From 5cd2b50afc289a1bd956311e5e9a35917946adb8 Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Fri, 5 Oct 2018 11:58:54 -0700 Subject: [PATCH 01/15] initial stab at mkdocs --- Pipfile | 13 +++++ Pipfile.lock | 125 ++++++++++++++++++++++++++++++++++++++++++++ circleci/config.yml | 26 +++++++++ mkdocs.yml | 18 +++++++ src/index.md | 3 ++ 5 files changed, 185 insertions(+) create mode 100644 Pipfile create mode 100644 Pipfile.lock create mode 100644 circleci/config.yml create mode 100644 mkdocs.yml create mode 100644 src/index.md diff --git a/Pipfile b/Pipfile new file mode 100644 index 0000000000..af8e8060a2 --- /dev/null +++ b/Pipfile @@ -0,0 +1,13 @@ +[[source]] +url = "https://pypi.org/simple" +verify_ssl = true +name = "pypi" + +[packages] +mkdocs = "==1.0.4" +mkdocs-material = "==3.0.4" + +[dev-packages] + +[requires] +python_version = "3.6" diff --git a/Pipfile.lock b/Pipfile.lock new file mode 100644 index 0000000000..27ed029995 --- /dev/null +++ b/Pipfile.lock @@ -0,0 +1,125 @@ +{ + "_meta": { + "hash": { + "sha256": "580a32c021d6bda5d1823a0bfb462bfbb5dfaa567bcef30b058c3af80cb67896" + }, + "pipfile-spec": 6, + "requires": { + "python_version": "3.6" + }, + "sources": [ + { + "name": "pypi", + "url": "https://pypi.org/simple", + "verify_ssl": true + } + ] + }, + "default": { + "click": { + "hashes": [ + "sha256:2335065e6395b9e67ca716de5f7526736bfa6ceead690adf616d925bdc622b13", + "sha256:5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7" + ], + "markers": "python_version != '3.0.*' and python_version != '3.3.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.2.*'", + "version": "==7.0" + }, + "jinja2": { + "hashes": [ + "sha256:74c935a1b8bb9a3947c50a54766a969d4846290e1e788ea44c1392163723c3bd", + "sha256:f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4" + ], + "version": "==2.10" + }, + "livereload": { + "hashes": [ + "sha256:583179dc8d49b040a9da79bd33de59e160d2a8802b939e304eb359a4419f6498", + "sha256:dd4469a8f5a6833576e9f5433f1439c306de15dbbfeceabd32479b1123380fa5" + ], + "markers": "python_version != '3.0.*' and python_version != '3.3.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.2.*'", + "version": "==2.5.2" + }, + "markdown": { + "hashes": [ + "sha256:c00429bd503a47ec88d5e30a751e147dcb4c6889663cd3e2ba0afe858e009baa", + "sha256:d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c" + ], + "markers": "python_version != '3.0.*' and python_version != '3.3.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.2.*'", + "version": "==3.0.1" + }, + "markupsafe": { + "hashes": [ + "sha256:a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665" + ], + "version": "==1.0" + }, + "mkdocs": { + "hashes": [ + "sha256:17d34329aad75d5de604b9ed4e31df3a4d235afefdc46ce7b1964fddb2e1e939", + "sha256:8cc8b38325456b9e942c981a209eaeb1e9f3f77b493ad755bfef889b9c8d356a" + ], + "index": "pypi", + "version": "==1.0.4" + }, + "mkdocs-material": { + "hashes": [ + "sha256:2f6987ee2c70f9da0870079a4626f2d309f8528806f08e1a7da842b6c58e7c5c", + "sha256:3905942fc8e659bd690420f5fd56bc1f31505067b574377aa8508011389696f0" + ], + "index": "pypi", + "version": "==3.0.4" + }, + "pygments": { + "hashes": [ + "sha256:78f3f434bcc5d6ee09020f92ba487f95ba50f1e3ef83ae96b9d5ffa1bab25c5d", + "sha256:dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc" + ], + "version": "==2.2.0" + }, + "pymdown-extensions": { + "hashes": [ + "sha256:2e1d8f4a4c351cfa6c5ad88a0f2f4a3a30af481a942fdf8f9db0936e12ff37c2", + "sha256:54675680f6ad3ee8242fcb8926703b30ea3dcbeb9e21b7f7f19077f0ec982a82" + ], + "markers": "python_version != '3.0.*' and python_version != '3.3.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.2.*'", + "version": "==5.0" + }, + "pyyaml": { + "hashes": [ + "sha256:3d7da3009c0f3e783b2c873687652d83b1bbfd5c88e9813fb7e5b03c0dd3108b", + "sha256:3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf", + "sha256:40c71b8e076d0550b2e6380bada1f1cd1017b882f7e16f09a65be98e017f211a", + "sha256:558dd60b890ba8fd982e05941927a3911dc409a63dcb8b634feaa0cda69330d3", + "sha256:a7c28b45d9f99102fa092bb213aa12e0aaf9a6a1f5e395d36166639c1f96c3a1", + "sha256:aa7dd4a6a427aed7df6fb7f08a580d68d9b118d90310374716ae90b710280af1", + "sha256:bc558586e6045763782014934bfaf39d48b8ae85a2713117d16c39864085c613", + "sha256:d46d7982b62e0729ad0175a9bc7e10a566fc07b224d2c79fafb5e032727eaa04", + "sha256:d5eef459e30b09f5a098b9cea68bebfeb268697f78d647bd255a085371ac7f3f", + "sha256:e01d3203230e1786cd91ccfdc8f8454c8069c91bee3962ad93b87a4b2860f537", + "sha256:e170a9e6fcfd19021dd29845af83bb79236068bf5fd4df3327c1be18182b2531" + ], + "version": "==3.13" + }, + "six": { + "hashes": [ + "sha256:70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9", + "sha256:832dc0e10feb1aa2c68dcc57dbb658f1c7e65b9b61af69048abc87a2db00a0eb" + ], + "version": "==1.11.0" + }, + "tornado": { + "hashes": [ + "sha256:0662d28b1ca9f67108c7e3b77afabfb9c7e87bde174fbda78186ecedc2499a9d", + "sha256:4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409", + "sha256:732e836008c708de2e89a31cb2fa6c0e5a70cb60492bee6f1ea1047500feaf7f", + "sha256:8154ec22c450df4e06b35f131adc4f2f3a12ec85981a203301d310abf580500f", + "sha256:8e9d728c4579682e837c92fdd98036bd5cdefa1da2aaf6acf26947e6dd0c01c5", + "sha256:d4b3e5329f572f055b587efc57d29bd051589fb5a43ec8898c77a47ec2fa2bbb", + "sha256:e5f2585afccbff22390cddac29849df463b252b711aa2ce7c5f3f342a5b3b444" + ], + "markers": "python_version != '3.0.*' and python_version != '3.3.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.2.*'", + "version": "==5.1.1" + } + }, + "develop": {} +} diff --git a/circleci/config.yml b/circleci/config.yml new file mode 100644 index 0000000000..56dbaa2dd6 --- /dev/null +++ b/circleci/config.yml @@ -0,0 +1,26 @@ +version: 2 +jobs: + build-docs: + docker: + - image: circleci/python:3.6.6 + steps: + - checkout + - run: sudo chown -R circleci:circleci /usr/local/bin + - run: sudo chown -R circleci:circleci /usr/local/lib/python3.6/site-packages + - restore_cache: # ensure this step occurs *before* installing dependencies + key: deps9-{{ .Branch }}-{{ checksum "Pipfile.lock" }} + - run: + command: | + sudo pip install pipenv + pipenv install + - save_cache: + key: deps9-{{ .Branch }}-{{ checksum "Pipfile.lock" }} + paths: + - ".venv" + - "/usr/local/bin" + - "/usr/local/lib/python3.6/site-packages" + - run: + name: generate docs + command: pipenv run mkdocs build --clean --strict --verbose + - store_artifacts: + path: site diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000000..c58c0be714 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,18 @@ +site_name: Brain Imaging Data Structure +theme: material +plugins: + - search +docs_dir: 'src' +nav: + - About: index.md + - Specification: + - Introduction: 01-introduction.md + - Common principles: 02-common-principles.md + - Modality agnostic files: 03-modality-agnostic-files.md + - Modality specific files: + - Magnetic Resonance Imaging: 04-modality-specific-files/01-magnetic-resonance-imaging-data.md + - Magnetoencephalography: 04-modality-specific-files/02-magnetoencephalography.md + - Task events: 04-modality-specific-files/03-task-events.md + - Physiological and other continous recordings: 04-modality-specific-files/04-physiological-and-other-continous-recordings.md + - Behavioral experiments (with no MRI): 04-modality-specific-files/05-behavioural-experiments.md + - Longitudinal and multi-site studies: 05-longitudinal-and-multi-site-studies.md diff --git a/src/index.md b/src/index.md new file mode 100644 index 0000000000..b55e16cb17 --- /dev/null +++ b/src/index.md @@ -0,0 +1,3 @@ +# Brain Imaging Data Structure + +Placeholder for the instroduction to the project From a74d20116ddbe4921e409acb6ab343b3ced325af Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Fri, 5 Oct 2018 12:02:40 -0700 Subject: [PATCH 02/15] circle trigger --- src/index.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/index.md b/src/index.md index b55e16cb17..eae94ab702 100644 --- a/src/index.md +++ b/src/index.md @@ -1,3 +1,4 @@ # Brain Imaging Data Structure -Placeholder for the instroduction to the project +Placeholder for the instroduction to the project. Mkdocs requires an index.md +file which becomes the landing page. From dd02f98c4376a80c63359b7dfcc8739665fb6468 Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Fri, 5 Oct 2018 12:06:06 -0700 Subject: [PATCH 03/15] circle config fix --- {circleci => .circleci}/config.yml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {circleci => .circleci}/config.yml (100%) diff --git a/circleci/config.yml b/.circleci/config.yml similarity index 100% rename from circleci/config.yml rename to .circleci/config.yml From f45021b8c22b2e6f6b4762b06c955834838d8e81 Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Fri, 5 Oct 2018 12:08:13 -0700 Subject: [PATCH 04/15] default job name --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 56dbaa2dd6..3ef7940f09 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -1,6 +1,6 @@ version: 2 jobs: - build-docs: + build: docker: - image: circleci/python:3.6.6 steps: From 9fd1af52f01a2e4925ac6db81edb4b3997a9b0bb Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Fri, 5 Oct 2018 12:16:06 -0700 Subject: [PATCH 05/15] urls to make circle artifacts work --- mkdocs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/mkdocs.yml b/mkdocs.yml index c58c0be714..d44648b2c1 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -3,6 +3,7 @@ theme: material plugins: - search docs_dir: 'src' +use_directory_urls: false nav: - About: index.md - Specification: From b8b61bb6578935694a0768710cc0bef08e7b40bd Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Fri, 5 Oct 2018 12:26:43 -0700 Subject: [PATCH 06/15] PDF export --- .circleci/config.yml | 5 ++ Pipfile | 1 + Pipfile.lock | 171 ++++++++++++++++++++++++++++++++++++++++++- mkdocs.yml | 4 +- 4 files changed, 179 insertions(+), 2 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 3ef7940f09..443e74f086 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -9,6 +9,11 @@ jobs: - run: sudo chown -R circleci:circleci /usr/local/lib/python3.6/site-packages - restore_cache: # ensure this step occurs *before* installing dependencies key: deps9-{{ .Branch }}-{{ checksum "Pipfile.lock" }} + - run: | + sudo apt-get install build-essential python3-dev python3-pip \ + python3-setuptools python3-wheel python3-cffi \ + libcairo2 libpango-1.0-0 libpangocairo-1.0-0 \ + libgdk-pixbuf2.0-0 libffi-dev shared-mime-info - run: command: | sudo pip install pipenv diff --git a/Pipfile b/Pipfile index af8e8060a2..8555e74fb7 100644 --- a/Pipfile +++ b/Pipfile @@ -6,6 +6,7 @@ name = "pypi" [packages] mkdocs = "==1.0.4" mkdocs-material = "==3.0.4" +mkdocs-pdf-export-plugin = "*" [dev-packages] diff --git a/Pipfile.lock b/Pipfile.lock index 27ed029995..de26ed7747 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "580a32c021d6bda5d1823a0bfb462bfbb5dfaa567bcef30b058c3af80cb67896" + "sha256": "02c8775b26cf90ce86f0fe8f644c48f8f784673bc04882769fec628af801a058" }, "pipfile-spec": 6, "requires": { @@ -16,6 +16,67 @@ ] }, "default": { + "beautifulsoup4": { + "hashes": [ + "sha256:194ec62a25438adcb3fdb06378b26559eda1ea8a747367d34c33cef9c7f48d57", + "sha256:90f8e61121d6ae58362ce3bed8cd997efb00c914eae0ff3d363c32f9a9822d10", + "sha256:f0abd31228055d698bb392a826528ea08ebb9959e6bea17c606fd9c9009db938" + ], + "version": "==4.6.3" + }, + "cairocffi": { + "hashes": [ + "sha256:15386c3a9e08823d6826c4491eaccc7b7254b1dc587a3b9ce60c350c3f990337" + ], + "markers": "python_version != '3.2.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.3.*' and python_version != '3.0.*'", + "version": "==0.9.0" + }, + "cairosvg": { + "hashes": [ + "sha256:93c5b3204478c4e20c4baeb33807db5311b4420c21db2f21034a6deda998cb14", + "sha256:f331e6024ee4c7f3eca3b0caa909dd893fa4d7414f50a6b206acbe2df20d95a9" + ], + "markers": "python_version >= '3.0'", + "version": "==2.2.1" + }, + "cffi": { + "hashes": [ + "sha256:151b7eefd035c56b2b2e1eb9963c90c6302dc15fbd8c1c0a83a163ff2c7d7743", + "sha256:1553d1e99f035ace1c0544050622b7bc963374a00c467edafac50ad7bd276aef", + "sha256:1b0493c091a1898f1136e3f4f991a784437fac3673780ff9de3bcf46c80b6b50", + "sha256:2ba8a45822b7aee805ab49abfe7eec16b90587f7f26df20c71dd89e45a97076f", + "sha256:3bb6bd7266598f318063e584378b8e27c67de998a43362e8fce664c54ee52d30", + "sha256:3c85641778460581c42924384f5e68076d724ceac0f267d66c757f7535069c93", + "sha256:3eb6434197633b7748cea30bf0ba9f66727cdce45117a712b29a443943733257", + "sha256:495c5c2d43bf6cebe0178eb3e88f9c4aa48d8934aa6e3cddb865c058da76756b", + "sha256:4c91af6e967c2015729d3e69c2e51d92f9898c330d6a851bf8f121236f3defd3", + "sha256:57b2533356cb2d8fac1555815929f7f5f14d68ac77b085d2326b571310f34f6e", + "sha256:770f3782b31f50b68627e22f91cb182c48c47c02eb405fd689472aa7b7aa16dc", + "sha256:79f9b6f7c46ae1f8ded75f68cf8ad50e5729ed4d590c74840471fc2823457d04", + "sha256:7a33145e04d44ce95bcd71e522b478d282ad0eafaf34fe1ec5bbd73e662f22b6", + "sha256:857959354ae3a6fa3da6651b966d13b0a8bed6bbc87a0de7b38a549db1d2a359", + "sha256:87f37fe5130574ff76c17cab61e7d2538a16f843bb7bca8ebbc4b12de3078596", + "sha256:95d5251e4b5ca00061f9d9f3d6fe537247e145a8524ae9fd30a2f8fbce993b5b", + "sha256:9d1d3e63a4afdc29bd76ce6aa9d58c771cd1599fbba8cf5057e7860b203710dd", + "sha256:a36c5c154f9d42ec176e6e620cb0dd275744aa1d804786a71ac37dc3661a5e95", + "sha256:a6a5cb8809091ec9ac03edde9304b3ad82ad4466333432b16d78ef40e0cce0d5", + "sha256:ae5e35a2c189d397b91034642cb0eab0e346f776ec2eb44a49a459e6615d6e2e", + "sha256:b0f7d4a3df8f06cf49f9f121bead236e328074de6449866515cea4907bbc63d6", + "sha256:b75110fb114fa366b29a027d0c9be3709579602ae111ff61674d28c93606acca", + "sha256:ba5e697569f84b13640c9e193170e89c13c6244c24400fc57e88724ef610cd31", + "sha256:be2a9b390f77fd7676d80bc3cdc4f8edb940d8c198ed2d8c0be1319018c778e1", + "sha256:ca1bd81f40adc59011f58159e4aa6445fc585a32bb8ac9badf7a2c1aa23822f2", + "sha256:d5d8555d9bfc3f02385c1c37e9f998e2011f0db4f90e250e5bc0c0a85a813085", + "sha256:e55e22ac0a30023426564b1059b035973ec82186ddddbac867078435801c7801", + "sha256:e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4", + "sha256:ecbb7b01409e9b782df5ded849c178a0aa7c906cf8c5a67368047daab282b184", + "sha256:ed01918d545a38998bfa5902c7c00e0fee90e957ce036a4000a88e3fe2264917", + "sha256:edabd457cd23a02965166026fd9bfd196f4324fe6032e866d0f3bd0301cd486f", + "sha256:fdf1c1dc5bafc32bc5d08b054f94d659422b05aba244d6be4ddc1c72d9aa70fb" + ], + "markers": "python_version != '3.2.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.3.*' and python_version != '3.0.*'", + "version": "==1.11.5" + }, "click": { "hashes": [ "sha256:2335065e6395b9e67ca716de5f7526736bfa6ceead690adf616d925bdc622b13", @@ -24,6 +85,27 @@ "markers": "python_version != '3.0.*' and python_version != '3.3.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.2.*'", "version": "==7.0" }, + "cssselect2": { + "hashes": [ + "sha256:267eebc7378ade2e8be710cd0179606ad9c95ecc673138fccfcfba42c5ce153d", + "sha256:505d2ce3d3a1d390ddb52f7d0864b7efeb115a5b852a91861b498b92424503ab" + ], + "version": "==0.2.1" + }, + "defusedxml": { + "hashes": [ + "sha256:24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4", + "sha256:702a91ade2968a82beb0db1e0766a6a273f33d4616a6ce8cde475d8e09853b20" + ], + "version": "==0.5.0" + }, + "html5lib": { + "hashes": [ + "sha256:20b159aa3badc9d5ee8f5c647e5efd02ed2a66ab8d354930bd9ff139fc1dc0a3", + "sha256:66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736" + ], + "version": "==1.0.1" + }, "jinja2": { "hashes": [ "sha256:74c935a1b8bb9a3947c50a54766a969d4846290e1e788ea44c1392163723c3bd", @@ -69,6 +151,64 @@ "index": "pypi", "version": "==3.0.4" }, + "mkdocs-pdf-export-plugin": { + "hashes": [ + "sha256:58856671dbaba1686f684cbda666676bb15793b568e47de8b2ea99157178093f", + "sha256:acbecb5826d1cc1835c6d1fa8f9c675e1bdb11eccfdb1bc2ff5f7a346d21b46d" + ], + "index": "pypi", + "version": "==0.3.0" + }, + "pdfrw": { + "hashes": [ + "sha256:0dc0494a0e6561b268542b28ede2280387c2728114f117d3bb5d8e4787b93ef4", + "sha256:758289edaa3b672e9a1a67504be73c18ec668d4e5b9d5ac9cbc0dc753d8d196b" + ], + "version": "==0.4" + }, + "pillow": { + "hashes": [ + "sha256:00203f406818c3f45d47bb8fe7e67d3feddb8dcbbd45a289a1de7dd789226360", + "sha256:0616f800f348664e694dddb0b0c88d26761dd5e9f34e1ed7b7a7d2da14b40cb7", + "sha256:1f7908aab90c92ad85af9d2fec5fc79456a89b3adcc26314d2cde0e238bd789e", + "sha256:2ea3517cd5779843de8a759c2349a3cd8d3893e03ab47053b66d5ec6f8bc4f93", + "sha256:48a9f0538c91fc136b3a576bee0e7cd174773dc9920b310c21dcb5519722e82c", + "sha256:5280ebc42641a1283b7b1f2c20e5b936692198b9dd9995527c18b794850be1a8", + "sha256:5e34e4b5764af65551647f5cc67cf5198c1d05621781d5173b342e5e55bf023b", + "sha256:63b120421ab85cad909792583f83b6ca3584610c2fe70751e23f606a3c2e87f0", + "sha256:696b5e0109fe368d0057f484e2e91717b49a03f1e310f857f133a4acec9f91dd", + 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"sha256:c2b62d3df80e694c0e4a0ed47754c9480521e25642251b3ab1dff050a4e60409", + "sha256:c5e2be6c263b64f6f7656e23e18a4a9980cffc671442795682e8c4e4f815dd9f", + "sha256:c99aa3c63104e0818ec566f8ff3942fb7c7a8f35f9912cb63fd8e12318b214b2", + "sha256:dae06620d3978da346375ebf88b9e2dd7d151335ba668c995aea9ed07af7add4", + "sha256:db5499d0710823fa4fb88206050d46544e8f0e0136a9a5f5570b026584c8fd74", + "sha256:f36baafd82119c4a114b9518202f2a983819101dcc14b26e43fc12cbefdce00e", + "sha256:f52b79c8796d81391ab295b04e520bda6feed54d54931708872e8f9ae9db0ea1", + "sha256:ff8cff01582fa1a7e533cb97f628531c4014af4b5f38e33cdcfe5eec29b6d888" + ], + "markers": "python_version != '3.2.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.3.*' and python_version != '3.0.*'", + "version": "==5.3.0" + }, + "pycparser": { + "hashes": [ + "sha256:a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3" + ], + "markers": "python_version != '3.2.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.3.*' and python_version != '3.0.*'", + "version": "==2.19" + }, "pygments": { "hashes": [ "sha256:78f3f434bcc5d6ee09020f92ba487f95ba50f1e3ef83ae96b9d5ffa1bab25c5d", @@ -84,6 +224,13 @@ "markers": "python_version != '3.0.*' and python_version != '3.3.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.2.*'", "version": "==5.0" }, + "pyphen": { + "hashes": [ + "sha256:3b633a50873156d777e1f1075ba4d8e96a6ad0a3ca42aa3ea9a6259f93f18921", + "sha256:e172faf10992c8c9d369bdc83e36dbcf1121f4ed0d881f1a0b521935aee583b5" + ], + "version": "==0.9.5" + }, "pyyaml": { "hashes": [ "sha256:3d7da3009c0f3e783b2c873687652d83b1bbfd5c88e9813fb7e5b03c0dd3108b", @@ -107,6 +254,13 @@ ], "version": "==1.11.0" }, + "tinycss2": { + "hashes": [ + "sha256:5e881eaa263bf4dc5c050d43cd6d2203ade1e3a3cda61f5511cf878972e83b78", + "sha256:7c53c2c0e914c7711c295b3101bcc78e0b7eda23ff20228a936efe11cdcc7136" + ], + "version": "==0.6.1" + }, "tornado": { "hashes": [ "sha256:0662d28b1ca9f67108c7e3b77afabfb9c7e87bde174fbda78186ecedc2499a9d", @@ -119,6 +273,21 @@ ], "markers": "python_version != '3.0.*' and python_version != '3.3.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.2.*'", "version": "==5.1.1" + }, + "weasyprint": { + "hashes": [ + "sha256:4d35e37cf9d2cea199ddfe4b038c80024619e8a05a2f2eb99b80a2bfb6063eb7", + "sha256:a9d198afb74cf4f29275cca7dc5d42eafd2d6abed3edb76c2d0d0429fead3907" + ], + "markers": "python_version != '3.2.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.3.*' and python_version != '3.0.*'", + "version": "==0.42.3" + }, + "webencodings": { + "hashes": [ + "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78", + "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923" + ], + "version": "==0.5.1" } }, "develop": {} diff --git a/mkdocs.yml b/mkdocs.yml index d44648b2c1..a8cd72791b 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -2,8 +2,10 @@ site_name: Brain Imaging Data Structure theme: material plugins: - search + - pdf-export: + verbose: true docs_dir: 'src' -use_directory_urls: false +use_directory_urls: false nav: - About: index.md - Specification: From 2170a8b3312407ebfafc5fa36307f1f69d79438f Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Fri, 5 Oct 2018 12:46:15 -0700 Subject: [PATCH 07/15] Revert "PDF export" This reverts commit b8b61bb6578935694a0768710cc0bef08e7b40bd. --- .circleci/config.yml | 5 -- Pipfile | 1 - Pipfile.lock | 171 +------------------------------------------ mkdocs.yml | 4 +- 4 files changed, 2 insertions(+), 179 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 443e74f086..3ef7940f09 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -9,11 +9,6 @@ jobs: - run: sudo chown -R circleci:circleci /usr/local/lib/python3.6/site-packages - restore_cache: # ensure this step occurs *before* installing dependencies key: deps9-{{ .Branch }}-{{ checksum "Pipfile.lock" }} - - run: | - sudo apt-get install build-essential python3-dev python3-pip \ - python3-setuptools python3-wheel python3-cffi \ - libcairo2 libpango-1.0-0 libpangocairo-1.0-0 \ - libgdk-pixbuf2.0-0 libffi-dev shared-mime-info - run: command: | sudo pip install pipenv diff --git a/Pipfile b/Pipfile index 8555e74fb7..af8e8060a2 100644 --- a/Pipfile +++ b/Pipfile @@ -6,7 +6,6 @@ name = "pypi" [packages] mkdocs = "==1.0.4" mkdocs-material = "==3.0.4" -mkdocs-pdf-export-plugin = "*" [dev-packages] diff --git a/Pipfile.lock b/Pipfile.lock index de26ed7747..27ed029995 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "02c8775b26cf90ce86f0fe8f644c48f8f784673bc04882769fec628af801a058" + "sha256": "580a32c021d6bda5d1823a0bfb462bfbb5dfaa567bcef30b058c3af80cb67896" }, "pipfile-spec": 6, "requires": { @@ -16,67 +16,6 @@ ] }, "default": { - "beautifulsoup4": { - "hashes": [ - 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"sha256:c99aa3c63104e0818ec566f8ff3942fb7c7a8f35f9912cb63fd8e12318b214b2", - "sha256:dae06620d3978da346375ebf88b9e2dd7d151335ba668c995aea9ed07af7add4", - "sha256:db5499d0710823fa4fb88206050d46544e8f0e0136a9a5f5570b026584c8fd74", - "sha256:f36baafd82119c4a114b9518202f2a983819101dcc14b26e43fc12cbefdce00e", - "sha256:f52b79c8796d81391ab295b04e520bda6feed54d54931708872e8f9ae9db0ea1", - "sha256:ff8cff01582fa1a7e533cb97f628531c4014af4b5f38e33cdcfe5eec29b6d888" - ], - "markers": "python_version != '3.2.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.3.*' and python_version != '3.0.*'", - "version": "==5.3.0" - }, - "pycparser": { - "hashes": [ - "sha256:a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3" - ], - "markers": "python_version != '3.2.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.3.*' and python_version != '3.0.*'", - "version": "==2.19" - }, "pygments": { "hashes": [ "sha256:78f3f434bcc5d6ee09020f92ba487f95ba50f1e3ef83ae96b9d5ffa1bab25c5d", @@ -224,13 +84,6 @@ "markers": "python_version != '3.0.*' and python_version != '3.3.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.2.*'", "version": "==5.0" }, - "pyphen": { - "hashes": [ - "sha256:3b633a50873156d777e1f1075ba4d8e96a6ad0a3ca42aa3ea9a6259f93f18921", - "sha256:e172faf10992c8c9d369bdc83e36dbcf1121f4ed0d881f1a0b521935aee583b5" - ], - "version": "==0.9.5" - }, "pyyaml": { "hashes": [ "sha256:3d7da3009c0f3e783b2c873687652d83b1bbfd5c88e9813fb7e5b03c0dd3108b", @@ -254,13 +107,6 @@ ], "version": "==1.11.0" }, - "tinycss2": { - "hashes": [ - "sha256:5e881eaa263bf4dc5c050d43cd6d2203ade1e3a3cda61f5511cf878972e83b78", - "sha256:7c53c2c0e914c7711c295b3101bcc78e0b7eda23ff20228a936efe11cdcc7136" - ], - "version": "==0.6.1" - }, "tornado": { "hashes": [ "sha256:0662d28b1ca9f67108c7e3b77afabfb9c7e87bde174fbda78186ecedc2499a9d", @@ -273,21 +119,6 @@ ], "markers": "python_version != '3.0.*' and python_version != '3.3.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.2.*'", "version": "==5.1.1" - }, - "weasyprint": { - "hashes": [ - "sha256:4d35e37cf9d2cea199ddfe4b038c80024619e8a05a2f2eb99b80a2bfb6063eb7", - "sha256:a9d198afb74cf4f29275cca7dc5d42eafd2d6abed3edb76c2d0d0429fead3907" - ], - "markers": "python_version != '3.2.*' and python_version >= '2.7' and python_version != '3.1.*' and python_version != '3.3.*' and python_version != '3.0.*'", - "version": "==0.42.3" - }, - "webencodings": { - "hashes": [ - "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78", - "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923" - ], - "version": "==0.5.1" } }, "develop": {} diff --git a/mkdocs.yml b/mkdocs.yml index a8cd72791b..d44648b2c1 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -2,10 +2,8 @@ site_name: Brain Imaging Data Structure theme: material plugins: - search - - pdf-export: - verbose: true docs_dir: 'src' -use_directory_urls: false +use_directory_urls: false nav: - About: index.md - Specification: From 51234b869cf679a792d0212e3d9a0d622a0e2140 Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Fri, 5 Oct 2018 13:54:24 -0700 Subject: [PATCH 08/15] mkdocs-combine + pandoc --- .circleci/config.yml | 6 ++++++ Pipfile | 1 + Pipfile.lock | 6 +++++- 3 files changed, 12 insertions(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 3ef7940f09..6bde4c1012 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -13,6 +13,8 @@ jobs: command: | sudo pip install pipenv pipenv install + - run: + command: apt-get install -y pandoc - save_cache: key: deps9-{{ .Branch }}-{{ checksum "Pipfile.lock" }} paths: @@ -22,5 +24,9 @@ jobs: - run: name: generate docs command: pipenv run mkdocs build --clean --strict --verbose + - run: + command: pipenv run mkdocscombine --no-titles -o mydocs.pd + - run: + command: pandoc --toc -f markdown+grid_tables+table_captions -o site/specification.pdf mydocs.pd - store_artifacts: path: site diff --git a/Pipfile b/Pipfile index af8e8060a2..9825e729fa 100644 --- a/Pipfile +++ b/Pipfile @@ -6,6 +6,7 @@ name = "pypi" [packages] mkdocs = "==1.0.4" mkdocs-material = "==3.0.4" +mkdocs-combine = {git = "https://github.com/o2r-project/mkdocs-combine.git"} [dev-packages] diff --git a/Pipfile.lock b/Pipfile.lock index 27ed029995..98bbac2548 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "580a32c021d6bda5d1823a0bfb462bfbb5dfaa567bcef30b058c3af80cb67896" + "sha256": "8d9bb744b26707f99ea5c2f36b74be398d9d208d03c203a8ca8b22e7df0eda39" }, "pipfile-spec": 6, "requires": { @@ -61,6 +61,10 @@ "index": "pypi", "version": "==1.0.4" }, + "mkdocs-combine": { + "git": "https://github.com/o2r-project/mkdocs-combine.git", + "ref": "4c1fa94c81a08c51ac65bf150fbf704c1de01c0e" + }, "mkdocs-material": { "hashes": [ "sha256:2f6987ee2c70f9da0870079a4626f2d309f8528806f08e1a7da842b6c58e7c5c", From 5c6b58cce6de4d523d293712bff45b16c08b96da Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Fri, 5 Oct 2018 13:55:36 -0700 Subject: [PATCH 09/15] sudo --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 6bde4c1012..fa7fd4d9b5 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -14,7 +14,7 @@ jobs: sudo pip install pipenv pipenv install - run: - command: apt-get install -y pandoc + command: sudo apt-get install -y pandoc - save_cache: key: deps9-{{ .Branch }}-{{ checksum "Pipfile.lock" }} paths: From 417b39b58c250a9c212c40b22613f97d100c5c48 Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Fri, 5 Oct 2018 13:58:41 -0700 Subject: [PATCH 10/15] other way to install deps --- .circleci/config.yml | 1 + Pipfile | 1 - Pipfile.lock | 6 +----- 3 files changed, 2 insertions(+), 6 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index fa7fd4d9b5..52cf5b7494 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -13,6 +13,7 @@ jobs: command: | sudo pip install pipenv pipenv install + - run: pipenv install git+https://github.com/o2r-project/mkdocs-combine.git#egg=mkdocs-combine - run: command: sudo apt-get install -y pandoc - save_cache: diff --git a/Pipfile b/Pipfile index 9825e729fa..af8e8060a2 100644 --- a/Pipfile +++ b/Pipfile @@ -6,7 +6,6 @@ name = "pypi" [packages] mkdocs = "==1.0.4" mkdocs-material = "==3.0.4" -mkdocs-combine = {git = "https://github.com/o2r-project/mkdocs-combine.git"} [dev-packages] diff --git a/Pipfile.lock b/Pipfile.lock index 98bbac2548..27ed029995 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "8d9bb744b26707f99ea5c2f36b74be398d9d208d03c203a8ca8b22e7df0eda39" + "sha256": "580a32c021d6bda5d1823a0bfb462bfbb5dfaa567bcef30b058c3af80cb67896" }, "pipfile-spec": 6, "requires": { @@ -61,10 +61,6 @@ "index": "pypi", "version": "==1.0.4" }, - "mkdocs-combine": { - "git": "https://github.com/o2r-project/mkdocs-combine.git", - "ref": "4c1fa94c81a08c51ac65bf150fbf704c1de01c0e" - }, "mkdocs-material": { "hashes": [ "sha256:2f6987ee2c70f9da0870079a4626f2d309f8528806f08e1a7da842b6c58e7c5c", From ccc170ab94b704feabcc58e69d0b855e1fe97bc6 Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Fri, 5 Oct 2018 14:01:13 -0700 Subject: [PATCH 11/15] other way to install deps --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 52cf5b7494..aefa0e3b3b 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -13,7 +13,7 @@ jobs: command: | sudo pip install pipenv pipenv install - - run: pipenv install git+https://github.com/o2r-project/mkdocs-combine.git#egg=mkdocs-combine + - run: pipenv run pip install git+https://github.com/o2r-project/mkdocs-combine.git#egg=mkdocs-combine - run: command: sudo apt-get install -y pandoc - save_cache: From c866d198aeaee02d2e6ac053f29c42b9d7c56fed Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Fri, 5 Oct 2018 14:05:46 -0700 Subject: [PATCH 12/15] install pdflatex --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index aefa0e3b3b..4d7d8981ff 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -15,7 +15,7 @@ jobs: pipenv install - run: pipenv run pip install git+https://github.com/o2r-project/mkdocs-combine.git#egg=mkdocs-combine - run: - command: sudo apt-get install -y pandoc + command: sudo apt-get install -y pandoc texlive-full - save_cache: key: deps9-{{ .Branch }}-{{ checksum "Pipfile.lock" }} paths: From f5c32a2766a940c9144581ebc95644276c5e7be6 Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Wed, 17 Oct 2018 22:12:51 -0700 Subject: [PATCH 13/15] fix pipenv version --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 4d7d8981ff..91b7604580 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -11,7 +11,7 @@ jobs: key: deps9-{{ .Branch }}-{{ checksum "Pipfile.lock" }} - run: command: | - sudo pip install pipenv + sudo pip install pipenv=2018.7.1 pipenv install - run: pipenv run pip install git+https://github.com/o2r-project/mkdocs-combine.git#egg=mkdocs-combine - run: From 4c9c3efa551766f0ee43e6a40a652547b48f4a8d Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Wed, 17 Oct 2018 22:13:46 -0700 Subject: [PATCH 14/15] fix pipenv version --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 91b7604580..a0f129801c 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -11,7 +11,7 @@ jobs: key: deps9-{{ .Branch }}-{{ checksum "Pipfile.lock" }} - run: command: | - sudo pip install pipenv=2018.7.1 + sudo pip install pipenv==2018.7.1 pipenv install - run: pipenv run pip install git+https://github.com/o2r-project/mkdocs-combine.git#egg=mkdocs-combine - run: From df932cc2ffa4f616bddaf6aa27b0883bf6a9ed28 Mon Sep 17 00:00:00 2001 From: Chris Gorgolewski Date: Wed, 17 Oct 2018 22:16:20 -0700 Subject: [PATCH 15/15] remove pdf creation --- .circleci/config.yml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index a0f129801c..42596b7d20 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -13,9 +13,6 @@ jobs: command: | sudo pip install pipenv==2018.7.1 pipenv install - - run: pipenv run pip install git+https://github.com/o2r-project/mkdocs-combine.git#egg=mkdocs-combine - - run: - command: sudo apt-get install -y pandoc texlive-full - save_cache: key: deps9-{{ .Branch }}-{{ checksum "Pipfile.lock" }} paths: @@ -25,9 +22,5 @@ jobs: - run: name: generate docs command: pipenv run mkdocs build --clean --strict --verbose - - run: - command: pipenv run mkdocscombine --no-titles -o mydocs.pd - - run: - command: pandoc --toc -f markdown+grid_tables+table_captions -o site/specification.pdf mydocs.pd - store_artifacts: path: site