From 97684efca862f449e6fc381033c114942c270906 Mon Sep 17 00:00:00 2001 From: You-Cyuan Jhang Date: Wed, 9 Sep 2020 10:56:11 -0700 Subject: [PATCH] Fix Sphinx-Click Issues on Readthedocs.org (#85) * Fix sphinx click extension * test trigger read the docs * Fix missing click doc * update readathedocs to use requirements.txt file * add dins dep --- .readthedocs.yml | 9 +- docs/Makefile | 6 +- docs/README.md | 19 ++- docs/requirements.txt | 190 +++++++++++++++++++++++ docs/source/conf.py | 2 +- docs/source/datasetinsights.commands.rst | 18 +++ docs/source/index.rst | 1 + poetry.lock | 85 +++++----- pyproject.toml | 3 - 9 files changed, 271 insertions(+), 62 deletions(-) create mode 100644 docs/requirements.txt diff --git a/.readthedocs.yml b/.readthedocs.yml index faf7eddb..625c8dc3 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -1,11 +1,12 @@ # .readthedocs.yml version: 2 -sphinx: - configuration: docs/source/conf.py +formats: all python: version: 3.7 install: + - requirements: docs/requirements.txt - method: pip path: . - extra_requirements: - - docs +sphinx: + builder: html + configuration: docs/source/conf.py diff --git a/docs/Makefile b/docs/Makefile index fe35e883..855c250a 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -12,11 +12,11 @@ help: clean: rm -rf $(BUILDDIR) - find $(SOURCEDIR) -name "*.rst" | grep -v index | xargs rm -f apidoc: - sphinx-apidoc -f --templatedir=$(TEMPLATEDIR) -o $(SOURCEDIR) -d 2 ../datasetinsights/ ../datasetinsights/stats/visualization ../datasetinsights/dashboard.py ../datasetinsights/datasets/protos -html: apidoc + sphinx-apidoc --templatedir=$(TEMPLATEDIR) -o $(SOURCEDIR) -d 2 ../datasetinsights/ ../datasetinsights/stats/visualization ../datasetinsights/dashboard.py ../datasetinsights/datasets/protos + +html: sphinx-build -b html $(SOURCEDIR) $(BUILDDIR)/html @echo @echo "Build finished. The HTML doumentation pages are in $(BUILDDIR)/html." diff --git a/docs/README.md b/docs/README.md index 669a2006..ea4ce76e 100644 --- a/docs/README.md +++ b/docs/README.md @@ -4,11 +4,14 @@ Building documentation Run the following commands from `docs` directory. Automatic generate of Sphinx sources using [sphinx-apidoc](https://www.sphinx-doc.org/en/master/man/sphinx-apidoc.html) + ```bash make apidoc ``` -Build html files +This command only applies to newly created modules. It will not update modules that already exist. You will have to modify `docs/datasetinsighs.module_name` manually. + +To build html files, run ```bash make html @@ -16,15 +19,19 @@ make html You can browse the documentation by opening `build/html/index.html` file directly in any web browser. -Cleanup build files +Cleanup build html files + ```bash make clean ``` - Known issues ------------ -When using commonmark to convert markdown files to rst files, links to headers cannot have `_` or `.`. -If the header has either of those characters, they should be replaced by dashes `-`. -e.g. if you have a header `#### annotation_definitions.json` in the markdown file, to link to that header the markdown needs to be `[click link](#annotation-definitions-json)` +1. Some of the documents are written in markdown format. We use [recommonmark](https://github.com/readthedocs/recommonmark) to generate documentations. It uses [CommonMark](http://commonmark.org/) to convert markdown files to rst files. Due to it's limitation, links to headers cannot have `_` or `.`. If the header has either of those characters, they should be replaced by dashes `-`. e.g. if you have a header `#### annotation_definitions.json` in the markdown file, to link to that header the markdown needs to be `[click link](#annotation-definitions-json)` + +2. `Readthedocs.org` does not currently support [poetry](https://python-poetry.org/) officially. Until then, we have to manually generated a `docs/requirements.txt` file when new requirements is added to the repo. This file can be generated using command: + +```bash +poetry export --dev --without-hashes -f requirements.txt > docs/requirements.txt +``` diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 00000000..17aaf27c --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,190 @@ +absl-py==0.10.0 +alabaster==0.7.12 +appdirs==1.4.4 +appnope==0.1.0; python_version >= "3.3" and sys_platform == "darwin" or platform_system == "Darwin" +argon2-cffi==20.1.0 +astunparse==1.6.3 +atomicwrites==1.4.0; sys_platform == "win32" +attrs==20.2.0 +babel==2.8.0 +backcall==0.2.0; python_version >= "3.3" +black==19.10b0 +bleach==3.1.5 +bokeh==2.2.1 +brotli==1.0.9 +cachetools==4.1.1 +certifi==2020.6.20 +cffi==1.14.2 +chardet==3.0.4 +click==7.1.2 +cloudpickle==1.6.0 +codetiming==1.2.0 +colorama==0.4.3; python_version >= "3.3" and sys_platform == "win32" or sys_platform == "win32" +commonmark==0.9.1 +coverage==5.2.1 +cycler==0.10.0 +cython==0.29.21 +dash==1.12.0 +dash-core-components==1.10.0 +dash-html-components==1.0.3 +dash-renderer==1.4.1 +dash-table==4.7.0 +dask==2.25.0 +decorator==4.4.2; python_version >= "3.3" +defusedxml==0.6.0 +deprecated==1.2.10 +descartes==1.1.0 +distributed==2.25.0 +docutils==0.16 +entrypoints==0.3 +flake8==3.8.3 +flask==1.1.2 +flask-compress==1.5.0 +fsspec==0.8.0 +future==0.18.2 +gast==0.3.3 +google-api-core==1.22.2 +google-auth==1.21.1 +google-auth-oauthlib==0.4.1 +google-cloud-core==1.4.1 +google-cloud-storage==1.28.1 +google-pasta==0.2.0 +google-resumable-media==0.5.1 +googleapis-common-protos==1.52.0 +grpcio==1.31.0 +h5py==2.10.0 +heapdict==1.0.1 +idna==2.10 +imagesize==1.2.0 +importlib-metadata==1.7.0; python_version < "3.8" +ipykernel==5.3.4 +ipython==7.18.1 +ipython-genutils==0.2.0 +ipywidgets==7.5.1 +isort==4.3.21 +itsdangerous==1.1.0 +jedi==0.17.2; python_version >= "3.3" +jinja2==2.11.2 +joblib==0.16.0 +jsonschema==3.2.0 +jupyter==1.0.0 +jupyter-client==6.1.7 +jupyter-console==6.2.0 +jupyter-core==4.6.3 +keras-preprocessing==1.1.2 +kfp==1.0.0 +kfp-server-api==1.0.0 +kiwisolver==1.2.0 +kornia==0.1.4.post2 +kubernetes==11.0.0 +locket==0.2.0 +markdown==3.2.2 +markupsafe==1.1.1 +matplotlib==3.3.1 +mccabe==0.6.1 +mistune==0.8.4 +more-itertools==8.5.0 +msgpack==1.0.0 +nbconvert==5.6.1 +nbformat==5.0.7 +notebook==6.1.4 +numpy==1.17.5 +nuscenes-devkit==1.0.2 +oauthlib==3.1.0 +opencv-python==4.4.0.42 +opt-einsum==3.3.0 +packaging==20.4 +pandas==1.1.2 +pandocfilters==1.4.2 +parso==0.7.1; python_version >= "3.3" +partd==1.1.0 +pathspec==0.8.0 +pbr==5.5.0 +pexpect==4.8.0; python_version >= "3.3" and sys_platform != "win32" +pickleshare==0.7.5; python_version >= "3.3" +pillow==7.2.0 +plotly==4.9.0 +pluggy==0.13.1 +prometheus-client==0.8.0 +prompt-toolkit==3.0.7 +protobuf==3.13.0 +psutil==5.7.2 +ptyprocess==0.6.0; python_version >= "3.3" and sys_platform != "win32" or os_name != "nt" +py==1.9.0 +pyasn1==0.4.8 +pyasn1-modules==0.2.8 +pycocotools==2.0.2 +pycodestyle==2.6.0 +pycparser==2.20 +pyflakes==2.2.0 +pygments==2.6.1 +pyparsing==2.4.7 +pyquaternion==0.9.5 +pyrsistent==0.17.0 +pytest==5.4.3 +pytest-cov==2.10.1 +python-dateutil==2.8.1 +pytorch-ignite==0.3.0 +pytz==2020.1 +pywin32==228; sys_platform == "win32" +pywinpty==0.5.7; os_name == "nt" +pyyaml==5.3.1 +pyzmq==19.0.2 +qtconsole==4.7.7 +qtpy==1.9.0 +recommonmark==0.6.0 +regex==2020.7.14 +requests==2.24.0 +requests-oauthlib==1.3.0 +requests-toolbelt==0.9.1 +responses==0.10.16 +retrying==1.3.3 +rsa==4.6; python_version >= "3.5" +scikit-learn==0.23.2 +scipy==1.4.1 +send2trash==1.5.0 +shapely==1.7.1 +six==1.15.0 +snowballstemmer==2.0.0 +sortedcontainers==2.2.2 +sphinx==3.2.1 +sphinx-click==2.5.0 +sphinx-rtd-theme==0.5.0 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==1.0.3 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.4 +strip-hints==0.1.9 +tabulate==0.8.7 +tblib==1.7.0 +tensorboard==2.3.0 +tensorboard-plugin-wit==1.7.0 +tensorboardx==2.1 +tensorflow==2.3.0 +tensorflow-estimator==2.3.0 +termcolor==1.1.0 +terminado==0.8.3 +testpath==0.4.4 +threadpoolctl==2.1.0 +toml==0.10.1 +toolz==0.10.0 +torch==1.4.0 +torchvision==0.5.0 +tornado==6.0.4 +tqdm==4.48.2 +traitlets==5.0.4 +typed-ast==1.4.1 +typing-extensions==3.7.4.3 +urllib3==1.25.10 +wcwidth==0.2.5 +webencodings==0.5.1 +websocket-client==0.57.0 +werkzeug==1.0.1 +wheel==0.35.1 +widgetsnbextension==3.5.1 +wrapt==1.12.1 +yacs==0.1.8 +zict==2.0.0 +zipp==3.1.0; python_version < "3.8" diff --git a/docs/source/conf.py b/docs/source/conf.py index 15d3cd8a..40ae9463 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -34,7 +34,7 @@ "sphinx.ext.autosectionlabel", "sphinx_rtd_theme", "sphinx.ext.napoleon", - "sphinx_click.ext", + "sphinx_click", ] source_suffix = { diff --git a/docs/source/datasetinsights.commands.rst b/docs/source/datasetinsights.commands.rst index 7f64f960..01f00669 100644 --- a/docs/source/datasetinsights.commands.rst +++ b/docs/source/datasetinsights.commands.rst @@ -5,6 +5,12 @@ datasetinsights.commands datasetinsights.commands.download --------------------------------- + +.. click:: datasetinsights.commands.download:cli + :prog: datasetinsights download + :show-nested: + + .. automodule:: datasetinsights.commands.download :members: :undoc-members: @@ -13,6 +19,12 @@ datasetinsights.commands.download datasetinsights.commands.evaluate --------------------------------- + +.. click:: datasetinsights.commands.evaluate:cli + :prog: datasetinsights evaluate + :show-nested: + + .. automodule:: datasetinsights.commands.evaluate :members: :undoc-members: @@ -21,6 +33,12 @@ datasetinsights.commands.evaluate datasetinsights.commands.train ------------------------------ + +.. click:: datasetinsights.commands.train:cli + :prog: datasetinsights train + :show-nested: + + .. automodule:: datasetinsights.commands.train :members: :undoc-members: diff --git a/docs/source/index.rst b/docs/source/index.rst index dc06ff18..32e693d3 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -92,6 +92,7 @@ Contents Synthetic_Dataset_Schema + Indices and tables ================== diff --git a/poetry.lock b/poetry.lock index 95a2f415..fbf0160b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -78,12 +78,13 @@ description = "Classes Without Boilerplate" name = "attrs" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -version = "20.1.0" +version = "20.2.0" [package.extras] dev = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "sphinx-rtd-theme", "pre-commit"] docs = ["sphinx", "sphinx-rtd-theme", "zope.interface"] tests = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"] +tests_no_zope = ["coverage (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"] [[package]] category = "dev" @@ -548,10 +549,10 @@ description = "Google API client core library" name = "google-api-core" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" -version = "1.22.1" +version = "1.22.2" [package.dependencies] -google-auth = ">=1.19.1,<2.0dev" +google-auth = ">=1.21.1,<2.0dev" googleapis-common-protos = ">=1.6.0,<2.0dev" protobuf = ">=3.12.0" pytz = "*" @@ -570,7 +571,7 @@ description = "Google Authentication Library" name = "google-auth" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" -version = "1.21.0" +version = "1.21.1" [package.dependencies] cachetools = ">=2.0.0,<5.0" @@ -1181,7 +1182,7 @@ description = "A web-based notebook environment for interactive computing" name = "notebook" optional = false python-versions = ">=3.5" -version = "6.1.3" +version = "6.1.4" [package.dependencies] Send2Trash = "*" @@ -1290,7 +1291,7 @@ description = "Powerful data structures for data analysis, time series, and stat name = "pandas" optional = false python-versions = ">=3.6.1" -version = "1.1.1" +version = "1.1.2" [package.dependencies] numpy = ">=1.15.4" @@ -1559,10 +1560,7 @@ description = "Persistent/Functional/Immutable data structures" name = "pyrsistent" optional = false python-versions = "*" -version = "0.16.0" - -[package.dependencies] -six = "*" +version = "0.17.0" [[package]] category = "dev" @@ -1675,7 +1673,7 @@ description = "Jupyter Qt console" name = "qtconsole" optional = false python-versions = "*" -version = "4.7.6" +version = "4.7.7" [package.dependencies] ipykernel = ">=4.1" @@ -2223,7 +2221,7 @@ description = "Traitlets Python configuration system" name = "traitlets" optional = false python-versions = ">=3.7" -version = "5.0.2" +version = "5.0.4" [package.dependencies] ipython-genutils = "*" @@ -2364,11 +2362,8 @@ version = "3.1.0" docs = ["sphinx", "jaraco.packaging (>=3.2)", "rst.linker (>=1.9)"] testing = ["jaraco.itertools", "func-timeout"] -[extras] -docs = [] - [metadata] -content-hash = "53c8d7460ff98fe71aa31b5b0f2dfe5be6763e32d30aa2fc16bc23c45ea78baa" +content-hash = "6946daf4e4c05199da432b66e0e28b9e6ccab159f4fee052cb8fda487afdff54" lock-version = "1.0" python-versions = "^3.7" @@ -2416,8 +2411,8 @@ atomicwrites = [ {file = "atomicwrites-1.4.0.tar.gz", hash = "sha256:ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a"}, ] attrs = [ - {file = "attrs-20.1.0-py2.py3-none-any.whl", hash = "sha256:2867b7b9f8326499ab5b0e2d12801fa5c98842d2cbd22b35112ae04bf85b4dff"}, - {file = "attrs-20.1.0.tar.gz", hash = "sha256:0ef97238856430dcf9228e07f316aefc17e8939fc8507e18c6501b761ef1a42a"}, + {file = "attrs-20.2.0-py2.py3-none-any.whl", hash = "sha256:fce7fc47dfc976152e82d53ff92fa0407700c21acd20886a13777a0d20e655dc"}, + {file = "attrs-20.2.0.tar.gz", hash = "sha256:26b54ddbbb9ee1d34d5d3668dd37d6cf74990ab23c828c2888dccdceee395594"}, ] babel = [ {file = "Babel-2.8.0-py2.py3-none-any.whl", hash = "sha256:d670ea0b10f8b723672d3a6abeb87b565b244da220d76b4dba1b66269ec152d4"}, @@ -2675,12 +2670,12 @@ gast = [ {file = "gast-0.3.3.tar.gz", hash = "sha256:b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57"}, ] google-api-core = [ - {file = "google-api-core-1.22.1.tar.gz", hash = "sha256:35cba563034d668ae90ffe1f03193a84e745b38f09592f60258358b5e5ee6238"}, - {file = "google_api_core-1.22.1-py2.py3-none-any.whl", hash = "sha256:431839101b7edc7b0e6cccca0441cb9015f728fc5f098e146e123bf523e8cf71"}, + {file = "google-api-core-1.22.2.tar.gz", hash = "sha256:779107f17e0fef8169c5239d56a8fbff03f9f72a3893c0c9e5842ec29dfedd54"}, + {file = "google_api_core-1.22.2-py2.py3-none-any.whl", hash = "sha256:67e33a852dcca7cb7eff49abc35c8cc2c0bb8ab11397dc8306d911505cae2990"}, ] google-auth = [ - 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