From 28f2cd41841a44c0abc162e7706f72b975fee8fa Mon Sep 17 00:00:00 2001 From: Ismail Ugur Bayindir Date: Wed, 11 Oct 2023 09:59:58 +0100 Subject: [PATCH] Sphinx integration (#41) * Sphinx integration * Updated pandasaurus_exceptions.py --- .github/workflows/documentation.yml | 25 - .github/workflows/publish-docs.yml | 34 + docs/Makefile | 20 + docs/conf.py | 47 + docs/index.rst | 22 + docs/introduction.rst | 14 + docs/make.bat | 35 + docs/pandasaurus/curie_validator.rst | 10 + docs/pandasaurus/graph/graph_generator.rst | 10 + .../graph/graph_generator_utils.rst | 13 + docs/pandasaurus/graph/index.rst | 16 + docs/pandasaurus/index.rst | 21 + docs/pandasaurus/query.rst | 10 + docs/pandasaurus/resources/index.rst | 16 + docs/pandasaurus/resources/slim.rst | 10 + docs/pandasaurus/resources/term.rst | 10 + docs/pandasaurus/slim_manager.rst | 10 + docs/pandasaurus/utils/index.rst | 17 + .../utils/pandasaurus_exceptions.rst | 12 + docs/pandasaurus/utils/query_utils.rst | 13 + docs/pandasaurus/utils/sparql_queries.rst | 13 + mkdocks.yml | 13 - pandasaurus/utils/pandasaurus_exceptions.py | 19 + poetry.lock | 964 +++++++++--------- pyproject.toml | 3 + 25 files changed, 874 insertions(+), 503 deletions(-) delete mode 100644 .github/workflows/documentation.yml create mode 100644 .github/workflows/publish-docs.yml create mode 100644 docs/Makefile create mode 100644 docs/conf.py create mode 100644 docs/index.rst create mode 100644 docs/introduction.rst create mode 100644 docs/make.bat create mode 100644 docs/pandasaurus/curie_validator.rst create mode 100644 docs/pandasaurus/graph/graph_generator.rst create mode 100644 docs/pandasaurus/graph/graph_generator_utils.rst create mode 100644 docs/pandasaurus/graph/index.rst create mode 100644 docs/pandasaurus/index.rst create mode 100644 docs/pandasaurus/query.rst create mode 100644 docs/pandasaurus/resources/index.rst create mode 100644 docs/pandasaurus/resources/slim.rst create mode 100644 docs/pandasaurus/resources/term.rst create mode 100644 docs/pandasaurus/slim_manager.rst create mode 100644 docs/pandasaurus/utils/index.rst create mode 100644 docs/pandasaurus/utils/pandasaurus_exceptions.rst create mode 100644 docs/pandasaurus/utils/query_utils.rst create mode 100644 docs/pandasaurus/utils/sparql_queries.rst delete mode 100644 mkdocks.yml diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml deleted file mode 100644 index c971f25..0000000 --- a/.github/workflows/documentation.yml +++ /dev/null @@ -1,25 +0,0 @@ -name: Publish mkdocs documentation - -on: - # Allows you to run this workflow manually from the Actions tab - workflow_dispatch: -# release: -# types: [created] - push: - branches: - - master - paths: - - 'docs/**' - -jobs: - build-and-publish: - name: Publish mkdocs documentation - runs-on: ubuntu-latest - steps: - - name: Checkout main - uses: actions/checkout@v3 - - name: Deploy docs - uses: mhausenblas/mkdocs-deploy-gh-pages@master - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - CONFIG_FILE: mkdocs.yml diff --git a/.github/workflows/publish-docs.yml b/.github/workflows/publish-docs.yml new file mode 100644 index 0000000..057951d --- /dev/null +++ b/.github/workflows/publish-docs.yml @@ -0,0 +1,34 @@ +name: Publish Documentation + +on: + push: + branches: + - main + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - name: Checkout Repository + uses: actions/checkout@v2 + + - name: Setup Python + uses: actions/setup-python@v2 + with: + python-version: 3.9 + + - name: Install Dependencies and Build Documentation + run: | + sudo apt-get install python3-sphinx + pip install sphinx-rtd-theme + cd docs + make html + + - name: Deploy documentation. + if: ${{ github.event_name == 'push' }} + uses: JamesIves/github-pages-deploy-action@v4.3.0 + with: + branch: gh-pages + force: true + folder: docs/_build/html diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d4bb2cb --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 0000000..d1cb5d9 --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,47 @@ +# Configuration file for the Sphinx documentation builder. +# +# For the full list of built-in configuration values, see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information + +project = 'pandasaurus' +copyright = '2023, Ugur Bayindir' +author = 'Ugur Bayindir' +release = '0.3.5' + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration + +extensions = [ + 'sphinx.ext.duration', + 'sphinx.ext.doctest', + "sphinx.ext.autodoc", + "sphinx.ext.githubpages", + "sphinx_rtd_theme", + "sphinx.ext.viewcode", + "sphinx.ext.napoleon", + "sphinx.ext.todo", + "sphinx.ext.coverage", +] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# source_suffix = ['.rst', '.md'] +source_suffix = [".rst", ".md"] + +templates_path = ['_templates'] +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = 'sphinx_rtd_theme' + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 0000000..ba9c09b --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,22 @@ +.. pandasaurus documentation master file, created by + sphinx-quickstart on Tue Oct 10 11:39:01 2023. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +pandasaurus's documentation! +======================================= + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + introduction + pandasaurus/index + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/introduction.rst b/docs/introduction.rst new file mode 100644 index 0000000..b473805 --- /dev/null +++ b/docs/introduction.rst @@ -0,0 +1,14 @@ +Pandasaurus +=========== + +.. image:: https://user-images.githubusercontent.com/112839/227489878-d253c381-75fd-4e92-b851-2b36df0fc5ed.png + :width: 100 + +STATUS: BETA +------------ + +A python library supporting simple queries over ontology annotations in dataframes, using UberGraph queries. + +The aim for now is to keep this as a very simple independent Python lib avoiding any complex dependencies. + +With the basic library in place, the first planned use for this is as a base for a library that provides simple enrichment and query-ability to AnnData Cell X Gene matrices following the `CZ single cell curation standard `_. diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..32bb245 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=. +set BUILDDIR=_build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/pandasaurus/curie_validator.rst b/docs/pandasaurus/curie_validator.rst new file mode 100644 index 0000000..847d4fd --- /dev/null +++ b/docs/pandasaurus/curie_validator.rst @@ -0,0 +1,10 @@ +Curie Validator +================== + +Documentation +------------- + +.. currentmodule:: pandasaurus.curie_validator + +.. autoclass:: CurieValidator + :members: \ No newline at end of file diff --git a/docs/pandasaurus/graph/graph_generator.rst b/docs/pandasaurus/graph/graph_generator.rst new file mode 100644 index 0000000..fad76f0 --- /dev/null +++ b/docs/pandasaurus/graph/graph_generator.rst @@ -0,0 +1,10 @@ +Graph Generator +================== + +Documentation +------------- + +.. currentmodule:: pandasaurus.graph.graph_generator + +.. autoclass:: GraphGenerator + :members: \ No newline at end of file diff --git a/docs/pandasaurus/graph/graph_generator_utils.rst b/docs/pandasaurus/graph/graph_generator_utils.rst new file mode 100644 index 0000000..356b977 --- /dev/null +++ b/docs/pandasaurus/graph/graph_generator_utils.rst @@ -0,0 +1,13 @@ +Graph Generator Utils +====================== + +Documentation +------------- + +.. currentmodule:: pandasaurus.graph.graph_generator_utils + +Functions +--------- + +.. automodule:: pandasaurus.graph.graph_generator_utils + :members: \ No newline at end of file diff --git a/docs/pandasaurus/graph/index.rst b/docs/pandasaurus/graph/index.rst new file mode 100644 index 0000000..0df12fa --- /dev/null +++ b/docs/pandasaurus/graph/index.rst @@ -0,0 +1,16 @@ +Library documentation +======================= + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + graph_generator + graph_generator_utils + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` \ No newline at end of file diff --git a/docs/pandasaurus/index.rst b/docs/pandasaurus/index.rst new file mode 100644 index 0000000..d996958 --- /dev/null +++ b/docs/pandasaurus/index.rst @@ -0,0 +1,21 @@ +Library documentation +======================= + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + curie_validator + query + slim_manager + graph/index + resources/index + utils/index + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` \ No newline at end of file diff --git a/docs/pandasaurus/query.rst b/docs/pandasaurus/query.rst new file mode 100644 index 0000000..a5b6cb2 --- /dev/null +++ b/docs/pandasaurus/query.rst @@ -0,0 +1,10 @@ +Query +================== + +Documentation +------------- + +.. currentmodule:: pandasaurus.query + +.. autoclass:: Query + :members: \ No newline at end of file diff --git a/docs/pandasaurus/resources/index.rst b/docs/pandasaurus/resources/index.rst new file mode 100644 index 0000000..f0cf81c --- /dev/null +++ b/docs/pandasaurus/resources/index.rst @@ -0,0 +1,16 @@ +Library documentation +======================= + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + slim + term + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` \ No newline at end of file diff --git a/docs/pandasaurus/resources/slim.rst b/docs/pandasaurus/resources/slim.rst new file mode 100644 index 0000000..de2d6d5 --- /dev/null +++ b/docs/pandasaurus/resources/slim.rst @@ -0,0 +1,10 @@ +Slim +================== + +Documentation +------------- + +.. currentmodule:: pandasaurus.resources.slim + +.. autoclass:: Slim + :members: \ No newline at end of file diff --git a/docs/pandasaurus/resources/term.rst b/docs/pandasaurus/resources/term.rst new file mode 100644 index 0000000..18c2730 --- /dev/null +++ b/docs/pandasaurus/resources/term.rst @@ -0,0 +1,10 @@ +Term +================== + +Documentation +------------- + +.. currentmodule:: pandasaurus.resources.term + +.. autoclass:: Term + :members: \ No newline at end of file diff --git a/docs/pandasaurus/slim_manager.rst b/docs/pandasaurus/slim_manager.rst new file mode 100644 index 0000000..cc33bf3 --- /dev/null +++ b/docs/pandasaurus/slim_manager.rst @@ -0,0 +1,10 @@ +Slim Manager +================== + +Documentation +------------- + +.. currentmodule:: pandasaurus.slim_manager + +.. autoclass:: SlimManager + :members: \ No newline at end of file diff --git a/docs/pandasaurus/utils/index.rst b/docs/pandasaurus/utils/index.rst new file mode 100644 index 0000000..6c04115 --- /dev/null +++ b/docs/pandasaurus/utils/index.rst @@ -0,0 +1,17 @@ +Library documentation +======================= + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + pandasaurus_exceptions + query_utils + sparql_queries + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` \ No newline at end of file diff --git a/docs/pandasaurus/utils/pandasaurus_exceptions.rst b/docs/pandasaurus/utils/pandasaurus_exceptions.rst new file mode 100644 index 0000000..8241e8d --- /dev/null +++ b/docs/pandasaurus/utils/pandasaurus_exceptions.rst @@ -0,0 +1,12 @@ +Exception Module +================= + +This module contains custom exception classes used in our project. + +Documentation +------------- + +.. automodule:: pandasaurus.utils.pandasaurus_exceptions + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/pandasaurus/utils/query_utils.rst b/docs/pandasaurus/utils/query_utils.rst new file mode 100644 index 0000000..cef4be4 --- /dev/null +++ b/docs/pandasaurus/utils/query_utils.rst @@ -0,0 +1,13 @@ +Query Utils +================== + +Documentation +------------- + +.. currentmodule:: pandasaurus.utils.query_utils + +Functions +--------- + +.. automodule:: pandasaurus.utils.query_utils + :members: \ No newline at end of file diff --git a/docs/pandasaurus/utils/sparql_queries.rst b/docs/pandasaurus/utils/sparql_queries.rst new file mode 100644 index 0000000..3efafa7 --- /dev/null +++ b/docs/pandasaurus/utils/sparql_queries.rst @@ -0,0 +1,13 @@ +Sparql Queries +================== + +Documentation +------------- + +.. currentmodule:: pandasaurus.utils.sparql_queries + +Functions +--------- + +.. automodule:: pandasaurus.utils.sparql_queries + :members: \ No newline at end of file diff --git a/mkdocks.yml b/mkdocks.yml deleted file mode 100644 index 60943d7..0000000 --- a/mkdocks.yml +++ /dev/null @@ -1,13 +0,0 @@ -site_name: PandaSaurus -theme: readthedocs -repo_url: https://github.com/INCATools/PandaSaurus -watch: ['src/'] - -plugins: -- search -- autorefs -- section-index -- mkdocstrings - -nav: - - Home: README.md diff --git a/pandasaurus/utils/pandasaurus_exceptions.py b/pandasaurus/utils/pandasaurus_exceptions.py index e2d4f9d..e3e5699 100644 --- a/pandasaurus/utils/pandasaurus_exceptions.py +++ b/pandasaurus/utils/pandasaurus_exceptions.py @@ -5,12 +5,24 @@ class InvalidTerm(Exception): def __init__(self, term_list: List[Term]): + """ + Exception raised for invalid ontology terms. + + Args: + term_list (List[Term]): A list of invalid Term objects. + """ self.message = f"The following terms are invalid: {', '.join([term.get_iri() for term in term_list])}" super().__init__(self.message) class ObsoletedTerm(Exception): def __init__(self, term_list: List[Term]): + """ + Exception raised for obsoleted ontology terms. + + Args: + term_list (List[Term]): A list of obsoleted Term objects. + """ self.message = ( f"The following terms are obsoleted: {', '.join([term.get_iri() for term in term_list])}, " f"and replaced by following terms: {', '.join([term.get_new_iri() for term in term_list])}. " @@ -21,6 +33,13 @@ def __init__(self, term_list: List[Term]): class InvalidOntology(Exception): def __init__(self, input_ontology: str, ontology_list: List[str]): + """ + Exception raised for invalid ontology names. + + Args: + input_ontology (str): The name of the invalid ontology. + ontology_list (List[str]): A list of valid ontology names. + """ self.message = ( f"The '{input_ontology}' ontology is invalid. \n" f"Please use one of the following ontologies: \n{', '.join(ontology_list)}" diff --git a/poetry.lock b/poetry.lock index 2ed03f6..6fcda78 100644 --- a/poetry.lock +++ b/poetry.lock @@ -17,13 +17,13 @@ parse = ["beautifulsoup4 (>=4.10.0,<5.0)", "requests (>=2.12.0,<3)"] [[package]] name = "annotated-types" -version = "0.5.0" +version = "0.6.0" description = "Reusable constraint types to use with typing.Annotated" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "annotated_types-0.5.0-py3-none-any.whl", hash = "sha256:58da39888f92c276ad970249761ebea80ba544b77acddaa1a4d6cf78287d45fd"}, - {file = "annotated_types-0.5.0.tar.gz", hash = "sha256:47cdc3490d9ac1506ce92c7aaa76c579dc3509ff11e098fc867e5130ab7be802"}, + {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, + {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, ] [[package]] @@ -67,15 +67,18 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte [[package]] name = "babel" -version = "2.12.1" +version = "2.13.0" description = "Internationalization utilities" optional = false python-versions = ">=3.7" files = [ - {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"}, - {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"}, + {file = "Babel-2.13.0-py3-none-any.whl", hash = "sha256:fbfcae1575ff78e26c7449136f1abbefc3c13ce542eeb13d43d50d8b047216ec"}, + {file = "Babel-2.13.0.tar.gz", hash = "sha256:04c3e2d28d2b7681644508f836be388ae49e0cfe91465095340395b60d00f210"}, ] +[package.extras] +dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] + [[package]] name = "bcp47" version = "0.0.4" @@ -200,86 +203,101 @@ files = [ [[package]] name = "charset-normalizer" -version = "3.2.0" +version = "3.3.0" description = "The Real First Universal Charset Detector. 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