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-msgpack-numpy = "^0.4.8" -more-itertools = "^9.0.0" -pluggy = "^1.0.0" -ruamel-yaml = "^0.17.21" -tqdm = "^4.64.1" -numpy = "^1.23.5" -pyjwt = "^2.4.0" -mako = "^1.2.2" -oauthlib = "^3.2.1" -aiohttp = "^3.7.4" -numba = {version = "^0.56.4", optional = true} +msgpack = ">=1.0.4" +msgpack-numpy = ">=0.4.8" +more-itertools = ">=9.0.0" +pluggy = ">=1.0.0" +ruamel-yaml = ">=0.17.21" +tqdm = ">=4.64.1" +numpy = ">=1.23.5" +pyjwt = ">=2.4.0" # dependabot: GHSA-ffqj-6fqr-9h24 +mako = ">=1.2.2" # dependabot: GHSA-v973-fxgf-6xhp +oauthlib = ">=3.2.2" # dependabot: GHSA-3pgj-pg6c-r5p7 +aiohttp = ">=3.9.0" # dependabot: GHSA-q3qx-c6g2-7pw2 +numba = {version = ">=0.56.4", optional = true} adlfs = {version = "<2021.10", optional = true} dask = {version = ">=2021.7.0", optional = true, extras = ["dataframe", "distributed"]} -odfpy = {version = "^1.4.1", optional = true} -openpyxl = {version = "^3.1.1", optional = true} -pyxlsb = {version = "^1.0.10", optional = true} -xlrd = {version = "^2.0.1", optional = true} +odfpy = {version = ">=1.4.1", optional = true} +openpyxl = {version = ">=3.1.1", optional = true} +pyxlsb = {version = ">=1.0.10", optional = true} +xlrd = {version = ">=2.0.1", optional = true} gcsfs = {version = ">=2021.7.0", optional = true} s3fs = {version = ">=2021.7.0", optional = true} torch = {version = ">=1.13.1", optional = true} -zarr = {version = "^2.10.3", optional = true} -pyarrow = {version = "^10.0.1", optional = true} +zarr = {version = ">=2.10.3", optional = true} +pyarrow = {version = ">=14.0.1", optional = true} # dependabot: GHSA-5wvp-7f3h-6wmm [tool.poetry.group.dev.dependencies] -twine = "^4.0.2" -wheel = "^0.38.4" -pytest = "^6.2.1" -pytest-timeout = "^2.1.0" -pytest-cov = "^4.0.0" -pytest-xdist = "^3.2.0" -wandb = "^0.13.10" -mlflow = "^2.1.1" -pre-commit = "^2.16.0" -pip-tools = "^6.6.2" +twine = ">=4.0.2" +wheel = ">=0.38.4" +pytest = ">=6.2.1" +pytest-timeout = ">=2.1.0" +pytest-cov = ">=4.0.0" +pytest-xdist = ">=3.2.0" +wandb = ">=0.13.10" +mlflow = ">=2.1.1" +pre-commit = ">=2.16.0" +pip-tools = ">=6.6.2" black = "22.8.0" autopep8 = "1.7.0" -hypothesis = "^6.91.1" -faker = "^20.1.0" +hypothesis = ">=6.91.1" +faker = ">=20.1.0" [tool.poetry.group.doc.dependencies] sphinx = "<4.0.0" jinja2 = "<3.1" click = "<8.1" -sphinx-versions = "^1.1.3" -sphinx-rtd-theme = "^1.2.0" -sphinx-autoapi = "^1.9.0" -sphinxcontrib-mermaid = "^0.8" -myst-nb = "^0.15.0" +sphinx-versions = ">=1.1.3" +sphinx-rtd-theme = ">=1.2.0" +sphinx-autoapi = ">=1.9.0" +sphinxcontrib-mermaid = ">=0.8" +myst-nb = ">=0.15.0" [tool.poetry.extras] azure = ["adlfs"] From 2c2b1e47c787b096c88b1c136a264d78ea4e8662 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Tue, 19 Dec 2023 17:19:40 +0100 Subject: [PATCH 02/41] Export requirements --- requirements.txt | 2002 +++------------------------------------------- 1 file changed, 117 insertions(+), 1885 deletions(-) diff --git a/requirements.txt b/requirements.txt index a2aa4cb..9913459 100644 --- 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--hash=sha256:b9c2130e1c632540fbf9c2c88341493797ddf58016e7cba02e311de9b0a96b67 \ - --hash=sha256:be596b44448aac14eb3614248c91586e2bc1728e020e82ef3197189aae556115 \ - --hash=sha256:c05349890804d846eca32ce0623ab66c06f8800db881af7a876dc073ac1c2225 \ - --hash=sha256:de4a045fbf388e120bb6ec66501458d3134f4729faed26ff95de52a754abddb1 \ - --hash=sha256:dff595686178b0e75580c24d316aa45a8f4d56e2418063865c114eef651a982e \ - --hash=sha256:f6383c29e796203a0bba74a250615ad262c4279d398e89d895a69d3069498305 -decorator==5.1.1 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330 \ - --hash=sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186 -defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69 \ - --hash=sha256:a352e7e428770286cc899e2542b6cdaedb2b4953ff269a210103ec58f6198a61 -distlib==0.3.6 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46 \ - --hash=sha256:f35c4b692542ca110de7ef0bea44d73981caeb34ca0b9b6b2e6d7790dda8f80e -distributed==2023.2.1 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:1347a4b3a1e5273672fd7a87471409e1bac470b4bdb6788c918313d45a22911b \ - --hash=sha256:34e9266af2bd24f14e4449934d900300ad994bb2c6929a56fbe7d0e398a3ed07 -docker-pycreds==0.4.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:6ce3270bcaf404cc4c3e27e4b6c70d3521deae82fb508767870fdbf772d584d4 \ - --hash=sha256:7266112468627868005106ec19cd0d722702d2b7d5912a28e19b826c3d37af49 -docker==6.0.1 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97 \ - --hash=sha256:dbcb3bd2fa80dca0788ed908218bf43972772009b881ed1e20dfc29a65e49782 -docutils==0.16 ; python_version >= "3.8" and python_version < 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--hash=sha256:04fbecc94300436f628517b05741b7ea009506ce8f946d40996567c669318490 \ - --hash=sha256:4a30d6315a68c253cfa8f963b9697246315aa3db89f98b97235e345dedfb0b8e -filelock==3.9.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:7b319f24340b51f55a2bf7a12ac0755a9b03e718311dac567a0f4f7fabd2f5de \ - --hash=sha256:f58d535af89bb9ad5cd4df046f741f8553a418c01a7856bf0d173bbc9f6bd16d -flask==2.2.5 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:58107ed83443e86067e41eff4631b058178191a355886f8e479e347fa1285fdf \ - --hash=sha256:edee9b0a7ff26621bd5a8c10ff484ae28737a2410d99b0bb9a6850c7fb977aa0 -fonttools==4.38.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:2bb244009f9bf3fa100fc3ead6aeb99febe5985fa20afbfbaa2f8946c2fbdaf1 \ - --hash=sha256:820466f43c8be8c3009aef8b87e785014133508f0de64ec469e4efb643ae54fb frozenlist==1.3.3 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:008a054b75d77c995ea26629ab3a0c0d7281341f2fa7e1e85fa6153ae29ae99c \ --hash=sha256:02c9ac843e3390826a265e331105efeab489ffaf4dd86384595ee8ce6d35ae7f \ @@ -654,360 +165,12 @@ frozenlist==1.3.3 ; python_version >= "3.8" and python_version < "4.0" \ fsspec==2023.1.0 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:b833e2e541e9e8cde0ab549414187871243177feb3d344f9d27b25a93f5d8139 \ --hash=sha256:fbae7f20ff801eb5f7d0bedf81f25c787c0dfac5e982d98fa3884a9cde2b5411 -gcsfs==2023.1.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:0a7b7ca8c1affa126a14ba35d7b7dff81c49e2aaceedda9732c7f159a4837a26 \ - --hash=sha256:62c491b9e2a8e9e58b8a899eec2ce111f827718a65539019ff3cadf447e48f41 -gitdb==4.0.10 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:6eb990b69df4e15bad899ea868dc46572c3f75339735663b81de79b06f17eb9a \ - --hash=sha256:c286cf298426064079ed96a9e4a9d39e7f3e9bf15ba60701e95f5492f28415c7 -gitpython==3.1.31 ; python_version >= 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python_version < "4.0" \ - --hash=sha256:08fb8465cffd03d10b9dd34a5c3fea908e20391a2a90b88d66362cb05beed186 \ - --hash=sha256:3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff markupsafe==2.1.2 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:0576fe974b40a400449768941d5d0858cc624e3249dfd1e0c33674e5c7ca7aed \ --hash=sha256:085fd3201e7b12809f9e6e9bc1e5c96a368c8523fad5afb02afe3c051ae4afcc \ @@ -1059,69 +222,9 @@ markupsafe==2.1.2 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:f1cd098434e83e656abf198f103a8207a8187c0fc110306691a2e94a78d0abb2 \ --hash=sha256:f2bfb563d0211ce16b63c7cb9395d2c682a23187f54c3d79bfec33e6705473c6 \ --hash=sha256:f8ffb705ffcf5ddd0e80b65ddf7bed7ee4f5a441ea7d3419e861a12eaf41af58 -matplotlib-inline==0.1.6 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:f1f41aab5328aa5aaea9b16d083b128102f8712542f819fe7e6a420ff581b311 \ - 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--hash=sha256:de20eb1247725a2f889173d391a6d9e7e0f2540feda24030748283108b0478ec \ - --hash=sha256:eb2e76cd429058d8954121c334dddfcd11a6186c6975bca61f3f248c99031b05 \ - --hash=sha256:f336e7014889c38c59029ebacc35c59236a852e4b23836708cfd3f43d1eaeed5 \ - --hash=sha256:f4ddac5f59e78d04b20469bc43853a8e619bb6505c7eac8ffb343ff2c516d72f \ - --hash=sha256:f910d924da8b9fb066b5beae0b85e34ed1b6293014892baadcf2a51da1c65807 \ - --hash=sha256:f91d35b3ef51d29d9c661069b9e4ba431ce283ffc533b981506889e144b5b40e \ - --hash=sha256:fb0304c1cd802e9a25743414c887e8a7cd51d96c9ec96d388625d2cd1c137ae3 -mdit-py-plugins==0.3.4 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:3278aab2e2b692539082f05e1243f24742194ffd92481f48844f057b51971283 \ - --hash=sha256:4f1441264ac5cb39fa40a5901921c2acf314ea098d75629750c138f80d552cdf -mdurl==0.1.2 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8 \ - --hash=sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba -mlflow==2.4.2 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:0b1a71b0ff4679dce8ff2ae9733e996ec0b6c106db93412e0df8606f791867c8 \ - --hash=sha256:0d7618d497e5b54aea5a9303268f771a64c14e695f002997b05defdbf10b036e more-itertools==9.1.0 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:cabaa341ad0389ea83c17a94566a53ae4c9d07349861ecb14dc6d0345cf9ac5d \ --hash=sha256:d2bc7f02446e86a68911e58ded76d6561eea00cddfb2a91e7019bbb586c799f3 -msal-extensions==1.0.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:91e3db9620b822d0ed2b4d1850056a0f133cba04455e62f11612e40f5502f2ee \ - --hash=sha256:c676aba56b0cce3783de1b5c5ecfe828db998167875126ca4b47dc6436451354 -msal==1.22.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:8a82f5375642c1625c89058018430294c109440dce42ea667d466c2cab520acd \ - --hash=sha256:9120b7eafdf061c92f7b3d744e5f325fca35873445fa8ffebb40b1086a13dd58 msgpack-numpy==0.4.8 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:773c19d4dfbae1b3c7b791083e2caf66983bb19b40901646f61d8731554ae3da \ --hash=sha256:c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69 @@ -1253,42 +356,7 @@ multidict==6.0.4 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:f70b98cd94886b49d91170ef23ec5c0e8ebb6f242d734ed7ed677b24d50c82cf \ --hash=sha256:fc35cb4676846ef752816d5be2193a1e8367b4c1397b74a565a9d0389c433a1d \ --hash=sha256:ff959bee35038c4624250473988b24f846cbeb2c6639de3602c073f10410ceba -mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d \ - --hash=sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782 -myst-nb==0.15.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:30cba4116274b7998eef1fec0f43763c5452da184f701fd63e135ca283ace9cf \ - --hash=sha256:fdce98e47e7f020d8c0fb479bfbcc609a67b8c0ed79f0a50dd4e758a9142aaff -myst-parser==0.17.2 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:1635ce3c18965a528d6de980f989ff64d6a1effb482e1f611b1bfb79e38f3d98 \ - --hash=sha256:4c076d649e066f9f5c7c661bae2658be1ca06e76b002bb97f02a09398707686c -nbclient==0.5.13 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:40c52c9b5e3c31faecaee69f202b3f53e38d7c1c563de0fadde9d7eda0fdafe8 \ - --hash=sha256:47ac905af59379913c1f8f541098d2550153cf8dc58553cbe18c702b181518b0 -nbformat==5.7.3 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:22a98a6516ca216002b0a34591af5bcb8072ca6c63910baffc901cfa07fefbf0 \ - --hash=sha256:4b021fca24d3a747bf4e626694033d792d594705829e5e35b14ee3369f9f6477 -nest-asyncio==1.5.6 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:b9a953fb40dceaa587d109609098db21900182b16440652454a146cffb06e8b8 \ - --hash=sha256:d267cc1ff794403f7df692964d1d2a3fa9418ffea2a3f6859a439ff482fef290 -nodeenv==1.7.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:27083a7b96a25f2f5e1d8cb4b6317ee8aeda3bdd121394e5ac54e498028a042e \ - --hash=sha256:e0e7f7dfb85fc5394c6fe1e8fa98131a2473e04311a45afb6508f7cf1836fa2b -numcodecs==0.11.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:0c240858bf29e0ff254b1db60430e8b2658b8c8328b684f80033289d94807a7c \ - --hash=sha256:0fabc7dfdf64a9555bf8a34911e05b415793c67a1377207dc79cd96342291fa1 \ - --hash=sha256:11596b71267417425ea8afb407477a67d684f434c8b07b1dd59c25a97d5c3ccb \ - --hash=sha256:32697785b786bb0039d3feeaabdc10f25eda6c149700cde954653aaa47637832 \ - --hash=sha256:694dc2e80b1f169b7deb14bdd0a04b20e5f17ef32cb0f81b71ab690406ec6bd9 \ - --hash=sha256:6c058b321de84a1729299b0eae4d652b2e48ea1ca7f9df0da65cb13470e635eb \ - --hash=sha256:7dae3f5678f247336c84e7315a0c59a4fec7c33eb7db72d78ff5c776479a812e \ - --hash=sha256:8c2f36b21162c6ebccc05d3fe896f86b91dcf8709946809f730cc23a37f8234d \ - --hash=sha256:bd05cdb853c7bcfde2efc809a9df2c5e205b96f70405b810e5788b45d0d81f73 \ - --hash=sha256:bf3925eeb37aed0e6c04d7fb9614133a3c8426dc77f8bda54c99c601a44b3bd3 \ - --hash=sha256:c0bc116752be45b4f9dca4315e5a2b4185e3b46f68c997dbb84aef334ceb5a1d \ - --hash=sha256:c27dfca402f69fbfa01c46fb572086e77f38121192160cc8ed1177dc30702c52 \ - --hash=sha256:ee5bda16e9d26a7a39fc20b6c1cec23b4debc314df5cfae3ed505149c2eeafc4 -numpy==1.23.5 ; python_version < "4.0" and python_version >= "3.8" \ +numpy==1.23.5 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:01dd17cbb340bf0fc23981e52e1d18a9d4050792e8fb8363cecbf066a84b827d \ --hash=sha256:06005a2ef6014e9956c09ba07654f9837d9e26696a0470e42beedadb78c11b07 \ --hash=sha256:09b7847f7e83ca37c6e627682f145856de331049013853f344f37b0c9690e3df \ @@ -1317,481 +385,52 @@ numpy==1.23.5 ; python_version < "4.0" and python_version >= "3.8" \ --hash=sha256:e9f4c4e51567b616be64e05d517c79a8a22f3606499941d97bb76f2ca59f982d \ --hash=sha256:f063b69b090c9d918f9df0a12116029e274daf0181df392839661c4c7ec9018a \ --hash=sha256:f9a909a8bae284d46bbfdefbdd4a262ba19d3bc9921b1e76126b1d21c3c34135 -nvidia-cublas-cu11==11.10.3.66 ; python_version >= "3.8" and python_version < "4.0" and platform_system == "Linux" \ - --hash=sha256:8ac17ba6ade3ed56ab898a036f9ae0756f1e81052a317bf98f8c6d18dc3ae49e \ - --hash=sha256:d32e4d75f94ddfb93ea0a5dda08389bcc65d8916a25cb9f37ac89edaeed3bded -nvidia-cuda-nvrtc-cu11==11.7.99 ; python_version >= "3.8" and python_version < "4.0" and platform_system == "Linux" \ - --hash=sha256:9f1562822ea264b7e34ed5930567e89242d266448e936b85bc97a3370feabb03 \ - --hash=sha256:f2effeb1309bdd1b3854fc9b17eaf997808f8b25968ce0c7070945c4265d64a3 \ - --hash=sha256:f7d9610d9b7c331fa0da2d1b2858a4a8315e6d49765091d28711c8946e7425e7 -nvidia-cuda-runtime-cu11==11.7.99 ; python_version >= 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python_version < "4.0" \ - --hash=sha256:5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb \ - --hash=sha256:fb33085c39dd998ac16d1431ebc293a8b3eedd00fd4a32de0ff79002c19511b4 -unidecode==1.3.6 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:547d7c479e4f377b430dd91ac1275d593308dce0fc464fb2ab7d41f82ec653be \ - --hash=sha256:fed09cf0be8cf415b391642c2a5addfc72194407caee4f98719e40ec2a72b830 -urllib3==1.26.14 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:076907bf8fd355cde77728471316625a4d2f7e713c125f51953bb5b3eecf4f72 \ - --hash=sha256:75edcdc2f7d85b137124a6c3c9fc3933cdeaa12ecb9a6a959f22797a0feca7e1 -virtualenv==20.19.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:37a640ba82ed40b226599c522d411e4be5edb339a0c0de030c0dc7b646d61590 \ - --hash=sha256:54eb59e7352b573aa04d53f80fc9736ed0ad5143af445a1e539aada6eb947dd1 -waitress==2.1.2 ; python_version >= "3.8" and python_version < "4.0" and platform_system == 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--hash=sha256:3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40 \ - --hash=sha256:cdf5877568b7e83aa7cf2244ab56a3213de587bbe0ce9d8b9600fc77b455d89e -werkzeug==2.2.3 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:2e1ccc9417d4da358b9de6f174e3ac094391ea1d4fbef2d667865d819dfd0afe \ - --hash=sha256:56433961bc1f12533306c624f3be5e744389ac61d722175d543e1751285da612 -wheel==0.38.4 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:965f5259b566725405b05e7cf774052044b1ed30119b5d586b2703aafe8719ac \ - --hash=sha256:b60533f3f5d530e971d6737ca6d58681ee434818fab630c83a734bb10c083ce8 -wrapt==1.15.0 ; python_version < "4.0" and python_version >= "3.8" \ - --hash=sha256:02fce1852f755f44f95af51f69d22e45080102e9d00258053b79367d07af39c0 \ - --hash=sha256:077ff0d1f9d9e4ce6476c1a924a3332452c1406e59d90a2cf24aeb29eeac9420 \ - --hash=sha256:078e2a1a86544e644a68422f881c48b84fef6d18f8c7a957ffd3f2e0a74a0d4a \ - 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--hash=sha256:b0724f05c396b0a4c36a3226c31648385deb6a65d8992644c12a4963c70326ba \ - --hash=sha256:b130fe77361d6771ecf5a219d8e0817d61b236b7d8b37cc045172e574ed219e6 \ - --hash=sha256:b56d5519e470d3f2fe4aa7585f0632b060d532d0696c5bdfb5e8319e1d0f69a2 \ - --hash=sha256:b67b819628e3b748fd3c2192c15fb951f549d0f47c0449af0764d7647302fda3 \ - --hash=sha256:ba1711cda2d30634a7e452fc79eabcadaffedf241ff206db2ee93dd2c89a60e7 \ - --hash=sha256:bbeccb1aa40ab88cd29e6c7d8585582c99548f55f9b2581dfc5ba68c59a85752 \ - --hash=sha256:bd84395aab8e4d36263cd1b9308cd504f6cf713b7d6d3ce25ea55670baec5416 \ - --hash=sha256:c99f4309f5145b93eca6e35ac1a988f0dc0a7ccf9ccdcd78d3c0adf57224e62f \ - --hash=sha256:ca1cccf838cd28d5a0883b342474c630ac48cac5df0ee6eacc9c7290f76b11c1 \ - --hash=sha256:cd525e0e52a5ff16653a3fc9e3dd827981917d34996600bbc34c05d048ca35cc \ - --hash=sha256:cdb4f085756c96a3af04e6eca7f08b1345e94b53af8921b25c72f096e704e145 \ - --hash=sha256:ce42618f67741d4697684e501ef02f29e758a123aa2d669e2d964ff734ee00ee \ - --hash=sha256:d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a \ - --hash=sha256:d5fe3e099cf07d0fb5a1e23d399e5d4d1ca3e6dfcbe5c8570ccff3e9208274f7 \ - --hash=sha256:d6bcbfc99f55655c3d93feb7ef3800bd5bbe963a755687cbf1f490a71fb7794b \ - --hash=sha256:d787272ed958a05b2c86311d3a4135d3c2aeea4fc655705f074130aa57d71653 \ - --hash=sha256:e169e957c33576f47e21864cf3fc9ff47c223a4ebca8960079b8bd36cb014fd0 \ - --hash=sha256:e20076a211cd6f9b44a6be58f7eeafa7ab5720eb796975d0c03f05b47d89eb90 \ - --hash=sha256:e826aadda3cae59295b95343db8f3d965fb31059da7de01ee8d1c40a60398b29 \ - --hash=sha256:eef4d64c650f33347c1f9266fa5ae001440b232ad9b98f1f43dfe7a79435c0a6 \ - --hash=sha256:f2e69b3ed24544b0d3dbe2c5c0ba5153ce50dcebb576fdc4696d52aa22db6034 \ - --hash=sha256:f87ec75864c37c4c6cb908d282e1969e79763e0d9becdfe9fe5473b7bb1e5f09 \ - --hash=sha256:fbec11614dba0424ca72f4e8ba3c420dba07b4a7c206c8c8e4e73f2e98f4c559 \ - --hash=sha256:fd69666217b62fa5d7c6aa88e507493a34dec4fa20c5bd925e4bc12fce586639 -xlrd==2.0.1 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:6a33ee89877bd9abc1158129f6e94be74e2679636b8a205b43b85206c3f0bbdd \ - --hash=sha256:f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88 yarl==1.8.2 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:009a028127e0a1755c38b03244c0bea9d5565630db9c4cf9572496e947137a87 \ --hash=sha256:0414fd91ce0b763d4eadb4456795b307a71524dbacd015c657bb2a39db2eab89 \ @@ -2309,12 +550,3 @@ yarl==1.8.2 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:fb742dcdd5eec9f26b61224c23baea46c9055cf16f62475e11b9b15dfd5c117b \ --hash=sha256:fc77086ce244453e074e445104f0ecb27530d6fd3a46698e33f6c38951d5a0f1 \ --hash=sha256:ff205b58dc2929191f68162633d5e10e8044398d7a45265f90a0f1d51f85f72c -zarr==2.14.2 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:68ec59b8ebdfc4fee5e32bd6c0ce273f72f7d4ed017454b45327c673c60907bc \ - --hash=sha256:feb72d6ccc43c447661861020dbf2e685a8367e80d890b6f5905954400394ed2 -zict==2.2.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:d7366c2e2293314112dcf2432108428a67b927b00005619feefc310d12d833f3 \ - --hash=sha256:dabcc8c8b6833aa3b6602daad50f03da068322c1a90999ff78aed9eecc8fa92c -zipp==3.15.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b \ - --hash=sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556 From 0156dc891f2082f98d56bda183cbdbb2d051a467 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Tue, 19 Dec 2023 17:20:36 +0100 Subject: [PATCH 03/41] poetry export --- requirements.txt | 1768 +++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 1766 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index 9913459..38cca64 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,3 +1,11 @@ +adal==1.2.7 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:2a7451ed7441ddbc57703042204a3e30ef747478eea022c70f789fc7f084bc3d \ + --hash=sha256:d74f45b81317454d96e982fd1c50e6fb5c99ac2223728aea8764433a39f566f1 +adlfs==2021.9.1 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:0d9cae55be36b937d1dc6e803b83dcb415ea887279dd7757b040b4f1a39b65ea +aiobotocore==2.4.2 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:0603b74a582dffa7511ce7548d07dc9b10ec87bc5fb657eb0b34f9bd490958bf \ + --hash=sha256:4acd1ebe2e44be4b100aa553910bda899f6dc090b3da2bc1cf3d5de2146ed208 aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:02ab6006ec3c3463b528374c4cdce86434e7b89ad355e7bf29e2f16b46c7dd6f \ --hash=sha256:04fa38875e53eb7e354ece1607b1d2fdee2d175ea4e4d745f6ec9f751fe20c7c \ @@ -75,18 +83,488 @@ aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:f694dc8a6a3112059258a725a4ebe9acac5fe62f11c77ac4dcf896edfa78ca28 \ --hash=sha256:f800164276eec54e0af5c99feb9494c295118fc10a11b997bbb1348ba1a52065 \ --hash=sha256:ffcd828e37dc219a72c9012ec44ad2e7e3066bec6ff3aaa19e7d435dbf4032ca +aioitertools==0.11.0 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:04b95e3dab25b449def24d7df809411c10e62aab0cbe31a50ca4e68748c43394 \ + --hash=sha256:42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831 aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc \ --hash=sha256:f8376fb07dd1e86a584e4fcdec80b36b7f81aac666ebc724e2c090300dd83b17 +alabaster==0.7.13 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3 \ + --hash=sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2 +alembic==1.9.4 ; python_version >= "3.8" and 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+mdit-py-plugins==0.3.4 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:3278aab2e2b692539082f05e1243f24742194ffd92481f48844f057b51971283 \ + --hash=sha256:4f1441264ac5cb39fa40a5901921c2acf314ea098d75629750c138f80d552cdf +mdurl==0.1.2 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8 \ + --hash=sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba +mlflow==2.9.2 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:25f2ad3d0b0e78bd32296058fb4c315dff4379515cd669ac6137f39507b9dfe9 \ + --hash=sha256:5c1aac70238636bfc798f41925b93c6cce3a8835287311e97b7dbc90d07a8777 more-itertools==9.1.0 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:cabaa341ad0389ea83c17a94566a53ae4c9d07349861ecb14dc6d0345cf9ac5d \ --hash=sha256:d2bc7f02446e86a68911e58ded76d6561eea00cddfb2a91e7019bbb586c799f3 +msal-extensions==1.0.0 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:91e3db9620b822d0ed2b4d1850056a0f133cba04455e62f11612e40f5502f2ee \ + --hash=sha256:c676aba56b0cce3783de1b5c5ecfe828db998167875126ca4b47dc6436451354 +msal==1.22.0 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:8a82f5375642c1625c89058018430294c109440dce42ea667d466c2cab520acd \ + --hash=sha256:9120b7eafdf061c92f7b3d744e5f325fca35873445fa8ffebb40b1086a13dd58 msgpack-numpy==0.4.8 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:773c19d4dfbae1b3c7b791083e2caf66983bb19b40901646f61d8731554ae3da \ --hash=sha256:c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69 @@ -356,7 +1238,42 @@ multidict==6.0.4 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:f70b98cd94886b49d91170ef23ec5c0e8ebb6f242d734ed7ed677b24d50c82cf \ --hash=sha256:fc35cb4676846ef752816d5be2193a1e8367b4c1397b74a565a9d0389c433a1d \ --hash=sha256:ff959bee35038c4624250473988b24f846cbeb2c6639de3602c073f10410ceba -numpy==1.23.5 ; python_version >= "3.8" and python_version < "4.0" \ +mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d \ + --hash=sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782 +myst-nb==0.15.0 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:30cba4116274b7998eef1fec0f43763c5452da184f701fd63e135ca283ace9cf \ + --hash=sha256:fdce98e47e7f020d8c0fb479bfbcc609a67b8c0ed79f0a50dd4e758a9142aaff +myst-parser==0.17.2 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:1635ce3c18965a528d6de980f989ff64d6a1effb482e1f611b1bfb79e38f3d98 \ + --hash=sha256:4c076d649e066f9f5c7c661bae2658be1ca06e76b002bb97f02a09398707686c +nbclient==0.5.13 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:40c52c9b5e3c31faecaee69f202b3f53e38d7c1c563de0fadde9d7eda0fdafe8 \ + --hash=sha256:47ac905af59379913c1f8f541098d2550153cf8dc58553cbe18c702b181518b0 +nbformat==5.7.3 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:22a98a6516ca216002b0a34591af5bcb8072ca6c63910baffc901cfa07fefbf0 \ + --hash=sha256:4b021fca24d3a747bf4e626694033d792d594705829e5e35b14ee3369f9f6477 +nest-asyncio==1.5.6 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:b9a953fb40dceaa587d109609098db21900182b16440652454a146cffb06e8b8 \ + --hash=sha256:d267cc1ff794403f7df692964d1d2a3fa9418ffea2a3f6859a439ff482fef290 +nodeenv==1.7.0 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:27083a7b96a25f2f5e1d8cb4b6317ee8aeda3bdd121394e5ac54e498028a042e \ + --hash=sha256:e0e7f7dfb85fc5394c6fe1e8fa98131a2473e04311a45afb6508f7cf1836fa2b +numcodecs==0.11.0 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:0c240858bf29e0ff254b1db60430e8b2658b8c8328b684f80033289d94807a7c \ + --hash=sha256:0fabc7dfdf64a9555bf8a34911e05b415793c67a1377207dc79cd96342291fa1 \ + --hash=sha256:11596b71267417425ea8afb407477a67d684f434c8b07b1dd59c25a97d5c3ccb \ + --hash=sha256:32697785b786bb0039d3feeaabdc10f25eda6c149700cde954653aaa47637832 \ + --hash=sha256:694dc2e80b1f169b7deb14bdd0a04b20e5f17ef32cb0f81b71ab690406ec6bd9 \ + --hash=sha256:6c058b321de84a1729299b0eae4d652b2e48ea1ca7f9df0da65cb13470e635eb \ + --hash=sha256:7dae3f5678f247336c84e7315a0c59a4fec7c33eb7db72d78ff5c776479a812e \ + --hash=sha256:8c2f36b21162c6ebccc05d3fe896f86b91dcf8709946809f730cc23a37f8234d \ + --hash=sha256:bd05cdb853c7bcfde2efc809a9df2c5e205b96f70405b810e5788b45d0d81f73 \ + --hash=sha256:bf3925eeb37aed0e6c04d7fb9614133a3c8426dc77f8bda54c99c601a44b3bd3 \ + --hash=sha256:c0bc116752be45b4f9dca4315e5a2b4185e3b46f68c997dbb84aef334ceb5a1d \ + --hash=sha256:c27dfca402f69fbfa01c46fb572086e77f38121192160cc8ed1177dc30702c52 \ + --hash=sha256:ee5bda16e9d26a7a39fc20b6c1cec23b4debc314df5cfae3ed505149c2eeafc4 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python_version < "4.0" and platform_system == "Linux" \ + --hash=sha256:9f1562822ea264b7e34ed5930567e89242d266448e936b85bc97a3370feabb03 \ + --hash=sha256:f2effeb1309bdd1b3854fc9b17eaf997808f8b25968ce0c7070945c4265d64a3 \ + --hash=sha256:f7d9610d9b7c331fa0da2d1b2858a4a8315e6d49765091d28711c8946e7425e7 +nvidia-cuda-runtime-cu11==11.7.99 ; python_version >= "3.8" and python_version < "4.0" and platform_system == "Linux" \ + --hash=sha256:bc77fa59a7679310df9d5c70ab13c4e34c64ae2124dd1efd7e5474b71be125c7 \ + --hash=sha256:cc768314ae58d2641f07eac350f40f99dcb35719c4faff4bc458a7cd2b119e31 +nvidia-cudnn-cu11==8.5.0.96 ; python_version >= "3.8" and python_version < "4.0" and platform_system == "Linux" \ + --hash=sha256:402f40adfc6f418f9dae9ab402e773cfed9beae52333f6d86ae3107a1b9527e7 \ + --hash=sha256:71f8111eb830879ff2836db3cccf03bbd735df9b0d17cd93761732ac50a8a108 oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "4.0" \ 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--hash=sha256:b67b819628e3b748fd3c2192c15fb951f549d0f47c0449af0764d7647302fda3 \ + --hash=sha256:ba1711cda2d30634a7e452fc79eabcadaffedf241ff206db2ee93dd2c89a60e7 \ + --hash=sha256:bbeccb1aa40ab88cd29e6c7d8585582c99548f55f9b2581dfc5ba68c59a85752 \ + --hash=sha256:bd84395aab8e4d36263cd1b9308cd504f6cf713b7d6d3ce25ea55670baec5416 \ + --hash=sha256:c99f4309f5145b93eca6e35ac1a988f0dc0a7ccf9ccdcd78d3c0adf57224e62f \ + --hash=sha256:ca1cccf838cd28d5a0883b342474c630ac48cac5df0ee6eacc9c7290f76b11c1 \ + --hash=sha256:cd525e0e52a5ff16653a3fc9e3dd827981917d34996600bbc34c05d048ca35cc \ + --hash=sha256:cdb4f085756c96a3af04e6eca7f08b1345e94b53af8921b25c72f096e704e145 \ + --hash=sha256:ce42618f67741d4697684e501ef02f29e758a123aa2d669e2d964ff734ee00ee \ + --hash=sha256:d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a \ + --hash=sha256:d5fe3e099cf07d0fb5a1e23d399e5d4d1ca3e6dfcbe5c8570ccff3e9208274f7 \ + --hash=sha256:d6bcbfc99f55655c3d93feb7ef3800bd5bbe963a755687cbf1f490a71fb7794b \ + --hash=sha256:d787272ed958a05b2c86311d3a4135d3c2aeea4fc655705f074130aa57d71653 \ + --hash=sha256:e169e957c33576f47e21864cf3fc9ff47c223a4ebca8960079b8bd36cb014fd0 \ + --hash=sha256:e20076a211cd6f9b44a6be58f7eeafa7ab5720eb796975d0c03f05b47d89eb90 \ + --hash=sha256:e826aadda3cae59295b95343db8f3d965fb31059da7de01ee8d1c40a60398b29 \ + --hash=sha256:eef4d64c650f33347c1f9266fa5ae001440b232ad9b98f1f43dfe7a79435c0a6 \ + --hash=sha256:f2e69b3ed24544b0d3dbe2c5c0ba5153ce50dcebb576fdc4696d52aa22db6034 \ + --hash=sha256:f87ec75864c37c4c6cb908d282e1969e79763e0d9becdfe9fe5473b7bb1e5f09 \ + --hash=sha256:fbec11614dba0424ca72f4e8ba3c420dba07b4a7c206c8c8e4e73f2e98f4c559 \ + --hash=sha256:fd69666217b62fa5d7c6aa88e507493a34dec4fa20c5bd925e4bc12fce586639 +xlrd==2.0.1 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:6a33ee89877bd9abc1158129f6e94be74e2679636b8a205b43b85206c3f0bbdd \ + --hash=sha256:f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88 yarl==1.8.2 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:009a028127e0a1755c38b03244c0bea9d5565630db9c4cf9572496e947137a87 \ --hash=sha256:0414fd91ce0b763d4eadb4456795b307a71524dbacd015c657bb2a39db2eab89 \ @@ -550,3 +2305,12 @@ yarl==1.8.2 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:fb742dcdd5eec9f26b61224c23baea46c9055cf16f62475e11b9b15dfd5c117b \ --hash=sha256:fc77086ce244453e074e445104f0ecb27530d6fd3a46698e33f6c38951d5a0f1 \ --hash=sha256:ff205b58dc2929191f68162633d5e10e8044398d7a45265f90a0f1d51f85f72c +zarr==2.14.2 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:68ec59b8ebdfc4fee5e32bd6c0ce273f72f7d4ed017454b45327c673c60907bc \ + --hash=sha256:feb72d6ccc43c447661861020dbf2e685a8367e80d890b6f5905954400394ed2 +zict==2.2.0 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:d7366c2e2293314112dcf2432108428a67b927b00005619feefc310d12d833f3 \ + --hash=sha256:dabcc8c8b6833aa3b6602daad50f03da068322c1a90999ff78aed9eecc8fa92c +zipp==3.15.0 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b \ + --hash=sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556 From 1b914eabdf49c7f9597a597b36403be0a11eb1ed Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Wed, 20 Dec 2023 16:43:08 +0100 Subject: [PATCH 04/41] Introducing multiple pins for faster resolution --- poetry.lock | 4676 ++++++++++++--------------- pyproject.toml | 75 +- test/test_iterstream/test_stream.py | 4 +- 3 files changed, 2174 insertions(+), 2581 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4c6842f..16247f7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,60 +1,47 @@ # This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. -[[package]] -name = "adal" -version = "1.2.7" -description = "Note: This library is already replaced by MSAL Python, available here: https://pypi.org/project/msal/ .ADAL Python remains available here as a legacy. 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"pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [extras] all = ["adlfs", "dask", "gcsfs", "odfpy", "openpyxl", "pyarrow", "pyxlsb", "s3fs", "torch", "xlrd", "zarr"] @@ -5646,4 +5236,4 @@ zarr = ["zarr"] [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "9248e0b250ad28f0eb5182835e22acc3f015e2dbc6ad7ccadf3423e695f8ed73" +content-hash = "b4f78f1eef65fd300ca1306fb9d844d30f9ec49d9b4c12f14e31adc86c8e52c5" diff --git a/pyproject.toml b/pyproject.toml index a187fd8..3d654db 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,56 +21,59 @@ classifiers = [ [tool.poetry.dependencies] python = "^3.8" -fsspec = ">=2021.7.0" -msgpack = ">=1.0.4" +fsspec = ">=2023.12.2" +msgpack = ">=1.0.7" msgpack-numpy = ">=0.4.8" -more-itertools = ">=9.0.0" -pluggy = ">=1.0.0" -ruamel-yaml = ">=0.17.21" -tqdm = ">=4.64.1" -numpy = ">=1.23.5" -pyjwt = ">=2.4.0" # dependabot: GHSA-ffqj-6fqr-9h24 -mako = ">=1.2.2" # dependabot: GHSA-v973-fxgf-6xhp +more-itertools = ">=10.1.0" +pluggy = ">=1.3.0" +ruamel-yaml = ">=0.18.5" +tqdm = ">=4.66.1" +numpy = "^1.23.5" +pyjwt = ">=2.8.0" # dependabot: GHSA-ffqj-6fqr-9h24 +mako = ">=1.3.0" # dependabot: GHSA-v973-fxgf-6xhp oauthlib = ">=3.2.2" # dependabot: GHSA-3pgj-pg6c-r5p7 -aiohttp = ">=3.9.0" # dependabot: GHSA-q3qx-c6g2-7pw2 -numba = {version = ">=0.56.4", optional = true} -adlfs = {version = "<2021.10", optional = true} -dask = {version = ">=2021.7.0", optional = true, extras = ["dataframe", "distributed"]} +aiohttp = ">=3.9.1" # dependabot: GHSA-q3qx-c6g2-7pw2 +urllib3 = "1.26.16" # pin for faster resolution, follows from current versions of s3fs +pandas = ">=1.2.0" # pin for dask compatibility +numba = {version = "^0.56.4", optional = true} +adlfs = {version = ">=2023.10.0", optional = true} +dask = {version = "^2023.4.0", optional = true, extras = ["dataframe", "distributed"]} odfpy = {version = ">=1.4.1", optional = true} openpyxl = {version = ">=3.1.1", optional = true} pyxlsb = {version = ">=1.0.10", optional = true} xlrd = {version = ">=2.0.1", optional = true} -gcsfs = {version = ">=2021.7.0", optional = true} -s3fs = {version = ">=2021.7.0", optional = true} +gcsfs = {version = ">=2023.12.0", optional = true} +s3fs = {version = ">=2023.12.0", optional = true} torch = {version = ">=1.13.1", optional = true} -zarr = {version = ">=2.10.3", optional = true} +zarr = {version = ">=2.16.1", optional = true} pyarrow = {version = ">=14.0.1", optional = true} # dependabot: GHSA-5wvp-7f3h-6wmm [tool.poetry.group.dev.dependencies] -twine = ">=4.0.2" -wheel = ">=0.38.4" -pytest = ">=6.2.1" -pytest-timeout = ">=2.1.0" -pytest-cov = ">=4.0.0" -pytest-xdist = ">=3.2.0" -wandb = ">=0.13.10" -mlflow = ">=2.1.1" -pre-commit = ">=2.16.0" -pip-tools = ">=6.6.2" -black = "22.8.0" autopep8 = "1.7.0" +black = "22.8.0" +faker = ">=21.0.0" hypothesis = ">=6.91.1" -faker = ">=20.1.0" +pip-tools = ">=7.3.0" +pre-commit = "^2.16.0" +pytest = "^7.0.2" +pytest-timeout = ">=2.2.0" +pytest-cov = "*" +pytest-xdist = "^3.2.0" +scipy = "*" +twine = "^4.0.2" +wandb = "0.16.1" +wheel = "^0.38.4" +#mlflow = ">=2.1.1" [tool.poetry.group.doc.dependencies] -sphinx = "<4.0.0" -jinja2 = "<3.1" -click = "<8.1" -sphinx-versions = ">=1.1.3" -sphinx-rtd-theme = ">=1.2.0" -sphinx-autoapi = ">=1.9.0" -sphinxcontrib-mermaid = ">=0.8" -myst-nb = ">=0.15.0" +sphinx = "5.0.0" # pin for faster resolution +jinja2 = ">2.7.2" # dependabot: GHSA-fqh9-2qgg-h84h +click = "^8.0.0" # pin for faster resolution any between 8.0.0 and 8.1.0 should work +sphinx-versions = "1.1.3" # pin for faster resolution - package does no longer seem to be maintained +sphinx-rtd-theme = "2.0.0" # pin for faster resolution any smaller should also work +sphinx-autoapi = "2.0.0" # pin for faster resolution any smaller should also work, larger requires sphinx >=5.2.0 +sphinxcontrib-mermaid = "0.9.2" # pin for faster resolution any smaller should also work +myst-nb = "0.17.2" # pin for faster resolution any <1.0.0 should work [tool.poetry.extras] azure = ["adlfs"] diff --git a/test/test_iterstream/test_stream.py b/test/test_iterstream/test_stream.py index 07abb06..9a060bb 100644 --- a/test/test_iterstream/test_stream.py +++ b/test/test_iterstream/test_stream.py @@ -7,7 +7,6 @@ from functools import partial import dask.distributed -import mlflow import numpy as np import pytest import wandb @@ -495,7 +494,7 @@ def test_metrics_tracking_with_wandb( .collect() ) - +@pytest.mark.skip("MLFlow dependency is being removed.") @pytest.mark.parametrize("metrics_conf_iops", [True, False]) @pytest.mark.parametrize("metrics_conf_throughput", [True, False]) @pytest.mark.parametrize("multi_points", [1, 2]) @@ -503,6 +502,7 @@ def test_metrics_tracking_with_mlflow( metrics_conf_iops: bool, metrics_conf_throughput: bool, create_all_iterable_source: Composable, multi_points: int ) -> None: """Smoke test for tracked iterable source, when callback set to be mlflow.log_metrics.""" + import mlflow conf = MetricsConf(iops=metrics_conf_iops, throughput=metrics_conf_throughput) it = create_all_iterable_source if multi_points == 1: From aee9b9ad2d17802b84a4922dff595b2abb9a6a8f Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Wed, 20 Dec 2023 16:56:30 +0100 Subject: [PATCH 05/41] Update deps --- poetry.lock | 264 ++++++++++++++++++++++++------------------------- pyproject.toml | 14 +-- 2 files changed, 135 insertions(+), 143 deletions(-) diff --git a/poetry.lock b/poetry.lock index 16247f7..80fe612 100644 --- a/poetry.lock +++ b/poetry.lock @@ -699,13 +699,13 @@ files = [ [[package]] name = "click" -version = "8.1.7" +version = "8.0.4" description = "Composable command line interface toolkit" optional = false -python-versions = ">=3.7" +python-versions = ">=3.6" files = [ - {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"}, - {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"}, + {file = "click-8.0.4-py3-none-any.whl", hash = "sha256:6a7a62563bbfabfda3a38f3023a1db4a35978c0abd76f6c9605ecd6554d6d9b1"}, + {file = "click-8.0.4.tar.gz", hash = "sha256:8458d7b1287c5fb128c90e23381cf99dcde74beaf6c7ff6384ce84d6fe090adb"}, ] [package.dependencies] @@ -1009,13 +1009,13 @@ six = ">=1.4.0" [[package]] name = "docutils" -version = "0.18.1" +version = "0.16" description = "Docutils -- Python Documentation Utilities" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ - {file = "docutils-0.18.1-py2.py3-none-any.whl", hash = "sha256:23010f129180089fbcd3bc08cfefccb3b890b0050e1ca00c867036e9d161b98c"}, - {file = "docutils-0.18.1.tar.gz", hash = "sha256:679987caf361a7539d76e584cbeddc311e3aee937877c87346f31debc63e9d06"}, + {file = "docutils-0.16-py2.py3-none-any.whl", hash = "sha256:0c5b78adfbf7762415433f5515cd5c9e762339e23369dbe8000d84a4bf4ab3af"}, + {file = "docutils-0.16.tar.gz", hash = "sha256:c2de3a60e9e7d07be26b7f2b00ca0309c207e06c100f9cc2a94931fc75a478fc"}, ] [[package]] @@ -1848,13 +1848,13 @@ trio = ["async_generator", "trio"] [[package]] name = "jinja2" -version = "3.1.2" +version = "3.0.3" description = "A very fast and expressive template engine." optional = false -python-versions = ">=3.7" +python-versions = ">=3.6" files = [ - {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"}, - {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"}, + {file = "Jinja2-3.0.3-py3-none-any.whl", hash = "sha256:077ce6014f7b40d03b47d1f1ca4b0fc8328a692bd284016f806ed0eaca390ad8"}, + {file = "Jinja2-3.0.3.tar.gz", hash = "sha256:611bb273cd68f3b993fabdc4064fc858c5b47a973cb5aa7999ec1ba405c87cd7"}, ] [package.dependencies] @@ -1914,30 +1914,30 @@ referencing = ">=0.31.0" [[package]] name = "jupyter-cache" -version = "0.6.1" +version = "0.5.0" description = "A defined interface for working with a cache of jupyter notebooks." optional = false -python-versions = "~=3.8" +python-versions = "~=3.7" files = [ - {file = "jupyter-cache-0.6.1.tar.gz", hash = "sha256:26f83901143edf4af2f3ff5a91e2d2ad298e46e2cee03c8071d37a23a63ccbfc"}, - {file = "jupyter_cache-0.6.1-py3-none-any.whl", hash = "sha256:2fce7d4975805c77f75bdfc1bc2e82bc538b8e5b1af27f2f5e06d55b9f996a82"}, + {file = "jupyter-cache-0.5.0.tar.gz", hash = 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"matplotlib", "nbdime", "nbformat (>=5.1)", "numpy", "pandas", "pytest (>=6,<7)", "pytest-cov", "pytest-regressions", "sympy"] [[package]] name = "jupyter-client" @@ -2442,79 +2442,80 @@ files = [ [[package]] name = "myst-nb" -version = "0.17.2" +version = "0.15.0" description = "A Jupyter Notebook Sphinx reader built on top of the MyST markdown parser." optional = false python-versions = ">=3.7" files = [ - {file = "myst-nb-0.17.2.tar.gz", hash = "sha256:0f61386515fab07c73646adca97fff2f69f41e90d313a260217c5bbe419d858b"}, - {file = "myst_nb-0.17.2-py3-none-any.whl", hash = "sha256:132ca4d0f5c308fdd4b6fdaba077712e28e119ccdafd04d6e41b51aac5483494"}, + {file = "myst-nb-0.15.0.tar.gz", hash = "sha256:fdce98e47e7f020d8c0fb479bfbcc609a67b8c0ed79f0a50dd4e758a9142aaff"}, + {file = "myst_nb-0.15.0-py3-none-any.whl", hash = "sha256:30cba4116274b7998eef1fec0f43763c5452da184f701fd63e135ca283ace9cf"}, ] [package.dependencies] +docutils = ">=0.15,<0.18" importlib_metadata = "*" ipykernel = "*" 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smaller should also work, larger requires sphinx >=5.2.0 -sphinxcontrib-mermaid = "0.9.2" # pin for faster resolution any smaller should also work -myst-nb = "0.17.2" # pin for faster resolution any <1.0.0 should work +sphinx-rtd-theme = "1.2.0" # pin for faster resolution any smaller should also work +sphinx-autoapi = "1.9.0" # pin for faster resolution any smaller should also work, larger requires sphinx >=5.2.0 +sphinxcontrib-mermaid = "0.8.1" # pin for faster resolution any smaller should also work +myst-nb = "0.15.0" # pin for faster resolution any <1.0.0 should work [tool.poetry.extras] azure = ["adlfs"] From 65ef3194b0ef09aabe43f56f2f01a553c00782c2 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Wed, 20 Dec 2023 17:06:09 +0100 Subject: [PATCH 06/41] More pins --- poetry.lock | 10 +++++----- pyproject.toml | 5 +++-- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/poetry.lock b/poetry.lock index 80fe612..c489f9d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -4460,17 +4460,17 @@ test = ["html5lib", "pytest"] [[package]] name = "sphinxcontrib-jquery" -version = "4.1" +version = "2.0.0" description = "Extension to include jQuery on newer Sphinx releases" optional = false python-versions = ">=2.7" files = [ - {file = "sphinxcontrib-jquery-4.1.tar.gz", hash = "sha256:1620739f04e36a2c779f1a131a2dfd49b2fd07351bf1968ced074365933abc7a"}, - {file = "sphinxcontrib_jquery-4.1-py2.py3-none-any.whl", hash = "sha256:f936030d7d0147dd026a4f2b5a57343d233f1fc7b363f68b3d4f1cb0993878ae"}, + {file = "sphinxcontrib-jquery-2.0.0.tar.gz", hash = "sha256:8fb65f6dba84bf7bcd1aea1f02ab3955ac34611d838bcc95d4983b805b234daa"}, + {file = "sphinxcontrib_jquery-2.0.0-py3-none-any.whl", hash = "sha256:ed47fa425c338ffebe3c37e1cdb56e30eb806116b85f01055b158c7057fdb995"}, ] [package.dependencies] -Sphinx = ">=1.8" +setuptools = "*" [[package]] name = "sphinxcontrib-jsmath" @@ -5228,4 +5228,4 @@ zarr = ["zarr"] [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "7b97e3bb3750e5016ae568e169594630354a93afdcb3f3b825318938df926a31" +content-hash = "93dd68c6ec8dcbdaf9cef7f963995eea9ba66d3361eb8b3007048a2249feb9db" diff --git a/pyproject.toml b/pyproject.toml index 468812a..b6c7abd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -69,10 +69,11 @@ wheel = "^0.38.4" sphinx = "3.5.4" # pin for faster resolution jinja2 = "3.0.3" # pin for faster resolution; dependabot: GHSA-fqh9-2qgg-h84h click = "8.0.4" # pin for faster resolution any between 8.0.0 and 8.1.0 should work -sphinx-versions = "1.1.3" # pin for faster resolution - package does no longer seem to be maintained -sphinx-rtd-theme = "1.2.0" # pin for faster resolution any smaller should also work sphinx-autoapi = "1.9.0" # pin for faster resolution any smaller should also work, larger requires sphinx >=5.2.0 +sphinxcontrib-jquery = "2.0.0" # pin for faster resolution sphinxcontrib-mermaid = "0.8.1" # pin for faster resolution any smaller should also work +sphinx-rtd-theme = "1.2.0" # pin for faster resolution any smaller should also work +sphinx-versions = "1.1.3" # pin for faster resolution - package does no longer seem to be maintained myst-nb = "0.15.0" # pin for faster resolution any <1.0.0 should work [tool.poetry.extras] From a8dba52cef27fe48ab4aa0b07e6b4527bfb4a555 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Wed, 20 Dec 2023 17:47:19 +0100 Subject: [PATCH 07/41] Pinning python --- poetry.lock | 742 +++++++++++++++++++++++++------------------------ pyproject.toml | 11 +- 2 files changed, 387 insertions(+), 366 deletions(-) diff --git a/poetry.lock b/poetry.lock index c489f9d..3002bf9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -178,6 +178,17 @@ files = [ {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, ] +[[package]] +name = "anyascii" +version = "0.3.2" +description = "Unicode to ASCII transliteration" +optional = false +python-versions = ">=3.3" +files = [ + {file = 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Weights and Biases API." optional = false -python-versions = ">=3.7" +python-versions = ">=3.6" files = [ - {file = "wandb-0.16.1-py3-none-any.whl", hash = "sha256:1d7423f92520984585bae9693bb637ae08d3e0c1d75ad4b34215bc44431f114c"}, - {file = "wandb-0.16.1.tar.gz", hash = "sha256:ffe6e8dd8cc8fcd72010c1246fb3d6d226b37c4f111f3f94308a1c0ae28a2fec"}, + {file = "wandb-0.13.10-py3-none-any.whl", hash = "sha256:d4a3397aed2790d5fa8adc5336e3607813dc498a49b1a0a48297f78d89a71b0b"}, + {file = "wandb-0.13.10.tar.gz", hash = "sha256:a2cde45dd6390ed1923ef3e1eca26487cb1e02e4732515856933c4494a975ad3"}, ] [package.dependencies] appdirs = ">=1.4.3" -Click = ">=7.1,<8.0.0 || >8.0.0" +Click = ">=7.0,<8.0.0 || >8.0.0" docker-pycreds = ">=0.4.0" -GitPython = ">=1.0.0,<3.1.29 || >3.1.29" +GitPython = ">=1.0.0" +pathtools = "*" protobuf = [ {version = ">=3.12.0,<4.21.0 || >4.21.0,<5", markers = "python_version < \"3.9\" and sys_platform == \"linux\""}, {version = ">=3.15.0,<4.21.0 || >4.21.0,<5", markers = "python_version == \"3.9\" and sys_platform == \"linux\""}, @@ -4930,16 +4980,14 @@ setuptools = "*" typing-extensions = {version = "*", markers = "python_version < \"3.10\""} [package.extras] -async = ["httpx (>=0.23.0)"] aws = ["boto3"] -azure = ["azure-identity", "azure-storage-blob"] -core = ["wandb-core (>=0.17.0b2)"] +azure = ["azure-storage-blob"] gcp = ["google-cloud-storage"] +grpc = ["grpcio (>=1.27.2)"] kubeflow = ["google-cloud-storage", "kubernetes", "minio", "sh"] -launch = ["PyYAML (>=6.0.0)", "awscli", "azure-containerregistry", "azure-identity", "azure-storage-blob", "boto3", "botocore", "chardet", "google-auth", "google-cloud-aiplatform", "google-cloud-artifact-registry", "google-cloud-compute", "google-cloud-storage", "iso8601", "kubernetes", "kubernetes-asyncio", "nbconvert", "nbformat", "optuna", "typing-extensions"] +launch = ["boto3", "botocore", "chardet", "google-cloud-storage", "iso8601", "kubernetes", "nbconvert", "nbformat", "typing-extensions"] media = ["bokeh", "moviepy", "numpy", "pillow", "plotly", "rdkit-pypi", "soundfile"] models = ["cloudpickle"] -perf = ["orjson"] sweeps = ["sweeps (>=0.2.0)"] [[package]] @@ -4971,7 +5019,7 @@ test = ["pytest (>=3.0.0)"] name = "wrapt" version = "1.16.0" description = "Module for decorators, wrappers and monkey patching." -optional = true +optional = false python-versions = ">=3.6" files = [ {file = "wrapt-1.16.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ffa565331890b90056c01db69c0fe634a776f8019c143a5ae265f9c6bc4bd6d4"}, @@ -5228,4 +5276,4 @@ zarr = ["zarr"] [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "93dd68c6ec8dcbdaf9cef7f963995eea9ba66d3361eb8b3007048a2249feb9db" +content-hash = "727b7874ac17af66ac497f22f9dcbc199ac9cf539a3098b5d5eb172a908a046c" diff --git a/pyproject.toml b/pyproject.toml index d71b234..acd283f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,52 +21,57 @@ classifiers = [ [tool.poetry.dependencies] python = "^3.8" -fsspec = ">=2023.12.2" -msgpack = ">=1.0.7" -msgpack-numpy = ">=0.4.8" -more-itertools = ">=10.1.0" -pluggy = ">=1.3.0" -ruamel-yaml = ">=0.18.5" -tqdm = ">=4.66.1" +fsspec = ">=2021.7.0" +msgpack = "^1.0.4" +msgpack-numpy = "^0.4.8" +more-itertools = "^9.0.0" +pluggy = "^1.0.0" +ruamel-yaml = "^0.17.21" +tqdm = "^4.64.1" numpy = "^1.23.5" -pyjwt = ">=2.8.0" # dependabot: GHSA-ffqj-6fqr-9h24 -mako = ">=1.3.0" # dependabot: GHSA-v973-fxgf-6xhp +pyjwt = "2.6.0" # dependabot: GHSA-ffqj-6fqr-9h24 +mako = "1.2.4" # dependabot: GHSA-v973-fxgf-6xhp oauthlib = ">=3.2.2" # dependabot: GHSA-3pgj-pg6c-r5p7 -aiohttp = ">=3.9.1" # dependabot: GHSA-q3qx-c6g2-7pw2 +aiohttp = "3.8.4" # dependabot: GHSA-q3qx-c6g2-7pw2 urllib3 = "1.26.16" # pin for faster resolution, follows from current versions of s3fs -pandas = ">=1.2.0" # pin for dask compatibility +pandas = "1.5.3" # pin for dask compatibility numba = {version = "^0.56.4", optional = true} -adlfs = {version = ">=2023.10.0", optional = true} -dask = {version = "^2023.4.0", optional = true, extras = ["dataframe", "distributed"]} +adlfs = {version = "2021.9.1", optional = true} +dask = {version = "2023.2.1", optional = true, extras = ["dataframe", "distributed"]} odfpy = {version = ">=1.4.1", optional = true} -openpyxl = {version = ">=3.1.1", optional = true} +openpyxl = {version = "3.1.1", optional = true} pyxlsb = {version = ">=1.0.10", optional = true} xlrd = {version = ">=2.0.1", optional = true} -gcsfs = {version = ">=2023.12.0", optional = true} -s3fs = {version = ">=2023.12.0", optional = true} +gcsfs = {version = ">=2021.7.0", optional = true} +s3fs = {version = ">=2021.7.0", optional = true} torch = {version = ">=1.13.1", optional = true} -zarr = {version = ">=2.16.1", optional = true} -pyarrow = {version = ">=14.0.1", optional = true} # dependabot: GHSA-5wvp-7f3h-6wmm +zarr = {version = ">=2.10.3", optional = true} +pyarrow = {version = "10.0.1", optional = true} # dependabot: GHSA-5wvp-7f3h-6wmm [tool.poetry.group.dev.dependencies] +# dev dependencies pinned for faster resolution autopep8 = "1.7.0" black = "22.8.0" -faker = ">=21.0.0" -hypothesis = ">=6.91.1" -pip-tools = ">=7.3.0" +faker = "20.1.0" +hypothesis = "6.91.1" +pip-tools = "6.12.2" pre-commit = "^2.16.0" -pytest = "^7.0.2" -pytest-timeout = ">=2.2.0" -pytest-cov = "*" -pytest-xdist = "^3.2.0" +pytest = "6.2.5" +pytest-timeout = "2.1.0" +pytest-cov = "4.0.0" +pytest-xdist = "3.2.0" scipy = "*" -twine = "^4.0.2" -wandb = "0.16.1" +setuptools = "67.4.0" +twine = "4.0.2" +wandb = "0.13.10" wheel = "^0.38.4" #mlflow = ">=2.1.1" [tool.poetry.group.doc.dependencies] + +# doc dependencies are pinned for faster resolution sphinx = "3.5.4" +astroid = "2.14.2" # newer versions seem to break sphinx-autoapi jinja2 = "3.0.3" click = "8.0.4" sphinx-autoapi = "1.9.0" @@ -77,12 +82,12 @@ sphinxcontrib-mermaid = "0.8.1" myst-nb = "0.15.0" # updated doc dependencies for python >=3.9 -# sphinx = "6.2.1" # pin for faster resolution +# sphinx = "6.2.1" # click = "<8.1.0" # pin for faster resolution any between 8.0.0 and 8.1.0 should work # sphinx-autoapi = "3.0.0" # pin for faster resolution - package does no longer seem to be maintained -# sphinxcontrib-mermaid = "0.8.1" # pin for faster resolution -# sphinx-rtd-theme = "1.2.0" # pin for faster resolution -# sphinx-versions = "1.1.3" # pin for faster resolution +# sphinxcontrib-mermaid = "0.8.1" +# sphinx-rtd-theme = "1.2.0" +# sphinx-versions = "1.1.3" # myst-nb = "1.0.0" # pin for faster resolution any <1.0.0 should work [tool.poetry.extras] From 24a434373d962ecc6c5d200e085d80fb634c39b5 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Thu, 21 Dec 2023 17:28:40 +0100 Subject: [PATCH 10/41] First solution satisfying both tests and docs --- poetry.lock | 484 ++++++++++++++++++++++++------------------------- pyproject.toml | 32 ++-- 2 files changed, 252 insertions(+), 264 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4a76336..72961e3 100644 --- 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= ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] +[[package]] +name = "waitress" +version = "2.1.2" +description = "Waitress WSGI server" +optional = false +python-versions = ">=3.7.0" +files = [ + {file = "waitress-2.1.2-py3-none-any.whl", hash = "sha256:7500c9625927c8ec60f54377d590f67b30c8e70ef4b8894214ac6e4cad233d2a"}, + {file = "waitress-2.1.2.tar.gz", hash = "sha256:780a4082c5fbc0fde6a2fcfe5e26e6efc1e8f425730863c04085769781f51eba"}, +] + +[package.extras] +docs = ["Sphinx (>=1.8.1)", "docutils", "pylons-sphinx-themes (>=1.0.9)"] +testing = ["coverage (>=5.0)", "pytest", "pytest-cover"] + [[package]] name = "wandb" version = "0.16.1" @@ -4964,6 +5745,39 @@ files = [ {file = "wcwidth-0.2.12.tar.gz", hash = "sha256:f01c104efdf57971bcb756f054dd58ddec5204dd15fa31d6503ea57947d97c02"}, ] +[[package]] +name = "websocket-client" +version = "1.7.0" +description = "WebSocket client for Python with low level API options" +optional = false +python-versions = ">=3.8" +files = [ + {file = "websocket-client-1.7.0.tar.gz", hash = "sha256:10e511ea3a8c744631d3bd77e61eb17ed09304c413ad42cf6ddfa4c7787e8fe6"}, + {file = "websocket_client-1.7.0-py3-none-any.whl", hash = "sha256:f4c3d22fec12a2461427a29957ff07d35098ee2d976d3ba244e688b8b4057588"}, +] + +[package.extras] +docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"] +optional = ["python-socks", "wsaccel"] +test = ["websockets"] + +[[package]] +name = "werkzeug" +version = "3.0.1" +description = "The comprehensive WSGI web application library." +optional = false +python-versions = ">=3.8" +files = [ + {file = "werkzeug-3.0.1-py3-none-any.whl", hash = "sha256:90a285dc0e42ad56b34e696398b8122ee4c681833fb35b8334a095d82c56da10"}, + {file = "werkzeug-3.0.1.tar.gz", hash = "sha256:507e811ecea72b18a404947aded4b3390e1db8f826b494d76550ef45bb3b1dcc"}, +] + +[package.dependencies] +MarkupSafe = ">=2.1.1" + +[package.extras] +watchdog = ["watchdog (>=2.3)"] + [[package]] name = "wheel" version = "0.42.0" @@ -5239,4 +6053,4 @@ zarr = ["zarr"] [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "003525a9c9d4619c0a44ffb379d08f6bfda6cda43a54618f1dc6f6b7213d4514" +content-hash = "0095dbc6d3b6abbd77000e5c4aefe7e295b80eb9445ee624e67feae7496c2a2f" diff --git a/pyproject.toml b/pyproject.toml index 33ea577..3e32a88 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,7 +64,7 @@ setuptools = "69.0.2" twine = "4.0.2" wandb = "0.16.1" wheel = "0.42.0" -#mlflow = ">=2.1.1" +mlflow = "2.9.2" [tool.poetry.group.doc.dependencies] diff --git a/test/test_iterstream/test_stream.py b/test/test_iterstream/test_stream.py index 9a060bb..83aa14a 100644 --- a/test/test_iterstream/test_stream.py +++ b/test/test_iterstream/test_stream.py @@ -7,6 +7,7 @@ from functools import partial import dask.distributed +import mlflow import numpy as np import pytest import wandb @@ -494,7 +495,6 @@ def test_metrics_tracking_with_wandb( .collect() ) -@pytest.mark.skip("MLFlow dependency is being removed.") @pytest.mark.parametrize("metrics_conf_iops", [True, False]) @pytest.mark.parametrize("metrics_conf_throughput", [True, False]) @pytest.mark.parametrize("multi_points", [1, 2]) @@ -502,7 +502,6 @@ def test_metrics_tracking_with_mlflow( metrics_conf_iops: bool, metrics_conf_throughput: bool, create_all_iterable_source: Composable, multi_points: int ) -> None: """Smoke test for tracked iterable source, when callback set to be mlflow.log_metrics.""" - import mlflow conf = MetricsConf(iops=metrics_conf_iops, throughput=metrics_conf_throughput) it = create_all_iterable_source if multi_points == 1: From 47067268b7b8266fbd18f04cdba63bb4e6b047e6 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Fri, 22 Dec 2023 09:25:20 +0100 Subject: [PATCH 14/41] Fixing tests --- test/test_iterstream/test_stream.py | 1 + test/test_iterstream/test_torch_composables.py | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/test/test_iterstream/test_stream.py b/test/test_iterstream/test_stream.py index 83aa14a..07abb06 100644 --- a/test/test_iterstream/test_stream.py +++ b/test/test_iterstream/test_stream.py @@ -495,6 +495,7 @@ def test_metrics_tracking_with_wandb( .collect() ) + @pytest.mark.parametrize("metrics_conf_iops", [True, False]) @pytest.mark.parametrize("metrics_conf_throughput", [True, False]) @pytest.mark.parametrize("multi_points", [1, 2]) diff --git a/test/test_iterstream/test_torch_composables.py b/test/test_iterstream/test_torch_composables.py index b3787c5..e3fb601 100644 --- a/test/test_iterstream/test_torch_composables.py +++ b/test/test_iterstream/test_torch_composables.py @@ -93,7 +93,7 @@ def test_multi_worker_torch_iterable_async_map(samples: List[int]) -> None: @mock.patch("torch.distributed.is_available", mock.MagicMock(return_value=True)) @mock.patch("torch.distributed.is_initialized", mock.MagicMock(return_value=True)) -@mock.patch("torch.distributed.group.WORLD", mock.MagicMock(return_value="WORLD")) +# @mock.patch("torch.distributed.group.WORLD", mock.MagicMock(return_value="WORLD")) @mock.patch("torch.distributed.get_world_size") @mock.patch("torch.distributed.get_rank") def test_multi_rank_torch_iterable(mock_get_rank: int, mock_get_world_size: int, samples: List[int]) -> None: @@ -109,7 +109,7 @@ def test_multi_rank_torch_iterable(mock_get_rank: int, mock_get_world_size: int, @mock.patch("torch.distributed.is_available", mock.MagicMock(return_value=True)) @mock.patch("torch.distributed.is_initialized", mock.MagicMock(return_value=True)) -@mock.patch("torch.distributed.group.WORLD", mock.MagicMock(return_value="WORLD")) +# @mock.patch("torch.distributed.group.WORLD", mock.MagicMock(return_value="WORLD")) @mock.patch("torch.distributed.get_world_size") @mock.patch("torch.distributed.get_rank") def test_multi_rank_multi_worker_torch_iterable( @@ -181,7 +181,7 @@ def _cb(x: Any) -> Any: @mock.patch("torch.distributed.is_available", mock.MagicMock(return_value=True)) @mock.patch("torch.distributed.is_initialized", mock.MagicMock(return_value=True)) -@mock.patch("torch.distributed.group.WORLD", mock.MagicMock(return_value="WORLD")) +# @mock.patch("torch.distributed.group.WORLD", mock.MagicMock(return_value="WORLD")) @mock.patch("torch.distributed.get_rank", mock.MagicMock(return_value=4)) @mock.patch("torch.distributed.get_world_size", mock.MagicMock(return_value=4)) @mock.patch("torch.utils.data.get_worker_info") From 8a2735766d20cff956d613391595dd00183e1030 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Fri, 22 Dec 2023 09:36:03 +0100 Subject: [PATCH 15/41] Workaround poetry --- poetry.lock | 19 +- pyproject.toml | 2 + requirements.txt | 3757 ++++++++++++++++++++++++---------------------- 3 files changed, 1983 insertions(+), 1795 deletions(-) diff --git a/poetry.lock b/poetry.lock index d936719..36dee48 100644 --- a/poetry.lock +++ b/poetry.lock @@ -5640,23 +5640,6 @@ brotli = ["brotli (==1.0.9)", "brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotl secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"] socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] -[[package]] -name = "urllib3" -version = "2.0.7" -description = "HTTP library with thread-safe connection pooling, file post, and more." -optional = false -python-versions = ">=3.7" -files = [ - {file = "urllib3-2.0.7-py3-none-any.whl", hash = "sha256:fdb6d215c776278489906c2f8916e6e7d4f5a9b602ccbcfdf7f016fc8da0596e"}, - {file = "urllib3-2.0.7.tar.gz", hash = "sha256:c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84"}, -] - -[package.extras] -brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] -secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"] -socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] -zstd = ["zstandard (>=0.18.0)"] - [[package]] name = "virtualenv" version = "20.25.0" @@ -6053,4 +6036,4 @@ zarr = ["zarr"] [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "0095dbc6d3b6abbd77000e5c4aefe7e295b80eb9445ee624e67feae7496c2a2f" +content-hash = "514c7714cc2f911eff0cd5d8f3b477bc4e5892f0fb960b99a5389357eb73a020" diff --git a/pyproject.toml b/pyproject.toml index 3e32a88..79cc4a0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,6 +34,8 @@ mako = ">=1.2.4" # dependabot: GHSA-v973-fxgf-6xhp oauthlib = ">=3.2.2" # dependabot: GHSA-3pgj-pg6c-r5p7 aiohttp = ">=3.8.4" # dependabot: GHSA-q3qx-c6g2-7pw2 pandas = "<=1.5.3" # pin for dask compatibility (afterwards core.strings.Stringmethods is not available anymore) +# workaround for: https://github.com/python-poetry/poetry-plugin-export/issues/183 +urllib3 = ">=1.25.4,<1.27" numba = {version = ">=0.56.4", optional = true} adlfs = {version = "<2021.10", optional = true} dask = {version = ">=2021.10.0", optional = true, extras = ["dataframe", "distributed"]} # dependabot: GHSA-hwqr-f3v9-hwxr diff --git a/requirements.txt b/requirements.txt index 38cca64..2a307f7 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,11 +1,8 @@ -adal==1.2.7 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:2a7451ed7441ddbc57703042204a3e30ef747478eea022c70f789fc7f084bc3d \ - --hash=sha256:d74f45b81317454d96e982fd1c50e6fb5c99ac2223728aea8764433a39f566f1 adlfs==2021.9.1 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:0d9cae55be36b937d1dc6e803b83dcb415ea887279dd7757b040b4f1a39b65ea -aiobotocore==2.4.2 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:0603b74a582dffa7511ce7548d07dc9b10ec87bc5fb657eb0b34f9bd490958bf \ - --hash=sha256:4acd1ebe2e44be4b100aa553910bda899f6dc090b3da2bc1cf3d5de2146ed208 +aiobotocore==2.9.0 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:4dc1e20da4561ae662219ca95b20f923328c3106764a741bec00e98eb6680f7e \ + --hash=sha256:acf5e49644e6e434b9ecc26284ae7e05d557effbdcdd8185e2eb08925f011853 aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:02ab6006ec3c3463b528374c4cdce86434e7b89ad355e7bf29e2f16b46c7dd6f \ --hash=sha256:04fa38875e53eb7e354ece1607b1d2fdee2d175ea4e4d745f6ec9f751fe20c7c \ @@ -92,13 +89,16 @@ aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "4.0" \ alabaster==0.7.13 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3 \ --hash=sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2 -alembic==1.9.4 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:4d3bd32ecdbb7bbfb48a9fe9e6d6fd6a831a1b59d03e26e292210237373e7db5 \ - --hash=sha256:6f1c2207369bf4f49f952057a33bb017fbe5c148c2a773b46906b806ea6e825f +alembic==1.13.1 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:2edcc97bed0bd3272611ce3a98d98279e9c209e7186e43e75bbb1b2bdfdbcc43 \ + --hash=sha256:4932c8558bf68f2ee92b9bbcb8218671c627064d5b08939437af6d77dc05e595 +anyio==4.2.0 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:745843b39e829e108e518c489b31dc757de7d2131d53fac32bd8df268227bfee \ + --hash=sha256:e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f appdirs==1.4.4 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41 \ --hash=sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128 -appnope==0.1.3 ; python_version >= "3.8" and python_version < "4.0" and platform_system == "Darwin" or python_version >= "3.8" and python_version < "4.0" and sys_platform == "darwin" \ +appnope==0.1.3 ; python_version >= "3.8" and python_version < "4.0" and (platform_system == "Darwin" or sys_platform == "darwin") \ --hash=sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24 \ --hash=sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e asciitree==0.3.3 ; python_version >= "3.8" and python_version < "4.0" \ @@ -106,429 +106,412 @@ asciitree==0.3.3 ; python_version >= "3.8" and python_version < "4.0" \ astroid==2.14.2 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:0e0e3709d64fbffd3037e4ff403580550f14471fd3eaae9fa11cc9a5c7901153 \ --hash=sha256:a3cf9f02c53dd259144a7e8f3ccd75d67c9a8c716ef183e0c1f291bc5d7bb3cf -asttokens==2.2.1 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:4622110b2a6f30b77e1473affaa97e711bc2f07d3f10848420ff1898edbe94f3 \ - --hash=sha256:6b0ac9e93fb0335014d382b8fa9b3afa7df546984258005da0b9e7095b3deb1c -async-timeout==4.0.2 ; python_version >= "3.8" and python_version < "3.11" \ - --hash=sha256:2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15 \ - --hash=sha256:8ca1e4fcf50d07413d66d1a5e416e42cfdf5851c981d679a09851a6853383b3c -atomicwrites==1.4.1 ; python_version >= "3.8" and python_version < "4.0" and sys_platform == "win32" \ - --hash=sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11 -attrs==22.2.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:29e95c7f6778868dbd49170f98f8818f78f3dc5e0e37c0b1f474e3561b240836 \ - --hash=sha256:c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99 -autopep8==1.7.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:6f09e90a2be784317e84dc1add17ebfc7abe3924239957a37e5040e27d812087 \ - --hash=sha256:ca9b1a83e53a7fad65d731dc7a2a2d50aa48f43850407c59f6a1a306c4201142 -azure-core==1.26.3 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:acbd0daa9675ce88623da35c80d819cdafa91731dee6b2695c64d7ca9da82db4 \ - --hash=sha256:f7bad0a7b4d800d6e73733ea7e13a616016221ac111ff9a344fe4cba41e51bbe -azure-datalake-store==0.0.52 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:4198ddb32614d16d4502b43d5c9739f81432b7e0e4d75d30e05149fe6007fea2 \ - --hash=sha256:aaed72b9c856824aeab554f4dbe0ef2c6d0ff36700bdd8b93d8298793117c48e -azure-identity==1.12.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:2a58ce4a209a013e37eaccfd5937570ab99e9118b3e1acf875eed3a85d541b92 \ - --hash=sha256:7f9b1ae7d97ea7af3f38dd09305e19ab81a1e16ab66ea186b6579d85c1ca2347 -azure-storage-blob==12.15.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:08d8807c577c63a436740627927c1a03a97c963efc29af5c818aed906590e1cf \ - --hash=sha256:f8b8d582492740ab16744455408342fb8e4c8897b64a8a3fc31743844722c2f2 -babel==2.12.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:468e6cd1e2b571a1663110fc737e3a7d9069d038e0c9c4a7f158caeeafe4089c \ - --hash=sha256:8f8b752c803e9f9e03ff219b644aceb0dbcf081c55a88ea11f86291e60a7bb68 +asttokens==2.4.1 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24 \ + --hash=sha256:b03869718ba9a6eb027e134bfdf69f38a236d681c83c160d510768af11254ba0 +async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11" \ + --hash=sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f \ + --hash=sha256:7405140ff1230c310e51dc27b3145b9092d659ce68ff733fb0cefe3ee42be028 +attrs==23.1.0 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04 \ + --hash=sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015 +autopep8==2.0.4 ; python_version >= "3.8" and python_version < "4.0" \ + 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--hash=sha256:1347a4b3a1e5273672fd7a87471409e1bac470b4bdb6788c918313d45a22911b \ - --hash=sha256:34e9266af2bd24f14e4449934d900300ad994bb2c6929a56fbe7d0e398a3ed07 +distlib==0.3.8 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:034db59a0b96f8ca18035f36290806a9a6e6bd9d1ff91e45a7f172eb17e51784 \ + --hash=sha256:1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64 +distributed==2023.5.0 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:73ce33bd2460bd45ffc793ffdf9066bd2a3b6bbc65079f74f5147eafcda9b1cb \ + --hash=sha256:74e3f7f68d4dc435a3591ae1ad8ce7d5a11211fd22692e39c7e50aa11bf7e385 docker-pycreds==0.4.0 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:6ce3270bcaf404cc4c3e27e4b6c70d3521deae82fb508767870fdbf772d584d4 \ --hash=sha256:7266112468627868005106ec19cd0d722702d2b7d5912a28e19b826c3d37af49 -docker==6.0.1 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97 \ - --hash=sha256:dbcb3bd2fa80dca0788ed908218bf43972772009b881ed1e20dfc29a65e49782 +docker==6.1.3 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:aa6d17830045ba5ef0168d5eaa34d37beeb113948c413affe1d5991fc11f9a20 \ + --hash=sha256:aecd2277b8bf8e506e484f6ab7aec39abe0038e29fa4a6d3ba86c3fe01844ed9 docutils==0.16 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:0c5b78adfbf7762415433f5515cd5c9e762339e23369dbe8000d84a4bf4ab3af \ --hash=sha256:c2de3a60e9e7d07be26b7f2b00ca0309c207e06c100f9cc2a94931fc75a478fc @@ -541,132 +524,175 @@ et-xmlfile==1.1.0 ; python_version >= "3.8" and python_version < "4.0" \ exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11" \ --hash=sha256:4bfd3996ac73b41e9b9628b04e079f193850720ea5945fc96a08633c66912f14 \ --hash=sha256:91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68 -execnet==1.9.0 ; python_version >= 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--hash=sha256:e0381b4ce23ff92f8170080c97678040fc5b08da85e9e292292aba67fdac6c34 \ + --hash=sha256:e23a6d84d9d1738dbc6e38167776107e63307dfc8ad108e580548d1f2c587f42 \ + --hash=sha256:e516dc8baf7b380e6c1c26792610230f37147bb754d6426462ab115a02944385 \ + --hash=sha256:ea65804b5dc88dacd4a40279af0cdadcfe74b3e5b4c897aa0d81cf86927fee78 \ + --hash=sha256:ec61d826d80fc293ed46c9dd26995921e3a82146feacd952ef0757236fc137be \ + --hash=sha256:ee04010f26d5102399bd17f8df8bc38dc7ccd7701dc77f4a68c5b8d733406958 \ + --hash=sha256:f3bc6af6e2b8f92eced34ef6a96ffb248e863af20ef4fde9448cc8c9b858b749 \ + --hash=sha256:f7d6b36dd2e029b6bcb8a13cf19664c7b8e19ab3a58e0fefbb5b8461447ed5ec +zarr==2.16.1 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:4276cf4b4a653431042cd53ff2282bc4d292a6842411e88529964504fb073286 \ + --hash=sha256:de4882433ccb5b42cc1ec9872b95e64ca3a13581424666b28ed265ad76c7056f +zict==3.0.0 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:5796e36bd0e0cc8cf0fbc1ace6a68912611c1dbd74750a3f3026b9b9d6a327ae \ + --hash=sha256:e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5 +zipp==3.17.0 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31 \ + --hash=sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0 From 5acb682e156462e5bfeb9a0d38fa06ff4111811f Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Fri, 22 Dec 2023 09:38:59 +0100 Subject: [PATCH 16/41] Holy lint --- requirements.txt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/requirements.txt b/requirements.txt index 2a307f7..c67a6bc 100644 --- a/requirements.txt +++ b/requirements.txt @@ -98,7 +98,7 @@ anyio==4.2.0 ; python_version >= "3.8" and python_version < "4.0" \ appdirs==1.4.4 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41 \ --hash=sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128 -appnope==0.1.3 ; python_version >= "3.8" and python_version < "4.0" and (platform_system == "Darwin" or sys_platform == "darwin") \ +appnope==0.1.3 ; python_version >= "3.8" and python_version < "4.0" and platform_system == "Darwin" or python_version >= "3.8" and python_version < "4.0" and sys_platform == "darwin" \ --hash=sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24 \ --hash=sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e asciitree==0.3.3 ; python_version >= "3.8" and python_version < "4.0" \ @@ -324,7 +324,7 @@ click==8.0.4 ; python_version >= "3.8" and python_version < "4.0" \ cloudpickle==3.0.0 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:246ee7d0c295602a036e86369c77fecda4ab17b506496730f2f576d9016fd9c7 \ --hash=sha256:996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882 -colorama==0.4.6 ; python_version >= "3.8" and python_version < "4.0" and (platform_system == "Windows" or sys_platform == "win32" or os_name == "nt") \ +colorama==0.4.6 ; python_version >= "3.8" and python_version < "4.0" and platform_system == "Windows" or python_version >= "3.8" and python_version < "4.0" and sys_platform == "win32" or python_version >= "3.8" and python_version < "4.0" and os_name == "nt" \ --hash=sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44 \ --hash=sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6 colorclass==2.2.2 ; python_version >= "3.8" and python_version < "4.0" \ @@ -1574,7 +1574,7 @@ pre-commit==3.5.0 ; python_version >= "3.8" and python_version < "4.0" \ prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:3527b7af26106cbc65a040bcc84839a3566ec1b051bb0bfe953631e704b0ff7d \ --hash=sha256:a11a29cb3bf0a28a387fe5122cdb649816a957cd9261dcedf8c9f1fef33eacf6 -protobuf==4.25.1 ; python_version < "4.0" and python_version >= "3.8" \ +protobuf==4.25.1 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:0bf384e75b92c42830c0a679b0cd4d6e2b36ae0cf3dbb1e1dfdda48a244f4bcd \ --hash=sha256:0f881b589ff449bf0b931a711926e9ddaad3b35089cc039ce1af50b21a4ae8cb \ --hash=sha256:1484f9e692091450e7edf418c939e15bfc8fc68856e36ce399aed6889dae8bb0 \ @@ -1694,7 +1694,7 @@ pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "4.0" \ pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "4.0" and sys_platform == "win32" \ --hash=sha256:3426e063bdd5fd4df74a14fa3cf80a0b42845a87e1d1e81f6549f9daec593a60 \ --hash=sha256:bf490a1a709baf35d688fe0ecf980ed4de11d2b3e37b51e5442587a75d9957e7 -pywin32==306 ; python_version >= "3.8" and python_version < "4.0" and (sys_platform == "win32" or platform_system == "Windows") \ +pywin32==306 ; python_version >= "3.8" and python_version < "4.0" and sys_platform == "win32" or python_version >= "3.8" and python_version < "4.0" and platform_system == "Windows" \ --hash=sha256:06d3420a5155ba65f0b72f2699b5bacf3109f36acbe8923765c22938a69dfc8d \ --hash=sha256:1c73ea9a0d2283d889001998059f5eaaba3b6238f767c9cf2833b13e6a685f65 \ --hash=sha256:37257794c1ad39ee9be652da0462dc2e394c8159dfd913a8a4e8eb6fd346da0e \ @@ -2319,7 +2319,7 @@ typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "4.0" \ unidecode==1.3.7 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:3c90b4662aa0de0cb591884b934ead8d2225f1800d8da675a7750cbc3bd94610 \ --hash=sha256:663a537f506834ed836af26a81b210d90cbde044c47bfbdc0fbbc9f94c86a6e4 -urllib3==1.26.18 ; python_version >= "3.8" and python_version < "4.0" \ +urllib3==1.26.18 ; python_version < "4.0" and python_version >= "3.8" \ --hash=sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07 \ --hash=sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0 virtualenv==20.25.0 ; python_version >= "3.8" and python_version < "4.0" \ From 1f82dd5e37cdf0780025ba959cecc56252557f5c Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Mon, 23 Oct 2023 09:15:32 +0200 Subject: [PATCH 17/41] First stub --- squirrel/artifact_manager/__init__.py | 0 squirrel/artifact_manager/base.py | 89 +++++++++++++++++++ squirrel/artifact_manager/fs/__init__.py | 0 .../fs/fs_artifact_manager.py | 15 ++++ 4 files changed, 104 insertions(+) create mode 100644 squirrel/artifact_manager/__init__.py create mode 100644 squirrel/artifact_manager/base.py create mode 100644 squirrel/artifact_manager/fs/__init__.py create mode 100644 squirrel/artifact_manager/fs/fs_artifact_manager.py diff --git a/squirrel/artifact_manager/__init__.py b/squirrel/artifact_manager/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py new file mode 100644 index 0000000..5968d19 --- /dev/null +++ b/squirrel/artifact_manager/base.py @@ -0,0 +1,89 @@ +from abc import abstractmethod, ABC +from pathlib import Path +from typing import Optional, List, Union, Iterable, Tuple + +from squirrel.catalog import Catalog, Source +from squirrel.catalog.catalog import CatalogKey +from squirrel.iterstream import Composable +from squirrel.store import AbstractStore + + +class ArtifactManager(ABC): + def __init__(self, backend_store: AbstractStore): + self.backend: AbstractStore = backend_store + self._collection = "default" + + @abstractmethod + def _key_to_artifact(self, key: str) -> Tuple[str, str, str]: + """Transform key of underlying store to (collection, artifact, version) tuple.""" + raise NotImplementedError + + @abstractmethod + def _artifact_to_key(self, collection: str, artifact: str, version: str) -> str: + """Transform (collection, artifact, version) tuple to key of underlying store.""" + raise NotImplementedError + + @abstractmethod + def get_artifact_location(self, artifact, collection: Optional[str] = None, version: Optional[int] = None) -> str: + """Get full qualified path or wandb directory of artifact""" + raise NotImplementedError + + @property + def collection(self) -> str: + """ + Collections act as folders of artifacts. + + The manager maintains an 'active' collections which it logs to by default. + Depending on the backend, the collection can also point to a nested collection + (e.g. a subfolder on a filesystem). + """ + return self._collection + + @collection.setter + def collection(self, value: str) -> None: + """Do not allow access to anything beyond the root location of the artifact store""" + assert len(value) > 0 and "\\" not in value, "Invalid collection name - must not be empty and cannot be nested." + self._collection = value + + def get_catalog(self) -> Catalog: + """Return catalog of artifacts""" + cat = Catalog() + for key in self.backend.keys(): + collection, name, version = self._key_to_artifact(key) + cat[CatalogKey(f"{collection}/{name}", int(version))] = Source("file", ...) + return cat + + def get_collections(self) -> List[str]: + return list(set([self._key_to_artifact(entry)[0] for entry in self.backend.keys()])) + + def get_artifacts(self) -> Iterable: + """Iterator over all known artifacts""" + return Composable(self.backend.keys()).map(self._key_to_artifact) + + def get_collection_artifacts(self, collection: Optional[str] = None) -> List[str]: + """List all artifacts belonging to specific collection""" + if collection is None: + collection = self.collection + raise Composable(self.backend.keys()).map(self._key_to_artifact).filter(lambda x: x[0] == collection) + + def get_artifact_versions(self, artifact, collection: Optional[str] = None) -> List[str]: + """Get all available versions of artifact""" + raise NotImplementedError + + def fetch_artifact( + self, name: str, collection: Optional[str] = None, version: Optional[int] = None, to: Path = "./" + ): + """Retrieve file (from current collection) to specific location. Retrieve latest version unless specified.""" + raise NotImplementedError + + def fetch_collection(self, collection: Optional[str] = None, to: Path = "./"): + """Retrieve file (from current collection) to specific location. Retrieve latest version unless specified.""" + raise NotImplementedError + + def log_artifact(self, local_path: Path, name: str, collection: Optional[str] = None) -> None: + """Upload file into (current) collection, increment version automatically""" + raise NotImplementedError + + def log_collection(self, files: Union[Path, List[Path]], collection_name: Optional[str] = None) -> None: + """Upload folder or collection of files""" + raise NotImplementedError diff --git a/squirrel/artifact_manager/fs/__init__.py b/squirrel/artifact_manager/fs/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/squirrel/artifact_manager/fs/fs_artifact_manager.py b/squirrel/artifact_manager/fs/fs_artifact_manager.py new file mode 100644 index 0000000..8503cdb --- /dev/null +++ b/squirrel/artifact_manager/fs/fs_artifact_manager.py @@ -0,0 +1,15 @@ +from squirrel.artifact_manager.base import ArtifactManager +from squirrel.serialization import MessagepackSerializer +from squirrel.store import FilesystemStore + + +class FileSystemArtifactManager(ArtifactManager): + def __init__(self, url): + # TODO serialise to deltalake instead of messagepack underneath + # TODO introduce buffer logic to avoid single entry additions into deltalake + fs_store = FilesystemStore(url=url, serializer=MessagepackSerializer()) + super(FileSystemArtifactManager, self).__init__(fs_store) + + + + # TODO allow schema to be configured at initialisation \ No newline at end of file From 6ed3ba251c846000986ec07d29b675ea1a41b6e6 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Tue, 24 Oct 2023 16:40:14 +0200 Subject: [PATCH 18/41] Updated interface proposal --- squirrel/artifact_manager/base.py | 105 +++++++++--------- .../fs/fs_artifact_manager.py | 9 +- 2 files changed, 56 insertions(+), 58 deletions(-) diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index 5968d19..14f1f05 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -1,41 +1,31 @@ from abc import abstractmethod, ABC from pathlib import Path -from typing import Optional, List, Union, Iterable, Tuple +from typing import Optional, List, Union, Any, Iterable -from squirrel.catalog import Catalog, Source -from squirrel.catalog.catalog import CatalogKey -from squirrel.iterstream import Composable +from squirrel.catalog import Catalog +from squirrel.catalog.catalog import CatalogSource from squirrel.store import AbstractStore class ArtifactManager(ABC): def __init__(self, backend_store: AbstractStore): + """ + Artifact manager interface for various backends + + Maintains a mapping of artifact names to backend objects to facilitate logging and retrieval of arbitrary + artifacts. + """ self.backend: AbstractStore = backend_store self._collection = "default" - @abstractmethod - def _key_to_artifact(self, key: str) -> Tuple[str, str, str]: - """Transform key of underlying store to (collection, artifact, version) tuple.""" - raise NotImplementedError - - @abstractmethod - def _artifact_to_key(self, collection: str, artifact: str, version: str) -> str: - """Transform (collection, artifact, version) tuple to key of underlying store.""" - raise NotImplementedError - - @abstractmethod - def get_artifact_location(self, artifact, collection: Optional[str] = None, version: Optional[int] = None) -> str: - """Get full qualified path or wandb directory of artifact""" - raise NotImplementedError - @property def collection(self) -> str: """ Collections act as folders of artifacts. The manager maintains an 'active' collections which it logs to by default. - Depending on the backend, the collection can also point to a nested collection - (e.g. a subfolder on a filesystem). + To avoid incompatibility between different backends, collections cannot be nested (e.g. as subfolders on a + filesystem). """ return self._collection @@ -45,45 +35,54 @@ def collection(self, value: str) -> None: assert len(value) > 0 and "\\" not in value, "Invalid collection name - must not be empty and cannot be nested." self._collection = value - def get_catalog(self) -> Catalog: - """Return catalog of artifacts""" - cat = Catalog() - for key in self.backend.keys(): - collection, name, version = self._key_to_artifact(key) - cat[CatalogKey(f"{collection}/{name}", int(version))] = Source("file", ...) - return cat - - def get_collections(self) -> List[str]: - return list(set([self._key_to_artifact(entry)[0] for entry in self.backend.keys()])) - - def get_artifacts(self) -> Iterable: - """Iterator over all known artifacts""" - return Composable(self.backend.keys()).map(self._key_to_artifact) - - def get_collection_artifacts(self, collection: Optional[str] = None) -> List[str]: - """List all artifacts belonging to specific collection""" - if collection is None: - collection = self.collection - raise Composable(self.backend.keys()).map(self._key_to_artifact).filter(lambda x: x[0] == collection) - - def get_artifact_versions(self, artifact, collection: Optional[str] = None) -> List[str]: - """Get all available versions of artifact""" + @abstractmethod + def list_collection_names(self) -> Iterable: + """Return list of all collections in the artifact store""" raise NotImplementedError - def fetch_artifact( - self, name: str, collection: Optional[str] = None, version: Optional[int] = None, to: Path = "./" - ): - """Retrieve file (from current collection) to specific location. Retrieve latest version unless specified.""" + @abstractmethod + def store_to_catalog(self) -> Catalog: + """Provide a catalog of all stored artifacts.""" raise NotImplementedError - def fetch_collection(self, collection: Optional[str] = None, to: Path = "./"): - """Retrieve file (from current collection) to specific location. Retrieve latest version unless specified.""" + @abstractmethod + def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: + """Catalog of all artifacts within a specific collection.""" + + @abstractmethod + def get_artifact(self, artifact: str, collection: Optional[str] = None) -> CatalogSource: + """Catalog entry for a specific artifact""" raise NotImplementedError - def log_artifact(self, local_path: Path, name: str, collection: Optional[str] = None) -> None: - """Upload file into (current) collection, increment version automatically""" + @abstractmethod + def get_artifact_location( + self, artifact_name: str, collection: Optional[str] = None, version: Optional[int] = None + ) -> str: + """Get full qualified path or wandb directory of artifact""" raise NotImplementedError - def log_collection(self, files: Union[Path, List[Path]], collection_name: Optional[str] = None) -> None: + @abstractmethod + def log_file(self, local_path: Path, name: str, collection: Optional[str] = None) -> CatalogSource: + """Upload file into (current) collection, increment version automatically""" + + @abstractmethod + def log_collection(self, files: Union[Path, List[Path]], collection_name: Optional[str] = None) -> Catalog: """Upload folder or collection of files""" raise NotImplementedError + + @abstractmethod + def log_object(self, obj: Any, name: str, collection: Optional[str] = None) -> CatalogSource: + """Log an arbitrary python object""" + raise NotImplementedError + + @abstractmethod + def download_artifact( + self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None, to: Path = "./" + ) -> None: + """Retrieve file (from current collection) to specific location. Retrieve latest version unless specified.""" + raise NotImplementedError + + @abstractmethod + def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> None: + """Retrieve file (from current collection) to specific location. Retrieve latest version of all artifacts.""" + raise NotImplementedError diff --git a/squirrel/artifact_manager/fs/fs_artifact_manager.py b/squirrel/artifact_manager/fs/fs_artifact_manager.py index 8503cdb..00f6a02 100644 --- a/squirrel/artifact_manager/fs/fs_artifact_manager.py +++ b/squirrel/artifact_manager/fs/fs_artifact_manager.py @@ -4,12 +4,11 @@ class FileSystemArtifactManager(ArtifactManager): - def __init__(self, url): + def __init__(self, url: str): + """Artifact manager based by local or cloud filesystem.""" # TODO serialise to deltalake instead of messagepack underneath # TODO introduce buffer logic to avoid single entry additions into deltalake fs_store = FilesystemStore(url=url, serializer=MessagepackSerializer()) - super(FileSystemArtifactManager, self).__init__(fs_store) + super().__init__(fs_store) - - - # TODO allow schema to be configured at initialisation \ No newline at end of file + # TODO allow schema to be configured at initialisation From ce0aefd3da0ef35f0288f9b34703c72420b92861 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Thu, 26 Oct 2023 16:23:46 +0200 Subject: [PATCH 19/41] First draft of file artifact manager --- squirrel/artifact_manager/base.py | 22 +- .../fs/fs_artifact_manager.py | 196 +++++++++++++++++- test/test_artifact_manager/__init__.py | 0 test/test_artifact_manager/test_logging.py | 59 ++++++ 4 files changed, 258 insertions(+), 19 deletions(-) create mode 100644 test/test_artifact_manager/__init__.py create mode 100644 test/test_artifact_manager/test_logging.py diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index 14f1f05..4351fc5 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -2,20 +2,17 @@ from pathlib import Path from typing import Optional, List, Union, Any, Iterable -from squirrel.catalog import Catalog -from squirrel.catalog.catalog import CatalogSource -from squirrel.store import AbstractStore +from squirrel.catalog import Catalog, Source class ArtifactManager(ABC): - def __init__(self, backend_store: AbstractStore): + def __init__(self): """ Artifact manager interface for various backends Maintains a mapping of artifact names to backend objects to facilitate logging and retrieval of arbitrary artifacts. """ - self.backend: AbstractStore = backend_store self._collection = "default" @property @@ -50,7 +47,12 @@ def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: """Catalog of all artifacts within a specific collection.""" @abstractmethod - def get_artifact(self, artifact: str, collection: Optional[str] = None) -> CatalogSource: + def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None) -> Any: + """Retrieve specific artifact value.""" + raise NotImplementedError + + @abstractmethod + def get_artifact_source(self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None) -> Source: """Catalog entry for a specific artifact""" raise NotImplementedError @@ -62,7 +64,7 @@ def get_artifact_location( raise NotImplementedError @abstractmethod - def log_file(self, local_path: Path, name: str, collection: Optional[str] = None) -> CatalogSource: + def log_file(self, local_path: Path, name: str, collection: Optional[str] = None) -> Source: """Upload file into (current) collection, increment version automatically""" @abstractmethod @@ -71,18 +73,18 @@ def log_collection(self, files: Union[Path, List[Path]], collection_name: Option raise NotImplementedError @abstractmethod - def log_object(self, obj: Any, name: str, collection: Optional[str] = None) -> CatalogSource: + def log_object(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: """Log an arbitrary python object""" raise NotImplementedError @abstractmethod def download_artifact( self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None, to: Path = "./" - ) -> None: + ) -> Source: """Retrieve file (from current collection) to specific location. Retrieve latest version unless specified.""" raise NotImplementedError @abstractmethod - def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> None: + def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> Catalog: """Retrieve file (from current collection) to specific location. Retrieve latest version of all artifacts.""" raise NotImplementedError diff --git a/squirrel/artifact_manager/fs/fs_artifact_manager.py b/squirrel/artifact_manager/fs/fs_artifact_manager.py index 00f6a02..10a8aa3 100644 --- a/squirrel/artifact_manager/fs/fs_artifact_manager.py +++ b/squirrel/artifact_manager/fs/fs_artifact_manager.py @@ -1,14 +1,192 @@ +import typing as t +import os +from pathlib import Path +from typing import Optional, Any, Union, List, Iterable + from squirrel.artifact_manager.base import ArtifactManager -from squirrel.serialization import MessagepackSerializer +from squirrel.catalog import Catalog, Source +from squirrel.serialization import MessagepackSerializer, JsonSerializer, SquirrelSerializer from squirrel.store import FilesystemStore +from squirrel.store.filesystem import get_random_key + +Serializers = { + MessagepackSerializer: "messagepack", + JsonSerializer: "jsonl", +} + + +class ArtifactFileStore(FilesystemStore): + def complete_key(self, key: str, **open_kwargs) -> List[str]: + """Returns a list of possible key continuations given a partial key.""" + if not self.fs.exists(f"{self.url}/{key}", **open_kwargs): + return [] + return [os.path.relpath(path, f"{self.url}/{key}") for path in self.fs.ls(f"{self.url}/{key}", detail=False, **open_kwargs)] + + def key_exists(self, key: str, **open_kwargs) -> bool: + """Checks if a key exists.""" + return self.fs.exists(f"{self.url}/{key}", **open_kwargs) + + def get(self, key: str, mode: str = "rb", **open_kwargs) -> t.Any: + """Retrieves an item with the given key.""" + if self.fs.exists(f"{self.url}/{key}/{Serializers[self.serializer.__class__]}", **open_kwargs): + return super(ArtifactFileStore, self).get(f"{key}/{Serializers[self.serializer.__class__]}", mode, + **open_kwargs) + elif self.fs.exists(f"{self.url}/{key}/file", **open_kwargs): + return self.fs.cat(f"{self.url}/{key}/file", **open_kwargs) + else: + raise ValueError(f"Key {key} does not exist!") + + def set(self, value: t.Any, key: t.Optional[str] = None, mode: str = "wb", **open_kwargs) -> None: + """Persists an item with the given key.""" + if key is None: + key = get_random_key() + if isinstance(value, Path): + self.fs.cp(value, f"{self.url}/{key}/file", **open_kwargs) + else: + super(ArtifactFileStore, self).set(value, f"{key}/{Serializers[self.serializer.__class__]}", mode, + **open_kwargs) class FileSystemArtifactManager(ArtifactManager): - def __init__(self, url: str): - """Artifact manager based by local or cloud filesystem.""" - # TODO serialise to deltalake instead of messagepack underneath - # TODO introduce buffer logic to avoid single entry additions into deltalake - fs_store = FilesystemStore(url=url, serializer=MessagepackSerializer()) - super().__init__(fs_store) - - # TODO allow schema to be configured at initialisation + def __init__(self, url: str, serializer: Optional[SquirrelSerializer] = MessagepackSerializer(), **fs_kwargs): + super().__init__() + self.backend = ArtifactFileStore(url=url, serializer=serializer, **fs_kwargs) + + def list_collection_names(self) -> Iterable: + return self.backend.keys(nested=False) + + def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None) -> Any: + """Retrieve specific artifact value.""" + if collection is None: + collection = self.collection + if version is None: + version = len(self.backend.complete_key(os.path.join(collection, artifact))) + if not self.backend.key_exists(os.path.join(collection, artifact, str(version))): + raise ValueError(f"Artifact {artifact} does not exist in collection {collection} with version {version}!") + path = os.path.join(collection, artifact, str(version)) + return self.backend.get(path) + + def get_artifact_source( + self, + artifact: str, + collection: Optional[str] = None, + version: Optional[int] = None + ) -> Source: + """Catalog entry for a specific artifact""" + if collection is None: + collection = self.collection + if version is None: + version = len(self.backend.complete_key(os.path.join(collection, artifact))) + if not self.backend.key_exists(os.path.join(collection, artifact, str(version))): + raise ValueError(f"Artifact {artifact} does not exist in collection {collection} with version {version}!") + + if (encoding := Serializers[self.backend.serializer.__class__]) in self.backend.complete_key(os.path.join(collection, artifact, str(version))): + return Source( + driver_name=encoding, + driver_kwargs={ + "url": os.path.join(self.backend.url, collection, artifact, str(version), encoding), + "storage_options": self.backend.storage_options + }, + metadata={ + "collection": collection, + "artifact": artifact, + "version": version + } + ) + elif self.backend.fs.exists(os.path.join(collection, artifact, str(version), "file")): + return Source( + driver_name="file", + driver_kwargs={ + "url": os.path.join(self.backend.url, collection, artifact, str(version), "file"), + "storage_options": self.backend.storage_options + }, + metadata={ + "collection": collection, + "artifact": artifact, + "version": version + } + ) + else: + raise ValueError(f"Could not read artifact {artifact} in collection {collection} with version {version}!") + + def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: + """Provide catalog of all artifacts and their versions contained within specific collection""" + if collection is None: + collection = self.collection + catalog = Catalog() + for artifact in self.backend.complete_key(collection): + for version in self.backend.complete_key(os.path.join(collection, artifact)): + catalog[os.path.join(collection, artifact)] = self.get_artifact_source(artifact, collection, int(version)) + return catalog + + def store_to_catalog(self) -> Catalog: + """Provide Catalog of all artifacts stored in backend""" + catalog = Catalog() + for collection in self.list_collection_names(): + catalog.update(self.collection_to_catalog(collection)) + return catalog + + def get_artifact_location(self, artifact: str, collection: Optional[str] = None, + version: Optional[int] = None) -> str: + """Get full qualified path or wandb directory of artifact""" + return self.get_artifact_source(artifact, collection, version).driver_kwargs["url"] + + def log_file(self, local_path: Path, name: str, collection: Optional[str] = None) -> Source: + """Upload local file to artifact store without serialisation""" + if collection is None: + collection = self.collection + version = len(self.backend.complete_key(os.path.join(collection, name))) + 1 + self.backend.set(local_path, os.path.join(collection, name, str(version))) + return self.get_artifact_source(name, collection) + + def log_collection(self, files: Union[Path, List[Path]], collection_name: Optional[str] = None) -> Catalog: + """Log folder or set of local paths as collection of artifacts into store""" + if isinstance(files, Path) and files.is_dir(): + if collection_name is None: + collection_name = files + files = list(files.iterdir()) + elif isinstance(files, Path): + raise ValueError(f"Path {files} is not a directory!") + else: + if collection_name is None: + raise ValueError("Collection name must be specified if files is not a directory!") + for file in files: + if file.is_file(): + self.log_file(file, file.name, collection_name) + return self.collection_to_catalog(collection_name) + + def log_object(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: + """Log an arbitrary python object using store serialisation.""" + if collection is None: + collection = self.collection + if self.backend.key_exists(os.path.join(collection, name)): + version = len(self.backend.complete_key(os.path.join(collection, name))) + 1 + else: + version = 1 + self.backend.set(obj, os.path.join(collection, name, str(version))) + return self.get_artifact_source(name, collection) + + def download_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None, + to: Path = "./") -> Source: + location = self.get_artifact_location(artifact, collection, version) + if self.backend.fs.exists(location): + self.backend.fs.cp(location, to) + return Source( + driver_name="file", + driver_kwargs={ + "url": str(to), + "storage_options": self.backend.storage_options + }, + metadata={ + "collection": collection, + "artifact": artifact, + "version": version + } + ) + + def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> Catalog: + catalog = self.collection_to_catalog(collection) + for artifact in catalog.values(): + artifact_name = artifact.metadata["artifact"] + self.download_artifact(artifact_name, to=to / artifact_name) + return catalog diff --git a/test/test_artifact_manager/__init__.py b/test/test_artifact_manager/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/test/test_artifact_manager/test_logging.py b/test/test_artifact_manager/test_logging.py new file mode 100644 index 0000000..f95c5d4 --- /dev/null +++ b/test/test_artifact_manager/test_logging.py @@ -0,0 +1,59 @@ +import tempfile + +from squirrel.artifact_manager.fs.fs_artifact_manager import FileSystemArtifactManager + + +def test_log_object() -> None: + """ + Log an object to the default collection and check details of the catalog entry. + """ + obj = {"name": "John", "age": 30} + artifact_name = "john" + collection = "my_collection" + + tmpdir = tempfile.TemporaryDirectory() + manager = FileSystemArtifactManager(url=tmpdir.name, auto_mkdir=True) + source = manager.log_object(obj, artifact_name) + + assert source.driver_name == "messagepack" + assert source.driver_kwargs["url"] == f"{tmpdir.name}/default/{artifact_name}/1/messagepack" + assert source.metadata["collection"] == "default" + assert source.metadata["artifact"] == artifact_name + assert source.metadata["version"] == 1 + + obj2 = {"name": "John", "age": 15} + artifact_name = "young_john" + + source2 = manager.log_object(obj2, artifact_name, collection) + assert source2.driver_kwargs["url"] == f"{tmpdir.name}/{collection}/{artifact_name}/1/messagepack" + assert source2.metadata["collection"] == collection + assert source2.metadata["artifact"] == artifact_name + assert source2.metadata["version"] == 1 + + source2 = manager.log_object(obj2, artifact_name, collection) + assert source2.driver_kwargs["url"] == f"{tmpdir.name}/{collection}/{artifact_name}/2/messagepack" + assert source2.metadata["collection"] == collection + assert source2.metadata["artifact"] == artifact_name + assert source2.metadata["version"] == 2 + tmpdir.cleanup() + + +def test_get_artifact() -> None: + """Test logging multiple versions of the same object and retrieving different versions.""" + obj = {"name": "John", "age": 10} + obj1 = {"name": "John", "age": 20} + obj2 = {"name": "John", "age": 30} + artifact_name = "john" + collection = "my_collection" + + tmpdir = tempfile.TemporaryDirectory() + manager = FileSystemArtifactManager(url=tmpdir.name, auto_mkdir=True) + manager.log_object(obj, artifact_name, collection) + assert manager.get_artifact("john", collection) == obj + manager.log_object(obj1, artifact_name, collection) + assert manager.get_artifact("john", collection) == obj1 + manager.log_object(obj2, artifact_name, collection) + assert manager.get_artifact(artifact_name, collection) == obj2 + assert manager.get_artifact(artifact_name, collection, 2) == obj1 + assert manager.get_artifact(artifact_name, collection, 1) == obj + From 458270ac7508dd9264d98a686aaec16987dc189b Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Thu, 26 Oct 2023 18:12:10 +0200 Subject: [PATCH 20/41] Linting --- squirrel/artifact_manager/base.py | 4 +- .../{fs/fs_artifact_manager.py => fs.py} | 79 ++++++++++--------- squirrel/artifact_manager/fs/__init__.py | 0 squirrel/artifact_manager/wandb.py | 46 +++++++++++ test/test_artifact_manager/test_logging.py | 7 +- 5 files changed, 91 insertions(+), 45 deletions(-) rename squirrel/artifact_manager/{fs/fs_artifact_manager.py => fs.py} (77%) delete mode 100644 squirrel/artifact_manager/fs/__init__.py create mode 100644 squirrel/artifact_manager/wandb.py diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index 4351fc5..6d242e6 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -52,7 +52,9 @@ def get_artifact(self, artifact: str, collection: Optional[str] = None, version: raise NotImplementedError @abstractmethod - def get_artifact_source(self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None) -> Source: + def get_artifact_source( + self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None + ) -> Source: """Catalog entry for a specific artifact""" raise NotImplementedError diff --git a/squirrel/artifact_manager/fs/fs_artifact_manager.py b/squirrel/artifact_manager/fs.py similarity index 77% rename from squirrel/artifact_manager/fs/fs_artifact_manager.py rename to squirrel/artifact_manager/fs.py index 10a8aa3..cacda51 100644 --- a/squirrel/artifact_manager/fs/fs_artifact_manager.py +++ b/squirrel/artifact_manager/fs.py @@ -20,7 +20,10 @@ def complete_key(self, key: str, **open_kwargs) -> List[str]: """Returns a list of possible key continuations given a partial key.""" if not self.fs.exists(f"{self.url}/{key}", **open_kwargs): return [] - return [os.path.relpath(path, f"{self.url}/{key}") for path in self.fs.ls(f"{self.url}/{key}", detail=False, **open_kwargs)] + return [ + os.path.relpath(path, f"{self.url}/{key}") + for path in self.fs.ls(f"{self.url}/{key}", detail=False, **open_kwargs) + ] def key_exists(self, key: str, **open_kwargs) -> bool: """Checks if a key exists.""" @@ -29,8 +32,7 @@ def key_exists(self, key: str, **open_kwargs) -> bool: def get(self, key: str, mode: str = "rb", **open_kwargs) -> t.Any: """Retrieves an item with the given key.""" if self.fs.exists(f"{self.url}/{key}/{Serializers[self.serializer.__class__]}", **open_kwargs): - return super(ArtifactFileStore, self).get(f"{key}/{Serializers[self.serializer.__class__]}", mode, - **open_kwargs) + return super().get(f"{key}/{Serializers[self.serializer.__class__]}", mode, **open_kwargs) elif self.fs.exists(f"{self.url}/{key}/file", **open_kwargs): return self.fs.cat(f"{self.url}/{key}/file", **open_kwargs) else: @@ -43,16 +45,19 @@ def set(self, value: t.Any, key: t.Optional[str] = None, mode: str = "wb", **ope if isinstance(value, Path): self.fs.cp(value, f"{self.url}/{key}/file", **open_kwargs) else: - super(ArtifactFileStore, self).set(value, f"{key}/{Serializers[self.serializer.__class__]}", mode, - **open_kwargs) + super().set(value, f"{key}/{Serializers[self.serializer.__class__]}", mode, **open_kwargs) class FileSystemArtifactManager(ArtifactManager): - def __init__(self, url: str, serializer: Optional[SquirrelSerializer] = MessagepackSerializer(), **fs_kwargs): + def __init__(self, url: str, serializer: Optional[SquirrelSerializer] = None, **fs_kwargs): + """Artifactmanager backed by fsspec filesystems.""" super().__init__() + if serializer is None: + serializer = MessagepackSerializer() self.backend = ArtifactFileStore(url=url, serializer=serializer, **fs_kwargs) def list_collection_names(self) -> Iterable: + """List all collections managed by this ArtifactManager.""" return self.backend.keys(nested=False) def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None) -> Any: @@ -67,10 +72,7 @@ def get_artifact(self, artifact: str, collection: Optional[str] = None, version: return self.backend.get(path) def get_artifact_source( - self, - artifact: str, - collection: Optional[str] = None, - version: Optional[int] = None + self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None ) -> Source: """Catalog entry for a specific artifact""" if collection is None: @@ -80,31 +82,31 @@ def get_artifact_source( if not self.backend.key_exists(os.path.join(collection, artifact, str(version))): raise ValueError(f"Artifact {artifact} does not exist in collection {collection} with version {version}!") - if (encoding := Serializers[self.backend.serializer.__class__]) in self.backend.complete_key(os.path.join(collection, artifact, str(version))): + if Serializers[self.backend.serializer.__class__] in self.backend.complete_key( + os.path.join(collection, artifact, str(version)) + ): return Source( - driver_name=encoding, + driver_name=Serializers[self.backend.serializer.__class__], driver_kwargs={ - "url": os.path.join(self.backend.url, collection, artifact, str(version), encoding), - "storage_options": self.backend.storage_options + "url": os.path.join( + self.backend.url, + collection, + artifact, + str(version), + Serializers[self.backend.serializer.__class__], + ), + "storage_options": self.backend.storage_options, }, - metadata={ - "collection": collection, - "artifact": artifact, - "version": version - } + metadata={"collection": collection, "artifact": artifact, "version": version}, ) elif self.backend.fs.exists(os.path.join(collection, artifact, str(version), "file")): return Source( driver_name="file", driver_kwargs={ "url": os.path.join(self.backend.url, collection, artifact, str(version), "file"), - "storage_options": self.backend.storage_options + "storage_options": self.backend.storage_options, }, - metadata={ - "collection": collection, - "artifact": artifact, - "version": version - } + metadata={"collection": collection, "artifact": artifact, "version": version}, ) else: raise ValueError(f"Could not read artifact {artifact} in collection {collection} with version {version}!") @@ -116,7 +118,9 @@ def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: catalog = Catalog() for artifact in self.backend.complete_key(collection): for version in self.backend.complete_key(os.path.join(collection, artifact)): - catalog[os.path.join(collection, artifact)] = self.get_artifact_source(artifact, collection, int(version)) + catalog[os.path.join(collection, artifact)] = self.get_artifact_source( + artifact, collection, int(version) + ) return catalog def store_to_catalog(self) -> Catalog: @@ -126,8 +130,9 @@ def store_to_catalog(self) -> Catalog: catalog.update(self.collection_to_catalog(collection)) return catalog - def get_artifact_location(self, artifact: str, collection: Optional[str] = None, - version: Optional[int] = None) -> str: + def get_artifact_location( + self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None + ) -> str: """Get full qualified path or wandb directory of artifact""" return self.get_artifact_source(artifact, collection, version).driver_kwargs["url"] @@ -166,25 +171,21 @@ def log_object(self, obj: Any, name: str, collection: Optional[str] = None) -> S self.backend.set(obj, os.path.join(collection, name, str(version))) return self.get_artifact_source(name, collection) - def download_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None, - to: Path = "./") -> Source: + def download_artifact( + self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None, to: Path = "./" + ) -> Source: + """Download artifact to local path.""" location = self.get_artifact_location(artifact, collection, version) if self.backend.fs.exists(location): self.backend.fs.cp(location, to) return Source( driver_name="file", - driver_kwargs={ - "url": str(to), - "storage_options": self.backend.storage_options - }, - metadata={ - "collection": collection, - "artifact": artifact, - "version": version - } + driver_kwargs={"url": str(to), "storage_options": self.backend.storage_options}, + metadata={"collection": collection, "artifact": artifact, "version": version}, ) def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> Catalog: + """Download all artifacts in collection to local directory.""" catalog = self.collection_to_catalog(collection) for artifact in catalog.values(): artifact_name = artifact.metadata["artifact"] diff --git a/squirrel/artifact_manager/fs/__init__.py b/squirrel/artifact_manager/fs/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/squirrel/artifact_manager/wandb.py b/squirrel/artifact_manager/wandb.py new file mode 100644 index 0000000..15b9cff --- /dev/null +++ b/squirrel/artifact_manager/wandb.py @@ -0,0 +1,46 @@ +from pathlib import Path +from typing import Optional, Any, Union, List, Iterable + +from squirrel.artifact_manager.base import ArtifactManager +from squirrel.catalog import Catalog, Source + + +class WandbArtifactManager(ArtifactManager): + def list_collection_names(self) -> Iterable: + pass + + def store_to_catalog(self) -> Catalog: + pass + + def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: + pass + + def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None) -> Any: + pass + + def get_artifact_source(self, artifact: str, collection: Optional[str] = None, + version: Optional[int] = None) -> Source: + pass + + def get_artifact_location(self, artifact_name: str, collection: Optional[str] = None, + version: Optional[int] = None) -> str: + pass + + def log_file(self, local_path: Path, name: str, collection: Optional[str] = None) -> Source: + pass + + def log_collection(self, files: Union[Path, List[Path]], collection_name: Optional[str] = None) -> Catalog: + pass + + def log_object(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: + pass + + def download_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None, + to: Path = "./") -> Source: + pass + + def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> Catalog: + pass + + def __init__(self): + super().__init__() diff --git a/test/test_artifact_manager/test_logging.py b/test/test_artifact_manager/test_logging.py index f95c5d4..d186617 100644 --- a/test/test_artifact_manager/test_logging.py +++ b/test/test_artifact_manager/test_logging.py @@ -1,12 +1,10 @@ import tempfile -from squirrel.artifact_manager.fs.fs_artifact_manager import FileSystemArtifactManager +from squirrel.artifact_manager.fs.fs import FileSystemArtifactManager def test_log_object() -> None: - """ - Log an object to the default collection and check details of the catalog entry. - """ + """Log an object to the default collection and check details of the catalog entry.""" obj = {"name": "John", "age": 30} artifact_name = "john" collection = "my_collection" @@ -56,4 +54,3 @@ def test_get_artifact() -> None: assert manager.get_artifact(artifact_name, collection) == obj2 assert manager.get_artifact(artifact_name, collection, 2) == obj1 assert manager.get_artifact(artifact_name, collection, 1) == obj - From 51fe46a500809748f9063d6dc98e7b1a6c478e89 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Tue, 7 Nov 2023 14:05:37 +0100 Subject: [PATCH 21/41] Integrating first round of feedback --- squirrel/artifact_manager/base.py | 15 ++-- squirrel/artifact_manager/fs.py | 92 ++++++++++++---------- squirrel/artifact_manager/wandb.py | 4 + test/test_artifact_manager/test_logging.py | 20 ++--- 4 files changed, 74 insertions(+), 57 deletions(-) diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index 6d242e6..56788fb 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -1,3 +1,4 @@ +import re from abc import abstractmethod, ABC from pathlib import Path from typing import Optional, List, Union, Any, Iterable @@ -13,7 +14,7 @@ def __init__(self): Maintains a mapping of artifact names to backend objects to facilitate logging and retrieval of arbitrary artifacts. """ - self._collection = "default" + self._active_collection = "default" @property def collection(self) -> str: @@ -24,13 +25,15 @@ def collection(self) -> str: To avoid incompatibility between different backends, collections cannot be nested (e.g. as subfolders on a filesystem). """ - return self._collection + return self._active_collection @collection.setter def collection(self, value: str) -> None: """Do not allow access to anything beyond the root location of the artifact store""" - assert len(value) > 0 and "\\" not in value, "Invalid collection name - must not be empty and cannot be nested." - self._collection = value + assert re.match(r'^[a-zA-Z0-9\-_:]+$', value), \ + ("Invalid collection name - must not be empty and can only contain alphanumerics, dashes, underscores and " + "colons.") + self._active_collection = value @abstractmethod def list_collection_names(self) -> Iterable: @@ -70,12 +73,12 @@ def log_file(self, local_path: Path, name: str, collection: Optional[str] = None """Upload file into (current) collection, increment version automatically""" @abstractmethod - def log_collection(self, files: Union[Path, List[Path]], collection_name: Optional[str] = None) -> Catalog: + def log_collection(self, files: Union[Path, List[Path]], collection: Optional[str] = None) -> Catalog: """Upload folder or collection of files""" raise NotImplementedError @abstractmethod - def log_object(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: + def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: """Log an arbitrary python object""" raise NotImplementedError diff --git a/squirrel/artifact_manager/fs.py b/squirrel/artifact_manager/fs.py index cacda51..d0a96dc 100644 --- a/squirrel/artifact_manager/fs.py +++ b/squirrel/artifact_manager/fs.py @@ -1,5 +1,4 @@ import typing as t -import os from pathlib import Path from typing import Optional, Any, Union, List, Iterable @@ -16,41 +15,52 @@ class ArtifactFileStore(FilesystemStore): - def complete_key(self, key: str, **open_kwargs) -> List[str]: + def complete_key(self, partial_key: Path, **open_kwargs) -> List[str]: """Returns a list of possible key continuations given a partial key.""" - if not self.fs.exists(f"{self.url}/{key}", **open_kwargs): + full_path = Path(self.url, partial_key) + if not self.fs.exists(full_path, **open_kwargs): return [] return [ - os.path.relpath(path, f"{self.url}/{key}") - for path in self.fs.ls(f"{self.url}/{key}", detail=False, **open_kwargs) + str(Path(path).relative_to(full_path)) + for path in self.fs.ls(full_path, detail=False, **open_kwargs) ] - def key_exists(self, key: str, **open_kwargs) -> bool: + def key_exists(self, key: Path, **open_kwargs) -> bool: """Checks if a key exists.""" - return self.fs.exists(f"{self.url}/{key}", **open_kwargs) + return self.fs.exists(Path(self.url) / key, **open_kwargs) - def get(self, key: str, mode: str = "rb", **open_kwargs) -> t.Any: + def get(self, key: Path, mode: str = "rb", **open_kwargs) -> t.Any: """Retrieves an item with the given key.""" - if self.fs.exists(f"{self.url}/{key}/{Serializers[self.serializer.__class__]}", **open_kwargs): - return super().get(f"{key}/{Serializers[self.serializer.__class__]}", mode, **open_kwargs) - elif self.fs.exists(f"{self.url}/{key}/file", **open_kwargs): - return self.fs.cat(f"{self.url}/{key}/file", **open_kwargs) + if self.fs.exists(Path(self.url, key, Serializers[self.serializer.__class__]), **open_kwargs): + return super().get(str(Path(key, Serializers[self.serializer.__class__])), mode, **open_kwargs) + elif self.fs.exists(Path(self.url, key, "file"), **open_kwargs): + return self.fs.cat(Path(self.url, key, "file"), **open_kwargs) else: raise ValueError(f"Key {key} does not exist!") - def set(self, value: t.Any, key: t.Optional[str] = None, mode: str = "wb", **open_kwargs) -> None: + def set(self, value: t.Any, key: t.Optional[Path] = None, mode: str = "wb", **open_kwargs) -> None: """Persists an item with the given key.""" if key is None: key = get_random_key() if isinstance(value, Path): - self.fs.cp(value, f"{self.url}/{key}/file", **open_kwargs) + self.fs.cp(value, Path(self.url, key, "file"), **open_kwargs) else: - super().set(value, f"{key}/{Serializers[self.serializer.__class__]}", mode, **open_kwargs) + super().set(value, str(Path(key, Serializers[self.serializer.__class__])), mode, **open_kwargs) class FileSystemArtifactManager(ArtifactManager): def __init__(self, url: str, serializer: Optional[SquirrelSerializer] = None, **fs_kwargs): - """Artifactmanager backed by fsspec filesystems.""" + """ + Artifactmanager backed by fsspec filesystems. + + The manager logs artifacts according to the following file structure: + url/collection/artifact/version/serializer + url: root directory of the artifact store + collection: the name of the collection defaults to 'default' + artifact: (human-readable) name of the artifact + version: version number starting at 1 which is automatically incremented + serializer: the name of the serializer used to store the artifact (e.g. file, messagepack) + """ super().__init__() if serializer is None: serializer = MessagepackSerializer() @@ -65,10 +75,10 @@ def get_artifact(self, artifact: str, collection: Optional[str] = None, version: if collection is None: collection = self.collection if version is None: - version = len(self.backend.complete_key(os.path.join(collection, artifact))) - if not self.backend.key_exists(os.path.join(collection, artifact, str(version))): + version = len(self.backend.complete_key(Path(collection) / Path(artifact))) + if not self.backend.key_exists(Path(collection, artifact, str(version))): raise ValueError(f"Artifact {artifact} does not exist in collection {collection} with version {version}!") - path = os.path.join(collection, artifact, str(version)) + path = Path(collection, artifact, str(version)) return self.backend.get(path) def get_artifact_source( @@ -78,32 +88,32 @@ def get_artifact_source( if collection is None: collection = self.collection if version is None: - version = len(self.backend.complete_key(os.path.join(collection, artifact))) - if not self.backend.key_exists(os.path.join(collection, artifact, str(version))): + version = len(self.backend.complete_key(Path(collection, artifact))) + if not self.backend.key_exists(Path(collection, artifact, str(version))): raise ValueError(f"Artifact {artifact} does not exist in collection {collection} with version {version}!") if Serializers[self.backend.serializer.__class__] in self.backend.complete_key( - os.path.join(collection, artifact, str(version)) + Path(collection, artifact, str(version)) ): return Source( driver_name=Serializers[self.backend.serializer.__class__], driver_kwargs={ - "url": os.path.join( + "url": Path( self.backend.url, collection, artifact, str(version), Serializers[self.backend.serializer.__class__], - ), + ).as_uri(), "storage_options": self.backend.storage_options, }, metadata={"collection": collection, "artifact": artifact, "version": version}, ) - elif self.backend.fs.exists(os.path.join(collection, artifact, str(version), "file")): + elif self.backend.fs.exists(Path(collection, artifact, str(version), "file")): return Source( driver_name="file", driver_kwargs={ - "url": os.path.join(self.backend.url, collection, artifact, str(version), "file"), + "url": Path(self.backend.url, collection, artifact, str(version), "file").as_uri(), "storage_options": self.backend.storage_options, }, metadata={"collection": collection, "artifact": artifact, "version": version}, @@ -116,9 +126,9 @@ def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: if collection is None: collection = self.collection catalog = Catalog() - for artifact in self.backend.complete_key(collection): - for version in self.backend.complete_key(os.path.join(collection, artifact)): - catalog[os.path.join(collection, artifact)] = self.get_artifact_source( + for artifact in self.backend.complete_key(Path(collection)): + for version in self.backend.complete_key(Path(collection, artifact)): + catalog[str(Path(collection, artifact))] = self.get_artifact_source( artifact, collection, int(version) ) return catalog @@ -140,35 +150,35 @@ def log_file(self, local_path: Path, name: str, collection: Optional[str] = None """Upload local file to artifact store without serialisation""" if collection is None: collection = self.collection - version = len(self.backend.complete_key(os.path.join(collection, name))) + 1 - self.backend.set(local_path, os.path.join(collection, name, str(version))) + version = len(self.backend.complete_key(Path(collection, name))) + 1 + self.backend.set(local_path, Path(collection, name, str(version))) return self.get_artifact_source(name, collection) - def log_collection(self, files: Union[Path, List[Path]], collection_name: Optional[str] = None) -> Catalog: + def log_collection(self, files: Union[Path, List[Path]], collection: Optional[str] = None) -> Catalog: """Log folder or set of local paths as collection of artifacts into store""" if isinstance(files, Path) and files.is_dir(): - if collection_name is None: - collection_name = files + if collection is None: + collection = files.name files = list(files.iterdir()) elif isinstance(files, Path): raise ValueError(f"Path {files} is not a directory!") else: - if collection_name is None: + if collection is None: raise ValueError("Collection name must be specified if files is not a directory!") for file in files: if file.is_file(): - self.log_file(file, file.name, collection_name) - return self.collection_to_catalog(collection_name) + self.log_file(file, file.name, collection) + return self.collection_to_catalog(collection) - def log_object(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: + def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: """Log an arbitrary python object using store serialisation.""" if collection is None: collection = self.collection - if self.backend.key_exists(os.path.join(collection, name)): - version = len(self.backend.complete_key(os.path.join(collection, name))) + 1 + if self.backend.key_exists(Path(collection, name)): + version = len(self.backend.complete_key(Path(collection, name))) + 1 else: version = 1 - self.backend.set(obj, os.path.join(collection, name, str(version))) + self.backend.set(obj, Path(collection, name, str(version))) return self.get_artifact_source(name, collection) def download_artifact( diff --git a/squirrel/artifact_manager/wandb.py b/squirrel/artifact_manager/wandb.py index 15b9cff..408c685 100644 --- a/squirrel/artifact_manager/wandb.py +++ b/squirrel/artifact_manager/wandb.py @@ -6,6 +6,10 @@ class WandbArtifactManager(ArtifactManager): + """Dummy placeholder for now + + TODO: Implement this based on the wandb Artifact API + """ def list_collection_names(self) -> Iterable: pass diff --git a/test/test_artifact_manager/test_logging.py b/test/test_artifact_manager/test_logging.py index d186617..f5d9cee 100644 --- a/test/test_artifact_manager/test_logging.py +++ b/test/test_artifact_manager/test_logging.py @@ -1,6 +1,6 @@ import tempfile -from squirrel.artifact_manager.fs.fs import FileSystemArtifactManager +from squirrel.artifact_manager.fs import FileSystemArtifactManager def test_log_object() -> None: @@ -11,10 +11,10 @@ def test_log_object() -> None: tmpdir = tempfile.TemporaryDirectory() manager = FileSystemArtifactManager(url=tmpdir.name, auto_mkdir=True) - source = manager.log_object(obj, artifact_name) + source = manager.log_artifact(obj, artifact_name) assert source.driver_name == "messagepack" - assert source.driver_kwargs["url"] == f"{tmpdir.name}/default/{artifact_name}/1/messagepack" + assert source.driver_kwargs["url"] == f"file://{tmpdir.name}/default/{artifact_name}/1/messagepack" assert source.metadata["collection"] == "default" assert source.metadata["artifact"] == artifact_name assert source.metadata["version"] == 1 @@ -22,14 +22,14 @@ def test_log_object() -> None: obj2 = {"name": "John", "age": 15} artifact_name = "young_john" - source2 = manager.log_object(obj2, artifact_name, collection) - assert source2.driver_kwargs["url"] == f"{tmpdir.name}/{collection}/{artifact_name}/1/messagepack" + source2 = manager.log_artifact(obj2, artifact_name, collection) + assert source2.driver_kwargs["url"] == f"file://{tmpdir.name}/{collection}/{artifact_name}/1/messagepack" assert source2.metadata["collection"] == collection assert source2.metadata["artifact"] == artifact_name assert source2.metadata["version"] == 1 - source2 = manager.log_object(obj2, artifact_name, collection) - assert source2.driver_kwargs["url"] == f"{tmpdir.name}/{collection}/{artifact_name}/2/messagepack" + source2 = manager.log_artifact(obj2, artifact_name, collection) + assert source2.driver_kwargs["url"] == f"file://{tmpdir.name}/{collection}/{artifact_name}/2/messagepack" assert source2.metadata["collection"] == collection assert source2.metadata["artifact"] == artifact_name assert source2.metadata["version"] == 2 @@ -46,11 +46,11 @@ def test_get_artifact() -> None: tmpdir = tempfile.TemporaryDirectory() manager = FileSystemArtifactManager(url=tmpdir.name, auto_mkdir=True) - manager.log_object(obj, artifact_name, collection) + manager.log_artifact(obj, artifact_name, collection) assert manager.get_artifact("john", collection) == obj - manager.log_object(obj1, artifact_name, collection) + manager.log_artifact(obj1, artifact_name, collection) assert manager.get_artifact("john", collection) == obj1 - manager.log_object(obj2, artifact_name, collection) + manager.log_artifact(obj2, artifact_name, collection) assert manager.get_artifact(artifact_name, collection) == obj2 assert manager.get_artifact(artifact_name, collection, 2) == obj1 assert manager.get_artifact(artifact_name, collection, 1) == obj From 18d074f49995c934c313e68a44b3d02fc98a206f Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Tue, 7 Nov 2023 14:23:01 +0100 Subject: [PATCH 22/41] Refactor logging of multiple files --- squirrel/artifact_manager/base.py | 19 +++++++++----- squirrel/artifact_manager/fs.py | 41 ++++++++++++++---------------- squirrel/artifact_manager/wandb.py | 16 +++++++----- 3 files changed, 41 insertions(+), 35 deletions(-) diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index 56788fb..5015d2f 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -1,7 +1,7 @@ import re from abc import abstractmethod, ABC from pathlib import Path -from typing import Optional, List, Union, Any, Iterable +from typing import Optional, List, Any, Iterable from squirrel.catalog import Catalog, Source @@ -30,9 +30,10 @@ def collection(self) -> str: @collection.setter def collection(self, value: str) -> None: """Do not allow access to anything beyond the root location of the artifact store""" - assert re.match(r'^[a-zA-Z0-9\-_:]+$', value), \ - ("Invalid collection name - must not be empty and can only contain alphanumerics, dashes, underscores and " - "colons.") + assert re.match(r"^[a-zA-Z0-9\-_:]+$", value), ( + "Invalid collection name - must not be empty and can only contain alphanumerics, dashes, underscores and " + "colons." + ) self._active_collection = value @abstractmethod @@ -73,8 +74,12 @@ def log_file(self, local_path: Path, name: str, collection: Optional[str] = None """Upload file into (current) collection, increment version automatically""" @abstractmethod - def log_collection(self, files: Union[Path, List[Path]], collection: Optional[str] = None) -> Catalog: - """Upload folder or collection of files""" + def log_files(self, local_paths: List[Path], collection: Optional[str] = None) -> Catalog: + """Upload a collection of file into a (current) collection""" + + @abstractmethod + def log_folder(self, files: Path, collection: Optional[str] = None) -> Catalog: + """Upload folder as collection of artifacts into store""" raise NotImplementedError @abstractmethod @@ -91,5 +96,5 @@ def download_artifact( @abstractmethod def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> Catalog: - """Retrieve file (from current collection) to specific location. Retrieve latest version of all artifacts.""" + """Retrieve files (from current collection) to specific location. Retrieve latest version of all artifacts.""" raise NotImplementedError diff --git a/squirrel/artifact_manager/fs.py b/squirrel/artifact_manager/fs.py index d0a96dc..da8d525 100644 --- a/squirrel/artifact_manager/fs.py +++ b/squirrel/artifact_manager/fs.py @@ -1,6 +1,6 @@ import typing as t from pathlib import Path -from typing import Optional, Any, Union, List, Iterable +from typing import Optional, Any, List, Iterable from squirrel.artifact_manager.base import ArtifactManager from squirrel.catalog import Catalog, Source @@ -20,10 +20,7 @@ def complete_key(self, partial_key: Path, **open_kwargs) -> List[str]: full_path = Path(self.url, partial_key) if not self.fs.exists(full_path, **open_kwargs): return [] - return [ - str(Path(path).relative_to(full_path)) - for path in self.fs.ls(full_path, detail=False, **open_kwargs) - ] + return [str(Path(path).relative_to(full_path)) for path in self.fs.ls(full_path, detail=False, **open_kwargs)] def key_exists(self, key: Path, **open_kwargs) -> bool: """Checks if a key exists.""" @@ -128,9 +125,7 @@ def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: catalog = Catalog() for artifact in self.backend.complete_key(Path(collection)): for version in self.backend.complete_key(Path(collection, artifact)): - catalog[str(Path(collection, artifact))] = self.get_artifact_source( - artifact, collection, int(version) - ) + catalog[str(Path(collection, artifact))] = self.get_artifact_source(artifact, collection, int(version)) return catalog def store_to_catalog(self) -> Catalog: @@ -154,22 +149,24 @@ def log_file(self, local_path: Path, name: str, collection: Optional[str] = None self.backend.set(local_path, Path(collection, name, str(version))) return self.get_artifact_source(name, collection) - def log_collection(self, files: Union[Path, List[Path]], collection: Optional[str] = None) -> Catalog: - """Log folder or set of local paths as collection of artifacts into store""" - if isinstance(files, Path) and files.is_dir(): - if collection is None: - collection = files.name - files = list(files.iterdir()) - elif isinstance(files, Path): - raise ValueError(f"Path {files} is not a directory!") - else: - if collection is None: - raise ValueError("Collection name must be specified if files is not a directory!") - for file in files: - if file.is_file(): - self.log_file(file, file.name, collection) + def log_files(self, local_paths: List[Path], collection: Optional[str] = None) -> Catalog: + """Upload a collection of file into a (current) collection""" + if collection is None: + collection = self.collection + for local_path in local_paths: + self.log_file(local_path, local_path.name, collection) return self.collection_to_catalog(collection) + def log_folder(self, file: Path, collection: Optional[str] = None) -> Catalog: + """Log folder as collection of artifacts into store""" + if not file.is_dir(): + raise ValueError(f"Path {file} is not a directory!") + + if collection is None: + collection = file.name + + return self.log_files([f for f in file.iterdir() if f.is_file()], collection) + def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: """Log an arbitrary python object using store serialisation.""" if collection is None: diff --git a/squirrel/artifact_manager/wandb.py b/squirrel/artifact_manager/wandb.py index 408c685..847f4fc 100644 --- a/squirrel/artifact_manager/wandb.py +++ b/squirrel/artifact_manager/wandb.py @@ -10,6 +10,7 @@ class WandbArtifactManager(ArtifactManager): TODO: Implement this based on the wandb Artifact API """ + def list_collection_names(self) -> Iterable: pass @@ -22,12 +23,14 @@ def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None) -> Any: pass - def get_artifact_source(self, artifact: str, collection: Optional[str] = None, - version: Optional[int] = None) -> Source: + def get_artifact_source( + self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None + ) -> Source: pass - def get_artifact_location(self, artifact_name: str, collection: Optional[str] = None, - version: Optional[int] = None) -> str: + def get_artifact_location( + self, artifact_name: str, collection: Optional[str] = None, version: Optional[int] = None + ) -> str: pass def log_file(self, local_path: Path, name: str, collection: Optional[str] = None) -> Source: @@ -39,8 +42,9 @@ def log_collection(self, files: Union[Path, List[Path]], collection_name: Option def log_object(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: pass - def download_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None, - to: Path = "./") -> Source: + def download_artifact( + self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None, to: Path = "./" + ) -> Source: pass def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> Catalog: From 718ccc3717e7730d25d422f4c0ee1e9aaa650806 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Tue, 7 Nov 2023 14:25:35 +0100 Subject: [PATCH 23/41] Renaming collection parameter --- squirrel/artifact_manager/base.py | 6 +++--- squirrel/artifact_manager/fs.py | 12 ++++++------ 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index 5015d2f..0b5a41b 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -17,7 +17,7 @@ def __init__(self): self._active_collection = "default" @property - def collection(self) -> str: + def active_collection(self) -> str: """ Collections act as folders of artifacts. @@ -27,8 +27,8 @@ def collection(self) -> str: """ return self._active_collection - @collection.setter - def collection(self, value: str) -> None: + @active_collection.setter + def active_collection(self, value: str) -> None: """Do not allow access to anything beyond the root location of the artifact store""" assert re.match(r"^[a-zA-Z0-9\-_:]+$", value), ( "Invalid collection name - must not be empty and can only contain alphanumerics, dashes, underscores and " diff --git a/squirrel/artifact_manager/fs.py b/squirrel/artifact_manager/fs.py index da8d525..39589c9 100644 --- a/squirrel/artifact_manager/fs.py +++ b/squirrel/artifact_manager/fs.py @@ -70,7 +70,7 @@ def list_collection_names(self) -> Iterable: def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None) -> Any: """Retrieve specific artifact value.""" if collection is None: - collection = self.collection + collection = self.active_collection if version is None: version = len(self.backend.complete_key(Path(collection) / Path(artifact))) if not self.backend.key_exists(Path(collection, artifact, str(version))): @@ -83,7 +83,7 @@ def get_artifact_source( ) -> Source: """Catalog entry for a specific artifact""" if collection is None: - collection = self.collection + collection = self.active_collection if version is None: version = len(self.backend.complete_key(Path(collection, artifact))) if not self.backend.key_exists(Path(collection, artifact, str(version))): @@ -121,7 +121,7 @@ def get_artifact_source( def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: """Provide catalog of all artifacts and their versions contained within specific collection""" if collection is None: - collection = self.collection + collection = self.active_collection catalog = Catalog() for artifact in self.backend.complete_key(Path(collection)): for version in self.backend.complete_key(Path(collection, artifact)): @@ -144,7 +144,7 @@ def get_artifact_location( def log_file(self, local_path: Path, name: str, collection: Optional[str] = None) -> Source: """Upload local file to artifact store without serialisation""" if collection is None: - collection = self.collection + collection = self.active_collection version = len(self.backend.complete_key(Path(collection, name))) + 1 self.backend.set(local_path, Path(collection, name, str(version))) return self.get_artifact_source(name, collection) @@ -152,7 +152,7 @@ def log_file(self, local_path: Path, name: str, collection: Optional[str] = None def log_files(self, local_paths: List[Path], collection: Optional[str] = None) -> Catalog: """Upload a collection of file into a (current) collection""" if collection is None: - collection = self.collection + collection = self.active_collection for local_path in local_paths: self.log_file(local_path, local_path.name, collection) return self.collection_to_catalog(collection) @@ -170,7 +170,7 @@ def log_folder(self, file: Path, collection: Optional[str] = None) -> Catalog: def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: """Log an arbitrary python object using store serialisation.""" if collection is None: - collection = self.collection + collection = self.active_collection if self.backend.key_exists(Path(collection, name)): version = len(self.backend.complete_key(Path(collection, name))) + 1 else: From a3f9e72afcf50f48a62be610ac152e1a63ee2513 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Thu, 14 Dec 2023 14:05:58 +0100 Subject: [PATCH 24/41] Extended tests --- squirrel/artifact_manager/base.py | 49 ++--- squirrel/artifact_manager/fs.py | 51 +++-- test/test_artifact_manager/test_fs_logging.py | 180 ++++++++++++++++++ test/test_artifact_manager/test_logging.py | 56 ------ 4 files changed, 242 insertions(+), 94 deletions(-) create mode 100644 test/test_artifact_manager/test_fs_logging.py delete mode 100644 test/test_artifact_manager/test_logging.py diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index 0b5a41b..1910980 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -21,19 +21,29 @@ def active_collection(self) -> str: """ Collections act as folders of artifacts. - The manager maintains an 'active' collections which it logs to by default. + It is ultimately up to the user how to structure their artifact store and the collections therein. All + operations accessing artifacts allow explicit specification of the collection to use. + Therefore, users could use collections to separate different artifact types or different experiments / runs. + To facilitate the latter use case in particular, the manager maintains an 'active' collection which it logs to + by default. This can be set once at the run start when the manager is initialized and then left unchanged. + To avoid incompatibility between different backends, collections cannot be nested (e.g. as subfolders on a - filesystem). + filesystem) as in particular the WandB backend has no real notion of nested folder structures. """ return self._active_collection @active_collection.setter def active_collection(self, value: str) -> None: - """Do not allow access to anything beyond the root location of the artifact store""" - assert re.match(r"^[a-zA-Z0-9\-_:]+$", value), ( - "Invalid collection name - must not be empty and can only contain alphanumerics, dashes, underscores and " - "colons." - ) + """ + Sets the active collections that is being logged to by default. + + The provided values is verified to ensure that no nested collections are used. + """ + if not re.match(r"^[a-zA-Z0-9\-_:]+$", value): + raise ValueError( + "Invalid collection name - must not be empty and can only contain alphanumerics, dashes, underscores " + "and colons." + ) self._active_collection = value @abstractmethod @@ -55,27 +65,15 @@ def get_artifact(self, artifact: str, collection: Optional[str] = None, version: """Retrieve specific artifact value.""" raise NotImplementedError - @abstractmethod - def get_artifact_source( - self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None - ) -> Source: - """Catalog entry for a specific artifact""" - raise NotImplementedError - - @abstractmethod - def get_artifact_location( - self, artifact_name: str, collection: Optional[str] = None, version: Optional[int] = None - ) -> str: - """Get full qualified path or wandb directory of artifact""" - raise NotImplementedError - @abstractmethod def log_file(self, local_path: Path, name: str, collection: Optional[str] = None) -> Source: """Upload file into (current) collection, increment version automatically""" + raise NotImplementedError @abstractmethod def log_files(self, local_paths: List[Path], collection: Optional[str] = None) -> Catalog: - """Upload a collection of file into a (current) collection""" + """Upload a collection of files into a (current) collection""" + raise NotImplementedError @abstractmethod def log_folder(self, files: Path, collection: Optional[str] = None) -> Catalog: @@ -84,7 +82,12 @@ def log_folder(self, files: Path, collection: Optional[str] = None) -> Catalog: @abstractmethod def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: - """Log an arbitrary python object""" + """ + Log an arbitrary python object + + The serialisation method used is backend dependent. When using a simple FileStore backend any SquirrelSerializer + can be chosen. For WandB objects serialisation is handled by WandB itself. + """ raise NotImplementedError @abstractmethod diff --git a/squirrel/artifact_manager/fs.py b/squirrel/artifact_manager/fs.py index 39589c9..90691cf 100644 --- a/squirrel/artifact_manager/fs.py +++ b/squirrel/artifact_manager/fs.py @@ -15,6 +15,14 @@ class ArtifactFileStore(FilesystemStore): + """ + A FilesystemStore serving as the backend for the FileSystemArtifactManager. + + The get and set methods are altered to allow for storing serialized data as well as raw files. + If the final path component is a serializer name, the data is stored as a serialized file. + If the final path component is "file", the data is stored as a raw file. + """ + def complete_key(self, partial_key: Path, **open_kwargs) -> List[str]: """Returns a list of possible key continuations given a partial key.""" full_path = Path(self.url, partial_key) @@ -40,7 +48,7 @@ def set(self, value: t.Any, key: t.Optional[Path] = None, mode: str = "wb", **op if key is None: key = get_random_key() if isinstance(value, Path): - self.fs.cp(value, Path(self.url, key, "file"), **open_kwargs) + self.fs.cp_file(value, Path(self.url, key, "file"), **open_kwargs) else: super().set(value, str(Path(key, Serializers[self.serializer.__class__])), mode, **open_kwargs) @@ -72,7 +80,7 @@ def get_artifact(self, artifact: str, collection: Optional[str] = None, version: if collection is None: collection = self.active_collection if version is None: - version = len(self.backend.complete_key(Path(collection) / Path(artifact))) + version = max(int(vs) for vs in self.backend.complete_key(Path(collection) / Path(artifact))) if not self.backend.key_exists(Path(collection, artifact, str(version))): raise ValueError(f"Artifact {artifact} does not exist in collection {collection} with version {version}!") path = Path(collection, artifact, str(version)) @@ -85,7 +93,7 @@ def get_artifact_source( if collection is None: collection = self.active_collection if version is None: - version = len(self.backend.complete_key(Path(collection, artifact))) + version = max(int(vs) for vs in self.backend.complete_key(Path(collection) / Path(artifact))) if not self.backend.key_exists(Path(collection, artifact, str(version))): raise ValueError(f"Artifact {artifact} does not exist in collection {collection} with version {version}!") @@ -104,16 +112,32 @@ def get_artifact_source( ).as_uri(), "storage_options": self.backend.storage_options, }, - metadata={"collection": collection, "artifact": artifact, "version": version}, + metadata={ + "collection": collection, + "artifact": artifact, + "version": version, + "location": Path( + self.backend.url, + collection, + artifact, + str(version), + Serializers[self.backend.serializer.__class__], + ).as_uri(), + }, ) - elif self.backend.fs.exists(Path(collection, artifact, str(version), "file")): + elif self.backend.key_exists(Path(collection, artifact, str(version), "file")): return Source( driver_name="file", driver_kwargs={ "url": Path(self.backend.url, collection, artifact, str(version), "file").as_uri(), "storage_options": self.backend.storage_options, }, - metadata={"collection": collection, "artifact": artifact, "version": version}, + metadata={ + "collection": collection, + "artifact": artifact, + "version": version, + "location": Path(self.backend.url, collection, artifact, str(version), "file").as_uri(), + }, ) else: raise ValueError(f"Could not read artifact {artifact} in collection {collection} with version {version}!") @@ -135,14 +159,11 @@ def store_to_catalog(self) -> Catalog: catalog.update(self.collection_to_catalog(collection)) return catalog - def get_artifact_location( - self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None - ) -> str: - """Get full qualified path or wandb directory of artifact""" - return self.get_artifact_source(artifact, collection, version).driver_kwargs["url"] - def log_file(self, local_path: Path, name: str, collection: Optional[str] = None) -> Source: """Upload local file to artifact store without serialisation""" + if isinstance(local_path, str): + local_path = Path(local_path) + assert isinstance(local_path, Path), "Path to file must be passed as a pathlib.Path object!" if collection is None: collection = self.active_collection version = len(self.backend.complete_key(Path(collection, name))) + 1 @@ -182,13 +203,13 @@ def download_artifact( self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None, to: Path = "./" ) -> Source: """Download artifact to local path.""" - location = self.get_artifact_location(artifact, collection, version) + location = self.get_artifact_source(artifact, collection, version).metadata["location"] if self.backend.fs.exists(location): - self.backend.fs.cp(location, to) + self.backend.fs.cp_file(location, to) return Source( driver_name="file", driver_kwargs={"url": str(to), "storage_options": self.backend.storage_options}, - metadata={"collection": collection, "artifact": artifact, "version": version}, + metadata={"collection": collection, "artifact": artifact, "version": version, "location": str(to)}, ) def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> Catalog: diff --git a/test/test_artifact_manager/test_fs_logging.py b/test/test_artifact_manager/test_fs_logging.py new file mode 100644 index 0000000..144272d --- /dev/null +++ b/test/test_artifact_manager/test_fs_logging.py @@ -0,0 +1,180 @@ +import tempfile +from pathlib import Path + +import pytest + +from squirrel.artifact_manager.fs import FileSystemArtifactManager +from squirrel.catalog import Source +from squirrel.serialization import JsonSerializer, MessagepackSerializer, SquirrelSerializer + + +@pytest.mark.parametrize( + "serializer,name,target", + [ + (JsonSerializer(), "jsonl", b'{"name": "John", "age": 30}'), + (MessagepackSerializer(), "messagepack", b"\x82\xa4name\xa4John\xa3age\x1e"), + ], +) +def test_serializer(serializer: SquirrelSerializer, name: str, target: str) -> None: + """Test that artifacts are correctly serialised.""" + obj = {"name": "John", "age": 30} + artifact_name = "john" + + tmpdir = tempfile.TemporaryDirectory() + # message pack serialization + manager = FileSystemArtifactManager(url=tmpdir.name, serializer=serializer, auto_mkdir=True) + source = manager.log_artifact(obj, artifact_name) + + assert source.metadata["location"] == f"file://{tmpdir.name}/default/{artifact_name}/1/{name}" + with open(f"{tmpdir.name}/default/{artifact_name}/1/{name}", "rb") as f: + assert f.read() == target + + tmpdir.cleanup() + + +def test_multi_serializer() -> None: + """Test that multiple artifact stores with differing backends are correctly interacting.""" + obj = {"name": "John", "age": 30} + artifact_name = "john" + + tmpdir = tempfile.TemporaryDirectory() + # message pack serialization + msgpack_manager = FileSystemArtifactManager(url=tmpdir.name, serializer=MessagepackSerializer(), auto_mkdir=True) + msgpack_source = msgpack_manager.log_artifact(obj, artifact_name) + jsonl_manager = FileSystemArtifactManager(url=tmpdir.name, serializer=JsonSerializer(), auto_mkdir=True) + jsonl_source = jsonl_manager.log_artifact(obj, artifact_name) + + assert msgpack_source == Source( + driver_name="messagepack", + driver_kwargs={ + "url": f"file://{tmpdir.name}/default/john/1/messagepack", + "storage_options": {"auto_mkdir": True}, + }, + metadata={ + "collection": "default", + "artifact": "john", + "version": 1, + "location": f"file://{tmpdir.name}/default/john/1/messagepack", + }, + ) + assert jsonl_source == Source( + driver_name="jsonl", + driver_kwargs={"url": f"file://{tmpdir.name}/default/john/2/jsonl", "storage_options": {"auto_mkdir": True}}, + metadata={ + "collection": "default", + "artifact": "john", + "version": 2, + "location": f"file://{tmpdir.name}/default/john/2/jsonl", + }, + ) + tmpdir.cleanup() + + +def test_log_object() -> None: + """Log an object to the default collection and check details of the catalog entry.""" + obj = {"name": "John", "age": 30} + artifact_name = "john" + collection = "my_collection" + + tmpdir = tempfile.TemporaryDirectory() + manager = FileSystemArtifactManager(url=tmpdir.name, auto_mkdir=True) + source = manager.log_artifact(obj, artifact_name) + + assert source.driver_name == "messagepack" + assert source.driver_kwargs["url"] == f"file://{tmpdir.name}/default/{artifact_name}/1/messagepack" + assert source.metadata["collection"] == "default" + assert source.metadata["artifact"] == artifact_name + assert source.metadata["version"] == 1 + + obj2 = {"name": "John", "age": 15} + artifact_name = "young_john" + + source2 = manager.log_artifact(obj2, artifact_name, collection) + assert source2.driver_kwargs["url"] == f"file://{tmpdir.name}/{collection}/{artifact_name}/1/messagepack" + assert source2.metadata["collection"] == collection + assert source2.metadata["artifact"] == artifact_name + assert source2.metadata["version"] == 1 + + source2 = manager.log_artifact(obj2, artifact_name, collection) + assert source2.driver_kwargs["url"] == f"file://{tmpdir.name}/{collection}/{artifact_name}/2/messagepack" + assert source2.metadata["collection"] == collection + assert source2.metadata["artifact"] == artifact_name + assert source2.metadata["version"] == 2 + tmpdir.cleanup() + + +def test_get_artifact() -> None: + """Test logging multiple versions of the same object and retrieving different versions.""" + obj = {"name": "John", "age": 10} + obj1 = {"name": "John", "age": 20} + obj2 = {"name": "John", "age": 30} + artifact_name = "john" + collection = "my_collection" + + tmpdir = tempfile.TemporaryDirectory() + manager = FileSystemArtifactManager(url=tmpdir.name, auto_mkdir=True) + manager.log_artifact(obj, artifact_name, collection) + assert manager.get_artifact("john", collection) == obj + manager.log_artifact(obj1, artifact_name, collection) + assert manager.get_artifact("john", collection) == obj1 + manager.log_artifact(obj2, artifact_name, collection) + assert manager.get_artifact(artifact_name, collection) == obj2 + assert manager.get_artifact(artifact_name, collection, 2) == obj1 + assert manager.get_artifact(artifact_name, collection, 1) == obj + + +def test_log_file() -> None: + """Test logging files to the artifact store.""" + src_dir = tempfile.TemporaryDirectory() + collection = "my_collection" + + store_dir = tempfile.TemporaryDirectory() + manager = FileSystemArtifactManager(url=store_dir.name, auto_mkdir=True) + + for (filename, artifact_name, version, content) in [ + ("foo.txt", "foo_file", 1, "Test: Foo"), + ("bar.txt", "bar_file", 1, "Test: Bar"), + ("baz.txt", "bar_file", 2, "Test: Baz"), + ]: + with open(f"{src_dir.name}/{filename}", "w") as f: + f.write(content) + + source = manager.log_file(Path(f"{src_dir.name}/{filename}"), artifact_name, collection) + + assert source.driver_name == "file" + assert source.metadata["collection"] == collection + assert source.metadata["artifact"] == artifact_name + assert source.metadata["version"] == version + + with open(f"{store_dir.name}/{collection}/{artifact_name}/{version}/file") as f: + assert f.read() == content + src_dir.cleanup() + store_dir.cleanup() + + +def test_get_file() -> None: + """Test retrieval of logged files from the artifact store.""" + src_dir = tempfile.TemporaryDirectory() + collection = "my_collection" + + store_dir = tempfile.TemporaryDirectory() + manager = FileSystemArtifactManager(url=store_dir.name, auto_mkdir=True) + + file_descriptions = [ + ("bar.txt", "bar_file", 1, "Test: Bar"), + ("baz.txt", "bar_file", 2, "Test: Baz"), + ] + + for (filename, artifact_name, _, content) in file_descriptions: + with open(f"{src_dir.name}/{filename}", "w") as f: + f.write(content) + + manager.log_file(Path(f"{src_dir.name}/{filename}"), artifact_name, collection) + + for (filename, artifact_name, version, content) in file_descriptions: + manager.download_artifact(artifact_name, collection, version, Path(f"{src_dir.name}/downloaded_{filename}")) + with open(f"{src_dir.name}/downloaded_{filename}") as f: + assert f.read() == content + + src_dir.cleanup() + store_dir.cleanup() diff --git a/test/test_artifact_manager/test_logging.py b/test/test_artifact_manager/test_logging.py deleted file mode 100644 index f5d9cee..0000000 --- a/test/test_artifact_manager/test_logging.py +++ /dev/null @@ -1,56 +0,0 @@ -import tempfile - -from squirrel.artifact_manager.fs import FileSystemArtifactManager - - -def test_log_object() -> None: - """Log an object to the default collection and check details of the catalog entry.""" - obj = {"name": "John", "age": 30} - artifact_name = "john" - collection = "my_collection" - - tmpdir = tempfile.TemporaryDirectory() - manager = FileSystemArtifactManager(url=tmpdir.name, auto_mkdir=True) - source = manager.log_artifact(obj, artifact_name) - - assert source.driver_name == "messagepack" - assert source.driver_kwargs["url"] == f"file://{tmpdir.name}/default/{artifact_name}/1/messagepack" - assert source.metadata["collection"] == "default" - assert source.metadata["artifact"] == artifact_name - assert source.metadata["version"] == 1 - - obj2 = {"name": "John", "age": 15} - artifact_name = "young_john" - - source2 = manager.log_artifact(obj2, artifact_name, collection) - assert source2.driver_kwargs["url"] == f"file://{tmpdir.name}/{collection}/{artifact_name}/1/messagepack" - assert source2.metadata["collection"] == collection - assert source2.metadata["artifact"] == artifact_name - assert source2.metadata["version"] == 1 - - source2 = manager.log_artifact(obj2, artifact_name, collection) - assert source2.driver_kwargs["url"] == f"file://{tmpdir.name}/{collection}/{artifact_name}/2/messagepack" - assert source2.metadata["collection"] == collection - assert source2.metadata["artifact"] == artifact_name - assert source2.metadata["version"] == 2 - tmpdir.cleanup() - - -def test_get_artifact() -> None: - """Test logging multiple versions of the same object and retrieving different versions.""" - obj = {"name": "John", "age": 10} - obj1 = {"name": "John", "age": 20} - obj2 = {"name": "John", "age": 30} - artifact_name = "john" - collection = "my_collection" - - tmpdir = tempfile.TemporaryDirectory() - manager = FileSystemArtifactManager(url=tmpdir.name, auto_mkdir=True) - manager.log_artifact(obj, artifact_name, collection) - assert manager.get_artifact("john", collection) == obj - manager.log_artifact(obj1, artifact_name, collection) - assert manager.get_artifact("john", collection) == obj1 - manager.log_artifact(obj2, artifact_name, collection) - assert manager.get_artifact(artifact_name, collection) == obj2 - assert manager.get_artifact(artifact_name, collection, 2) == obj1 - assert manager.get_artifact(artifact_name, collection, 1) == obj From 3fc564691ec11ec821bc7ee371a26196456fb8b8 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Fri, 15 Dec 2023 18:02:22 +0100 Subject: [PATCH 25/41] First wandb version --- pyproject.toml | 5 +- squirrel/artifact_manager/base.py | 53 +++-- squirrel/artifact_manager/fs.py | 77 ++----- squirrel/artifact_manager/wandb.py | 193 ++++++++++++++---- test/test_artifact_manager/test_fs_logging.py | 43 ++-- 5 files changed, 238 insertions(+), 133 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 79cc4a0..f9d94a9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -97,12 +97,13 @@ dask = ["dask"] excel = ["odfpy", "openpyxl", "pyxlsb", "xlrd"] feather = ["pyarrow"] gcp = ["gcsfs"] +numba = ["numba"] parquet = ["pyarrow"] s3 = ["s3fs"] torch = ["torch"] +wandb = ["wandb"] zarr = ["zarr"] -all = ["adlfs", "dask", "odfpy", "openpyxl", "pyxlsb", "xlrd", "pyarrow", "gcsfs", "s3fs", "torch", "zarr"] -numba = ["numba"] +all = ["adlfs", "dask", "odfpy", "openpyxl", "pyxlsb", "xlrd", "pyarrow", "gcsfs", "s3fs", "torch", "zarr", "wandb", "numba"] [build-system] requires = ["poetry-core"] diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index 1910980..9175f08 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -51,17 +51,12 @@ def list_collection_names(self) -> Iterable: """Return list of all collections in the artifact store""" raise NotImplementedError - @abstractmethod - def store_to_catalog(self) -> Catalog: - """Provide a catalog of all stored artifacts.""" - raise NotImplementedError - @abstractmethod def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: """Catalog of all artifacts within a specific collection.""" @abstractmethod - def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None) -> Any: + def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None) -> Any: """Retrieve specific artifact value.""" raise NotImplementedError @@ -70,16 +65,6 @@ def log_file(self, local_path: Path, name: str, collection: Optional[str] = None """Upload file into (current) collection, increment version automatically""" raise NotImplementedError - @abstractmethod - def log_files(self, local_paths: List[Path], collection: Optional[str] = None) -> Catalog: - """Upload a collection of files into a (current) collection""" - raise NotImplementedError - - @abstractmethod - def log_folder(self, files: Path, collection: Optional[str] = None) -> Catalog: - """Upload folder as collection of artifacts into store""" - raise NotImplementedError - @abstractmethod def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: """ @@ -92,12 +77,40 @@ def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> @abstractmethod def download_artifact( - self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None, to: Path = "./" + self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Path = "./" ) -> Source: """Retrieve file (from current collection) to specific location. Retrieve latest version unless specified.""" raise NotImplementedError - @abstractmethod + def store_to_catalog(self) -> Catalog: + """Provide Catalog of all artifacts stored in backend.""" + catalog = Catalog() + for collection in self.list_collection_names(): + catalog.update(self.collection_to_catalog(collection)) + return catalog + + def log_files(self, local_paths: List[Path], collection: Optional[str] = None) -> Catalog: + """Upload a collection of file into a (current) collection""" + if collection is None: + collection = self.active_collection + for local_path in local_paths: + self.log_file(local_path, local_path.name, collection) + return self.collection_to_catalog(collection) + + def log_folder(self, folder: Path, collection: Optional[str] = None) -> Catalog: + """Log folder as collection of artifacts into store""" + if not folder.is_dir(): + raise ValueError(f"Path {folder} is not a directory!") + + if collection is None: + collection = folder.name + + return self.log_files([f for f in folder.iterdir() if f.is_file()], collection) + def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> Catalog: - """Retrieve files (from current collection) to specific location. Retrieve latest version of all artifacts.""" - raise NotImplementedError + """Download all artifacts in collection to local directory.""" + catalog = self.collection_to_catalog(collection) + for artifact in catalog.values(): + artifact_name = artifact.metadata["artifact"] + self.download_artifact(artifact_name, to=to / artifact_name) + return catalog diff --git a/squirrel/artifact_manager/fs.py b/squirrel/artifact_manager/fs.py index 90691cf..fe47ca1 100644 --- a/squirrel/artifact_manager/fs.py +++ b/squirrel/artifact_manager/fs.py @@ -75,30 +75,30 @@ def list_collection_names(self) -> Iterable: """List all collections managed by this ArtifactManager.""" return self.backend.keys(nested=False) - def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None) -> Any: + def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None) -> Any: """Retrieve specific artifact value.""" if collection is None: collection = self.active_collection - if version is None: - version = max(int(vs) for vs in self.backend.complete_key(Path(collection) / Path(artifact))) - if not self.backend.key_exists(Path(collection, artifact, str(version))): + if version is None or version == "latest": + version = f"v{max(int(vs[1:]) for vs in self.backend.complete_key(Path(collection) / Path(artifact)))}" + if not self.backend.key_exists(Path(collection, artifact, version)): raise ValueError(f"Artifact {artifact} does not exist in collection {collection} with version {version}!") - path = Path(collection, artifact, str(version)) + path = Path(collection, artifact, version) return self.backend.get(path) def get_artifact_source( - self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None + self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None ) -> Source: """Catalog entry for a specific artifact""" if collection is None: collection = self.active_collection - if version is None: - version = max(int(vs) for vs in self.backend.complete_key(Path(collection) / Path(artifact))) - if not self.backend.key_exists(Path(collection, artifact, str(version))): + if version is None or version == "latest": + version = f"v{max(int(vs[1:]) for vs in self.backend.complete_key(Path(collection) / Path(artifact)))}" + if not self.backend.key_exists(Path(collection, artifact, version)): raise ValueError(f"Artifact {artifact} does not exist in collection {collection} with version {version}!") if Serializers[self.backend.serializer.__class__] in self.backend.complete_key( - Path(collection, artifact, str(version)) + Path(collection, artifact, version) ): return Source( driver_name=Serializers[self.backend.serializer.__class__], @@ -107,7 +107,7 @@ def get_artifact_source( self.backend.url, collection, artifact, - str(version), + version, Serializers[self.backend.serializer.__class__], ).as_uri(), "storage_options": self.backend.storage_options, @@ -120,23 +120,23 @@ def get_artifact_source( self.backend.url, collection, artifact, - str(version), + version, Serializers[self.backend.serializer.__class__], ).as_uri(), }, ) - elif self.backend.key_exists(Path(collection, artifact, str(version), "file")): + elif self.backend.key_exists(Path(collection, artifact, version, "file")): return Source( driver_name="file", driver_kwargs={ - "url": Path(self.backend.url, collection, artifact, str(version), "file").as_uri(), + "url": Path(self.backend.url, collection, artifact, version, "file").as_uri(), "storage_options": self.backend.storage_options, }, metadata={ "collection": collection, "artifact": artifact, "version": version, - "location": Path(self.backend.url, collection, artifact, str(version), "file").as_uri(), + "location": Path(self.backend.url, collection, artifact, version, "file").as_uri(), }, ) else: @@ -149,14 +149,7 @@ def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: catalog = Catalog() for artifact in self.backend.complete_key(Path(collection)): for version in self.backend.complete_key(Path(collection, artifact)): - catalog[str(Path(collection, artifact))] = self.get_artifact_source(artifact, collection, int(version)) - return catalog - - def store_to_catalog(self) -> Catalog: - """Provide Catalog of all artifacts stored in backend""" - catalog = Catalog() - for collection in self.list_collection_names(): - catalog.update(self.collection_to_catalog(collection)) + catalog[str(Path(collection, artifact))] = self.get_artifact_source(artifact, collection, version) return catalog def log_file(self, local_path: Path, name: str, collection: Optional[str] = None) -> Source: @@ -166,41 +159,23 @@ def log_file(self, local_path: Path, name: str, collection: Optional[str] = None assert isinstance(local_path, Path), "Path to file must be passed as a pathlib.Path object!" if collection is None: collection = self.active_collection - version = len(self.backend.complete_key(Path(collection, name))) + 1 - self.backend.set(local_path, Path(collection, name, str(version))) + version = f"v{len(self.backend.complete_key(Path(collection, name)))}" + self.backend.set(local_path, Path(collection, name, version)) return self.get_artifact_source(name, collection) - def log_files(self, local_paths: List[Path], collection: Optional[str] = None) -> Catalog: - """Upload a collection of file into a (current) collection""" - if collection is None: - collection = self.active_collection - for local_path in local_paths: - self.log_file(local_path, local_path.name, collection) - return self.collection_to_catalog(collection) - - def log_folder(self, file: Path, collection: Optional[str] = None) -> Catalog: - """Log folder as collection of artifacts into store""" - if not file.is_dir(): - raise ValueError(f"Path {file} is not a directory!") - - if collection is None: - collection = file.name - - return self.log_files([f for f in file.iterdir() if f.is_file()], collection) - def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: """Log an arbitrary python object using store serialisation.""" if collection is None: collection = self.active_collection if self.backend.key_exists(Path(collection, name)): - version = len(self.backend.complete_key(Path(collection, name))) + 1 + version = f"v{len(self.backend.complete_key(Path(collection, name)))}" else: - version = 1 - self.backend.set(obj, Path(collection, name, str(version))) + version = "v0" + self.backend.set(obj, Path(collection, name, version)) return self.get_artifact_source(name, collection) def download_artifact( - self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None, to: Path = "./" + self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Path = "./" ) -> Source: """Download artifact to local path.""" location = self.get_artifact_source(artifact, collection, version).metadata["location"] @@ -211,11 +186,3 @@ def download_artifact( driver_kwargs={"url": str(to), "storage_options": self.backend.storage_options}, metadata={"collection": collection, "artifact": artifact, "version": version, "location": str(to)}, ) - - def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> Catalog: - """Download all artifacts in collection to local directory.""" - catalog = self.collection_to_catalog(collection) - for artifact in catalog.values(): - artifact_name = artifact.metadata["artifact"] - self.download_artifact(artifact_name, to=to / artifact_name) - return catalog diff --git a/squirrel/artifact_manager/wandb.py b/squirrel/artifact_manager/wandb.py index 847f4fc..7403510 100644 --- a/squirrel/artifact_manager/wandb.py +++ b/squirrel/artifact_manager/wandb.py @@ -1,54 +1,177 @@ +import itertools from pathlib import Path -from typing import Optional, Any, Union, List, Iterable +from typing import Optional, Any, Iterable + +import logging +import wandb from squirrel.artifact_manager.base import ArtifactManager from squirrel.catalog import Catalog, Source +logger = logging.getLogger(__name__) -class WandbArtifactManager(ArtifactManager): - """Dummy placeholder for now - - TODO: Implement this based on the wandb Artifact API - """ - def list_collection_names(self) -> Iterable: - pass +class WandbArtifactManager(ArtifactManager): + def __init__(self, project: Optional[str] = None): + """ + Artifact manager using Weights & Biases as backend. - def store_to_catalog(self) -> Catalog: - pass + Aligning this with the FileSystemArtifactManager, the collections correspond to WandB artifact types. However, a + single WandB artifact can contain multiple files allowing the assignment of a single shared version to groups of + files. - def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: - pass + Note: This assumes that wandb.init() has been called before initializing this class. + """ + super().__init__() + if project is not None: + self.project = project + elif wandb.run is not None: + self.project = wandb.run.project + else: + raise ValueError("No project name was provided and no wandb run is active.") + if wandb.Api().settings["entity"] is not None: + self.entity = wandb.Api().settings["entity"] + else: + self.entity = wandb.Api().project(self.project).entity - def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None) -> Any: - pass + def list_collection_names(self) -> Iterable: + """ + List all collections managed by this ArtifactManager. + + Collections correspond to Wandb artifact types. + """ + return itertools.chain( + *[ + [artifact.name for artifact in collection.collections()] + for collection in wandb.Api().artifact_types(project=self.project) + ] + ) + + def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None) -> Any: + """ + Retrieve specific artifact value. + + This assumes that the artifact was logged as a wandb serialised object. If the artifact was a file upload, + the file contents should be retrieved using download instead. + """ + if collection is None: + collection = self._active_collection + if version is None: + version = "latest" + if wandb.run is None: + artifact = wandb.Api().artifact(f"{self.entity}/{self.project}/{artifact}:{version}", type=collection) + else: + artifact = wandb.run.use_artifact(f"{self.entity}/{self.project}/{artifact}:{version}", type=collection) + + value = artifact.get("data") + if value is not None: + return value + else: + raise ValueError(f"Artifact {artifact} was a file upload, please use download instead.") def get_artifact_source( - self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None + self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None ) -> Source: - pass + """Catalog entry for a specific artifact""" + if collection is None: + collection = self.active_collection + if version is None: + version = "latest" + + return Source( + driver_name="wandb", + driver_kwargs={ + "url": Path( + wandb.Api().settings["base_url"], + self.entity, + self.project, + collection, + artifact, + version, + ), + }, + metadata={ + "project": self.project, + "collection": collection, + "artifact": artifact, + "version": version, + "location": Path( + wandb.Api().settings["base_url"], self.entity, self.project, collection, artifact, version + ), + }, + ) - def get_artifact_location( - self, artifact_name: str, collection: Optional[str] = None, version: Optional[int] = None - ) -> str: - pass + def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: + """Construct a catalog listing artifacts within a specific collection.""" + if collection is None: + collection = self._active_collection + artifact_names = [ + artifact.name + for artifact in wandb.Api().artifact_type(type_name=collection, project=self.project).collections() + ] + catalog = Catalog() + for artifact in artifact_names: + for instance in wandb.Api().artifact_versions(type_name=collection, name=f"{self.project}/{artifact}"): + catalog[str(Path(collection, artifact))] = self.get_artifact_source( + artifact, collection, instance.version + ) + return catalog def log_file(self, local_path: Path, name: str, collection: Optional[str] = None) -> Source: - pass - - def log_collection(self, files: Union[Path, List[Path]], collection_name: Optional[str] = None) -> Catalog: - pass - - def log_object(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: - pass + """Upload a single file to artifact store without serialisation.""" + if collection is None: + collection = self._active_collection + artifact = wandb.Artifact(name, type=collection) + artifact.add_file(str(local_path), "data") + artifact.save() + artifact.wait() + return self.get_artifact_source(name, collection) + + def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: + """Log serialisable object to artifact store.""" + if not isinstance(obj, wandb.data_types.WBValue): + raise ValueError( + f"Object {obj} is not a wandb serializable object. Please convert to a subclass of" + f" wandb.data_types.WBValue first. See https://docs.wandb.ai/ref/python/data-types/" + ) + if wandb.run is None: + raise ValueError("No wandb run is active. Please call wandb.init() before logging artifacts.") + if collection is None: + collection = self._active_collection + artifact = wandb.Artifact(name, type=collection) + artifact.add(obj, "data") + artifact.save() + artifact.wait() + return self.get_artifact_source(name, collection, artifact.version) def download_artifact( - self, artifact: str, collection: Optional[str] = None, version: Optional[int] = None, to: Path = "./" + self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Path = "./" ) -> Source: - pass - - def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> Catalog: - pass - - def __init__(self): - super().__init__() + """ + Download a specific artifact to a local path. + + WandB serialised objects would be downloaded in a nested folder structure and are therefore discouraged right + now. + """ + if collection is None: + collection = self._active_collection + if version is None: + version = "latest" + if wandb.run is None: + art = wandb.Api().artifact(f"{self.entity}/{self.project}/{artifact}:{version}", type=collection) + else: + art = wandb.run.use_artifact(f"{self.entity}/{self.project}/{artifact}:{version}", type=collection) + + if art.get("data") is not None: + logger.warning( + "Artifact was a serialised object, the directory structure was created by WandB and may contain " + "nested folders." + ) + art.download(str(to)) + + art.download(str(to)) + return Source( + driver_name="file", + driver_kwargs={"url": str(to)}, + metadata={"collection": collection, "artifact": artifact, "version": version, "location": str(to)}, + ) diff --git a/test/test_artifact_manager/test_fs_logging.py b/test/test_artifact_manager/test_fs_logging.py index 144272d..96f146a 100644 --- a/test/test_artifact_manager/test_fs_logging.py +++ b/test/test_artifact_manager/test_fs_logging.py @@ -21,12 +21,13 @@ def test_serializer(serializer: SquirrelSerializer, name: str, target: str) -> N artifact_name = "john" tmpdir = tempfile.TemporaryDirectory() + # message pack serialization manager = FileSystemArtifactManager(url=tmpdir.name, serializer=serializer, auto_mkdir=True) source = manager.log_artifact(obj, artifact_name) - assert source.metadata["location"] == f"file://{tmpdir.name}/default/{artifact_name}/1/{name}" - with open(f"{tmpdir.name}/default/{artifact_name}/1/{name}", "rb") as f: + assert source.metadata["location"] == f"file://{tmpdir.name}/default/{artifact_name}/v0/{name}" + with open(f"{tmpdir.name}/default/{artifact_name}/v0/{name}", "rb") as f: assert f.read() == target tmpdir.cleanup() @@ -47,24 +48,24 @@ def test_multi_serializer() -> None: assert msgpack_source == Source( driver_name="messagepack", driver_kwargs={ - "url": f"file://{tmpdir.name}/default/john/1/messagepack", + "url": f"file://{tmpdir.name}/default/john/v0/messagepack", "storage_options": {"auto_mkdir": True}, }, metadata={ "collection": "default", "artifact": "john", - "version": 1, - "location": f"file://{tmpdir.name}/default/john/1/messagepack", + "version": "v0", + "location": f"file://{tmpdir.name}/default/john/v0/messagepack", }, ) assert jsonl_source == Source( driver_name="jsonl", - driver_kwargs={"url": f"file://{tmpdir.name}/default/john/2/jsonl", "storage_options": {"auto_mkdir": True}}, + driver_kwargs={"url": f"file://{tmpdir.name}/default/john/v1/jsonl", "storage_options": {"auto_mkdir": True}}, metadata={ "collection": "default", "artifact": "john", - "version": 2, - "location": f"file://{tmpdir.name}/default/john/2/jsonl", + "version": "v1", + "location": f"file://{tmpdir.name}/default/john/v1/jsonl", }, ) tmpdir.cleanup() @@ -81,25 +82,25 @@ def test_log_object() -> None: source = manager.log_artifact(obj, artifact_name) assert source.driver_name == "messagepack" - assert source.driver_kwargs["url"] == f"file://{tmpdir.name}/default/{artifact_name}/1/messagepack" + assert source.driver_kwargs["url"] == f"file://{tmpdir.name}/default/{artifact_name}/v0/messagepack" assert source.metadata["collection"] == "default" assert source.metadata["artifact"] == artifact_name - assert source.metadata["version"] == 1 + assert source.metadata["version"] == "v0" obj2 = {"name": "John", "age": 15} artifact_name = "young_john" source2 = manager.log_artifact(obj2, artifact_name, collection) - assert source2.driver_kwargs["url"] == f"file://{tmpdir.name}/{collection}/{artifact_name}/1/messagepack" + assert source2.driver_kwargs["url"] == f"file://{tmpdir.name}/{collection}/{artifact_name}/v0/messagepack" assert source2.metadata["collection"] == collection assert source2.metadata["artifact"] == artifact_name - assert source2.metadata["version"] == 1 + assert source2.metadata["version"] == "v0" source2 = manager.log_artifact(obj2, artifact_name, collection) - assert source2.driver_kwargs["url"] == f"file://{tmpdir.name}/{collection}/{artifact_name}/2/messagepack" + assert source2.driver_kwargs["url"] == f"file://{tmpdir.name}/{collection}/{artifact_name}/v1/messagepack" assert source2.metadata["collection"] == collection assert source2.metadata["artifact"] == artifact_name - assert source2.metadata["version"] == 2 + assert source2.metadata["version"] == "v1" tmpdir.cleanup() @@ -119,8 +120,8 @@ def test_get_artifact() -> None: assert manager.get_artifact("john", collection) == obj1 manager.log_artifact(obj2, artifact_name, collection) assert manager.get_artifact(artifact_name, collection) == obj2 - assert manager.get_artifact(artifact_name, collection, 2) == obj1 - assert manager.get_artifact(artifact_name, collection, 1) == obj + assert manager.get_artifact(artifact_name, collection, "v1") == obj1 + assert manager.get_artifact(artifact_name, collection, "v0") == obj def test_log_file() -> None: @@ -132,9 +133,9 @@ def test_log_file() -> None: manager = FileSystemArtifactManager(url=store_dir.name, auto_mkdir=True) for (filename, artifact_name, version, content) in [ - ("foo.txt", "foo_file", 1, "Test: Foo"), - ("bar.txt", "bar_file", 1, "Test: Bar"), - ("baz.txt", "bar_file", 2, "Test: Baz"), + ("foo.txt", "foo_file", "v0", "Test: Foo"), + ("bar.txt", "bar_file", "v0", "Test: Bar"), + ("baz.txt", "bar_file", "v1", "Test: Baz"), ]: with open(f"{src_dir.name}/{filename}", "w") as f: f.write(content) @@ -161,8 +162,8 @@ def test_get_file() -> None: manager = FileSystemArtifactManager(url=store_dir.name, auto_mkdir=True) file_descriptions = [ - ("bar.txt", "bar_file", 1, "Test: Bar"), - ("baz.txt", "bar_file", 2, "Test: Baz"), + ("bar.txt", "bar_file", "v0", "Test: Bar"), + ("baz.txt", "bar_file", "v1", "Test: Baz"), ] for (filename, artifact_name, _, content) in file_descriptions: From 57cd1754c001def3e3d90d8f3692ca25950f4b9b Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Mon, 18 Dec 2023 18:09:20 +0100 Subject: [PATCH 26/41] API update --- squirrel/artifact_manager/base.py | 93 ++++++++++++++---- squirrel/artifact_manager/fs.py | 146 ++++++++++++++--------------- squirrel/artifact_manager/wandb.py | 117 ++++++++++++----------- 3 files changed, 204 insertions(+), 152 deletions(-) diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index 9175f08..b3bfdf4 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -1,11 +1,66 @@ -import re from abc import abstractmethod, ABC +import logging from pathlib import Path -from typing import Optional, List, Any, Iterable +import re +import tempfile +from types import TracebackType +from typing import Optional, List, Any, Iterable, Type from squirrel.catalog import Catalog, Source +logger = logging.getLogger(__name__) + + +class DirectoryLogger: + """ + Class to be used as a context for logging a directory as an artifact. + When entering the scope it creates a local dir with a valid afid and returns the filepath to it. + You can then write files to that dir and after exiting the scope the dir gets logged through the artifactmanager. + """ + + def __init__(self, artifact_manager: "ArtifactManager", artifact: str, collection: Optional[str]) -> None: + """ + Initializes the DirectoryLogger. + + Args: + artifact_manager: An artifact manager instance to use for logging the final artifact. + artifact: The name of the artifact to log. + collection: The name of the collection to log to, if None the active collection of the artifact manager is used. + """ + self.artifact_manager = artifact_manager + self.artifact = artifact + self.collection = collection + self.tempdir = None + + def __enter__(self) -> str: + """ + Called when we enter the context. Creates folder under /tmp with the artifacts id if it doesn't exist yet. + + Returns: Absolute path to artifact folder as str + """ + self.tempdir = tempfile.TemporaryDirectory() + return str(Path(self.tempdir.name) / Path(self.artifact)) + + def __exit__( + self, + exctype: Optional[Type[BaseException]] = None, + excinst: Optional[BaseException] = None, + exctb: Optional[TracebackType] = None, + ) -> None: + """Called when we exit the context. Logs the artifact folder with mlflow if its not empty.""" + + path = Path(self.tempdir.name) / Path(self.artifact) + files = [p for p in path.glob("*")] + if len(files) > 0: + self.artifact_manager.log_files(path, self.artifact, self.collection) + else: + logger.info(f"Did not log artifact folder at {path} as it seems to be empty") + + if self.tempdir is not None: + self.tempdir.cleanup() + + class ArtifactManager(ABC): def __init__(self): """ @@ -51,6 +106,11 @@ def list_collection_names(self) -> Iterable: """Return list of all collections in the artifact store""" raise NotImplementedError + @abstractmethod + def exists_in_collection(self, artifact: str, collection: Optional[str] = None) -> bool: + """Check if artifact exists in specified collection.""" + raise NotImplementedError + @abstractmethod def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: """Catalog of all artifacts within a specific collection.""" @@ -61,7 +121,7 @@ def get_artifact(self, artifact: str, collection: Optional[str] = None, version: raise NotImplementedError @abstractmethod - def log_file(self, local_path: Path, name: str, collection: Optional[str] = None) -> Source: + def log_files(self, local_path: Path, name: str, collection: Optional[str] = None) -> Source: """Upload file into (current) collection, increment version automatically""" raise NotImplementedError @@ -82,6 +142,10 @@ def download_artifact( """Retrieve file (from current collection) to specific location. Retrieve latest version unless specified.""" raise NotImplementedError + def exists(self, artifact: str) -> bool: + """Check if artifact exists in specified collection.""" + return any([self.exists_in_collection(artifact, collection) for collection in self.list_collection_names()]) + def store_to_catalog(self) -> Catalog: """Provide Catalog of all artifacts stored in backend.""" catalog = Catalog() @@ -89,23 +153,14 @@ def store_to_catalog(self) -> Catalog: catalog.update(self.collection_to_catalog(collection)) return catalog - def log_files(self, local_paths: List[Path], collection: Optional[str] = None) -> Catalog: - """Upload a collection of file into a (current) collection""" - if collection is None: - collection = self.active_collection - for local_path in local_paths: - self.log_file(local_path, local_path.name, collection) - return self.collection_to_catalog(collection) - - def log_folder(self, folder: Path, collection: Optional[str] = None) -> Catalog: - """Log folder as collection of artifacts into store""" - if not folder.is_dir(): - raise ValueError(f"Path {folder} is not a directory!") - - if collection is None: - collection = folder.name + def log_folder(self, artifact: str, collection: Optional[str] = None) -> DirectoryLogger: + """ + Context manager for logging a directory as an artifact. - return self.log_files([f for f in folder.iterdir() if f.is_file()], collection) + When entering the scope it creates a local dir with a valid afid and returns the filepath to it. + You can then write files to that dir and after exiting the scope the dir gets logged through the artifactmanager. + """ + return DirectoryLogger(self, artifact, collection) def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> Catalog: """Download all artifacts in collection to local directory.""" diff --git a/squirrel/artifact_manager/fs.py b/squirrel/artifact_manager/fs.py index fe47ca1..c9c78d4 100644 --- a/squirrel/artifact_manager/fs.py +++ b/squirrel/artifact_manager/fs.py @@ -1,4 +1,3 @@ -import typing as t from pathlib import Path from typing import Optional, Any, List, Iterable @@ -34,32 +33,42 @@ def key_exists(self, key: Path, **open_kwargs) -> bool: """Checks if a key exists.""" return self.fs.exists(Path(self.url) / key, **open_kwargs) - def get(self, key: Path, mode: str = "rb", **open_kwargs) -> t.Any: + def get(self, key: Path, mode: str = "rb", **open_kwargs) -> Any: """Retrieves an item with the given key.""" if self.fs.exists(Path(self.url, key, Serializers[self.serializer.__class__]), **open_kwargs): return super().get(str(Path(key, Serializers[self.serializer.__class__])), mode, **open_kwargs) - elif self.fs.exists(Path(self.url, key, "file"), **open_kwargs): - return self.fs.cat(Path(self.url, key, "file"), **open_kwargs) + elif self.fs.exists(Path(self.url, key, "files"), **open_kwargs): + return self.fs.cat(Path(self.url, key, "files"), **open_kwargs) else: raise ValueError(f"Key {key} does not exist!") - def set(self, value: t.Any, key: t.Optional[Path] = None, mode: str = "wb", **open_kwargs) -> None: + def set(self, value: Any, key: Optional[Path] = None, mode: str = "wb", **open_kwargs) -> None: """Persists an item with the given key.""" if key is None: key = get_random_key() + # construct path under which to store the data + target = Path(self.url, key, Serializers.get(self.serializer.__class__, "files"), open_kwargs.pop("suffix")) + + if self.fs.exists(target, **open_kwargs): + raise ValueError(f"Key {key} already exists!") + if isinstance(value, Path): - self.fs.cp_file(value, Path(self.url, key, "file"), **open_kwargs) + if value.is_dir(): + self.fs.cp_dir(value, target, **open_kwargs) + else: + self.fs.cp_file(value, target, mode, **open_kwargs) else: - super().set(value, str(Path(key, Serializers[self.serializer.__class__])), mode, **open_kwargs) + super().set(value, str(target), mode, **open_kwargs) class FileSystemArtifactManager(ArtifactManager): + def __init__(self, url: str, serializer: Optional[SquirrelSerializer] = None, **fs_kwargs): """ Artifactmanager backed by fsspec filesystems. The manager logs artifacts according to the following file structure: - url/collection/artifact/version/serializer + url/collection/artifact/version/serializer/ url: root directory of the artifact store collection: the name of the collection defaults to 'default' artifact: (human-readable) name of the artifact @@ -75,16 +84,11 @@ def list_collection_names(self) -> Iterable: """List all collections managed by this ArtifactManager.""" return self.backend.keys(nested=False) - def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None) -> Any: - """Retrieve specific artifact value.""" + def exists_in_collection(self, artifact: str, collection: Optional[str] = None) -> bool: + """Check if artifact exists in specified collection.""" if collection is None: collection = self.active_collection - if version is None or version == "latest": - version = f"v{max(int(vs[1:]) for vs in self.backend.complete_key(Path(collection) / Path(artifact)))}" - if not self.backend.key_exists(Path(collection, artifact, version)): - raise ValueError(f"Artifact {artifact} does not exist in collection {collection} with version {version}!") - path = Path(collection, artifact, version) - return self.backend.get(path) + return self.backend.key_exists(Path(collection, artifact)) def get_artifact_source( self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None @@ -97,50 +101,20 @@ def get_artifact_source( if not self.backend.key_exists(Path(collection, artifact, version)): raise ValueError(f"Artifact {artifact} does not exist in collection {collection} with version {version}!") - if Serializers[self.backend.serializer.__class__] in self.backend.complete_key( - Path(collection, artifact, version) - ): - return Source( - driver_name=Serializers[self.backend.serializer.__class__], - driver_kwargs={ - "url": Path( - self.backend.url, - collection, - artifact, - version, - Serializers[self.backend.serializer.__class__], - ).as_uri(), - "storage_options": self.backend.storage_options, - }, - metadata={ - "collection": collection, - "artifact": artifact, - "version": version, - "location": Path( - self.backend.url, - collection, - artifact, - version, - Serializers[self.backend.serializer.__class__], - ).as_uri(), - }, - ) - elif self.backend.key_exists(Path(collection, artifact, version, "file")): - return Source( - driver_name="file", - driver_kwargs={ - "url": Path(self.backend.url, collection, artifact, version, "file").as_uri(), - "storage_options": self.backend.storage_options, - }, - metadata={ - "collection": collection, - "artifact": artifact, - "version": version, - "location": Path(self.backend.url, collection, artifact, version, "file").as_uri(), - }, - ) - else: - raise ValueError(f"Could not read artifact {artifact} in collection {collection} with version {version}!") + # TODO: Vary source (driver) description when support for serialised python values is added + return Source( + driver_name="file", + driver_kwargs={ + "url": Path(self.backend.url, collection, artifact, version, "file").as_uri(), + "storage_options": self.backend.storage_options, + }, + metadata={ + "collection": collection, + "artifact": artifact, + "version": version, + "location": Path(self.backend.url, collection, artifact, version).as_uri(), + }, + ) def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: """Provide catalog of all artifacts and their versions contained within specific collection""" @@ -152,27 +126,43 @@ def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: catalog[str(Path(collection, artifact))] = self.get_artifact_source(artifact, collection, version) return catalog - def log_file(self, local_path: Path, name: str, collection: Optional[str] = None) -> Source: - """Upload local file to artifact store without serialisation""" - if isinstance(local_path, str): - local_path = Path(local_path) - assert isinstance(local_path, Path), "Path to file must be passed as a pathlib.Path object!" - if collection is None: - collection = self.active_collection - version = f"v{len(self.backend.complete_key(Path(collection, name)))}" - self.backend.set(local_path, Path(collection, name, version)) - return self.get_artifact_source(name, collection) - def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: """Log an arbitrary python object using store serialisation.""" + raise NotImplementedError("Logging and retrieving python objects is not yet supported. Please serialize your" + "objects and log resulting files with 'log_file' or 'log_folder'.") + # Implementation for logging python objects can make use of + # self.backend.set(obj, Path(collection, name, version)) + + def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None) -> Any: + """Retrieve specific artifact value.""" + raise NotImplementedError("Logging and retrieving python objects is not yet supported. Please serialize your" + "objects and retrieve the logged files with 'download_artifact' instead.") + + def log_files( + self, + artifact_name: str, + local_path: Path, + collection: Optional[str] = None, + artifact_path: Optional[Path] = None + ) -> Source: + """Upload local file or folder to artifact store without serialisation""" + if not isinstance(local_path, (str, Path)): + raise ValueError("Path to file should be passed as a pathlib.Path object!") + + if artifact_path is not None and not isinstance(artifact_name, (str, Path)): + raise ValueError("Artifact path should be passed as a pathlib.Path object!") + if collection is None: collection = self.active_collection - if self.backend.key_exists(Path(collection, name)): - version = f"v{len(self.backend.complete_key(Path(collection, name)))}" - else: - version = "v0" - self.backend.set(obj, Path(collection, name, version)) - return self.get_artifact_source(name, collection) + + version = f"v{len(self.backend.complete_key(Path(collection, artifact_name)))}" + + if artifact_path is None: + artifact_path = Path(local_path) + + self.backend.set(local_path, Path(collection, artifact_name, version), suffix=artifact_path) + + return self.get_artifact_source(artifact_name, collection) def download_artifact( self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Path = "./" @@ -180,7 +170,7 @@ def download_artifact( """Download artifact to local path.""" location = self.get_artifact_source(artifact, collection, version).metadata["location"] if self.backend.fs.exists(location): - self.backend.fs.cp_file(location, to) + self.backend.fs.cp(Path(location, "files"), to) return Source( driver_name="file", driver_kwargs={"url": str(to), "storage_options": self.backend.storage_options}, diff --git a/squirrel/artifact_manager/wandb.py b/squirrel/artifact_manager/wandb.py index 7403510..8e2c12c 100644 --- a/squirrel/artifact_manager/wandb.py +++ b/squirrel/artifact_manager/wandb.py @@ -12,7 +12,7 @@ class WandbArtifactManager(ArtifactManager): - def __init__(self, project: Optional[str] = None): + def __init__(self, entity: Optional[str] = None, project: Optional[str] = None): """ Artifact manager using Weights & Biases as backend. @@ -20,16 +20,23 @@ def __init__(self, project: Optional[str] = None): single WandB artifact can contain multiple files allowing the assignment of a single shared version to groups of files. - Note: This assumes that wandb.init() has been called before initializing this class. + Note: For storing objects it is assumed that wandb.init() has been called so that artifacts can be associated + with a run. """ super().__init__() if project is not None: self.project = project elif wandb.run is not None: self.project = wandb.run.project + elif wandb.Api().settings["project"] is not None: + self.project = wandb.Api().settings["project"] else: - raise ValueError("No project name was provided and no wandb run is active.") - if wandb.Api().settings["entity"] is not None: + raise ValueError("No project name was provided and no active project could be identified.") + if entity is not None: + self.entity = entity + elif wandb.run is not None: + self.entity = wandb.run.entity + elif wandb.Api().settings["entity"] is not None: self.entity = wandb.Api().settings["entity"] else: self.entity = wandb.Api().project(self.project).entity @@ -47,27 +54,15 @@ def list_collection_names(self) -> Iterable: ] ) - def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None) -> Any: + def exists_in_collection(self, artifact: str, collection: Optional[str] = None) -> bool: """ - Retrieve specific artifact value. + Check if artifact exists in specified collection. - This assumes that the artifact was logged as a wandb serialised object. If the artifact was a file upload, - the file contents should be retrieved using download instead. + Note: This is not supported by the WandB API and therefore requires listing all artifacts in a collection. """ if collection is None: - collection = self._active_collection - if version is None: - version = "latest" - if wandb.run is None: - artifact = wandb.Api().artifact(f"{self.entity}/{self.project}/{artifact}:{version}", type=collection) - else: - artifact = wandb.run.use_artifact(f"{self.entity}/{self.project}/{artifact}:{version}", type=collection) - - value = artifact.get("data") - if value is not None: - return value - else: - raise ValueError(f"Artifact {artifact} was a file upload, please use download instead.") + collection = self.active_collection + return artifact in [artifact.name for artifact in wandb.Api().artifact_type(type_name=collection).collections()] def get_artifact_source( self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None @@ -81,13 +76,15 @@ def get_artifact_source( return Source( driver_name="wandb", driver_kwargs={ - "url": Path( - wandb.Api().settings["base_url"], - self.entity, - self.project, - collection, - artifact, - version, + "url": str( + Path( + wandb.Api().settings["base_url"], + self.entity, + self.project, + collection, + artifact, + version, + ) ), }, metadata={ @@ -117,32 +114,49 @@ def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: ) return catalog - def log_file(self, local_path: Path, name: str, collection: Optional[str] = None) -> Source: - """Upload a single file to artifact store without serialisation.""" - if collection is None: - collection = self._active_collection - artifact = wandb.Artifact(name, type=collection) - artifact.add_file(str(local_path), "data") - artifact.save() - artifact.wait() - return self.get_artifact_source(name, collection) - def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: """Log serialisable object to artifact store.""" - if not isinstance(obj, wandb.data_types.WBValue): - raise ValueError( - f"Object {obj} is not a wandb serializable object. Please convert to a subclass of" - f" wandb.data_types.WBValue first. See https://docs.wandb.ai/ref/python/data-types/" - ) - if wandb.run is None: - raise ValueError("No wandb run is active. Please call wandb.init() before logging artifacts.") + raise NotImplementedError("Logging and retrieving python objects is not yet supported. Please serialize your" + "objects and log resulting files with 'log_files' or log_folder.") + # Implementation for logging python objects can make use of + # if not isinstance(obj, wandb.data_types.WBValue): + # raise ValueError( + # f"Object {obj} is not a wandb serializable object. Please convert to a subclass of" + # f" wandb.data_types.WBValue first. See https://docs.wandb.ai/ref/python/data-types/" + # ) + # if wandb.run is None: + # raise ValueError("No wandb run is active. Please call wandb.init() before logging artifacts.") + + def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None) -> Any: + """ + Retrieve specific artifact value. + + This assumes that the artifact was logged as a wandb serialised object. If the artifact was a file upload, + the file contents should be retrieved using download instead. + """ + raise NotImplementedError("Logging and retrieving python objects is not yet supported. Please serialize your" + "objects and retrieve the logged files with 'download_artifact' instead.") + + def log_files( + self, + artifact_name: str, + local_path: Path, + collection: Optional[str] = None, + artifact_path: Optional[Path] = None + ) -> Source: + """Upload a single file to artifact store without serialisation.""" if collection is None: collection = self._active_collection - artifact = wandb.Artifact(name, type=collection) - artifact.add(obj, "data") + artifact = wandb.Artifact(artifact_name, type=collection) + if artifact_path is not None: + artifact_path = str(artifact_path) + if local_path.is_dir(): + artifact.add_dir(str(local_path), name=artifact_path) + else: + artifact.add_file(str(local_path), name=artifact_path) artifact.save() artifact.wait() - return self.get_artifact_source(name, collection, artifact.version) + return self.get_artifact_source(artifact_name, collection) def download_artifact( self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Path = "./" @@ -162,13 +176,6 @@ def download_artifact( else: art = wandb.run.use_artifact(f"{self.entity}/{self.project}/{artifact}:{version}", type=collection) - if art.get("data") is not None: - logger.warning( - "Artifact was a serialised object, the directory structure was created by WandB and may contain " - "nested folders." - ) - art.download(str(to)) - art.download(str(to)) return Source( driver_name="file", From a4d91feb4d85f88e4e97e3fe21e7e8d696c776d9 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Tue, 19 Dec 2023 10:21:46 +0100 Subject: [PATCH 27/41] Fixing filesystem tests --- squirrel/artifact_manager/fs.py | 46 +++++++++++------ test/test_artifact_manager/test_fs_logging.py | 39 +++++++++++--- test/test_artifact_manager/wandb_script.py | 51 +++++++++++++++++++ 3 files changed, 114 insertions(+), 22 deletions(-) create mode 100644 test/test_artifact_manager/wandb_script.py diff --git a/squirrel/artifact_manager/fs.py b/squirrel/artifact_manager/fs.py index c9c78d4..cc7f204 100644 --- a/squirrel/artifact_manager/fs.py +++ b/squirrel/artifact_manager/fs.py @@ -36,9 +36,21 @@ def key_exists(self, key: Path, **open_kwargs) -> bool: def get(self, key: Path, mode: str = "rb", **open_kwargs) -> Any: """Retrieves an item with the given key.""" if self.fs.exists(Path(self.url, key, Serializers[self.serializer.__class__]), **open_kwargs): + # retrieve and deserialize data return super().get(str(Path(key, Serializers[self.serializer.__class__])), mode, **open_kwargs) elif self.fs.exists(Path(self.url, key, "files"), **open_kwargs): - return self.fs.cat(Path(self.url, key, "files"), **open_kwargs) + if "target" in open_kwargs: + if not open_kwargs["target"].exists(): + open_kwargs["target"].mkdir(parents=True) + self.fs.cp( + str(Path(self.url, key, "files/*")), + str(open_kwargs.pop("target")), + recursive=True, + **open_kwargs + ) + # retrieve raw file + else: + return self.fs.cat(Path(self.url, key, "files"), **open_kwargs) else: raise ValueError(f"Key {key} does not exist!") @@ -47,16 +59,19 @@ def set(self, value: Any, key: Optional[Path] = None, mode: str = "wb", **open_k if key is None: key = get_random_key() # construct path under which to store the data - target = Path(self.url, key, Serializers.get(self.serializer.__class__, "files"), open_kwargs.pop("suffix")) + if isinstance(value, Path): + target = Path(self.url, key, "files", open_kwargs.pop("suffix", "")) + else: + target = Path(self.url, key, Serializers[self.serializer.__class__], open_kwargs.pop("suffix")) if self.fs.exists(target, **open_kwargs): raise ValueError(f"Key {key} already exists!") if isinstance(value, Path): if value.is_dir(): - self.fs.cp_dir(value, target, **open_kwargs) + self.fs.cp(str(value), str(target), recursive=True, **open_kwargs) else: - self.fs.cp_file(value, target, mode, **open_kwargs) + self.fs.cp_file(value, target, **open_kwargs) else: super().set(value, str(target), mode, **open_kwargs) @@ -157,10 +172,10 @@ def log_files( version = f"v{len(self.backend.complete_key(Path(collection, artifact_name)))}" - if artifact_path is None: - artifact_path = Path(local_path) - - self.backend.set(local_path, Path(collection, artifact_name, version), suffix=artifact_path) + open_kwargs = {"auto_mkdir": True} + if artifact_path is not None: + open_kwargs["suffix"] = artifact_path + self.backend.set(local_path, Path(collection, artifact_name, version), **open_kwargs) return self.get_artifact_source(artifact_name, collection) @@ -168,11 +183,10 @@ def download_artifact( self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Path = "./" ) -> Source: """Download artifact to local path.""" - location = self.get_artifact_source(artifact, collection, version).metadata["location"] - if self.backend.fs.exists(location): - self.backend.fs.cp(Path(location, "files"), to) - return Source( - driver_name="file", - driver_kwargs={"url": str(to), "storage_options": self.backend.storage_options}, - metadata={"collection": collection, "artifact": artifact, "version": version, "location": str(to)}, - ) + location = Path(collection, artifact, version) + self.backend.get(Path(location), target=to) + return Source( + driver_name="file", + driver_kwargs={"url": str(to), "storage_options": self.backend.storage_options}, + metadata={"collection": collection, "artifact": artifact, "version": version, "location": str(to)}, + ) diff --git a/test/test_artifact_manager/test_fs_logging.py b/test/test_artifact_manager/test_fs_logging.py index 96f146a..1c53c3f 100644 --- a/test/test_artifact_manager/test_fs_logging.py +++ b/test/test_artifact_manager/test_fs_logging.py @@ -8,6 +8,7 @@ from squirrel.serialization import JsonSerializer, MessagepackSerializer, SquirrelSerializer +@pytest.mark.skip(reason="Logging of python values not yet supported") @pytest.mark.parametrize( "serializer,name,target", [ @@ -26,13 +27,14 @@ def test_serializer(serializer: SquirrelSerializer, name: str, target: str) -> N manager = FileSystemArtifactManager(url=tmpdir.name, serializer=serializer, auto_mkdir=True) source = manager.log_artifact(obj, artifact_name) - assert source.metadata["location"] == f"file://{tmpdir.name}/default/{artifact_name}/v0/{name}" + assert source.metadata["location"] == f"file://{tmpdir.name}/default/{artifact_name}/v0/{name}/john" with open(f"{tmpdir.name}/default/{artifact_name}/v0/{name}", "rb") as f: assert f.read() == target tmpdir.cleanup() +@pytest.mark.skip(reason="Logging of python values not yet supported") def test_multi_serializer() -> None: """Test that multiple artifact stores with differing backends are correctly interacting.""" obj = {"name": "John", "age": 30} @@ -71,6 +73,7 @@ def test_multi_serializer() -> None: tmpdir.cleanup() +@pytest.mark.skip(reason="Logging of python values not yet supported") def test_log_object() -> None: """Log an object to the default collection and check details of the catalog entry.""" obj = {"name": "John", "age": 30} @@ -104,6 +107,7 @@ def test_log_object() -> None: tmpdir.cleanup() +@pytest.mark.skip(reason="Logging of python values not yet supported") def test_get_artifact() -> None: """Test logging multiple versions of the same object and retrieving different versions.""" obj = {"name": "John", "age": 10} @@ -132,6 +136,7 @@ def test_log_file() -> None: store_dir = tempfile.TemporaryDirectory() manager = FileSystemArtifactManager(url=store_dir.name, auto_mkdir=True) + # test logging of individual files for (filename, artifact_name, version, content) in [ ("foo.txt", "foo_file", "v0", "Test: Foo"), ("bar.txt", "bar_file", "v0", "Test: Bar"), @@ -140,15 +145,28 @@ def test_log_file() -> None: with open(f"{src_dir.name}/{filename}", "w") as f: f.write(content) - source = manager.log_file(Path(f"{src_dir.name}/{filename}"), artifact_name, collection) + source = manager.log_files(artifact_name, Path(f"{src_dir.name}/{filename}"), collection, Path(filename)) assert source.driver_name == "file" assert source.metadata["collection"] == collection assert source.metadata["artifact"] == artifact_name assert source.metadata["version"] == version + assert source.metadata["location"] == f"file://{store_dir.name}/{collection}/{artifact_name}/{version}" - with open(f"{store_dir.name}/{collection}/{artifact_name}/{version}/file") as f: + with open(f"{store_dir.name}/{collection}/{artifact_name}/{version}/files/{filename}") as f: assert f.read() == content + + # test logging of folder + source = manager.log_files("folder", Path(src_dir.name), collection) + + assert source.driver_name == "file" + assert source.metadata["collection"] == collection + assert source.metadata["artifact"] == "folder" + assert source.metadata["version"] == "v0" + assert source.metadata["location"] == f"file://{store_dir.name}/{collection}/folder/v0" + + assert len(list(Path(f"{store_dir.name}/{collection}/folder/v0/files").iterdir())) == 3 + src_dir.cleanup() store_dir.cleanup() @@ -170,11 +188,20 @@ def test_get_file() -> None: with open(f"{src_dir.name}/{filename}", "w") as f: f.write(content) - manager.log_file(Path(f"{src_dir.name}/{filename}"), artifact_name, collection) + manager.log_files(artifact_name, Path(f"{src_dir.name}/{filename}"), collection, Path(filename)) + + source = manager.log_files("folder", Path(src_dir.name), collection) + + # Test retrieval of specific files + for (filename, artifact_name, version, content) in file_descriptions: + manager.download_artifact(artifact_name, collection, version, Path(f"{src_dir.name}/downloaded")) + with open(f"{src_dir.name}/downloaded/{filename}") as f: + assert f.read() == content + # Test retrieval of entire folder + manager.download_artifact("folder", collection, "v0", Path(f"{src_dir.name}/downloaded2")) for (filename, artifact_name, version, content) in file_descriptions: - manager.download_artifact(artifact_name, collection, version, Path(f"{src_dir.name}/downloaded_{filename}")) - with open(f"{src_dir.name}/downloaded_{filename}") as f: + with open(f"{src_dir.name}/downloaded2/{filename}") as f: assert f.read() == content src_dir.cleanup() diff --git a/test/test_artifact_manager/wandb_script.py b/test/test_artifact_manager/wandb_script.py new file mode 100644 index 0000000..d0519a8 --- /dev/null +++ b/test/test_artifact_manager/wandb_script.py @@ -0,0 +1,51 @@ +from pathlib import Path + +import numpy as np +import pandas as pd +import tempfile +import wandb +from squirrel.artifact_manager.wandb import WandbArtifactManager + + +tbl_data = pd.DataFrame({"users": ["geoff", "juergen", "ada"], "feature_01": [1, 117, 42]}) +tbl = wandb.Table(data=tbl_data) + +pixels = np.random.randint(low=0, high=256, size=(100, 100, 3)) +image = wandb.Image(pixels, caption=f"random field") + +localdir = tempfile.TemporaryDirectory() +tbl_data.to_csv(f"{localdir.name}/tbl") +pixels.dump(f"{localdir.name}/image") + +test_run = wandb.init(project="sebastian-sandbox") + +artifact_manager = WandbArtifactManager(project="sebastian-sandbox") +# src1 = artifact_manager.log_artifact(tbl, "tbl", collection="test_objects") +# assert src1.metadata["collection"] == "test_objects" +# assert src1.metadata["artifact"] == "tbl" +# assert src1.metadata["version"] == "v0", f"First version should be v1, but is {src1.metadata['version']}" +# assert src1.metadata["location"] == Path("https://merantix-momentum.wandb.io/mxm/sebastian-sandbox/test_objects/tbl/v0"), \ +# f"Location is {src1.metadata['location']}" +# +# src2 = artifact_manager.log_artifact(image, "random_field", collection="test_data") +# assert src2.metadata["collection"] == "test_data" +# assert src2.metadata["artifact"] == "random_field", f"Name should be random_field, but is {src2.metadata['artifact']}" +# assert src2.metadata["version"] == "v0", f"First version should be v0, but is {src2.metadata['version']}" +# assert src2.metadata["location"] == Path("https://merantix-momentum.wandb.io/mxm/sebastian-sandbox/test_data/random_field/v0") +# +# catalog = artifact_manager.log_folder(Path(localdir.name), "test_objects") +# assert len(catalog) == 2, f"Catalog is {catalog}" +# assert "test_objects/tbl" in catalog and "test_objects/image" in catalog, f"Catalog is {catalog}" +# assert catalog["test_objects/tbl"].metadata["version"] == "v1", f"Catalog entry is {catalog['test_objects/tbl']}" +# assert catalog["test_objects/image"].metadata["version"] == "v0", f"Catalog entry is {catalog['test_objects/image']}" + +assert artifact_manager.get_artifact("tbl", collection="test_objects", version="v0") == tbl, artifact_manager.get_artifact("tbl", collection="test_objects") +assert ( + np.array(artifact_manager.get_artifact("random_field", collection="test_data").image.getdata()) + .reshape((100,100,3)) == pixels),\ + artifact_manager.get_artifact("random_field", collection="test_data") + +artifact_manager.download_collection(collection="test_objects", to=Path(localdir.name, "recovered")) + +wandb.finish() +localdir.cleanup() From 497156c07abc4025447927125b9428a7aba25a61 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Tue, 19 Dec 2023 11:51:13 +0100 Subject: [PATCH 28/41] Adding wandb tests --- squirrel/artifact_manager/fs.py | 5 +- squirrel/artifact_manager/wandb.py | 3 +- test/test_artifact_manager/test_fs_logging.py | 2 +- test/test_artifact_manager/wandb_script.py | 78 ++++++++++--------- 4 files changed, 45 insertions(+), 43 deletions(-) diff --git a/squirrel/artifact_manager/fs.py b/squirrel/artifact_manager/fs.py index cc7f204..dece65a 100644 --- a/squirrel/artifact_manager/fs.py +++ b/squirrel/artifact_manager/fs.py @@ -40,12 +40,11 @@ def get(self, key: Path, mode: str = "rb", **open_kwargs) -> Any: return super().get(str(Path(key, Serializers[self.serializer.__class__])), mode, **open_kwargs) elif self.fs.exists(Path(self.url, key, "files"), **open_kwargs): if "target" in open_kwargs: - if not open_kwargs["target"].exists(): - open_kwargs["target"].mkdir(parents=True) self.fs.cp( str(Path(self.url, key, "files/*")), str(open_kwargs.pop("target")), recursive=True, + mkdirs=True, **open_kwargs ) # retrieve raw file @@ -187,6 +186,6 @@ def download_artifact( self.backend.get(Path(location), target=to) return Source( driver_name="file", - driver_kwargs={"url": str(to), "storage_options": self.backend.storage_options}, + driver_kwargs={"url": str(to)}, metadata={"collection": collection, "artifact": artifact, "version": version, "location": str(to)}, ) diff --git a/squirrel/artifact_manager/wandb.py b/squirrel/artifact_manager/wandb.py index 8e2c12c..e88bc22 100644 --- a/squirrel/artifact_manager/wandb.py +++ b/squirrel/artifact_manager/wandb.py @@ -71,7 +71,8 @@ def get_artifact_source( if collection is None: collection = self.active_collection if version is None: - version = "latest" + versions = [instance.version for instance in wandb.Api().artifact_versions(type_name=collection, name=f"{self.project}/{artifact}")] + version = f"v{max([int(v[1:]) for v in versions])}" return Source( driver_name="wandb", diff --git a/test/test_artifact_manager/test_fs_logging.py b/test/test_artifact_manager/test_fs_logging.py index 1c53c3f..0d23cc8 100644 --- a/test/test_artifact_manager/test_fs_logging.py +++ b/test/test_artifact_manager/test_fs_logging.py @@ -190,7 +190,7 @@ def test_get_file() -> None: manager.log_files(artifact_name, Path(f"{src_dir.name}/{filename}"), collection, Path(filename)) - source = manager.log_files("folder", Path(src_dir.name), collection) + manager.log_files("folder", Path(src_dir.name), collection) # Test retrieval of specific files for (filename, artifact_name, version, content) in file_descriptions: diff --git a/test/test_artifact_manager/wandb_script.py b/test/test_artifact_manager/wandb_script.py index d0519a8..92567db 100644 --- a/test/test_artifact_manager/wandb_script.py +++ b/test/test_artifact_manager/wandb_script.py @@ -1,51 +1,53 @@ from pathlib import Path -import numpy as np -import pandas as pd import tempfile import wandb from squirrel.artifact_manager.wandb import WandbArtifactManager +src_dir = tempfile.TemporaryDirectory() -tbl_data = pd.DataFrame({"users": ["geoff", "juergen", "ada"], "feature_01": [1, 117, 42]}) -tbl = wandb.Table(data=tbl_data) +test_run = wandb.init(project="sebastian-sandbox") +artifact_manager = WandbArtifactManager(project="sebastian-sandbox") +collection = "test_objects" -pixels = np.random.randint(low=0, high=256, size=(100, 100, 3)) -image = wandb.Image(pixels, caption=f"random field") +file_descriptions = [ + ("foo.txt", "foo_file", "v0", "Test: Foo"), + ("bar.txt", "bar_file", "v0", "Test: Bar"), + ("baz.txt", "bar_file", "v1", "Test: Baz"), +] -localdir = tempfile.TemporaryDirectory() -tbl_data.to_csv(f"{localdir.name}/tbl") -pixels.dump(f"{localdir.name}/image") +for (filename, artifact_name, version, content) in file_descriptions: + with open(f"{src_dir.name}/{filename}", "w") as f: + f.write(content) -test_run = wandb.init(project="sebastian-sandbox") + source = artifact_manager.log_files(artifact_name, Path(f"{src_dir.name}/{filename}"), collection, Path(filename)) + + assert source.driver_name == "wandb" + assert source.metadata["collection"] == collection, f"Value {source.metadata['collection']} should be {collection}" + assert source.metadata["artifact"] == artifact_name, f"Value {source.metadata['artifact']} should be {artifact_name}" + assert source.metadata["version"] == version, f"Value {source.metadata['version']} should be {version}" + +# test logging of folder +source = artifact_manager.log_files("folder", Path(src_dir.name), collection) + +assert source.driver_name == "wandb" +assert source.metadata["collection"] == collection, f"Value {source.metadata['collection']} should be {collection}" +assert source.metadata["artifact"] == "folder", f"Value {source.metadata['artifact']} should be {artifact_name}" +assert source.metadata["version"] == "v0", f"Value {source.metadata['version']} should be {version}" + + +# Test retrieval of specific files +for (filename, artifact_name, version, content) in file_descriptions: + artifact_manager.download_artifact(artifact_name, collection, version, Path(f"{src_dir.name}/downloaded")) + with open(f"{src_dir.name}/downloaded/{filename}") as f: + assert f.read() == content + +# Test retrieval of entire folder +artifact_manager.download_artifact("folder", collection, "v0", Path(f"{src_dir.name}/downloaded2")) +for (filename, artifact_name, version, content) in file_descriptions: + with open(f"{src_dir.name}/downloaded2/{filename}") as f: + assert f.read() == content -artifact_manager = WandbArtifactManager(project="sebastian-sandbox") -# src1 = artifact_manager.log_artifact(tbl, "tbl", collection="test_objects") -# assert src1.metadata["collection"] == "test_objects" -# assert src1.metadata["artifact"] == "tbl" -# assert src1.metadata["version"] == "v0", f"First version should be v1, but is {src1.metadata['version']}" -# assert src1.metadata["location"] == Path("https://merantix-momentum.wandb.io/mxm/sebastian-sandbox/test_objects/tbl/v0"), \ -# f"Location is {src1.metadata['location']}" -# -# src2 = artifact_manager.log_artifact(image, "random_field", collection="test_data") -# assert src2.metadata["collection"] == "test_data" -# assert src2.metadata["artifact"] == "random_field", f"Name should be random_field, but is {src2.metadata['artifact']}" -# assert src2.metadata["version"] == "v0", f"First version should be v0, but is {src2.metadata['version']}" -# assert src2.metadata["location"] == Path("https://merantix-momentum.wandb.io/mxm/sebastian-sandbox/test_data/random_field/v0") -# -# catalog = artifact_manager.log_folder(Path(localdir.name), "test_objects") -# assert len(catalog) == 2, f"Catalog is {catalog}" -# assert "test_objects/tbl" in catalog and "test_objects/image" in catalog, f"Catalog is {catalog}" -# assert catalog["test_objects/tbl"].metadata["version"] == "v1", f"Catalog entry is {catalog['test_objects/tbl']}" -# assert catalog["test_objects/image"].metadata["version"] == "v0", f"Catalog entry is {catalog['test_objects/image']}" - -assert artifact_manager.get_artifact("tbl", collection="test_objects", version="v0") == tbl, artifact_manager.get_artifact("tbl", collection="test_objects") -assert ( - np.array(artifact_manager.get_artifact("random_field", collection="test_data").image.getdata()) - .reshape((100,100,3)) == pixels),\ - artifact_manager.get_artifact("random_field", collection="test_data") - -artifact_manager.download_collection(collection="test_objects", to=Path(localdir.name, "recovered")) wandb.finish() -localdir.cleanup() +src_dir.cleanup() From fe811e2e221aed3dc2bf230d2772413cce5d410a Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Tue, 19 Dec 2023 12:34:07 +0100 Subject: [PATCH 29/41] Fixing log_folder --- squirrel/artifact_manager/base.py | 30 ++++++++++--- squirrel/artifact_manager/fs.py | 2 +- test/test_artifact_manager/test_fs_logging.py | 44 +++++++++++++++++++ 3 files changed, 68 insertions(+), 8 deletions(-) diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index b3bfdf4..7db56b3 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -31,7 +31,7 @@ def __init__(self, artifact_manager: "ArtifactManager", artifact: str, collectio self.artifact_manager = artifact_manager self.artifact = artifact self.collection = collection - self.tempdir = None + self.tempdir = tempfile.TemporaryDirectory() def __enter__(self) -> str: """ @@ -39,8 +39,8 @@ def __enter__(self) -> str: Returns: Absolute path to artifact folder as str """ - self.tempdir = tempfile.TemporaryDirectory() - return str(Path(self.tempdir.name) / Path(self.artifact)) + Path(self.tempdir.name, self.artifact).mkdir(exist_ok=False) + return str(Path(self.tempdir.name, self.artifact)) def __exit__( self, @@ -53,7 +53,7 @@ def __exit__( path = Path(self.tempdir.name) / Path(self.artifact) files = [p for p in path.glob("*")] if len(files) > 0: - self.artifact_manager.log_files(path, self.artifact, self.collection) + self.artifact_manager.log_files(self.artifact, path, self.collection) else: logger.info(f"Did not log artifact folder at {path} as it seems to be empty") @@ -121,8 +121,22 @@ def get_artifact(self, artifact: str, collection: Optional[str] = None, version: raise NotImplementedError @abstractmethod - def log_files(self, local_path: Path, name: str, collection: Optional[str] = None) -> Source: - """Upload file into (current) collection, increment version automatically""" + def log_files( + self, + artifact_name: str, + local_path: Path, + collection: Optional[str] = None, + artifact_path: Optional[Path] = None + ) -> Source: + """ + Upload file into (current) collection, increment version automatically + + Args: + artifact_name: Name of artifact to log + local_path: Local path to the file or folder to log + collection: Name of collection to log to, defaults to the active collection + artifact_path: path under which to log the files within the artifact, defaults to "./" + """ raise NotImplementedError @abstractmethod @@ -164,8 +178,10 @@ def log_folder(self, artifact: str, collection: Optional[str] = None) -> Directo def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> Catalog: """Download all artifacts in collection to local directory.""" + if collection is None: + collection = self.active_collection catalog = self.collection_to_catalog(collection) for artifact in catalog.values(): artifact_name = artifact.metadata["artifact"] - self.download_artifact(artifact_name, to=to / artifact_name) + self.download_artifact(artifact_name, collection, to=to / artifact_name) return catalog diff --git a/squirrel/artifact_manager/fs.py b/squirrel/artifact_manager/fs.py index dece65a..714e3f9 100644 --- a/squirrel/artifact_manager/fs.py +++ b/squirrel/artifact_manager/fs.py @@ -61,7 +61,7 @@ def set(self, value: Any, key: Optional[Path] = None, mode: str = "wb", **open_k if isinstance(value, Path): target = Path(self.url, key, "files", open_kwargs.pop("suffix", "")) else: - target = Path(self.url, key, Serializers[self.serializer.__class__], open_kwargs.pop("suffix")) + target = Path(self.url, key, Serializers[self.serializer.__class__], open_kwargs.pop("suffix", "")) if self.fs.exists(target, **open_kwargs): raise ValueError(f"Key {key} already exists!") diff --git a/test/test_artifact_manager/test_fs_logging.py b/test/test_artifact_manager/test_fs_logging.py index 0d23cc8..8c95f9e 100644 --- a/test/test_artifact_manager/test_fs_logging.py +++ b/test/test_artifact_manager/test_fs_logging.py @@ -206,3 +206,47 @@ def test_get_file() -> None: src_dir.cleanup() store_dir.cleanup() + + +def test_log_folder() -> None: + store_dir = tempfile.TemporaryDirectory() + manager = FileSystemArtifactManager(url=store_dir.name, auto_mkdir=True) + collection = "my_collection" + test_files = [ + ("foo.txt", "Test: Foo"), + ("bar.txt", "Test: Bar"), + ("baz.txt", "Test: Baz"), + ] + with manager.log_folder("folder", collection) as folder: + for (filename, content) in test_files: + with open(f"{folder}/{filename}", "w") as file: + file.write(content) + + assert manager.exists_in_collection("folder", collection) + source = manager.collection_to_catalog(collection)['my_collection/folder'] + assert source.driver_name == "file" + assert source.metadata["collection"] == collection + assert source.metadata["artifact"] == "folder" + assert source.metadata["version"] == "v0" + assert source.metadata["location"] == f"file://{store_dir.name}/{collection}/folder/v0" + assert len(list(Path(f"{store_dir.name}/{collection}/folder/v0/files").iterdir())) == 3 + + local_dir = tempfile.TemporaryDirectory() + manager.download_artifact("folder", collection, "v0", Path(f"{local_dir.name}/downloaded")) + for (filename, content) in test_files: + with open(f"{local_dir.name}/downloaded/{filename}") as f: + assert f.read() == content + + local_dir.cleanup() + store_dir.cleanup() + + +def test_exists() -> None: + pass + +def test_store_to_catalog() -> None: + pass + +def test_download_collection() -> None: + pass + From 53c7b8a933c388f30894f34431ddae03b2775265 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Tue, 19 Dec 2023 14:11:38 +0100 Subject: [PATCH 30/41] Additional tests --- squirrel/artifact_manager/base.py | 6 +- squirrel/artifact_manager/fs.py | 10 +- test/test_artifact_manager/test_fs_logging.py | 97 ++++++++++++++++++- 3 files changed, 102 insertions(+), 11 deletions(-) diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index 7db56b3..b93872c 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -7,7 +7,7 @@ from typing import Optional, List, Any, Iterable, Type from squirrel.catalog import Catalog, Source - +from squirrel.catalog.catalog import CatalogSource logger = logging.getLogger(__name__) @@ -164,7 +164,7 @@ def store_to_catalog(self) -> Catalog: """Provide Catalog of all artifacts stored in backend.""" catalog = Catalog() for collection in self.list_collection_names(): - catalog.update(self.collection_to_catalog(collection)) + catalog = catalog.union(self.collection_to_catalog(collection)) return catalog def log_folder(self, artifact: str, collection: Optional[str] = None) -> DirectoryLogger: @@ -181,7 +181,7 @@ def download_collection(self, collection: Optional[str] = None, to: Path = "./") if collection is None: collection = self.active_collection catalog = self.collection_to_catalog(collection) - for artifact in catalog.values(): + for _, artifact in catalog: artifact_name = artifact.metadata["artifact"] self.download_artifact(artifact_name, collection, to=to / artifact_name) return catalog diff --git a/squirrel/artifact_manager/fs.py b/squirrel/artifact_manager/fs.py index 714e3f9..63c9f88 100644 --- a/squirrel/artifact_manager/fs.py +++ b/squirrel/artifact_manager/fs.py @@ -179,13 +179,17 @@ def log_files( return self.get_artifact_source(artifact_name, collection) def download_artifact( - self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Path = "./" + self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Path = Path("./") ) -> Source: """Download artifact to local path.""" + if collection is None: + collection = self.active_collection + if version is None or version == "latest": + version = f"v{max(int(vs[1:]) for vs in self.backend.complete_key(Path(collection) / Path(artifact)))}" location = Path(collection, artifact, version) self.backend.get(Path(location), target=to) return Source( driver_name="file", - driver_kwargs={"url": str(to)}, - metadata={"collection": collection, "artifact": artifact, "version": version, "location": str(to)}, + driver_kwargs={"url": str(Path(to, artifact))}, + metadata={"collection": collection, "artifact": artifact, "version": version, "location": str(Path(to, artifact))}, ) diff --git a/test/test_artifact_manager/test_fs_logging.py b/test/test_artifact_manager/test_fs_logging.py index 8c95f9e..3420175 100644 --- a/test/test_artifact_manager/test_fs_logging.py +++ b/test/test_artifact_manager/test_fs_logging.py @@ -171,6 +171,39 @@ def test_log_file() -> None: store_dir.cleanup() +def test_exists() -> None: + test_files = { + "my_collection": ["foo.txt", "bar.txt"], + "default": ["baz.txt"], + } + + src_dir = tempfile.TemporaryDirectory() + store_dir = tempfile.TemporaryDirectory() + manager = FileSystemArtifactManager(url=store_dir.name, auto_mkdir=True) + + for collection in test_files: + for filename in test_files[collection]: + with open(f"{src_dir.name}/{filename}", "w") as f: + f.write("Test") + + manager.log_files(filename[:3], Path(f"{src_dir.name}/{filename}"), collection, Path(filename)) + + assert manager.exists("foo") + assert manager.exists("bar") + assert manager.exists("baz") + + assert manager.exists_in_collection("foo", "my_collection") + assert manager.exists_in_collection("bar", "my_collection") + assert not manager.exists_in_collection("baz", "my_collection") + + assert not manager.exists_in_collection("foo", "default") + assert not manager.exists_in_collection("bar", "default") + assert manager.exists_in_collection("baz", "default") + + src_dir.cleanup() + store_dir.cleanup() + + def test_get_file() -> None: """Test retrieval of logged files from the artifact store.""" src_dir = tempfile.TemporaryDirectory() @@ -241,12 +274,66 @@ def test_log_folder() -> None: store_dir.cleanup() -def test_exists() -> None: - pass - def test_store_to_catalog() -> None: - pass + test_files = { + "my_collection": ["foo.txt", "bar.txt"], + "default": ["baz.txt"], + } + + src_dir = tempfile.TemporaryDirectory() + store_dir = tempfile.TemporaryDirectory() + manager = FileSystemArtifactManager(url=store_dir.name, auto_mkdir=True) + + for collection in test_files: + for filename in test_files[collection]: + with open(f"{src_dir.name}/{filename}", "w") as f: + f.write("Test") + + manager.log_files(filename[:3], Path(f"{src_dir.name}/{filename}"), collection, Path(filename)) + + collection_catalog = manager.collection_to_catalog("my_collection") + assert len(collection_catalog) == 2 + assert "my_collection/foo" in collection_catalog + assert "my_collection/bar" in collection_catalog + + default_catalog = manager.collection_to_catalog() + assert len(default_catalog) == 1 + assert "default/baz" in default_catalog + + catalog = manager.store_to_catalog() + assert len(catalog) == 3 + assert "my_collection/foo" in catalog + assert "my_collection/bar" in catalog + assert "default/baz" in catalog + + src_dir.cleanup() + store_dir.cleanup() + def test_download_collection() -> None: - pass + test_files = { + "my_collection": ["foo.txt", "bar.txt"], + "default": ["baz.txt"], + } + + src_dir = tempfile.TemporaryDirectory() + store_dir = tempfile.TemporaryDirectory() + manager = FileSystemArtifactManager(url=store_dir.name, auto_mkdir=True) + + for collection in test_files: + for filename in test_files[collection]: + with open(f"{src_dir.name}/{filename}", "w") as f: + f.write("Test") + + manager.log_files(filename[:3], Path(f"{src_dir.name}/{filename}"), collection, Path(filename)) + + manager.download_collection("my_collection", Path(src_dir.name, "downloaded/my_collection")) + manager.download_collection("default", Path(src_dir.name, "downloaded/default")) + for collection in test_files: + for filename in test_files[collection]: + with open(f"{src_dir.name}/downloaded/{collection}/{filename[:3]}/{filename}") as f: + assert f.read() == "Test" + + src_dir.cleanup() + store_dir.cleanup() From ce3de84e651d62e40e752f527242ab5e49e052a5 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Tue, 19 Dec 2023 15:48:11 +0100 Subject: [PATCH 31/41] Updating wandb test-suite --- squirrel/artifact_manager/wandb.py | 19 ++++---- test/test_artifact_manager/wandb_script.py | 51 ++++++++++++++++++++-- 2 files changed, 58 insertions(+), 12 deletions(-) diff --git a/squirrel/artifact_manager/wandb.py b/squirrel/artifact_manager/wandb.py index e88bc22..a375b8d 100644 --- a/squirrel/artifact_manager/wandb.py +++ b/squirrel/artifact_manager/wandb.py @@ -47,12 +47,9 @@ def list_collection_names(self) -> Iterable: Collections correspond to Wandb artifact types. """ - return itertools.chain( - *[ - [artifact.name for artifact in collection.collections()] - for collection in wandb.Api().artifact_types(project=self.project) - ] - ) + return [ + collection.name for collection in wandb.Api().artifact_types(project=self.project) + ] def exists_in_collection(self, artifact: str, collection: Optional[str] = None) -> bool: """ @@ -62,7 +59,9 @@ def exists_in_collection(self, artifact: str, collection: Optional[str] = None) """ if collection is None: collection = self.active_collection - return artifact in [artifact.name for artifact in wandb.Api().artifact_type(type_name=collection).collections()] + if collection not in self.list_collection_names(): + return False + return artifact in [artifact.name for artifact in wandb.Api().artifact_type(type_name=collection, project=self.project).collections()] def get_artifact_source( self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None @@ -93,9 +92,9 @@ def get_artifact_source( "collection": collection, "artifact": artifact, "version": version, - "location": Path( + "location": str(Path( wandb.Api().settings["base_url"], self.entity, self.project, collection, artifact, version - ), + )), }, ) @@ -103,6 +102,8 @@ def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: """Construct a catalog listing artifacts within a specific collection.""" if collection is None: collection = self._active_collection + if collection not in self.list_collection_names(): + raise ValueError(f"Collection {collection} does not exist.") artifact_names = [ artifact.name for artifact in wandb.Api().artifact_type(type_name=collection, project=self.project).collections() diff --git a/test/test_artifact_manager/wandb_script.py b/test/test_artifact_manager/wandb_script.py index 92567db..7543fe8 100644 --- a/test/test_artifact_manager/wandb_script.py +++ b/test/test_artifact_manager/wandb_script.py @@ -11,9 +11,9 @@ collection = "test_objects" file_descriptions = [ - ("foo.txt", "foo_file", "v0", "Test: Foo"), - ("bar.txt", "bar_file", "v0", "Test: Bar"), - ("baz.txt", "bar_file", "v1", "Test: Baz"), + ("foo.txt", "foo", "v0", "Test: Foo"), + ("bar.txt", "bar", "v0", "Test: Bar"), + ("baz.txt", "bar", "v1", "Test: Baz"), ] for (filename, artifact_name, version, content) in file_descriptions: @@ -48,6 +48,51 @@ with open(f"{src_dir.name}/downloaded2/{filename}") as f: assert f.read() == content +# test artifact existence checks +assert artifact_manager.exists("foo") +assert artifact_manager.exists("bar") + +assert artifact_manager.exists_in_collection("foo", collection) +assert artifact_manager.exists_in_collection("bar", collection) +assert not artifact_manager.exists_in_collection("foo", "other_collection") + +# test catalog retrieval +collection_catalog = artifact_manager.collection_to_catalog(collection) +assert f"{collection}/foo" in collection_catalog +assert f"{collection}/bar" in collection_catalog + +catalog = artifact_manager.store_to_catalog() +assert f"{collection}/foo" in catalog +assert f"{collection}/bar" in catalog + +# test log folder +with artifact_manager.log_folder("test_folder", collection) as folder: + for (filename, _, _, content) in file_descriptions: + with open(f"{folder}/{filename}", "w") as file: + file.write(content) + +assert artifact_manager.exists_in_collection("test_folder", collection) +source = artifact_manager.collection_to_catalog(collection)[f'{collection}/test_folder'] +assert source.driver_name == "wandb" +assert source.metadata["collection"] == collection +assert source.metadata["artifact"] == "test_folder" +assert source.metadata["version"] == "v0" + +local_dir = tempfile.TemporaryDirectory() +artifact_manager.download_artifact("test_folder", collection, "v0", Path(f"{local_dir.name}/downloaded3")) +for (filename, _, _, content) in file_descriptions: + with open(f"{local_dir.name}/downloaded3/{filename}") as f: + assert f.read() == content + +# test download collection +artifact_manager.download_collection(collection, Path(src_dir.name, "my_collection")) +for (filename, artifact_name, _, content) in file_descriptions: + with open(f"{src_dir.name}/my_collection/test_folder/{filename}") as f: + assert f.read() == content +with open(f"{src_dir.name}/my_collection/foo/foo.txt") as f: + assert f.read() == "Test: Foo" +with open(f"{src_dir.name}/my_collection/bar/baz.txt") as f: + assert f.read() == "Test: Baz" wandb.finish() src_dir.cleanup() From e4695b5c0a6990dbf3fe6a1122f48810ae645e42 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Tue, 19 Dec 2023 16:00:55 +0100 Subject: [PATCH 32/41] Linting --- squirrel/artifact_manager/base.py | 45 +++++++------------ squirrel/artifact_manager/fs.py | 36 +++++++++------ squirrel/artifact_manager/wandb.py | 43 ++++++++++-------- test/test_artifact_manager/test_fs_logging.py | 17 ++++--- test/test_artifact_manager/wandb_script.py | 10 +++-- 5 files changed, 81 insertions(+), 70 deletions(-) diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index b93872c..d60175a 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -4,10 +4,9 @@ import re import tempfile from types import TracebackType -from typing import Optional, List, Any, Iterable, Type +from typing import Optional, Any, Iterable, Type from squirrel.catalog import Catalog, Source -from squirrel.catalog.catalog import CatalogSource logger = logging.getLogger(__name__) @@ -16,7 +15,7 @@ class DirectoryLogger: """ Class to be used as a context for logging a directory as an artifact. When entering the scope it creates a local dir with a valid afid and returns the filepath to it. - You can then write files to that dir and after exiting the scope the dir gets logged through the artifactmanager. + You can then write files to that dir and after exiting the scope the dir gets logged through the artifact manager. """ def __init__(self, artifact_manager: "ArtifactManager", artifact: str, collection: Optional[str]) -> None: @@ -26,7 +25,7 @@ def __init__(self, artifact_manager: "ArtifactManager", artifact: str, collectio Args: artifact_manager: An artifact manager instance to use for logging the final artifact. artifact: The name of the artifact to log. - collection: The name of the collection to log to, if None the active collection of the artifact manager is used. + collection: The name of the collection to log to, defaults to the active collection of the artifact manager. """ self.artifact_manager = artifact_manager self.artifact = artifact @@ -35,7 +34,7 @@ def __init__(self, artifact_manager: "ArtifactManager", artifact: str, collectio def __enter__(self) -> str: """ - Called when we enter the context. Creates folder under /tmp with the artifacts id if it doesn't exist yet. + Called when entering the context. Creates folder under /tmp with the artifacts id if it doesn't exist yet. Returns: Absolute path to artifact folder as str """ @@ -48,14 +47,14 @@ def __exit__( excinst: Optional[BaseException] = None, exctb: Optional[TracebackType] = None, ) -> None: - """Called when we exit the context. Logs the artifact folder with mlflow if its not empty.""" + """Called when exiting the context. Logs the artifact folder if it's not empty.""" path = Path(self.tempdir.name) / Path(self.artifact) files = [p for p in path.glob("*")] if len(files) > 0: self.artifact_manager.log_files(self.artifact, path, self.collection) else: - logger.info(f"Did not log artifact folder at {path} as it seems to be empty") + logger.info(f"Did not log artifact folder at {path} as it seems to be empty.") if self.tempdir is not None: self.tempdir.cleanup() @@ -63,12 +62,7 @@ def __exit__( class ArtifactManager(ABC): def __init__(self): - """ - Artifact manager interface for various backends - - Maintains a mapping of artifact names to backend objects to facilitate logging and retrieval of arbitrary - artifacts. - """ + """Artifact manager interface for various backends.""" self._active_collection = "default" @property @@ -79,8 +73,8 @@ def active_collection(self) -> str: It is ultimately up to the user how to structure their artifact store and the collections therein. All operations accessing artifacts allow explicit specification of the collection to use. Therefore, users could use collections to separate different artifact types or different experiments / runs. - To facilitate the latter use case in particular, the manager maintains an 'active' collection which it logs to - by default. This can be set once at the run start when the manager is initialized and then left unchanged. + The manager maintains an 'active' collection which it logs to by default. This can be set at the run start + when the manager is initialized and then remain unchanged for the duration of the run. To avoid incompatibility between different backends, collections cannot be nested (e.g. as subfolders on a filesystem) as in particular the WandB backend has no real notion of nested folder structures. @@ -92,7 +86,7 @@ def active_collection(self, value: str) -> None: """ Sets the active collections that is being logged to by default. - The provided values is verified to ensure that no nested collections are used. + The provided value is verified to ensure that no nested collections are used. """ if not re.match(r"^[a-zA-Z0-9\-_:]+$", value): raise ValueError( @@ -122,14 +116,14 @@ def get_artifact(self, artifact: str, collection: Optional[str] = None, version: @abstractmethod def log_files( - self, - artifact_name: str, - local_path: Path, - collection: Optional[str] = None, - artifact_path: Optional[Path] = None + self, + artifact_name: str, + local_path: Path, + collection: Optional[str] = None, + artifact_path: Optional[Path] = None, ) -> Source: """ - Upload file into (current) collection, increment version automatically + Upload a file or folder into (current) collection, increment version automatically Args: artifact_name: Name of artifact to log @@ -168,12 +162,7 @@ def store_to_catalog(self) -> Catalog: return catalog def log_folder(self, artifact: str, collection: Optional[str] = None) -> DirectoryLogger: - """ - Context manager for logging a directory as an artifact. - - When entering the scope it creates a local dir with a valid afid and returns the filepath to it. - You can then write files to that dir and after exiting the scope the dir gets logged through the artifactmanager. - """ + """Create a context manager for logging a directory of files as a single artifact.""" return DirectoryLogger(self, artifact, collection) def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> Catalog: diff --git a/squirrel/artifact_manager/fs.py b/squirrel/artifact_manager/fs.py index 63c9f88..8ccf898 100644 --- a/squirrel/artifact_manager/fs.py +++ b/squirrel/artifact_manager/fs.py @@ -45,7 +45,7 @@ def get(self, key: Path, mode: str = "rb", **open_kwargs) -> Any: str(open_kwargs.pop("target")), recursive=True, mkdirs=True, - **open_kwargs + **open_kwargs, ) # retrieve raw file else: @@ -76,7 +76,6 @@ def set(self, value: Any, key: Optional[Path] = None, mode: str = "wb", **open_k class FileSystemArtifactManager(ArtifactManager): - def __init__(self, url: str, serializer: Optional[SquirrelSerializer] = None, **fs_kwargs): """ Artifactmanager backed by fsspec filesystems. @@ -142,22 +141,26 @@ def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: """Log an arbitrary python object using store serialisation.""" - raise NotImplementedError("Logging and retrieving python objects is not yet supported. Please serialize your" - "objects and log resulting files with 'log_file' or 'log_folder'.") + raise NotImplementedError( + "Logging and retrieving python objects is not yet supported. Please serialize your" + "objects and log resulting files with 'log_file' or 'log_folder'." + ) # Implementation for logging python objects can make use of # self.backend.set(obj, Path(collection, name, version)) def get_artifact(self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None) -> Any: """Retrieve specific artifact value.""" - raise NotImplementedError("Logging and retrieving python objects is not yet supported. Please serialize your" - "objects and retrieve the logged files with 'download_artifact' instead.") + raise NotImplementedError( + "Logging and retrieving python objects is not yet supported. Please serialize your" + "objects and retrieve the logged files with 'download_artifact' instead." + ) def log_files( - self, - artifact_name: str, - local_path: Path, - collection: Optional[str] = None, - artifact_path: Optional[Path] = None + self, + artifact_name: str, + local_path: Path, + collection: Optional[str] = None, + artifact_path: Optional[Path] = None, ) -> Source: """Upload local file or folder to artifact store without serialisation""" if not isinstance(local_path, (str, Path)): @@ -179,17 +182,24 @@ def log_files( return self.get_artifact_source(artifact_name, collection) def download_artifact( - self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Path = Path("./") + self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Path = "./" ) -> Source: """Download artifact to local path.""" if collection is None: collection = self.active_collection if version is None or version == "latest": version = f"v{max(int(vs[1:]) for vs in self.backend.complete_key(Path(collection) / Path(artifact)))}" + if isinstance(to, str): + to = Path(to) location = Path(collection, artifact, version) self.backend.get(Path(location), target=to) return Source( driver_name="file", driver_kwargs={"url": str(Path(to, artifact))}, - metadata={"collection": collection, "artifact": artifact, "version": version, "location": str(Path(to, artifact))}, + metadata={ + "collection": collection, + "artifact": artifact, + "version": version, + "location": str(Path(to, artifact)), + }, ) diff --git a/squirrel/artifact_manager/wandb.py b/squirrel/artifact_manager/wandb.py index a375b8d..c9ef5b0 100644 --- a/squirrel/artifact_manager/wandb.py +++ b/squirrel/artifact_manager/wandb.py @@ -1,4 +1,3 @@ -import itertools from pathlib import Path from typing import Optional, Any, Iterable @@ -47,9 +46,7 @@ def list_collection_names(self) -> Iterable: Collections correspond to Wandb artifact types. """ - return [ - collection.name for collection in wandb.Api().artifact_types(project=self.project) - ] + return [collection.name for collection in wandb.Api().artifact_types(project=self.project)] def exists_in_collection(self, artifact: str, collection: Optional[str] = None) -> bool: """ @@ -61,7 +58,10 @@ def exists_in_collection(self, artifact: str, collection: Optional[str] = None) collection = self.active_collection if collection not in self.list_collection_names(): return False - return artifact in [artifact.name for artifact in wandb.Api().artifact_type(type_name=collection, project=self.project).collections()] + return artifact in [ + artifact.name + for artifact in wandb.Api().artifact_type(type_name=collection, project=self.project).collections() + ] def get_artifact_source( self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None @@ -70,7 +70,10 @@ def get_artifact_source( if collection is None: collection = self.active_collection if version is None: - versions = [instance.version for instance in wandb.Api().artifact_versions(type_name=collection, name=f"{self.project}/{artifact}")] + versions = [ + instance.version + for instance in wandb.Api().artifact_versions(type_name=collection, name=f"{self.project}/{artifact}") + ] version = f"v{max([int(v[1:]) for v in versions])}" return Source( @@ -92,9 +95,9 @@ def get_artifact_source( "collection": collection, "artifact": artifact, "version": version, - "location": str(Path( - wandb.Api().settings["base_url"], self.entity, self.project, collection, artifact, version - )), + "location": str( + Path(wandb.Api().settings["base_url"], self.entity, self.project, collection, artifact, version) + ), }, ) @@ -118,8 +121,10 @@ def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: """Log serialisable object to artifact store.""" - raise NotImplementedError("Logging and retrieving python objects is not yet supported. Please serialize your" - "objects and log resulting files with 'log_files' or log_folder.") + raise NotImplementedError( + "Logging and retrieving python objects is not yet supported. Please serialize your" + "objects and log resulting files with 'log_files' or log_folder." + ) # Implementation for logging python objects can make use of # if not isinstance(obj, wandb.data_types.WBValue): # raise ValueError( @@ -136,15 +141,17 @@ def get_artifact(self, artifact: str, collection: Optional[str] = None, version: This assumes that the artifact was logged as a wandb serialised object. If the artifact was a file upload, the file contents should be retrieved using download instead. """ - raise NotImplementedError("Logging and retrieving python objects is not yet supported. Please serialize your" - "objects and retrieve the logged files with 'download_artifact' instead.") + raise NotImplementedError( + "Logging and retrieving python objects is not yet supported. Please serialize your" + "objects and retrieve the logged files with 'download_artifact' instead." + ) def log_files( - self, - artifact_name: str, - local_path: Path, - collection: Optional[str] = None, - artifact_path: Optional[Path] = None + self, + artifact_name: str, + local_path: Path, + collection: Optional[str] = None, + artifact_path: Optional[Path] = None, ) -> Source: """Upload a single file to artifact store without serialisation.""" if collection is None: diff --git a/test/test_artifact_manager/test_fs_logging.py b/test/test_artifact_manager/test_fs_logging.py index 3420175..d608969 100644 --- a/test/test_artifact_manager/test_fs_logging.py +++ b/test/test_artifact_manager/test_fs_logging.py @@ -172,6 +172,7 @@ def test_log_file() -> None: def test_exists() -> None: + """Test existence checks for artifacts in the artifact store.""" test_files = { "my_collection": ["foo.txt", "bar.txt"], "default": ["baz.txt"], @@ -233,7 +234,7 @@ def test_get_file() -> None: # Test retrieval of entire folder manager.download_artifact("folder", collection, "v0", Path(f"{src_dir.name}/downloaded2")) - for (filename, artifact_name, version, content) in file_descriptions: + for (filename, _, _, content) in file_descriptions: with open(f"{src_dir.name}/downloaded2/{filename}") as f: assert f.read() == content @@ -242,21 +243,22 @@ def test_get_file() -> None: def test_log_folder() -> None: + """Test logging of folders using the context manager provided by the artifact store.""" store_dir = tempfile.TemporaryDirectory() manager = FileSystemArtifactManager(url=store_dir.name, auto_mkdir=True) collection = "my_collection" test_files = [ - ("foo.txt", "Test: Foo"), - ("bar.txt", "Test: Bar"), - ("baz.txt", "Test: Baz"), - ] + ("foo.txt", "Test: Foo"), + ("bar.txt", "Test: Bar"), + ("baz.txt", "Test: Baz"), + ] with manager.log_folder("folder", collection) as folder: for (filename, content) in test_files: with open(f"{folder}/{filename}", "w") as file: file.write(content) assert manager.exists_in_collection("folder", collection) - source = manager.collection_to_catalog(collection)['my_collection/folder'] + source = manager.collection_to_catalog(collection)["my_collection/folder"] assert source.driver_name == "file" assert source.metadata["collection"] == collection assert source.metadata["artifact"] == "folder" @@ -275,6 +277,7 @@ def test_log_folder() -> None: def test_store_to_catalog() -> None: + """Test retrieval of catalog description of artifacts stored in the artifact store.""" test_files = { "my_collection": ["foo.txt", "bar.txt"], "default": ["baz.txt"], @@ -311,6 +314,7 @@ def test_store_to_catalog() -> None: def test_download_collection() -> None: + """Test retrieval of an entire collection from the artifact store.""" test_files = { "my_collection": ["foo.txt", "bar.txt"], "default": ["baz.txt"], @@ -336,4 +340,3 @@ def test_download_collection() -> None: src_dir.cleanup() store_dir.cleanup() - diff --git a/test/test_artifact_manager/wandb_script.py b/test/test_artifact_manager/wandb_script.py index 7543fe8..75e88f6 100644 --- a/test/test_artifact_manager/wandb_script.py +++ b/test/test_artifact_manager/wandb_script.py @@ -24,7 +24,9 @@ assert source.driver_name == "wandb" assert source.metadata["collection"] == collection, f"Value {source.metadata['collection']} should be {collection}" - assert source.metadata["artifact"] == artifact_name, f"Value {source.metadata['artifact']} should be {artifact_name}" + assert ( + source.metadata["artifact"] == artifact_name + ), f"Value {source.metadata['artifact']} should be {artifact_name}" assert source.metadata["version"] == version, f"Value {source.metadata['version']} should be {version}" # test logging of folder @@ -44,7 +46,7 @@ # Test retrieval of entire folder artifact_manager.download_artifact("folder", collection, "v0", Path(f"{src_dir.name}/downloaded2")) -for (filename, artifact_name, version, content) in file_descriptions: +for (filename, _, _, content) in file_descriptions: with open(f"{src_dir.name}/downloaded2/{filename}") as f: assert f.read() == content @@ -72,7 +74,7 @@ file.write(content) assert artifact_manager.exists_in_collection("test_folder", collection) -source = artifact_manager.collection_to_catalog(collection)[f'{collection}/test_folder'] +source = artifact_manager.collection_to_catalog(collection)[f"{collection}/test_folder"] assert source.driver_name == "wandb" assert source.metadata["collection"] == collection assert source.metadata["artifact"] == "test_folder" @@ -86,7 +88,7 @@ # test download collection artifact_manager.download_collection(collection, Path(src_dir.name, "my_collection")) -for (filename, artifact_name, _, content) in file_descriptions: +for (filename, _, _, content) in file_descriptions: with open(f"{src_dir.name}/my_collection/test_folder/{filename}") as f: assert f.read() == content with open(f"{src_dir.name}/my_collection/foo/foo.txt") as f: From 308df5d4fb3eb0fba430abfe13c43dd908f26212 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Tue, 19 Dec 2023 16:32:20 +0100 Subject: [PATCH 33/41] Small comment --- test/test_artifact_manager/wandb_script.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/test/test_artifact_manager/wandb_script.py b/test/test_artifact_manager/wandb_script.py index 75e88f6..ac74f61 100644 --- a/test/test_artifact_manager/wandb_script.py +++ b/test/test_artifact_manager/wandb_script.py @@ -1,3 +1,7 @@ +""" +Test script for the wandb artifact manager implementation. This is merely a substitute for a proper test suite until we +can figure out how to best mock the wandb API. +""" from pathlib import Path import tempfile From 7fbfc6e4490c61e50e1373aa4f4bc62f30b500b8 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze <93528995+SebS94@users.noreply.github.com> Date: Wed, 20 Dec 2023 16:28:40 +0100 Subject: [PATCH 34/41] Update squirrel/artifact_manager/fs.py Co-authored-by: miha g --- squirrel/artifact_manager/fs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/squirrel/artifact_manager/fs.py b/squirrel/artifact_manager/fs.py index 8ccf898..48e68b7 100644 --- a/squirrel/artifact_manager/fs.py +++ b/squirrel/artifact_manager/fs.py @@ -166,7 +166,7 @@ def log_files( if not isinstance(local_path, (str, Path)): raise ValueError("Path to file should be passed as a pathlib.Path object!") - if artifact_path is not None and not isinstance(artifact_name, (str, Path)): + if artifact_path is not None and not isinstance(artifact_path, (str, Path)): raise ValueError("Artifact path should be passed as a pathlib.Path object!") if collection is None: From 1124fd437d1f679d56e473bbbb9f934b1ef590e4 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Fri, 22 Dec 2023 10:24:33 +0100 Subject: [PATCH 35/41] Rebasing on updated requirements --- poetry.lock | 15 +++++++------ pyproject.toml | 27 +++++++++++------------ requirements.txt | 57 +++++++++++++++++++++++++++++++++++++++++++----- 3 files changed, 73 insertions(+), 26 deletions(-) diff --git a/poetry.lock b/poetry.lock index 36dee48..3907849 100644 --- a/poetry.lock +++ b/poetry.lock @@ -221,7 +221,7 @@ trio = ["trio (>=0.23)"] name = "appdirs" version = "1.4.4" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -optional = false +optional = true python-versions = "*" files = [ {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"}, @@ -1204,7 +1204,7 @@ ssh = ["paramiko (>=2.4.3)"] name = "docker-pycreds" version = "0.4.0" description = "Python bindings for the docker credentials store API" -optional = false +optional = true python-versions = "*" files = [ {file = "docker-pycreds-0.4.0.tar.gz", hash = "sha256:6ce3270bcaf404cc4c3e27e4b6c70d3521deae82fb508767870fdbf772d584d4"}, @@ -4843,7 +4843,7 @@ jeepney = ">=0.6" name = "sentry-sdk" version = "1.39.1" description = "Python client for Sentry (https://sentry.io)" -optional = false +optional = true python-versions = "*" files = [ {file = "sentry-sdk-1.39.1.tar.gz", hash = "sha256:320a55cdf9da9097a0bead239c35b7e61f53660ef9878861824fd6d9b2eaf3b5"}, @@ -4888,7 +4888,7 @@ tornado = ["tornado (>=5)"] name = "setproctitle" version = "1.3.3" description = "A Python module to customize the process title" -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "setproctitle-1.3.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:897a73208da48db41e687225f355ce993167079eda1260ba5e13c4e53be7f754"}, @@ -5679,7 +5679,7 @@ testing = ["coverage (>=5.0)", "pytest", "pytest-cover"] name = "wandb" version = "0.16.1" description = "A CLI and library for interacting with the Weights & Biases API." -optional = false +optional = true python-versions = ">=3.7" files = [ {file = "wandb-0.16.1-py3-none-any.whl", hash = "sha256:1d7423f92520984585bae9693bb637ae08d3e0c1d75ad4b34215bc44431f114c"}, @@ -6021,7 +6021,7 @@ docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.link testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [extras] -all = ["adlfs", "dask", "gcsfs", "odfpy", "openpyxl", "pyarrow", "pyxlsb", "s3fs", "torch", "xlrd", "zarr"] +all = ["adlfs", "dask", "gcsfs", "numba", "odfpy", "openpyxl", "pyarrow", "pyxlsb", "s3fs", "torch", "wandb", "xlrd", "zarr"] azure = ["adlfs"] dask = ["dask"] excel = ["odfpy", "openpyxl", "pyxlsb", "xlrd"] @@ -6031,9 +6031,10 @@ numba = ["numba"] parquet = ["pyarrow"] s3 = ["s3fs"] torch = ["torch"] +wandb = ["wandb"] zarr = ["zarr"] [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "514c7714cc2f911eff0cd5d8f3b477bc4e5892f0fb960b99a5389357eb73a020" +content-hash = "dde3fe856e9376bb3ee5575d857585244244696b88e266db5964f23cd86bdbcb" diff --git a/pyproject.toml b/pyproject.toml index f9d94a9..6055838 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,33 +21,34 @@ classifiers = [ [tool.poetry.dependencies] python = "^3.8" +aiohttp = ">=3.8.4" # dependabot: GHSA-q3qx-c6g2-7pw2 fsspec = ">=2021.7.0" +mako = ">=1.2.4" # dependabot: GHSA-v973-fxgf-6xhp msgpack = ">=1.0.4" msgpack-numpy = ">=0.4.8" more-itertools = ">=9.0.0" -pluggy = ">=1.0.0" -ruamel-yaml = ">=0.17.21" -tqdm = ">=4.64.1" # dependabot: GHSA-r7q7-xcjw-qx8q numpy = ">=1.23.5" -pyjwt = ">=2.6.0" # dependabot: GHSA-ffqj-6fqr-9h24 -mako = ">=1.2.4" # dependabot: GHSA-v973-fxgf-6xhp oauthlib = ">=3.2.2" # dependabot: GHSA-3pgj-pg6c-r5p7 -aiohttp = ">=3.8.4" # dependabot: GHSA-q3qx-c6g2-7pw2 pandas = "<=1.5.3" # pin for dask compatibility (afterwards core.strings.Stringmethods is not available anymore) -# workaround for: https://github.com/python-poetry/poetry-plugin-export/issues/183 -urllib3 = ">=1.25.4,<1.27" -numba = {version = ">=0.56.4", optional = true} +pluggy = ">=1.0.0" +pyjwt = ">=2.6.0" # dependabot: GHSA-ffqj-6fqr-9h24 +ruamel-yaml = ">=0.17.21" +tqdm = ">=4.64.1" # dependabot: GHSA-r7q7-xcjw-qx8q +urllib3 = ">=1.25.4,<1.27" # workaround for: https://github.com/python-poetry/poetry-plugin-export/issues/183 + adlfs = {version = "<2021.10", optional = true} dask = {version = ">=2021.10.0", optional = true, extras = ["dataframe", "distributed"]} # dependabot: GHSA-hwqr-f3v9-hwxr +gcsfs = {version = ">=2021.7.0", optional = true} +numba = {version = ">=0.56.4", optional = true} odfpy = {version = ">=1.4.1", optional = true} openpyxl = {version = ">=3.1.1", optional = true} # dependabot: GHSA-chqf-hx79-gxc6 +pyarrow = {version = ">=14.0.1", optional = true} # dependabot: GHSA-5wvp-7f3h-6wmm pyxlsb = {version = ">=1.0.10", optional = true} -xlrd = {version = ">=2.0.1", optional = true} -gcsfs = {version = ">=2021.7.0", optional = true} s3fs = {version = ">=2021.7.0", optional = true} torch = {version = ">=1.13.1", optional = true} # dependabot: GHSA-47fc-vmwq-366v +wandb = {version = "*", optional = true} +xlrd = {version = ">=2.0.1", optional = true} zarr = {version = ">=2.10.3", optional = true} -pyarrow = {version = ">=14.0.1", optional = true} # dependabot: GHSA-5wvp-7f3h-6wmm [tool.poetry.group.dev.dependencies] # dev dependencies pinned for faster resolution @@ -64,12 +65,10 @@ pytest-xdist = "3.5.0" scipy = "*" setuptools = "69.0.2" twine = "4.0.2" -wandb = "0.16.1" wheel = "0.42.0" mlflow = "2.9.2" [tool.poetry.group.doc.dependencies] - # doc dependencies are pinned for faster resolution sphinx = "3.5.4" astroid = "2.14.2" # newer versions seem to break sphinx-autoapi diff --git a/requirements.txt b/requirements.txt index c67a6bc..3b7e984 100644 --- a/requirements.txt +++ b/requirements.txt @@ -98,7 +98,7 @@ anyio==4.2.0 ; python_version >= "3.8" and python_version < "4.0" \ appdirs==1.4.4 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41 \ --hash=sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128 -appnope==0.1.3 ; python_version >= "3.8" and python_version < "4.0" and platform_system == "Darwin" or python_version >= "3.8" and python_version < "4.0" and sys_platform == "darwin" \ +appnope==0.1.3 ; python_version >= "3.8" and python_version < "4.0" and (platform_system == "Darwin" or sys_platform == "darwin") \ --hash=sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24 \ --hash=sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e asciitree==0.3.3 ; python_version >= "3.8" and python_version < "4.0" \ @@ -324,7 +324,7 @@ click==8.0.4 ; python_version >= "3.8" and python_version < "4.0" \ cloudpickle==3.0.0 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:246ee7d0c295602a036e86369c77fecda4ab17b506496730f2f576d9016fd9c7 \ --hash=sha256:996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882 -colorama==0.4.6 ; python_version >= "3.8" and python_version < "4.0" and platform_system == "Windows" or python_version >= "3.8" and python_version < "4.0" and sys_platform == "win32" or python_version >= "3.8" and python_version < "4.0" and os_name == "nt" \ +colorama==0.4.6 ; python_version >= "3.8" and python_version < "4.0" and (platform_system == "Windows" or sys_platform == "win32" or os_name == "nt") \ --hash=sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44 \ --hash=sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6 colorclass==2.2.2 ; python_version >= "3.8" and python_version < "4.0" \ @@ -1042,6 +1042,31 @@ lazy-object-proxy==1.10.0 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:e98c8af98d5707dcdecc9ab0863c0ea6e88545d42ca7c3feffb6b4d1e370c7ba \ --hash=sha256:edb45bb8278574710e68a6b021599a10ce730d156e5b254941754a9cc0b17d03 \ --hash=sha256:fec03caabbc6b59ea4a638bee5fce7117be8e99a4103d9d5ad77f15d6f81020c +llvmlite==0.41.1 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:04725975e5b2af416d685ea0769f4ecc33f97be541e301054c9f741003085802 \ + --hash=sha256:0dd0338da625346538f1173a17cabf21d1e315cf387ca21b294ff209d176e244 \ + --hash=sha256:150d0bc275a8ac664a705135e639178883293cf08c1a38de3bbaa2f693a0a867 \ + --hash=sha256:1eee5cf17ec2b4198b509272cf300ee6577229d237c98cc6e63861b08463ddc6 \ + --hash=sha256:210e458723436b2469d61b54b453474e09e12a94453c97ea3fbb0742ba5a83d8 \ + --hash=sha256:2181bb63ef3c607e6403813421b46982c3ac6bfc1f11fa16a13eaafb46f578e6 \ + --hash=sha256:24091a6b31242bcdd56ae2dbea40007f462260bc9bdf947953acc39dffd54f8f \ + --hash=sha256:2b76acee82ea0e9304be6be9d4b3840208d050ea0dcad75b1635fa06e949a0ae \ + --hash=sha256:2d92c51e6e9394d503033ffe3292f5bef1566ab73029ec853861f60ad5c925d0 \ + --hash=sha256:5940bc901fb0325970415dbede82c0b7f3e35c2d5fd1d5e0047134c2c46b3281 \ + --hash=sha256:8454c1133ef701e8c050a59edd85d238ee18bb9a0eb95faf2fca8b909ee3c89a \ + --hash=sha256:855f280e781d49e0640aef4c4af586831ade8f1a6c4df483fb901cbe1a48d127 \ + --hash=sha256:880cb57ca49e862e1cd077104375b9d1dfdc0622596dfa22105f470d7bacb309 \ + --hash=sha256:8b0a9a47c28f67a269bb62f6256e63cef28d3c5f13cbae4fab587c3ad506778b \ + --hash=sha256:92c32356f669e036eb01016e883b22add883c60739bc1ebee3a1cc0249a50828 \ + --hash=sha256:92f093986ab92e71c9ffe334c002f96defc7986efda18397d0f08534f3ebdc4d \ + --hash=sha256:9564c19b31a0434f01d2025b06b44c7ed422f51e719ab5d24ff03b7560066c9a \ + --hash=sha256:b67340c62c93a11fae482910dc29163a50dff3dfa88bc874872d28ee604a83be \ + --hash=sha256:bf14aa0eb22b58c231243dccf7e7f42f7beec48970f2549b3a6acc737d1a4ba4 \ + --hash=sha256:c1e1029d47ee66d3a0c4d6088641882f75b93db82bd0e6178f7bd744ebce42b9 \ + --hash=sha256:df75594e5a4702b032684d5481db3af990b69c249ccb1d32687b8501f0689432 \ + --hash=sha256:f19f767a018e6ec89608e1f6b13348fa2fcde657151137cb64e56d48598a92db \ + --hash=sha256:f8afdfa6da33f0b4226af8e64cfc2b28986e005528fbf944d0a24a72acfc9432 \ + --hash=sha256:fa1469901a2e100c17eb8fe2678e34bd4255a3576d1a543421356e9c14d6e2ae locket==1.0.0 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632 \ --hash=sha256:b6c819a722f7b6bd955b80781788e4a66a55628b858d347536b7e81325a3a5e3 @@ -1353,6 +1378,28 @@ nh3==0.2.15 ; python_version >= "3.8" and python_version < "4.0" \ nodeenv==1.8.0 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:d51e0c37e64fbf47d017feac3145cdbb58836d7eee8c6f6d3b6880c5456227d2 \ --hash=sha256:df865724bb3c3adc86b3876fa209771517b0cfe596beff01a92700e0e8be4cec +numba==0.58.1 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:07f2fa7e7144aa6f275f27260e73ce0d808d3c62b30cff8906ad1dec12d87bbe \ + --hash=sha256:240e7a1ae80eb6b14061dc91263b99dc8d6af9ea45d310751b780888097c1aaa \ + --hash=sha256:45698b995914003f890ad839cfc909eeb9c74921849c712a05405d1a79c50f68 \ + --hash=sha256:487ded0633efccd9ca3a46364b40006dbdaca0f95e99b8b83e778d1195ebcbaa \ + --hash=sha256:4e79b6cc0d2bf064a955934a2e02bf676bc7995ab2db929dbbc62e4c16551be6 \ + --hash=sha256:55a01e1881120e86d54efdff1be08381886fe9f04fc3006af309c602a72bc44d \ + --hash=sha256:5c765aef472a9406a97ea9782116335ad4f9ef5c9f93fc05fd44aab0db486954 \ + --hash=sha256:6fe7a9d8e3bd996fbe5eac0683227ccef26cba98dae6e5cee2c1894d4b9f16c1 \ + --hash=sha256:7bf1ddd4f7b9c2306de0384bf3854cac3edd7b4d8dffae2ec1b925e4c436233f \ + --hash=sha256:811305d5dc40ae43c3ace5b192c670c358a89a4d2ae4f86d1665003798ea7a1a \ + --hash=sha256:81fe5b51532478149b5081311b0fd4206959174e660c372b94ed5364cfb37c82 \ + --hash=sha256:898af055b03f09d33a587e9425500e5be84fc90cd2f80b3fb71c6a4a17a7e354 \ + --hash=sha256:9e9356e943617f5e35a74bf56ff6e7cc83e6b1865d5e13cee535d79bf2cae954 \ + --hash=sha256:a1eaa744f518bbd60e1f7ccddfb8002b3d06bd865b94a5d7eac25028efe0e0ff \ + --hash=sha256:bc2d904d0319d7a5857bd65062340bed627f5bfe9ae4a495aef342f072880d50 \ + --hash=sha256:bcecd3fb9df36554b342140a4d77d938a549be635d64caf8bd9ef6c47a47f8aa \ + --hash=sha256:bd3dda77955be03ff366eebbfdb39919ce7c2620d86c906203bed92124989032 \ + --hash=sha256:bf68df9c307fb0aa81cacd33faccd6e419496fdc621e83f1efce35cdc5e79cac \ + --hash=sha256:d3e2fe81fe9a59fcd99cc572002101119059d64d31eb6324995ee8b0f144a306 \ + --hash=sha256:e63d6aacaae1ba4ef3695f1c2122b30fa3d8ba039c8f517784668075856d79e2 \ + --hash=sha256:ea5bfcf7d641d351c6a80e8e1826eb4a145d619870016eeaf20bbd71ef5caa22 numcodecs==0.12.1 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:05d91a433733e7eef268d7e80ec226a0232da244289614a8f3826901aec1098e \ --hash=sha256:0e79bf9d1d37199ac00a60ff3adb64757523291d19d03116832e600cac391c51 \ @@ -1574,7 +1621,7 @@ pre-commit==3.5.0 ; python_version >= "3.8" and python_version < "4.0" \ prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:3527b7af26106cbc65a040bcc84839a3566ec1b051bb0bfe953631e704b0ff7d \ --hash=sha256:a11a29cb3bf0a28a387fe5122cdb649816a957cd9261dcedf8c9f1fef33eacf6 -protobuf==4.25.1 ; python_version >= "3.8" and python_version < "4.0" \ +protobuf==4.25.1 ; python_version < "4.0" and python_version >= "3.8" \ --hash=sha256:0bf384e75b92c42830c0a679b0cd4d6e2b36ae0cf3dbb1e1dfdda48a244f4bcd \ --hash=sha256:0f881b589ff449bf0b931a711926e9ddaad3b35089cc039ce1af50b21a4ae8cb \ --hash=sha256:1484f9e692091450e7edf418c939e15bfc8fc68856e36ce399aed6889dae8bb0 \ @@ -1694,7 +1741,7 @@ pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "4.0" \ pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "4.0" and sys_platform == "win32" \ --hash=sha256:3426e063bdd5fd4df74a14fa3cf80a0b42845a87e1d1e81f6549f9daec593a60 \ --hash=sha256:bf490a1a709baf35d688fe0ecf980ed4de11d2b3e37b51e5442587a75d9957e7 -pywin32==306 ; python_version >= "3.8" and python_version < "4.0" and sys_platform == "win32" or python_version >= "3.8" and python_version < "4.0" and platform_system == "Windows" \ +pywin32==306 ; python_version >= "3.8" and python_version < "4.0" and (sys_platform == "win32" or platform_system == "Windows") \ --hash=sha256:06d3420a5155ba65f0b72f2699b5bacf3109f36acbe8923765c22938a69dfc8d \ --hash=sha256:1c73ea9a0d2283d889001998059f5eaaba3b6238f767c9cf2833b13e6a685f65 \ --hash=sha256:37257794c1ad39ee9be652da0462dc2e394c8159dfd913a8a4e8eb6fd346da0e \ @@ -2319,7 +2366,7 @@ typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "4.0" \ unidecode==1.3.7 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:3c90b4662aa0de0cb591884b934ead8d2225f1800d8da675a7750cbc3bd94610 \ --hash=sha256:663a537f506834ed836af26a81b210d90cbde044c47bfbdc0fbbc9f94c86a6e4 -urllib3==1.26.18 ; python_version < "4.0" and python_version >= "3.8" \ +urllib3==1.26.18 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07 \ --hash=sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0 virtualenv==20.25.0 ; python_version >= "3.8" and python_version < "4.0" \ From ce7cb3af72342423c4e1b7b9c0cb377f4ca4d66b Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Fri, 22 Dec 2023 14:32:45 +0100 Subject: [PATCH 36/41] Revisiting local interactions --- squirrel/artifact_manager/__init__.py | 1 + squirrel/artifact_manager/base.py | 61 ++++++++++-- squirrel/artifact_manager/drivers.py | 31 ++++++ .../artifact_manager/{fs.py => filesystem.py} | 94 +++++++++++-------- squirrel/artifact_manager/wandb.py | 17 ++-- .../my_collection/folder/bar.txt | 1 + .../my_collection/folder/baz.txt | 1 + .../my_collection/folder/foo.txt | 1 + test/test_artifact_manager/test_fs_logging.py | 68 ++++++++++---- 9 files changed, 204 insertions(+), 71 deletions(-) create mode 100644 squirrel/artifact_manager/drivers.py rename squirrel/artifact_manager/{fs.py => filesystem.py} (76%) create mode 100644 test/test_artifact_manager/my_collection/folder/bar.txt create mode 100644 test/test_artifact_manager/my_collection/folder/baz.txt create mode 100644 test/test_artifact_manager/my_collection/folder/foo.txt diff --git a/squirrel/artifact_manager/__init__.py b/squirrel/artifact_manager/__init__.py index e69de29..3c9a7d6 100644 --- a/squirrel/artifact_manager/__init__.py +++ b/squirrel/artifact_manager/__init__.py @@ -0,0 +1 @@ +import squirrel.artifact_manager.drivers # noqa \ No newline at end of file diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index d60175a..9795726 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -6,11 +6,50 @@ from types import TracebackType from typing import Optional, Any, Iterable, Type -from squirrel.catalog import Catalog, Source +from squirrel.catalog import Catalog +from squirrel.catalog.catalog import CatalogSource logger = logging.getLogger(__name__) +class TmpArtifact: + """ + Class to be used as a context for temporarily downloading an artifact, interacting with it and the deleting it. + When entering the scope it downloads the artifact to a local dir with a valid afid and returns the filepath to it. + """ + def __init__(self, artifact_manager: "ArtifactManager", collection: str, artifact: str, version: str ) -> None: + """ + Initializes the TmpArtifact. + + Args: + artifact_manager: An artifact manager instance to use for downloading the artifact. + """ + self.artifact_manager = artifact_manager + self.tempdir = tempfile.TemporaryDirectory() + self.collection = collection + self.artifact = artifact + self.version = version + + def __enter__(self) -> tuple[CatalogSource, Path]: + """ + Called when entering the context. Downloads the artifact to a local dir with a valid afid and returns the filepath to it. + + Returns: Absolute path to artifact folder as str + """ + source, _ = self.artifact_manager.download_artifact(self.artifact, self.collection, self.version, Path(self.tempdir.name)) + return source, Path(self.tempdir.name, self.artifact) + + def __exit__( + self, + exctype: Optional[Type[BaseException]] = None, + excinst: Optional[BaseException] = None, + exctb: Optional[TracebackType] = None, + ) -> None: + """Called when exiting the context. Deletes the artifact folder.""" + if self.tempdir is not None: + self.tempdir.cleanup() + + class DirectoryLogger: """ Class to be used as a context for logging a directory as an artifact. @@ -61,9 +100,9 @@ def __exit__( class ArtifactManager(ABC): - def __init__(self): + def __init__(self, active_collection: str = "default"): """Artifact manager interface for various backends.""" - self._active_collection = "default" + self._active_collection = active_collection @property def active_collection(self) -> str: @@ -121,7 +160,7 @@ def log_files( local_path: Path, collection: Optional[str] = None, artifact_path: Optional[Path] = None, - ) -> Source: + ) -> CatalogSource: """ Upload a file or folder into (current) collection, increment version automatically @@ -134,7 +173,7 @@ def log_files( raise NotImplementedError @abstractmethod - def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: + def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> CatalogSource: """ Log an arbitrary python object @@ -145,9 +184,13 @@ def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> @abstractmethod def download_artifact( - self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Path = "./" - ) -> Source: - """Retrieve file (from current collection) to specific location. Retrieve latest version unless specified.""" + self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Optional[Path] = None + ) -> tuple[CatalogSource, Path]: + """ + Download artifact contents (from current collection) to specific location and return a source listing them. + + If no target location is specified, a temporary directory is created and the path to it is returned. + Retrieve latest version unless specified.""" raise NotImplementedError def exists(self, artifact: str) -> bool: @@ -172,5 +215,5 @@ def download_collection(self, collection: Optional[str] = None, to: Path = "./") catalog = self.collection_to_catalog(collection) for _, artifact in catalog: artifact_name = artifact.metadata["artifact"] - self.download_artifact(artifact_name, collection, to=to / artifact_name) + self.download_artifact(artifact_name, collection, to=to) return catalog diff --git a/squirrel/artifact_manager/drivers.py b/squirrel/artifact_manager/drivers.py new file mode 100644 index 0000000..0080369 --- /dev/null +++ b/squirrel/artifact_manager/drivers.py @@ -0,0 +1,31 @@ +from typing import Any, Optional + +from squirrel.driver.store import StoreDriver +from squirrel.framework.plugins.plugin_manager import register_driver +from squirrel.store import AbstractStore, FilesystemStore + + +class DirectoryDriver(StoreDriver): + name = "directory" + + def __init__(self, url: str, storage_options: Optional[dict[str, Any]] = None, **kwargs) -> None: + """Initializes FileSystemDriver. + + Args: + url (str): the url of the store + **kwargs: Keyword arguments to pass to the super class initializer. + """ + if "store" in kwargs: + raise ValueError("Store of DirectoryDriver is fixed, `store` cannot be provided.") + + super().__init__(url=url, serializer=None, storage_options=storage_options, **kwargs) + + @property + def store(self) -> AbstractStore: + """Store that is used by the driver.""" + if self._store is None: + self._store = FilesystemStore(url=self.url, serializer=self.serializer, **self.storage_options) + return self._store + + +register_driver(DirectoryDriver) \ No newline at end of file diff --git a/squirrel/artifact_manager/fs.py b/squirrel/artifact_manager/filesystem.py similarity index 76% rename from squirrel/artifact_manager/fs.py rename to squirrel/artifact_manager/filesystem.py index 48e68b7..e144300 100644 --- a/squirrel/artifact_manager/fs.py +++ b/squirrel/artifact_manager/filesystem.py @@ -1,8 +1,9 @@ from pathlib import Path -from typing import Optional, Any, List, Iterable +from typing import Optional, Any, List, Iterable, Union -from squirrel.artifact_manager.base import ArtifactManager -from squirrel.catalog import Catalog, Source +from squirrel.artifact_manager.base import ArtifactManager, TmpArtifact +from squirrel.catalog import Catalog +from squirrel.catalog.catalog import CatalogSource, Source from squirrel.serialization import MessagepackSerializer, JsonSerializer, SquirrelSerializer from squirrel.store import FilesystemStore from squirrel.store.filesystem import get_random_key @@ -19,7 +20,7 @@ class ArtifactFileStore(FilesystemStore): The get and set methods are altered to allow for storing serialized data as well as raw files. If the final path component is a serializer name, the data is stored as a serialized file. - If the final path component is "file", the data is stored as a raw file. + If the final path component is "files", the data is stored as a raw file. """ def complete_key(self, partial_key: Path, **open_kwargs) -> List[str]: @@ -90,7 +91,7 @@ def __init__(self, url: str, serializer: Optional[SquirrelSerializer] = None, ** """ super().__init__() if serializer is None: - serializer = MessagepackSerializer() + serializer = JsonSerializer() self.backend = ArtifactFileStore(url=url, serializer=serializer, **fs_kwargs) def list_collection_names(self) -> Iterable: @@ -104,9 +105,11 @@ def exists_in_collection(self, artifact: str, collection: Optional[str] = None) return self.backend.key_exists(Path(collection, artifact)) def get_artifact_source( - self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None - ) -> Source: + self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, catalog: Optional[Catalog] = None + ) -> CatalogSource: """Catalog entry for a specific artifact""" + if catalog is None: + catalog = Catalog() if collection is None: collection = self.active_collection if version is None or version == "latest": @@ -115,18 +118,23 @@ def get_artifact_source( raise ValueError(f"Artifact {artifact} does not exist in collection {collection} with version {version}!") # TODO: Vary source (driver) description when support for serialised python values is added - return Source( - driver_name="file", - driver_kwargs={ - "url": Path(self.backend.url, collection, artifact, version, "file").as_uri(), - "storage_options": self.backend.storage_options, - }, - metadata={ - "collection": collection, - "artifact": artifact, - "version": version, - "location": Path(self.backend.url, collection, artifact, version).as_uri(), - }, + return CatalogSource( + Source( + driver_name="directory", + driver_kwargs={ + "url": Path(self.backend.url, collection, artifact, version, "files").as_uri(), + "storage_options": self.backend.storage_options, + + }, + metadata={ + "collection": collection, + "artifact": artifact, + "version": version, + }, + ), + identifier=str(Path(collection, artifact)), + catalog=catalog, + version=int(version[1:]) + 1, # Squirrel Catalog version is 1-based ) def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: @@ -136,7 +144,8 @@ def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: catalog = Catalog() for artifact in self.backend.complete_key(Path(collection)): for version in self.backend.complete_key(Path(collection, artifact)): - catalog[str(Path(collection, artifact))] = self.get_artifact_source(artifact, collection, version) + src = self.get_artifact_source(artifact, collection, version, catalog=catalog) + catalog[str(Path(collection, artifact)), src.version] = src return catalog def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: @@ -161,7 +170,7 @@ def log_files( local_path: Path, collection: Optional[str] = None, artifact_path: Optional[Path] = None, - ) -> Source: + ) -> CatalogSource: """Upload local file or folder to artifact store without serialisation""" if not isinstance(local_path, (str, Path)): raise ValueError("Path to file should be passed as a pathlib.Path object!") @@ -182,24 +191,35 @@ def log_files( return self.get_artifact_source(artifact_name, collection) def download_artifact( - self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Path = "./" - ) -> Source: + self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Optional[Path] = None + ) -> Union[tuple[Source, Path], TmpArtifact]: """Download artifact to local path.""" if collection is None: collection = self.active_collection if version is None or version == "latest": version = f"v{max(int(vs[1:]) for vs in self.backend.complete_key(Path(collection) / Path(artifact)))}" - if isinstance(to, str): - to = Path(to) - location = Path(collection, artifact, version) - self.backend.get(Path(location), target=to) - return Source( - driver_name="file", - driver_kwargs={"url": str(Path(to, artifact))}, - metadata={ - "collection": collection, - "artifact": artifact, - "version": version, - "location": str(Path(to, artifact)), - }, - ) + + if to is not None: + if isinstance(to, str): + to = Path(to) + location = Path(collection, artifact, version) + self.backend.get(Path(location), target=to / artifact) + src = CatalogSource( + Source( + driver_name="directory", + driver_kwargs={ + "url": (to / artifact).as_uri(), + }, + metadata={ + "collection": collection, + "artifact": artifact, + "version": version, + }, + ), + identifier=str(Path(collection, artifact)), + catalog=Catalog(), + version=int(version[1:]) + 1, # Squirrel Catalog version is 1-based + ) + return src, to + else: + return TmpArtifact(self, collection, artifact, version) diff --git a/squirrel/artifact_manager/wandb.py b/squirrel/artifact_manager/wandb.py index c9ef5b0..a19eba4 100644 --- a/squirrel/artifact_manager/wandb.py +++ b/squirrel/artifact_manager/wandb.py @@ -27,18 +27,23 @@ def __init__(self, entity: Optional[str] = None, project: Optional[str] = None): self.project = project elif wandb.run is not None: self.project = wandb.run.project + logger.info(f"Using project {self.project} from active wandb run.") elif wandb.Api().settings["project"] is not None: self.project = wandb.Api().settings["project"] + logger.info(f"Using project {self.project} from wandb settings.") else: raise ValueError("No project name was provided and no active project could be identified.") if entity is not None: self.entity = entity - elif wandb.run is not None: + elif wandb.run is not None and wandb.run.entity is not None: self.entity = wandb.run.entity + logger.info(f"Using entity {self.entity} from active wandb run.") elif wandb.Api().settings["entity"] is not None: self.entity = wandb.Api().settings["entity"] + logger.info(f"Using entity {self.entity} from wandb settings.") else: self.entity = wandb.Api().project(self.project).entity + logger.info(f"Using entity {self.entity} from wandb project.") def list_collection_names(self) -> Iterable: """ @@ -72,7 +77,7 @@ def get_artifact_source( if version is None: versions = [ instance.version - for instance in wandb.Api().artifact_versions(type_name=collection, name=f"{self.project}/{artifact}") + for instance in wandb.Api().artifact_versions(type_name=collection, name=f"{self.entity}/{self.project}/{artifact}") ] version = f"v{max([int(v[1:]) for v in versions])}" @@ -113,7 +118,7 @@ def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: ] catalog = Catalog() for artifact in artifact_names: - for instance in wandb.Api().artifact_versions(type_name=collection, name=f"{self.project}/{artifact}"): + for instance in wandb.Api().artifact_versions(type_name=collection, name=f"{self.entity}/{self.project}/{artifact}"): catalog[str(Path(collection, artifact))] = self.get_artifact_source( artifact, collection, instance.version ) @@ -168,8 +173,8 @@ def log_files( return self.get_artifact_source(artifact_name, collection) def download_artifact( - self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Path = "./" - ) -> Source: + self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Optional[Path] = None + ) -> tuple[Source, Path]: """ Download a specific artifact to a local path. @@ -190,4 +195,4 @@ def download_artifact( driver_name="file", driver_kwargs={"url": str(to)}, metadata={"collection": collection, "artifact": artifact, "version": version, "location": str(to)}, - ) + ) \ No newline at end of file diff --git a/test/test_artifact_manager/my_collection/folder/bar.txt b/test/test_artifact_manager/my_collection/folder/bar.txt new file mode 100644 index 0000000..39f99de --- /dev/null +++ b/test/test_artifact_manager/my_collection/folder/bar.txt @@ -0,0 +1 @@ +Test: Bar \ No newline at end of file diff --git a/test/test_artifact_manager/my_collection/folder/baz.txt b/test/test_artifact_manager/my_collection/folder/baz.txt new file mode 100644 index 0000000..50f65cf --- /dev/null +++ b/test/test_artifact_manager/my_collection/folder/baz.txt @@ -0,0 +1 @@ +Test: Baz \ No newline at end of file diff --git a/test/test_artifact_manager/my_collection/folder/foo.txt b/test/test_artifact_manager/my_collection/folder/foo.txt new file mode 100644 index 0000000..a0b5f91 --- /dev/null +++ b/test/test_artifact_manager/my_collection/folder/foo.txt @@ -0,0 +1 @@ +Test: Foo \ No newline at end of file diff --git a/test/test_artifact_manager/test_fs_logging.py b/test/test_artifact_manager/test_fs_logging.py index d608969..dd95e96 100644 --- a/test/test_artifact_manager/test_fs_logging.py +++ b/test/test_artifact_manager/test_fs_logging.py @@ -3,7 +3,7 @@ import pytest -from squirrel.artifact_manager.fs import FileSystemArtifactManager +from squirrel.artifact_manager.filesystem import FileSystemArtifactManager from squirrel.catalog import Source from squirrel.serialization import JsonSerializer, MessagepackSerializer, SquirrelSerializer @@ -138,35 +138,34 @@ def test_log_file() -> None: # test logging of individual files for (filename, artifact_name, version, content) in [ - ("foo.txt", "foo_file", "v0", "Test: Foo"), - ("bar.txt", "bar_file", "v0", "Test: Bar"), - ("baz.txt", "bar_file", "v1", "Test: Baz"), + ("foo.txt", "foo_file", 0, "Test: Foo"), + ("bar.txt", "bar_file", 0, "Test: Bar"), + ("baz.txt", "bar_file", 1, "Test: Baz"), ]: with open(f"{src_dir.name}/{filename}", "w") as f: f.write(content) source = manager.log_files(artifact_name, Path(f"{src_dir.name}/{filename}"), collection, Path(filename)) - assert source.driver_name == "file" + assert source.driver_name == "directory" assert source.metadata["collection"] == collection assert source.metadata["artifact"] == artifact_name - assert source.metadata["version"] == version - assert source.metadata["location"] == f"file://{store_dir.name}/{collection}/{artifact_name}/{version}" + assert source.metadata["version"] == f"v{version}" + assert source.version == version + 1 - with open(f"{store_dir.name}/{collection}/{artifact_name}/{version}/files/{filename}") as f: + with open(f"{store_dir.name}/{collection}/{artifact_name}/v{version}/files/{filename}") as f: assert f.read() == content # test logging of folder source = manager.log_files("folder", Path(src_dir.name), collection) - assert source.driver_name == "file" + assert source.driver_name == "directory" assert source.metadata["collection"] == collection assert source.metadata["artifact"] == "folder" - assert source.metadata["version"] == "v0" - assert source.metadata["location"] == f"file://{store_dir.name}/{collection}/folder/v0" + assert source.version == 1 assert len(list(Path(f"{store_dir.name}/{collection}/folder/v0/files").iterdir())) == 3 - + assert len([x for x in source.get_driver().keys()]) == 3 src_dir.cleanup() store_dir.cleanup() @@ -229,13 +228,13 @@ def test_get_file() -> None: # Test retrieval of specific files for (filename, artifact_name, version, content) in file_descriptions: manager.download_artifact(artifact_name, collection, version, Path(f"{src_dir.name}/downloaded")) - with open(f"{src_dir.name}/downloaded/{filename}") as f: + with open(f"{src_dir.name}/downloaded/{artifact_name}/{filename}") as f: assert f.read() == content # Test retrieval of entire folder manager.download_artifact("folder", collection, "v0", Path(f"{src_dir.name}/downloaded2")) for (filename, _, _, content) in file_descriptions: - with open(f"{src_dir.name}/downloaded2/{filename}") as f: + with open(f"{src_dir.name}/downloaded2/folder/{filename}") as f: assert f.read() == content src_dir.cleanup() @@ -259,17 +258,17 @@ def test_log_folder() -> None: assert manager.exists_in_collection("folder", collection) source = manager.collection_to_catalog(collection)["my_collection/folder"] - assert source.driver_name == "file" + assert source.driver_name == "directory" assert source.metadata["collection"] == collection assert source.metadata["artifact"] == "folder" assert source.metadata["version"] == "v0" - assert source.metadata["location"] == f"file://{store_dir.name}/{collection}/folder/v0" + assert source.version == 1 assert len(list(Path(f"{store_dir.name}/{collection}/folder/v0/files").iterdir())) == 3 local_dir = tempfile.TemporaryDirectory() manager.download_artifact("folder", collection, "v0", Path(f"{local_dir.name}/downloaded")) for (filename, content) in test_files: - with open(f"{local_dir.name}/downloaded/{filename}") as f: + with open(f"{local_dir.name}/downloaded/folder/{filename}") as f: assert f.read() == content local_dir.cleanup() @@ -306,8 +305,17 @@ def test_store_to_catalog() -> None: catalog = manager.store_to_catalog() assert len(catalog) == 3 assert "my_collection/foo" in catalog + assert catalog["my_collection/foo"].metadata["collection"] == "my_collection" + assert catalog["my_collection/foo"].metadata["artifact"] == "foo" + assert catalog["my_collection/foo"].version == 1 assert "my_collection/bar" in catalog + assert catalog["my_collection/bar"].metadata["collection"] == "my_collection" + assert catalog["my_collection/bar"].metadata["artifact"] == "bar" + assert catalog["my_collection/bar"].version == 1 assert "default/baz" in catalog + assert catalog["default/baz"].metadata["collection"] == "default" + assert catalog["default/baz"].metadata["artifact"] == "baz" + assert catalog["default/baz"].version == 1 src_dir.cleanup() store_dir.cleanup() @@ -331,8 +339,10 @@ def test_download_collection() -> None: manager.log_files(filename[:3], Path(f"{src_dir.name}/{filename}"), collection, Path(filename)) - manager.download_collection("my_collection", Path(src_dir.name, "downloaded/my_collection")) - manager.download_collection("default", Path(src_dir.name, "downloaded/default")) + cat1 = manager.download_collection("my_collection", Path(src_dir.name, "downloaded/my_collection")) + assert len(cat1) == 2 + cat2 = manager.download_collection("default", Path(src_dir.name, "downloaded/default")) + assert len(cat2) == 1 for collection in test_files: for filename in test_files[collection]: with open(f"{src_dir.name}/downloaded/{collection}/{filename[:3]}/{filename}") as f: @@ -340,3 +350,23 @@ def test_download_collection() -> None: src_dir.cleanup() store_dir.cleanup() + + +def test_download_tmp(): + store_dir = tempfile.TemporaryDirectory() + manager = FileSystemArtifactManager(url=store_dir.name, auto_mkdir=True) + collection = "my_collection" + test_files = { + "foo.txt": "Test: Foo", + "bar.txt": "Test: Bar", + "baz.txt": "Test: Baz", + } + with manager.log_folder("folder", collection) as folder: + for (filename, content) in test_files.items(): + with open(f"{folder}/{filename}", "w") as file: + file.write(content) + + with manager.download_artifact("folder", collection, "v0") as (src, path): + for file in src.get_driver().keys(): + with open(f"{path}/{file}") as f: + assert f.read() == test_files[file] \ No newline at end of file From 90b1cd41e48b6c630d72547b1866f18d3c1373c3 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Fri, 22 Dec 2023 15:16:33 +0100 Subject: [PATCH 37/41] Simplified download --- requirements.txt | 10 +- squirrel/artifact_manager/__init__.py | 2 +- squirrel/artifact_manager/base.py | 15 +-- squirrel/artifact_manager/drivers.py | 2 +- squirrel/artifact_manager/filesystem.py | 31 ++----- squirrel/artifact_manager/wandb.py | 93 +++++++++++-------- .../my_collection/folder/bar.txt | 1 - .../my_collection/folder/baz.txt | 1 - .../my_collection/folder/foo.txt | 1 - test/test_artifact_manager/test_fs_logging.py | 7 +- test/test_artifact_manager/wandb_script.py | 8 +- 11 files changed, 85 insertions(+), 86 deletions(-) delete mode 100644 test/test_artifact_manager/my_collection/folder/bar.txt delete mode 100644 test/test_artifact_manager/my_collection/folder/baz.txt delete mode 100644 test/test_artifact_manager/my_collection/folder/foo.txt diff --git a/requirements.txt b/requirements.txt index 3b7e984..6d91f35 100644 --- a/requirements.txt +++ b/requirements.txt @@ -98,7 +98,7 @@ anyio==4.2.0 ; python_version >= "3.8" and python_version < "4.0" \ appdirs==1.4.4 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41 \ --hash=sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128 -appnope==0.1.3 ; python_version >= "3.8" and python_version < "4.0" and (platform_system == "Darwin" or sys_platform == "darwin") \ +appnope==0.1.3 ; python_version >= "3.8" and python_version < "4.0" and platform_system == "Darwin" or python_version >= "3.8" and python_version < "4.0" and sys_platform == "darwin" \ --hash=sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24 \ --hash=sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e asciitree==0.3.3 ; python_version >= "3.8" and python_version < "4.0" \ @@ -324,7 +324,7 @@ click==8.0.4 ; python_version >= "3.8" and python_version < "4.0" \ cloudpickle==3.0.0 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:246ee7d0c295602a036e86369c77fecda4ab17b506496730f2f576d9016fd9c7 \ --hash=sha256:996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882 -colorama==0.4.6 ; python_version >= "3.8" and python_version < "4.0" and (platform_system == "Windows" or sys_platform == "win32" or os_name == "nt") \ +colorama==0.4.6 ; python_version >= "3.8" and python_version < "4.0" and platform_system == "Windows" or python_version >= "3.8" and python_version < "4.0" and sys_platform == "win32" or python_version >= "3.8" and python_version < "4.0" and os_name == "nt" \ --hash=sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44 \ --hash=sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6 colorclass==2.2.2 ; python_version >= "3.8" and python_version < "4.0" \ @@ -1621,7 +1621,7 @@ pre-commit==3.5.0 ; python_version >= "3.8" and python_version < "4.0" \ prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:3527b7af26106cbc65a040bcc84839a3566ec1b051bb0bfe953631e704b0ff7d \ --hash=sha256:a11a29cb3bf0a28a387fe5122cdb649816a957cd9261dcedf8c9f1fef33eacf6 -protobuf==4.25.1 ; python_version < "4.0" and python_version >= "3.8" \ +protobuf==4.25.1 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:0bf384e75b92c42830c0a679b0cd4d6e2b36ae0cf3dbb1e1dfdda48a244f4bcd \ --hash=sha256:0f881b589ff449bf0b931a711926e9ddaad3b35089cc039ce1af50b21a4ae8cb \ --hash=sha256:1484f9e692091450e7edf418c939e15bfc8fc68856e36ce399aed6889dae8bb0 \ @@ -1741,7 +1741,7 @@ pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "4.0" \ pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "4.0" and sys_platform == "win32" \ --hash=sha256:3426e063bdd5fd4df74a14fa3cf80a0b42845a87e1d1e81f6549f9daec593a60 \ --hash=sha256:bf490a1a709baf35d688fe0ecf980ed4de11d2b3e37b51e5442587a75d9957e7 -pywin32==306 ; python_version >= "3.8" and python_version < "4.0" and (sys_platform == "win32" or platform_system == "Windows") \ +pywin32==306 ; python_version >= "3.8" and python_version < "4.0" and sys_platform == "win32" or python_version >= "3.8" and python_version < "4.0" and platform_system == "Windows" \ --hash=sha256:06d3420a5155ba65f0b72f2699b5bacf3109f36acbe8923765c22938a69dfc8d \ --hash=sha256:1c73ea9a0d2283d889001998059f5eaaba3b6238f767c9cf2833b13e6a685f65 \ --hash=sha256:37257794c1ad39ee9be652da0462dc2e394c8159dfd913a8a4e8eb6fd346da0e \ @@ -2366,7 +2366,7 @@ typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "4.0" \ unidecode==1.3.7 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:3c90b4662aa0de0cb591884b934ead8d2225f1800d8da675a7750cbc3bd94610 \ --hash=sha256:663a537f506834ed836af26a81b210d90cbde044c47bfbdc0fbbc9f94c86a6e4 -urllib3==1.26.18 ; python_version >= "3.8" and python_version < "4.0" \ +urllib3==1.26.18 ; python_version < "4.0" and python_version >= "3.8" \ --hash=sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07 \ --hash=sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0 virtualenv==20.25.0 ; python_version >= "3.8" and python_version < "4.0" \ diff --git a/squirrel/artifact_manager/__init__.py b/squirrel/artifact_manager/__init__.py index 3c9a7d6..2bd4c19 100644 --- a/squirrel/artifact_manager/__init__.py +++ b/squirrel/artifact_manager/__init__.py @@ -1 +1 @@ -import squirrel.artifact_manager.drivers # noqa \ No newline at end of file +import squirrel.artifact_manager.drivers # noqa diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index 9795726..0857f49 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -4,7 +4,7 @@ import re import tempfile from types import TracebackType -from typing import Optional, Any, Iterable, Type +from typing import Optional, Any, Iterable, Type, Union from squirrel.catalog import Catalog from squirrel.catalog.catalog import CatalogSource @@ -17,7 +17,8 @@ class TmpArtifact: Class to be used as a context for temporarily downloading an artifact, interacting with it and the deleting it. When entering the scope it downloads the artifact to a local dir with a valid afid and returns the filepath to it. """ - def __init__(self, artifact_manager: "ArtifactManager", collection: str, artifact: str, version: str ) -> None: + + def __init__(self, artifact_manager: "ArtifactManager", collection: str, artifact: str, version: str) -> None: """ Initializes the TmpArtifact. @@ -30,14 +31,16 @@ def __init__(self, artifact_manager: "ArtifactManager", collection: str, artifac self.artifact = artifact self.version = version - def __enter__(self) -> tuple[CatalogSource, Path]: + def __enter__(self) -> Path: """ Called when entering the context. Downloads the artifact to a local dir with a valid afid and returns the filepath to it. Returns: Absolute path to artifact folder as str """ - source, _ = self.artifact_manager.download_artifact(self.artifact, self.collection, self.version, Path(self.tempdir.name)) - return source, Path(self.tempdir.name, self.artifact) + self.artifact_manager.download_artifact( + self.artifact, self.collection, self.version, Path(self.tempdir.name) + ) + return Path(self.tempdir.name, self.artifact) def __exit__( self, @@ -185,7 +188,7 @@ def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> @abstractmethod def download_artifact( self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Optional[Path] = None - ) -> tuple[CatalogSource, Path]: + ) -> Union[Path, TmpArtifact]: """ Download artifact contents (from current collection) to specific location and return a source listing them. diff --git a/squirrel/artifact_manager/drivers.py b/squirrel/artifact_manager/drivers.py index 0080369..6aab5f9 100644 --- a/squirrel/artifact_manager/drivers.py +++ b/squirrel/artifact_manager/drivers.py @@ -28,4 +28,4 @@ def store(self) -> AbstractStore: return self._store -register_driver(DirectoryDriver) \ No newline at end of file +register_driver(DirectoryDriver) diff --git a/squirrel/artifact_manager/filesystem.py b/squirrel/artifact_manager/filesystem.py index e144300..795a4a9 100644 --- a/squirrel/artifact_manager/filesystem.py +++ b/squirrel/artifact_manager/filesystem.py @@ -105,7 +105,11 @@ def exists_in_collection(self, artifact: str, collection: Optional[str] = None) return self.backend.key_exists(Path(collection, artifact)) def get_artifact_source( - self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, catalog: Optional[Catalog] = None + self, + artifact: str, + collection: Optional[str] = None, + version: Optional[str] = None, + catalog: Optional[Catalog] = None, ) -> CatalogSource: """Catalog entry for a specific artifact""" if catalog is None: @@ -124,17 +128,16 @@ def get_artifact_source( driver_kwargs={ "url": Path(self.backend.url, collection, artifact, version, "files").as_uri(), "storage_options": self.backend.storage_options, - }, metadata={ "collection": collection, "artifact": artifact, "version": version, - }, + }, ), identifier=str(Path(collection, artifact)), catalog=catalog, - version=int(version[1:]) + 1, # Squirrel Catalog version is 1-based + version=int(version[1:]) + 1, # Squirrel Catalog version is 1-based ) def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: @@ -192,7 +195,7 @@ def log_files( def download_artifact( self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Optional[Path] = None - ) -> Union[tuple[Source, Path], TmpArtifact]: + ) -> Union[Path, TmpArtifact]: """Download artifact to local path.""" if collection is None: collection = self.active_collection @@ -204,22 +207,6 @@ def download_artifact( to = Path(to) location = Path(collection, artifact, version) self.backend.get(Path(location), target=to / artifact) - src = CatalogSource( - Source( - driver_name="directory", - driver_kwargs={ - "url": (to / artifact).as_uri(), - }, - metadata={ - "collection": collection, - "artifact": artifact, - "version": version, - }, - ), - identifier=str(Path(collection, artifact)), - catalog=Catalog(), - version=int(version[1:]) + 1, # Squirrel Catalog version is 1-based - ) - return src, to + return to / artifact else: return TmpArtifact(self, collection, artifact, version) diff --git a/squirrel/artifact_manager/wandb.py b/squirrel/artifact_manager/wandb.py index a19eba4..648cffc 100644 --- a/squirrel/artifact_manager/wandb.py +++ b/squirrel/artifact_manager/wandb.py @@ -1,11 +1,12 @@ from pathlib import Path -from typing import Optional, Any, Iterable +from typing import Optional, Any, Iterable, Union import logging import wandb -from squirrel.artifact_manager.base import ArtifactManager -from squirrel.catalog import Catalog, Source +from squirrel.artifact_manager.base import ArtifactManager, TmpArtifact +from squirrel.catalog import Catalog +from squirrel.catalog.catalog import CatalogSource, Source logger = logging.getLogger(__name__) @@ -69,41 +70,51 @@ def exists_in_collection(self, artifact: str, collection: Optional[str] = None) ] def get_artifact_source( - self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None - ) -> Source: + self, + artifact: str, + collection: Optional[str] = None, + version: Optional[str] = None, + catalog: Optional[Catalog] = None, + ) -> CatalogSource: """Catalog entry for a specific artifact""" + if catalog is None: + catalog = Catalog() if collection is None: collection = self.active_collection if version is None: versions = [ instance.version - for instance in wandb.Api().artifact_versions(type_name=collection, name=f"{self.entity}/{self.project}/{artifact}") + for instance in wandb.Api().artifact_versions( + type_name=collection, name=f"{self.entity}/{self.project}/{artifact}" + ) ] version = f"v{max([int(v[1:]) for v in versions])}" - return Source( - driver_name="wandb", - driver_kwargs={ - "url": str( - Path( - wandb.Api().settings["base_url"], - self.entity, - self.project, - collection, - artifact, - version, - ) - ), - }, - metadata={ - "project": self.project, - "collection": collection, - "artifact": artifact, - "version": version, - "location": str( - Path(wandb.Api().settings["base_url"], self.entity, self.project, collection, artifact, version) - ), - }, + return CatalogSource( + Source( + driver_name="wandb", + driver_kwargs={ + "url": str( + Path( + wandb.Api().settings["base_url"], + self.entity, + self.project, + collection, + artifact, + version, + ) + ), + }, + metadata={ + "project": self.project, + "collection": collection, + "artifact": artifact, + "version": version, + }, + ), + identifier=str(Path(collection, artifact)), + catalog=catalog, + version=int(version[1:]) + 1, # Squirrel Catalog version is 1-based ) def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: @@ -118,10 +129,11 @@ def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: ] catalog = Catalog() for artifact in artifact_names: - for instance in wandb.Api().artifact_versions(type_name=collection, name=f"{self.entity}/{self.project}/{artifact}"): - catalog[str(Path(collection, artifact))] = self.get_artifact_source( - artifact, collection, instance.version - ) + for instance in wandb.Api().artifact_versions( + type_name=collection, name=f"{self.entity}/{self.project}/{artifact}" + ): + src = self.get_artifact_source(artifact, collection, instance.version, catalog=catalog) + catalog[str(Path(collection, artifact)), src.version] = src return catalog def log_artifact(self, obj: Any, name: str, collection: Optional[str] = None) -> Source: @@ -157,7 +169,7 @@ def log_files( local_path: Path, collection: Optional[str] = None, artifact_path: Optional[Path] = None, - ) -> Source: + ) -> CatalogSource: """Upload a single file to artifact store without serialisation.""" if collection is None: collection = self._active_collection @@ -174,7 +186,7 @@ def log_files( def download_artifact( self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Optional[Path] = None - ) -> tuple[Source, Path]: + ) -> Union[Path, TmpArtifact]: """ Download a specific artifact to a local path. @@ -190,9 +202,8 @@ def download_artifact( else: art = wandb.run.use_artifact(f"{self.entity}/{self.project}/{artifact}:{version}", type=collection) - art.download(str(to)) - return Source( - driver_name="file", - driver_kwargs={"url": str(to)}, - metadata={"collection": collection, "artifact": artifact, "version": version, "location": str(to)}, - ) \ No newline at end of file + if to is not None: + art.download(str(to / artifact)) + return to / artifact + else: + return TmpArtifact(self, collection, artifact, version) diff --git a/test/test_artifact_manager/my_collection/folder/bar.txt b/test/test_artifact_manager/my_collection/folder/bar.txt deleted file mode 100644 index 39f99de..0000000 --- a/test/test_artifact_manager/my_collection/folder/bar.txt +++ /dev/null @@ -1 +0,0 @@ -Test: Bar \ No newline at end of file diff --git a/test/test_artifact_manager/my_collection/folder/baz.txt b/test/test_artifact_manager/my_collection/folder/baz.txt deleted file mode 100644 index 50f65cf..0000000 --- a/test/test_artifact_manager/my_collection/folder/baz.txt +++ /dev/null @@ -1 +0,0 @@ -Test: Baz \ No newline at end of file diff --git a/test/test_artifact_manager/my_collection/folder/foo.txt b/test/test_artifact_manager/my_collection/folder/foo.txt deleted file mode 100644 index a0b5f91..0000000 --- a/test/test_artifact_manager/my_collection/folder/foo.txt +++ /dev/null @@ -1 +0,0 @@ -Test: Foo \ No newline at end of file diff --git a/test/test_artifact_manager/test_fs_logging.py b/test/test_artifact_manager/test_fs_logging.py index dd95e96..6d8a450 100644 --- a/test/test_artifact_manager/test_fs_logging.py +++ b/test/test_artifact_manager/test_fs_logging.py @@ -1,3 +1,4 @@ +import os import tempfile from pathlib import Path @@ -366,7 +367,7 @@ def test_download_tmp(): with open(f"{folder}/{filename}", "w") as file: file.write(content) - with manager.download_artifact("folder", collection, "v0") as (src, path): - for file in src.get_driver().keys(): + with manager.download_artifact("folder", collection, "v0") as path: + for file in os.listdir(path): with open(f"{path}/{file}") as f: - assert f.read() == test_files[file] \ No newline at end of file + assert f.read() == test_files[file] diff --git a/test/test_artifact_manager/wandb_script.py b/test/test_artifact_manager/wandb_script.py index ac74f61..a499e89 100644 --- a/test/test_artifact_manager/wandb_script.py +++ b/test/test_artifact_manager/wandb_script.py @@ -31,7 +31,7 @@ assert ( source.metadata["artifact"] == artifact_name ), f"Value {source.metadata['artifact']} should be {artifact_name}" - assert source.metadata["version"] == version, f"Value {source.metadata['version']} should be {version}" + assert source.version == int(version[1:]) + 1, f"Value {source.metadata['version']} should be {version}" # test logging of folder source = artifact_manager.log_files("folder", Path(src_dir.name), collection) @@ -39,19 +39,19 @@ assert source.driver_name == "wandb" assert source.metadata["collection"] == collection, f"Value {source.metadata['collection']} should be {collection}" assert source.metadata["artifact"] == "folder", f"Value {source.metadata['artifact']} should be {artifact_name}" -assert source.metadata["version"] == "v0", f"Value {source.metadata['version']} should be {version}" +assert source.version == 1, f"Value {source.version} should be {version}" # Test retrieval of specific files for (filename, artifact_name, version, content) in file_descriptions: artifact_manager.download_artifact(artifact_name, collection, version, Path(f"{src_dir.name}/downloaded")) - with open(f"{src_dir.name}/downloaded/{filename}") as f: + with open(f"{src_dir.name}/downloaded/{artifact_name}/{filename}") as f: assert f.read() == content # Test retrieval of entire folder artifact_manager.download_artifact("folder", collection, "v0", Path(f"{src_dir.name}/downloaded2")) for (filename, _, _, content) in file_descriptions: - with open(f"{src_dir.name}/downloaded2/{filename}") as f: + with open(f"{src_dir.name}/downloaded2/folder/{filename}") as f: assert f.read() == content # test artifact existence checks From 705522c0cc26c2205dd824302afedd97c0b56221 Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Fri, 22 Dec 2023 15:25:27 +0100 Subject: [PATCH 38/41] Cleanup --- squirrel/artifact_manager/base.py | 12 +++++++----- squirrel/artifact_manager/drivers.py | 1 + test/test_artifact_manager/test_fs_logging.py | 3 ++- test/test_artifact_manager/wandb_script.py | 9 ++++++++- 4 files changed, 18 insertions(+), 7 deletions(-) diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index 0857f49..f691521 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -24,6 +24,9 @@ def __init__(self, artifact_manager: "ArtifactManager", collection: str, artifac Args: artifact_manager: An artifact manager instance to use for downloading the artifact. + collection: The name of the collection to download from. + artifact: The name of the artifact to download. + version: The version of the artifact to download. """ self.artifact_manager = artifact_manager self.tempdir = tempfile.TemporaryDirectory() @@ -33,13 +36,11 @@ def __init__(self, artifact_manager: "ArtifactManager", collection: str, artifac def __enter__(self) -> Path: """ - Called when entering the context. Downloads the artifact to a local dir with a valid afid and returns the filepath to it. + Called when entering the context. Downloads the artifact to a temporary dir and returns the filepath to it. Returns: Absolute path to artifact folder as str """ - self.artifact_manager.download_artifact( - self.artifact, self.collection, self.version, Path(self.tempdir.name) - ) + self.artifact_manager.download_artifact(self.artifact, self.collection, self.version, Path(self.tempdir.name)) return Path(self.tempdir.name, self.artifact) def __exit__( @@ -193,7 +194,8 @@ def download_artifact( Download artifact contents (from current collection) to specific location and return a source listing them. If no target location is specified, a temporary directory is created and the path to it is returned. - Retrieve latest version unless specified.""" + Retrieve latest version unless specified. + """ raise NotImplementedError def exists(self, artifact: str) -> bool: diff --git a/squirrel/artifact_manager/drivers.py b/squirrel/artifact_manager/drivers.py index 6aab5f9..bfb8f9d 100644 --- a/squirrel/artifact_manager/drivers.py +++ b/squirrel/artifact_manager/drivers.py @@ -13,6 +13,7 @@ def __init__(self, url: str, storage_options: Optional[dict[str, Any]] = None, * Args: url (str): the url of the store + storage_options (dict[str, Any], optional): Keyword arguments passed to filesystem handler. **kwargs: Keyword arguments to pass to the super class initializer. """ if "store" in kwargs: diff --git a/test/test_artifact_manager/test_fs_logging.py b/test/test_artifact_manager/test_fs_logging.py index 6d8a450..d8bb256 100644 --- a/test/test_artifact_manager/test_fs_logging.py +++ b/test/test_artifact_manager/test_fs_logging.py @@ -353,7 +353,8 @@ def test_download_collection() -> None: store_dir.cleanup() -def test_download_tmp(): +def test_download_tmp() -> None: + """Test temporary retrieval of artifacts.""" store_dir = tempfile.TemporaryDirectory() manager = FileSystemArtifactManager(url=store_dir.name, auto_mkdir=True) collection = "my_collection" diff --git a/test/test_artifact_manager/wandb_script.py b/test/test_artifact_manager/wandb_script.py index a499e89..c4f737c 100644 --- a/test/test_artifact_manager/wandb_script.py +++ b/test/test_artifact_manager/wandb_script.py @@ -84,12 +84,19 @@ assert source.metadata["artifact"] == "test_folder" assert source.metadata["version"] == "v0" +# test download folder local_dir = tempfile.TemporaryDirectory() artifact_manager.download_artifact("test_folder", collection, "v0", Path(f"{local_dir.name}/downloaded3")) for (filename, _, _, content) in file_descriptions: - with open(f"{local_dir.name}/downloaded3/{filename}") as f: + with open(f"{local_dir.name}/downloaded3/test_folder/{filename}") as f: assert f.read() == content +# test temporary download +with artifact_manager.download_artifact("test_folder", collection, "v0") as path: + for (filename, _, _, content) in file_descriptions: + with open(f"{path}/{filename}") as f: + assert f.read() == content + # test download collection artifact_manager.download_collection(collection, Path(src_dir.name, "my_collection")) for (filename, _, _, content) in file_descriptions: From d5f8bbc4aaaaf05a1ae43678fd6cc4666693c670 Mon Sep 17 00:00:00 2001 From: mg515 Date: Fri, 22 Dec 2023 15:33:29 +0100 Subject: [PATCH 39/41] collection constructor arg --- squirrel/artifact_manager/base.py | 10 +++++----- squirrel/artifact_manager/filesystem.py | 10 ++++++---- squirrel/artifact_manager/wandb.py | 8 ++++---- 3 files changed, 15 insertions(+), 13 deletions(-) diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index f691521..812ad31 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -1,10 +1,10 @@ -from abc import abstractmethod, ABC import logging -from pathlib import Path import re import tempfile +from abc import ABC, abstractmethod +from pathlib import Path from types import TracebackType -from typing import Optional, Any, Iterable, Type, Union +from typing import Any, Iterable, Optional, Type, Union from squirrel.catalog import Catalog from squirrel.catalog.catalog import CatalogSource @@ -104,9 +104,9 @@ def __exit__( class ArtifactManager(ABC): - def __init__(self, active_collection: str = "default"): + def __init__(self, collection: str = "default"): """Artifact manager interface for various backends.""" - self._active_collection = active_collection + self._active_collection = collection @property def active_collection(self) -> str: diff --git a/squirrel/artifact_manager/filesystem.py b/squirrel/artifact_manager/filesystem.py index 795a4a9..4b72ccc 100644 --- a/squirrel/artifact_manager/filesystem.py +++ b/squirrel/artifact_manager/filesystem.py @@ -1,10 +1,10 @@ from pathlib import Path -from typing import Optional, Any, List, Iterable, Union +from typing import Any, Iterable, List, Optional, Union from squirrel.artifact_manager.base import ArtifactManager, TmpArtifact from squirrel.catalog import Catalog from squirrel.catalog.catalog import CatalogSource, Source -from squirrel.serialization import MessagepackSerializer, JsonSerializer, SquirrelSerializer +from squirrel.serialization import JsonSerializer, MessagepackSerializer, SquirrelSerializer from squirrel.store import FilesystemStore from squirrel.store.filesystem import get_random_key @@ -77,7 +77,9 @@ def set(self, value: Any, key: Optional[Path] = None, mode: str = "wb", **open_k class FileSystemArtifactManager(ArtifactManager): - def __init__(self, url: str, serializer: Optional[SquirrelSerializer] = None, **fs_kwargs): + def __init__( + self, url: str, serializer: Optional[SquirrelSerializer] = None, collection: str = "default", **fs_kwargs + ): """ Artifactmanager backed by fsspec filesystems. @@ -89,7 +91,7 @@ def __init__(self, url: str, serializer: Optional[SquirrelSerializer] = None, ** version: version number starting at 1 which is automatically incremented serializer: the name of the serializer used to store the artifact (e.g. file, messagepack) """ - super().__init__() + super().__init__(collection=collection) if serializer is None: serializer = JsonSerializer() self.backend = ArtifactFileStore(url=url, serializer=serializer, **fs_kwargs) diff --git a/squirrel/artifact_manager/wandb.py b/squirrel/artifact_manager/wandb.py index 648cffc..0ee8e9f 100644 --- a/squirrel/artifact_manager/wandb.py +++ b/squirrel/artifact_manager/wandb.py @@ -1,7 +1,7 @@ +import logging from pathlib import Path -from typing import Optional, Any, Iterable, Union +from typing import Any, Iterable, Optional, Union -import logging import wandb from squirrel.artifact_manager.base import ArtifactManager, TmpArtifact @@ -12,7 +12,7 @@ class WandbArtifactManager(ArtifactManager): - def __init__(self, entity: Optional[str] = None, project: Optional[str] = None): + def __init__(self, entity: Optional[str] = None, project: Optional[str] = None, collection: str = "default"): """ Artifact manager using Weights & Biases as backend. @@ -23,7 +23,7 @@ def __init__(self, entity: Optional[str] = None, project: Optional[str] = None): Note: For storing objects it is assumed that wandb.init() has been called so that artifacts can be associated with a run. """ - super().__init__() + super().__init__(collection=collection) if project is not None: self.project = project elif wandb.run is not None: From 3c5c3d60c397848bce131de57d220d0fdeb15296 Mon Sep 17 00:00:00 2001 From: mg515 Date: Fri, 22 Dec 2023 16:16:01 +0100 Subject: [PATCH 40/41] collection optional, styling --- squirrel/artifact_manager/base.py | 7 +++---- squirrel/artifact_manager/filesystem.py | 15 +++++---------- squirrel/artifact_manager/wandb.py | 15 +++++---------- 3 files changed, 13 insertions(+), 24 deletions(-) diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index 812ad31..317399b 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -61,7 +61,7 @@ class DirectoryLogger: You can then write files to that dir and after exiting the scope the dir gets logged through the artifact manager. """ - def __init__(self, artifact_manager: "ArtifactManager", artifact: str, collection: Optional[str]) -> None: + def __init__(self, artifact_manager: "ArtifactManager", artifact: str, collection: Optional[str] = None) -> None: """ Initializes the DirectoryLogger. @@ -72,7 +72,7 @@ def __init__(self, artifact_manager: "ArtifactManager", artifact: str, collectio """ self.artifact_manager = artifact_manager self.artifact = artifact - self.collection = collection + self.collection = collection or artifact_manager.active_collection self.tempdir = tempfile.TemporaryDirectory() def __enter__(self) -> str: @@ -215,8 +215,7 @@ def log_folder(self, artifact: str, collection: Optional[str] = None) -> Directo def download_collection(self, collection: Optional[str] = None, to: Path = "./") -> Catalog: """Download all artifacts in collection to local directory.""" - if collection is None: - collection = self.active_collection + collection = collection or self.active_collection catalog = self.collection_to_catalog(collection) for _, artifact in catalog: artifact_name = artifact.metadata["artifact"] diff --git a/squirrel/artifact_manager/filesystem.py b/squirrel/artifact_manager/filesystem.py index 4b72ccc..d189dc9 100644 --- a/squirrel/artifact_manager/filesystem.py +++ b/squirrel/artifact_manager/filesystem.py @@ -102,8 +102,7 @@ def list_collection_names(self) -> Iterable: def exists_in_collection(self, artifact: str, collection: Optional[str] = None) -> bool: """Check if artifact exists in specified collection.""" - if collection is None: - collection = self.active_collection + collection = collection or self.active_collection return self.backend.key_exists(Path(collection, artifact)) def get_artifact_source( @@ -116,8 +115,7 @@ def get_artifact_source( """Catalog entry for a specific artifact""" if catalog is None: catalog = Catalog() - if collection is None: - collection = self.active_collection + collection = collection or self.active_collection if version is None or version == "latest": version = f"v{max(int(vs[1:]) for vs in self.backend.complete_key(Path(collection) / Path(artifact)))}" if not self.backend.key_exists(Path(collection, artifact, version)): @@ -144,8 +142,7 @@ def get_artifact_source( def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: """Provide catalog of all artifacts and their versions contained within specific collection""" - if collection is None: - collection = self.active_collection + collection = collection or self.active_collection catalog = Catalog() for artifact in self.backend.complete_key(Path(collection)): for version in self.backend.complete_key(Path(collection, artifact)): @@ -183,8 +180,7 @@ def log_files( if artifact_path is not None and not isinstance(artifact_path, (str, Path)): raise ValueError("Artifact path should be passed as a pathlib.Path object!") - if collection is None: - collection = self.active_collection + collection = collection or self.active_collection version = f"v{len(self.backend.complete_key(Path(collection, artifact_name)))}" @@ -199,8 +195,7 @@ def download_artifact( self, artifact: str, collection: Optional[str] = None, version: Optional[str] = None, to: Optional[Path] = None ) -> Union[Path, TmpArtifact]: """Download artifact to local path.""" - if collection is None: - collection = self.active_collection + collection = collection or self.active_collection if version is None or version == "latest": version = f"v{max(int(vs[1:]) for vs in self.backend.complete_key(Path(collection) / Path(artifact)))}" diff --git a/squirrel/artifact_manager/wandb.py b/squirrel/artifact_manager/wandb.py index 0ee8e9f..f613d5a 100644 --- a/squirrel/artifact_manager/wandb.py +++ b/squirrel/artifact_manager/wandb.py @@ -60,8 +60,7 @@ def exists_in_collection(self, artifact: str, collection: Optional[str] = None) Note: This is not supported by the WandB API and therefore requires listing all artifacts in a collection. """ - if collection is None: - collection = self.active_collection + collection = collection or self.active_collection if collection not in self.list_collection_names(): return False return artifact in [ @@ -79,8 +78,7 @@ def get_artifact_source( """Catalog entry for a specific artifact""" if catalog is None: catalog = Catalog() - if collection is None: - collection = self.active_collection + collection = collection or self.active_collection if version is None: versions = [ instance.version @@ -119,8 +117,7 @@ def get_artifact_source( def collection_to_catalog(self, collection: Optional[str] = None) -> Catalog: """Construct a catalog listing artifacts within a specific collection.""" - if collection is None: - collection = self._active_collection + collection = collection or self.active_collection if collection not in self.list_collection_names(): raise ValueError(f"Collection {collection} does not exist.") artifact_names = [ @@ -171,8 +168,7 @@ def log_files( artifact_path: Optional[Path] = None, ) -> CatalogSource: """Upload a single file to artifact store without serialisation.""" - if collection is None: - collection = self._active_collection + collection = collection or self.active_collection artifact = wandb.Artifact(artifact_name, type=collection) if artifact_path is not None: artifact_path = str(artifact_path) @@ -193,8 +189,7 @@ def download_artifact( WandB serialised objects would be downloaded in a nested folder structure and are therefore discouraged right now. """ - if collection is None: - collection = self._active_collection + collection = collection or self.active_collection if version is None: version = "latest" if wandb.run is None: From 73f3754e659e8ee50c8db6980e47dd1e0698c98e Mon Sep 17 00:00:00 2001 From: Sebastian Schulze Date: Fri, 22 Dec 2023 23:23:17 +0100 Subject: [PATCH 41/41] Bump version and minor clean up --- poetry.lock | 6 +++--- pyproject.toml | 2 +- requirements.txt | 6 +++--- squirrel/artifact_manager/base.py | 16 ++++++++-------- squirrel/artifact_manager/drivers.py | 5 +++-- 5 files changed, 18 insertions(+), 17 deletions(-) diff --git a/poetry.lock b/poetry.lock index 3907849..32a33c2 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1987,13 +1987,13 @@ files = [ [[package]] name = "importlib-metadata" -version = "7.0.0" +version = "7.0.1" description = "Read metadata from Python packages" optional = false python-versions = ">=3.8" files = [ - {file = "importlib_metadata-7.0.0-py3-none-any.whl", hash = "sha256:d97503976bb81f40a193d41ee6570868479c69d5068651eb039c40d850c59d67"}, - {file = "importlib_metadata-7.0.0.tar.gz", hash = "sha256:7fc841f8b8332803464e5dc1c63a2e59121f46ca186c0e2e182e80bf8c1319f7"}, + {file = "importlib_metadata-7.0.1-py3-none-any.whl", hash = "sha256:4805911c3a4ec7c3966410053e9ec6a1fecd629117df5adee56dfc9432a1081e"}, + {file = "importlib_metadata-7.0.1.tar.gz", hash = "sha256:f238736bb06590ae52ac1fab06a3a9ef1d8dce2b7a35b5ab329371d6c8f5d2cc"}, ] [package.dependencies] diff --git a/pyproject.toml b/pyproject.toml index 6055838..dc954c5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "squirrel-core" -version = "0.19.6" +version = "0.19.7" description = "Squirrel is a Python library that enables ML teams to share, load, and transform data in a collaborative, flexible and efficient way." authors = ["Merantix Momentum"] license = "Apache 2.0" diff --git a/requirements.txt b/requirements.txt index 6d91f35..f228b2b 100644 --- a/requirements.txt +++ b/requirements.txt @@ -842,9 +842,9 @@ idna==3.6 ; python_version >= "3.8" and python_version < "4.0" \ imagesize==1.4.1 ; python_version >= "3.8" and python_version < "4.0" \ --hash=sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b \ --hash=sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a -importlib-metadata==7.0.0 ; python_version >= "3.8" and python_version < "4.0" \ - --hash=sha256:7fc841f8b8332803464e5dc1c63a2e59121f46ca186c0e2e182e80bf8c1319f7 \ - --hash=sha256:d97503976bb81f40a193d41ee6570868479c69d5068651eb039c40d850c59d67 +importlib-metadata==7.0.1 ; python_version >= "3.8" and python_version < "4.0" \ + --hash=sha256:4805911c3a4ec7c3966410053e9ec6a1fecd629117df5adee56dfc9432a1081e \ + --hash=sha256:f238736bb06590ae52ac1fab06a3a9ef1d8dce2b7a35b5ab329371d6c8f5d2cc importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.10" \ --hash=sha256:3893a00122eafde6894c59914446a512f728a0c1a45f9bb9b63721b6bacf0b4a \ --hash=sha256:e8bf90d8213b486f428c9c39714b920041cb02c184686a3dee24905aaa8105d6 diff --git a/squirrel/artifact_manager/base.py b/squirrel/artifact_manager/base.py index 317399b..8790a6b 100644 --- a/squirrel/artifact_manager/base.py +++ b/squirrel/artifact_manager/base.py @@ -14,8 +14,8 @@ class TmpArtifact: """ - Class to be used as a context for temporarily downloading an artifact, interacting with it and the deleting it. - When entering the scope it downloads the artifact to a local dir with a valid afid and returns the filepath to it. + Class to be used as a context for temporarily downloading an artifact, interacting with it and then deleting it. + When entering the scope it downloads the artifact to a local dir and returns the filepath to it. """ def __init__(self, artifact_manager: "ArtifactManager", collection: str, artifact: str, version: str) -> None: @@ -38,7 +38,7 @@ def __enter__(self) -> Path: """ Called when entering the context. Downloads the artifact to a temporary dir and returns the filepath to it. - Returns: Absolute path to artifact folder as str + Returns: Absolute path to artifact folder """ self.artifact_manager.download_artifact(self.artifact, self.collection, self.version, Path(self.tempdir.name)) return Path(self.tempdir.name, self.artifact) @@ -56,7 +56,7 @@ def __exit__( class DirectoryLogger: """ - Class to be used as a context for logging a directory as an artifact. + Class to be used as a context for logging an entire directory as an artifact. When entering the scope it creates a local dir with a valid afid and returns the filepath to it. You can then write files to that dir and after exiting the scope the dir gets logged through the artifact manager. """ @@ -75,14 +75,14 @@ def __init__(self, artifact_manager: "ArtifactManager", artifact: str, collectio self.collection = collection or artifact_manager.active_collection self.tempdir = tempfile.TemporaryDirectory() - def __enter__(self) -> str: + def __enter__(self) -> Path: """ Called when entering the context. Creates folder under /tmp with the artifacts id if it doesn't exist yet. Returns: Absolute path to artifact folder as str """ Path(self.tempdir.name, self.artifact).mkdir(exist_ok=False) - return str(Path(self.tempdir.name, self.artifact)) + return Path(self.tempdir.name, self.artifact) def __exit__( self, @@ -193,8 +193,8 @@ def download_artifact( """ Download artifact contents (from current collection) to specific location and return a source listing them. - If no target location is specified, a temporary directory is created and the path to it is returned. - Retrieve latest version unless specified. + If no target location is specified, a context manager for a temporary directory is created and the path to it + is returned. Retrieve latest version unless specified. """ raise NotImplementedError diff --git a/squirrel/artifact_manager/drivers.py b/squirrel/artifact_manager/drivers.py index bfb8f9d..843f79a 100644 --- a/squirrel/artifact_manager/drivers.py +++ b/squirrel/artifact_manager/drivers.py @@ -9,10 +9,11 @@ class DirectoryDriver(StoreDriver): name = "directory" def __init__(self, url: str, storage_options: Optional[dict[str, Any]] = None, **kwargs) -> None: - """Initializes FileSystemDriver. + """ + Initializes DirectoryDriver iterating over all files in the root directory. Args: - url (str): the url of the store + url (str): the root url of the store storage_options (dict[str, Any], optional): Keyword arguments passed to filesystem handler. **kwargs: Keyword arguments to pass to the super class initializer. """