Added sphinx documentation for Python bindings

Added sphinx documentation for the opm.simulators.BlackOilSimulator Python module. Added GitHub action workflow to deploy sphinx documentation to GitHub Pages.
2024-07-04 11:33:06 -05:00 · 2024-03-05 07:34:20 +01:00 · 2024-03-05 07:34:20 +01:00 · 566a844fef
commit 566a844fef
parent 2e7a7a0c44
12 changed files with 789 additions and 1 deletions
--- a/.github/workflows/python_sphinx_docs.yml
+++ b/.github/workflows/python_sphinx_docs.yml
@ -0,0 +1,48 @@
+name: Build Python Sphinx Docs and push to gh-pages
+
+on:
+    push:
+        branches: main
+        paths:
+          - 'python/**'
+          - '.github/workflows/python_sphinx_docs.yml'
+    pull_request:
+        branches: main
+        paths:
+          - 'python/**'
+          - '.github/workflows/python_sphinx_docs.yml'
+permissions:
+    contents: write
+jobs:
+    build:
+      runs-on: ubuntu-latest
+      steps:
+        - name: checkout source code
+          uses: actions/checkout@v3
+        - name: Set up Python
+          uses: actions/setup-python@v4
+          with:
+            python-version: "3.11"
+        - name: Install poetry
+          uses: abatilo/actions-poetry@v2
+        - name: Install python dependencies
+          run: |
+            cd python/sphinx_docs
+            poetry install
+        - name: Build documentation
+          run: |
+            cd python
+            mkdir gh-pages
+            touch gh-pages/.nojekyll
+            cd sphinx_docs/docs/
+            poetry run sphinx-build -b html . _build
+        - name: Copy documentation to gh-pages
+          run: |
+            cd python/sphinx_docs/docs
+            cp -r _build/* ../../gh-pages/
+        - name: Deploy documentation
+          if: ${{ github.event_name == 'push' }}
+          uses: JamesIves/github-pages-deploy-action@v4
+          with:
+            branch: gh-pages
+            folder: python/gh-pages
--- a/.gitignore
+++ b/.gitignore
@ -34,4 +34,11 @@ build/
 *.dSYM

 # emacs directory setting:
-.dir-locals.el
+.dir-locals.el
+
+# Python sphinx build
+python/sphinx_docs/docs/_build/
+
+# Python cache directories
+**/__pycache__/
+
--- a/python/sphinx_docs/README.md
+++ b/python/sphinx_docs/README.md
@ -0,0 +1,23 @@
+# Python scripts for building opm-simulators sphinx documentation
+
+## Installation of the python scripts
+- Requires python3 >= 3.10
+
+### Using poetry
+For development it is recommended to use poetry:
+
+- Install [poetry](https://python-poetry.org/docs/)
+- Then run:
+```
+$ poetry install
+$ poetry shell
+```
+
+### Installation into virtual environment
+If you do not plan to change the code, you can do a regular installation into a VENV:
+
+```
+$ python -m venv .venv
+$ source .venv/bin/activate
+$ pip install .
+```
--- a/python/sphinx_docs/docs/Makefile
+++ b/python/sphinx_docs/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)
--- a/python/sphinx_docs/docs/conf.py
+++ b/python/sphinx_docs/docs/conf.py
@ -0,0 +1,44 @@
+# Configuration file for the Sphinx documentation builder.
+
+project = "opm.simulators"
+copyright = "2024 Equinor ASA"
+author = "Håkon Hægland"
+release = "0.1"
+
+# -- General configuration ---------------------------------------------------
+import os
+import sys
+
+# For regular Python packages, the path to the package is usually added to sys.path
+# here such that autodoc can find the modules. However, our Python module
+#  opm.simulators.BlackOilSimulator is not generated yet. Since it is a pybind11
+# extension module, it needs to be compiled as part of the opm-simulators build
+# process (which requires building opm-common first and so on). The full compilation
+# of opm-simulators requres time and storage resources, so we do not want to
+# do this as part of the documentation build. Instead, we will use a sphinx extension
+# (Python script) to generate documentation from a JSON input file. (This JSON file
+# is also is also used to generate a C++ header file with docstrings. The header file
+# is generated when opm-simulators is built and is then included
+# in the pybind11 binding code for the BlackOilSimulator class. In this way, the
+# opm.simulators.BlackOilSimulator Python module will also have access to the docstrings.)
+sys.path.insert(0, os.path.abspath("../src"))
+# Our sphinx extension that will use the docstrings.json file to generate documentation
+extensions = ["opm_simulators_docs.sphinx_ext_docstrings"]
+# Path to docstrings.json
+opm_simulators_docstrings_path = os.path.abspath('../../docstrings.json')
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# See: https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
+html_context = {
+    "display_github": True,
+    "github_user": "OPM",
+    "github_repo": "opm-simulators",
+    "github_version": "master",
+    "conf_py_path": "/python/docs/",
+}
--- a/python/sphinx_docs/docs/index.rst
+++ b/python/sphinx_docs/docs/index.rst
@ -0,0 +1,16 @@
+Welcome to the Python documentation for opm-simulators!
+=======================================================
+
+.. toctree::
+    :maxdepth: 1
+    :caption: Contents:
+
+    introduction
+    python
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
--- a/python/sphinx_docs/docs/introduction.rst
+++ b/python/sphinx_docs/docs/introduction.rst
@ -0,0 +1,4 @@
+Introduction
+============
+
+Documentation for the ``opm.simulators`` Python module.
--- a/python/sphinx_docs/docs/make.bat
+++ b/python/sphinx_docs/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
--- a/python/sphinx_docs/docs/python.rst
+++ b/python/sphinx_docs/docs/python.rst
@ -0,0 +1,4 @@
+Python Module Documentation
+===========================
+
+.. opm_simulators_docstrings::
--- a/python/sphinx_docs/poetry.lock
+++ b/python/sphinx_docs/poetry.lock
@ -0,0 +1,521 @@
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+
+[[package]]
+name = "alabaster"
+version = "0.7.16"
+description = "A light, configurable Sphinx theme"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
+    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
+]
+
+[[package]]
+name = "babel"
+version = "2.14.0"
+description = "Internationalization utilities"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
+    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
+]
+
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+
+[[package]]
+name = "certifi"
+version = "2024.2.2"
+description = "Python package for providing Mozilla's CA Bundle."
+optional = false
+python-versions = ">=3.6"
+files = [
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+]
+
+[[package]]
+name = "charset-normalizer"
+version = "3.3.2"
+description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
+optional = false
+python-versions = ">=3.7.0"
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+test = ["cython (>=3.0)", "filelock", "html5lib", "pytest (>=4.6)", "setuptools (>=67.0)"]
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+[[package]]
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+[package.extras]
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+
+[[package]]
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+description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
+optional = false
+python-versions = ">=3.9"
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+
+[[package]]
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+version = "1.0.6"
+description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
+optional = false
+python-versions = ">=3.9"
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+
+[[package]]
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+optional = false
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+
+[[package]]
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+description = "Extension to include jQuery on newer Sphinx releases"
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+[[package]]
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+
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+optional = false
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+h2 = ["h2 (>=4,<5)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["zstandard (>=0.18.0)"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.10"
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--- a/python/sphinx_docs/pyproject.toml
+++ b/python/sphinx_docs/pyproject.toml
@ -0,0 +1,20 @@
+[tool.poetry]
+name = "opm-simulators-docs"
+version = "0.1.0"
+description = """Helper scripts for generating sphinx documentation for the \
+                 opm-simulators Python bindings"""
+authors = ["Håkon Hægland <hakon.hagland@gmail.com>"]
+readme = "README.md"
+packages = [{ include = "opm_simulators_docs", from = "src"}]
+license = "GPL3"
+repository = "https://github.com/OPM/opm-simulators"
+
+[tool.poetry.dependencies]
+python = "^3.10"
+sphinx = "^7.2.5"
+sphinx-rtd-theme = "^1.3.0"
+click = "^8.1.7"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
--- a/python/sphinx_docs/src/opm_simulators_docs/sphinx_ext_docstrings.py
+++ b/python/sphinx_docs/src/opm_simulators_docs/sphinx_ext_docstrings.py
@ -0,0 +1,46 @@
+import json
+from sphinx.util.nodes import nested_parse_with_titles
+from docutils.statemachine import ViewList
+from sphinx.util.docutils import SphinxDirective
+from docutils import nodes
+
+class PybindDocstringsDirective(SphinxDirective):
+    required_arguments = 0
+    optional_arguments = 0
+    final_argument_whitespace = False
+    option_spec = {}
+
+    def run(self):
+        env = self.state.document.settings.env
+        docstrings_path = env.app.config.opm_simulators_docstrings_path
+        with open(docstrings_path, 'r') as file:
+            docstrings = json.load(file)
+        result = []
+        for func_name, doc_info in docstrings.items():
+            signature = doc_info.get('signature', '')
+            docstring = doc_info.get('doc', '')
+
+            # Create a ViewList instance for the function signature and docstring
+            rst = ViewList()
+
+            # Check if signature exists and prepend it to the docstring
+            signature_line = f".. py:function:: {signature}" if signature else f".. py:function:: {func_name}()"
+            rst.append(signature_line, source="")
+            rst.append("", source="")
+            # Add the docstring text if it exists
+            if docstring:
+                for line in docstring.split('\n'):
+                    rst.append(f"   {line}", source="")
+
+            # Create a node that will be populated by nested_parse_with_titles
+            node = nodes.section()
+            node.document = self.state.document
+            # Parse the rst content
+            nested_parse_with_titles(self.state, rst, node)
+
+            result.extend(node.children)
+        return result
+
+def setup(app):
+    app.add_config_value('opm_simulators_docstrings_path', None, 'env')
+    app.add_directive("opm_simulators_docstrings", PybindDocstringsDirective)