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urllib3 = ">=1.26.15,<2.0.0" [[package]] name = "requests" -version = "2.32.2" +version = "2.32.3" description = "Python HTTP for Humans." optional = false python-versions = ">=3.8" files = [ - {file = "requests-2.32.2-py3-none-any.whl", hash = "sha256:fc06670dd0ed212426dfeb94fc1b983d917c4f9847c863f313c9dfaaffb7c23c"}, - {file = "requests-2.32.2.tar.gz", hash = "sha256:dd951ff5ecf3e3b3aa26b40703ba77495dab41da839ae72ef3c8e5d8e2433289"}, + {file = "requests-2.32.3-py3-none-any.whl", hash = "sha256:70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6"}, + {file = "requests-2.32.3.tar.gz", hash = "sha256:55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760"}, ] [package.dependencies] @@ -2132,13 +2152,13 @@ typing-extensions = ">=3.7.4.3" [[package]] name = "typing-extensions" -version = "4.12.0" +version = "4.12.2" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" files = [ - {file = 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"jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.12" -content-hash = "97d89818fdaabc1edec1e25d15cf7b108f022a04bff4d7d5b4806f973a8b81a9" +content-hash = "a22825dceb910ccb3f839cf20b9cff0eaa5772e345d980fc10aa7a8edf5a9bb6" diff --git a/pyproject.toml b/pyproject.toml index c264b48..e8ab25c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "graph-validation-test-runners" -version = "0.1.4" +version = "0.1.5" description = "Validation of Translator Knowledge Graphs - TRAPI, Biolink Model and One Hop navigation" authors = [ "Richard Bruskiewich ", @@ -54,7 +54,7 @@ tqdm = "^4.66.2" requests = "^2.31.0" matplotlib = "^3.8.3" -reasoner-validator = "^4.2.3" +reasoner-validator = "^4.2.4" translator-testing-model = "^0.3.1" [tool.poetry.group.dev.dependencies] diff --git a/requirements.txt b/requirements.txt index b36f810..1975368 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,15 +7,15 @@ anyio==4.4.0 ; python_version >= "3.9" and python_version < "3.12" \ attrs==23.2.0 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30 \ --hash=sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1 -bioregistry==0.11.6 ; python_version >= "3.9" and python_version < "3.12" \ - --hash=sha256:335647a54a7aef6e62545bf168f9a71ea05b56c35053babda294adb9b53c2a15 \ - --hash=sha256:b0f6dc7b6396d0257e25ce66bd8fcfae9a6a6e797114b0365d56341095cb1d28 -bmt==1.4.2 ; python_version >= "3.9" and python_version < "3.12" \ - --hash=sha256:488583cfccab0d733b18f524a896e771e648deea032ae9d434f06e83ea64d329 \ - --hash=sha256:bc0714fe9a4072edbdee3f95ef929d2254c039e663567f02185944b55666f7c4 -certifi==2024.2.2 ; python_version >= "3.9" and python_version < "3.12" \ - --hash=sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f \ - --hash=sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1 +bioregistry==0.11.9 ; python_version >= "3.9" and python_version < "3.12" \ + --hash=sha256:a89b88121759586fd599204d06bbbc453de9b134f8e7f0a86732c0b537022da5 \ + --hash=sha256:b46462ab37faceaab3493f006ec3bcc51f07401676aa90101a67247282c0ae48 +bmt==1.4.3 ; python_version >= "3.9" and python_version < "3.12" \ + --hash=sha256:96bb9a6a6b979e46432282ac52b96ae530b52cd31a6d650f9faadc2b56424be9 \ + --hash=sha256:a5cbae7918e481eba985fee2de01b7c4d5c6b8d5590b587f52852ad6e0e2ffff +certifi==2024.6.2 ; python_version >= "3.9" and python_version < "3.12" \ + --hash=sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516 \ + --hash=sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56 charset-normalizer==3.3.2 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:06435b539f889b1f6f4ac1758871aae42dc3a8c0e24ac9e60c2384973ad73027 \ --hash=sha256:06a81e93cd441c56a9b65d8e1d043daeb97a3d0856d177d5c90ba85acb3db087 \ @@ -179,9 +179,9 @@ dictdiffer==0.9.0 ; python_version >= "3.9" and python_version < "3.12" \ dnspython==2.6.1 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:5ef3b9680161f6fa89daf8ad451b5f1a33b18ae8a1c6778cdf4b43f08c0a6e50 \ --hash=sha256:e8f0f9c23a7b7cb99ded64e6c3a6f3e701d78f50c55e002b839dea7225cff7cc -email-validator==2.1.1 ; python_version >= "3.9" and python_version < "3.12" \ - --hash=sha256:200a70680ba08904be6d1eef729205cc0d687634399a5924d842533efb824b84 \ - --hash=sha256:97d882d174e2a65732fb43bfce81a3a834cbc1bde8bf419e30ef5ea976370a05 +email-validator==2.1.2 ; python_version >= "3.9" and python_version < "3.12" \ + --hash=sha256:14c0f3d343c4beda37400421b39fa411bbe33a75df20825df73ad53e06a9f04c \ + --hash=sha256:d89f6324e13b1e39889eab7f9ca2f91dc9aebb6fa50a6d8bd4329ab50f251115 exceptiongroup==1.2.1 ; python_version >= "3.9" and python_version < "3.11" \ --hash=sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad \ --hash=sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16 @@ -191,49 +191,49 @@ fastapi-cli==0.0.4 ; python_version >= "3.9" and python_version < "3.12" \ fastapi==0.111.0 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:97ecbf994be0bcbdadedf88c3150252bed7b2087075ac99735403b1b76cc8fc0 \ 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--hash=sha256:ba9f09ff17f947392a855e3455a846f9855f6cf6bec33e9a427d3c1d254c712f \ + --hash=sha256:bb7273789f69b565d88e97e9e1da602b4ee7ba733caf35a6c2affd4334d4f005 \ + --hash=sha256:bd5bc124fae781a4422f61b98d1d7faa47985f663a64770b78f13d2c072410c2 \ + --hash=sha256:bff98816cb144fb7b85e4b5ba3888a33b56ecef075b0e95b95bcd0a5fbf20f06 \ + --hash=sha256:c4ee5a24e281fbd8261c6ab29faa7fd9a87a12e8c0eed485b705236c65999109 \ + --hash=sha256:c93ed66d32de1559b6fc348838c7572d5c0ac1e4a258e76763a5caddd8944002 \ + --hash=sha256:d1a24f51a3305362b94681120c508758a88f207fa0a681c16b5a4172e9e6c7a9 \ + --hash=sha256:d8f191a17369bd53a5557a5ee4bab91d5330ca3aefcdf17fab9a497b0e7cff7a \ + --hash=sha256:daaef7390e632283051e3cf3e16aff2b68b247e99aea916f64e578c0449c9c68 \ + --hash=sha256:e40013572bfb843d6794a3ce076c29ef4efd15937ab833f520117f8eccc84fd6 \ + --hash=sha256:eceef49f457253000e6a2d0f7bd08ff4e9fe96ec4ffce2dbcb32e34d9c1b8161 \ + --hash=sha256:ee595d7ba9bba130b2bec555a40aafa60c26ce68ed0cf509983e0f12d88674fd \ + --hash=sha256:ef50ec31649fbc3acf6afd261ed89d09eb909b97cc289d80476166df8438524d \ + --hash=sha256:fa1f3e34373aa16045484b4d9d352d4c6b5f9f77ac77a178252ccbc851e8b2ee \ + --hash=sha256:fca66d9ff2ac89b03f5aa17e0b21a97c21f3491c46b583bb131eb32c7bab33af h11==0.14.0 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d \ --hash=sha256:e3fe4ac4b851c468cc8363d500db52c2ead036020723024a109d37346efaa761 @@ -412,9 +412,9 @@ kiwisolver==1.4.5 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:fcc700eadbbccbf6bc1bcb9dbe0786b4b1cb91ca0dcda336eef5c2beed37b797 \ --hash=sha256:fd32ea360bcbb92d28933fc05ed09bffcb1704ba3fc7942e81db0fd4f81a7892 \ --hash=sha256:fdb7adb641a0d13bdcd4ef48e062363d8a9ad4a182ac7647ec88f695e719ae9f -linkml-runtime==1.7.5 ; python_version >= "3.9" and python_version < "3.12" \ - --hash=sha256:b31197a5398359441ae1ed43470c54377a1d08db961366dda670300dddcd71d7 \ - --hash=sha256:c58000c7c68fa97b7d76c50421a85a64e25f07eec5bcac464bc00c4cd79007a6 +linkml-runtime==1.7.7 ; python_version >= "3.9" and python_version < "3.12" \ + --hash=sha256:1556db30cda1191de2f70c3b949eb45c31b2ed66ca525bf38ee99f992f2451d7 \ + --hash=sha256:f471b765056b38ff3eb1372d167b86a67e188ef472c16abf4f6cd91097a82a11 markdown-it-py==3.0.0 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1 \ --hash=sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb @@ -515,96 +515,105 @@ mdurl==0.1.2 ; python_version >= "3.9" and python_version < "3.12" \ more-click==0.1.2 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:085da66d5a9b823c5d912a888dca1fa0c8b3a14ed1b21ea9c8a1b814857a3981 \ --hash=sha256:f6387af37ef7e7423bd94b72a81a53c79c5086a3bfe5cc035da534ff0c2a0a9e -numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.12" \ - 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--hash=sha256:1e2722cc9fbb45d9b87631ac70924c11d3a401b2d7f410cc0e3bbf249f2dca62 \ --hash=sha256:1fe35611261b29bd1de0070f0b2f47cb6ff71fa6595c077e42bd0c419fa27b98 \ --hash=sha256:28c119d996beec18c05208a8bd78cbe4007878c6dd15091efb73a30e90539696 \ + --hash=sha256:326c013efe8048858a6d312ddd31d56e468118ad4cdeda36c719bf5bb6192290 \ + --hash=sha256:40df9b996c2b73138957fe23a16a4f0ba614f4c0efce1e9406a184b6d07fa3a9 \ --hash=sha256:42f8152b8dbc4fe7d96729ec2b99c7097d656dc1213a3229ca5383f973a5ed6d \ + --hash=sha256:49a183be227561de579b4a36efbb21b3eab9651dd81b1858589f796549873dd6 \ --hash=sha256:4fb147e7a67ef577a588a0e2c17b6db51dda102c71de36f8549b6816a96e1867 \ --hash=sha256:50550eb667afee136e9a77d6dc71ae76a44df8b3e51e41b77f6de2932bfe0f47 \ --hash=sha256:510c9deebc5c0225e8c96813043e62b680ba2f9c50a08d3724c7f28a747d1486 \ @@ -875,11 +889,15 @@ pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:596106435fa6ad000c2991a98fa58eeb8656ef2325d7e158344fb33864ed87e3 \ --hash=sha256:6965a7bc3cf88e5a1c3bd2e0b5c22f8d677dc88a455344035f03399034eb3007 \ --hash=sha256:69b023b2b4daa7548bcfbd4aa3da05b3a74b772db9e23b982788168117739938 \ + --hash=sha256:6c22bec3fbe2524cde73d7ada88f6566758a8f7227bfbf93a408a9d86bcc12a0 \ --hash=sha256:704219a11b772aea0d8ecd7058d0082713c3562b4e271b849ad7dc4a5c90c13c \ --hash=sha256:7e07cbde391ba96ab58e532ff4803f79c4129397514e1413a7dc761ccd755735 \ --hash=sha256:81e0b275a9ecc9c0c0c07b4b90ba548307583c125f54d5b6946cfee6360c733d \ + --hash=sha256:855fb52b0dc35af121542a76b9a84f8d1cd886ea97c84703eaa6d88e37a2ad28 \ + --hash=sha256:8d4e9c88387b0f5c7d5f281e55304de64cf7f9c0021a3525bd3b1c542da3b0e4 \ --hash=sha256:9046c58c4395dff28dd494285c82ba00b546adfc7ef001486fbf0324bc174fba \ --hash=sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8 \ + --hash=sha256:a08c6f0fe150303c1c6b71ebcd7213c2858041a7e01975da3a99aed1e7a378ef \ --hash=sha256:a0cd17c15d3bb3fa06978b4e8958dcdc6e0174ccea823003a106c7d4d7899ac5 \ --hash=sha256:afd7e57eddb1a54f0f1a974bc4391af8bcce0b444685d936840f125cf046d5bd \ --hash=sha256:b1275ad35a5d18c62a7220633c913e1b42d44b46ee12554e5fd39c70a243d6a3 \ @@ -892,7 +910,9 @@ pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43 \ --hash=sha256:c8098ddcc2a85b61647b2590f825f3db38891662cfc2fc776415143f599bb859 \ --hash=sha256:d2b04aac4d386b172d5b9692e2d2da8de7bfb6c387fa4f801fbf6fb2e6ba4673 \ + --hash=sha256:d483d2cdf104e7c9fa60c544d92981f12ad66a457afae824d146093b8c294c54 \ --hash=sha256:d858aa552c999bc8a8d57426ed01e40bef403cd8ccdd0fc5f6f04a00414cac2a \ + --hash=sha256:e7d73685e87afe9f3b36c799222440d6cf362062f78be1013661b00c5c6f678b \ --hash=sha256:f003ed9ad21d6a4713f0a9b5a7a0a79e08dd0f221aff4525a2be4c346ee60aab \ --hash=sha256:f22ac1c3cac4dbc50079e965eba2c1058622631e526bd9afd45fedd49ba781fa \ --hash=sha256:faca3bdcf85b2fc05d06ff3fbc1f83e1391b3e724afa3feba7d13eeab355484c \ @@ -902,12 +922,12 @@ pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "3.12" \ rdflib==7.0.0 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:0438920912a642c866a513de6fe8a0001bd86ef975057d6962c79ce4771687cd \ --hash=sha256:9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae -reasoner-validator==4.2.3 ; python_version >= "3.9" and python_version < "3.12" \ - --hash=sha256:2cdecf7a249d26f4fa6746c0e0e919c2b00863a4cc1cf4a7041ab4157b107220 \ - --hash=sha256:368c073eabc06233d3390b3b088d3c30ba441b6a93593b8ecceebdab6e49a426 -requests==2.32.2 ; python_version >= "3.9" and python_version < "3.12" \ - --hash=sha256:dd951ff5ecf3e3b3aa26b40703ba77495dab41da839ae72ef3c8e5d8e2433289 \ - --hash=sha256:fc06670dd0ed212426dfeb94fc1b983d917c4f9847c863f313c9dfaaffb7c23c +reasoner-validator==4.2.4 ; python_version >= "3.9" and python_version < "3.12" \ + --hash=sha256:44ef9d50f1aa07951f5f70303531c26d45e232bc44032ba337a0d661c84670bb \ + --hash=sha256:9851407a444b1de6c31c1594650a6f6d577dad22e5eb6c83a5022f35a3d366fa +requests==2.32.3 ; python_version >= "3.9" and python_version < "3.12" \ + --hash=sha256:55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760 \ + --hash=sha256:70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6 rich==13.7.1 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:4edbae314f59eb482f54e9e30bf00d33350aaa94f4bfcd4e9e3110e64d0d7222 \ --hash=sha256:9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432 @@ -940,9 +960,9 @@ translator-testing-model==0.3.2 ; python_version >= "3.9" and python_version < " typer==0.12.3 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:070d7ca53f785acbccba8e7d28b08dcd88f79f1fbda035ade0aecec71ca5c914 \ --hash=sha256:49e73131481d804288ef62598d97a1ceef3058905aa536a1134f90891ba35482 -typing-extensions==4.12.0 ; python_version >= "3.9" and python_version < "3.12" \ - --hash=sha256:8cbcdc8606ebcb0d95453ad7dc5065e6237b6aa230a31e81d0f440c30fed5fd8 \ - --hash=sha256:b349c66bea9016ac22978d800cfff206d5f9816951f12a7d0ec5578b0a819594 +typing-extensions==4.12.2 ; python_version >= "3.9" and python_version < "3.12" \ + --hash=sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d \ + --hash=sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8 tzdata==2024.1 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd \ --hash=sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252 @@ -1025,12 +1045,12 @@ ujson==5.10.0 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:f77b74475c462cb8b88680471193064d3e715c7c6074b1c8c412cb526466efe9 \ --hash=sha256:f8ccb77b3e40b151e20519c6ae6d89bfe3f4c14e8e210d910287f778368bb3d1 \ --hash=sha256:fbd8fd427f57a03cff3ad6574b5e299131585d9727c8c366da4624a9069ed746 -urllib3==1.26.18 ; python_version >= "3.9" and python_version < "3.12" \ - --hash=sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07 \ - --hash=sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0 -uvicorn[standard]==0.30.0 ; python_version >= "3.9" and python_version < "3.12" \ - --hash=sha256:78fa0b5f56abb8562024a59041caeb555c86e48d0efdd23c3fe7de7a4075bdab \ - --hash=sha256:f678dec4fa3a39706bbf49b9ec5fc40049d42418716cea52b53f07828a60aa37 +urllib3==1.26.19 ; python_version >= "3.9" and python_version < "3.12" \ + --hash=sha256:37a0344459b199fce0e80b0d3569837ec6b6937435c5244e7fd73fa6006830f3 \ + --hash=sha256:3e3d753a8618b86d7de333b4223005f68720bcd6a7d2bcb9fbd2229ec7c1e429 +uvicorn[standard]==0.30.1 ; python_version >= "3.9" and python_version < "3.12" \ + --hash=sha256:cd17daa7f3b9d7a24de3617820e634d0933b69eed8e33a516071174427238c81 \ + --hash=sha256:d46cd8e0fd80240baffbcd9ec1012a712938754afcf81bce56c024c1656aece8 uvloop==0.19.0 ; (sys_platform != "win32" and sys_platform != "cygwin") and platform_python_implementation != "PyPy" and python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:0246f4fd1bf2bf702e06b0d45ee91677ee5c31242f39aab4ea6fe0c51aedd0fd \ --hash=sha256:02506dc23a5d90e04d4f65c7791e65cf44bd91b37f24cfc3ef6cf2aff05dc7ec \ @@ -1283,6 +1303,6 @@ wrapt==1.16.0 ; python_version >= "3.9" and python_version < "3.12" \ --hash=sha256:f6b2d0c6703c988d334f297aa5df18c45e97b0af3679bb75059e0e0bd8b1069d \ --hash=sha256:f8212564d49c50eb4565e502814f694e240c55551a5f1bc841d4fcaabb0a9b8a \ --hash=sha256:ffa565331890b90056c01db69c0fe634a776f8019c143a5ae265f9c6bc4bd6d4 -zipp==3.19.0 ; python_version >= "3.9" and python_version < "3.10" \ - --hash=sha256:952df858fb3164426c976d9338d3961e8e8b3758e2e059e0f754b8c4262625ee \ - --hash=sha256:96dc6ad62f1441bcaccef23b274ec471518daf4fbbc580341204936a5a3dddec +zipp==3.19.2 ; python_version >= "3.9" and python_version < "3.10" \ + --hash=sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19 \ + --hash=sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c