Merge pull request #84 from judithabk6/add_doc

Add documentation

.github/workflows/sphinx_doc.yml

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+name: documentation
+
+on: 
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs: 
+  # This workflow contains a single job called "build"
+  build: 
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: | 
+          python -m pip install --upgrade pip
+          pip install ghp-import sphinx sphinx_rtd_theme -e .
+
+      - name: Build HTML
+        run: | 
+          cd docs/
+          make html
+      - name: Run ghp-import
+        run: | 
+          ghp-import -n -p -f docs/_build/html

docs/Makefile

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+# 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)

docs/conf.py

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+import os
+import sys
+
+import med_bench
+import med_bench.get_estimation
+import med_bench.get_simulated_data
+import med_bench.mediation
+import med_bench.utils
+import med_bench.utils.utils
+import med_bench.utils.nuisances
+
+
+sys.path.insert(0, os.path.abspath('../'))
+
+project = 'med_bench'
+copyright = '2024, Judith Abecassis, Houssam Zenati, Bertrand Thirion, Hadrien Mariaccia, Mouad Zbakh'
+author = 'Judith Abecassis, Houssam Zenati, Bertrand Thirion, Hadrien Mariaccia, Mouad Zbakh'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.githubpages'
+]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '.venv']
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']

docs/index.rst

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+.. med_bench documentation master file, created by
+   sphinx-quickstart on Tue Apr  9 16:50:56 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to med_bench's documentation!
+=====================================
+
+.. toctree::
+   :maxdepth: 4
+   :caption: Contents:
+
+   modules
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

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+@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

docs/modules.rst

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+.. toctree::
+   :maxdepth: 4
+   :caption: Contents:
+
+
+med_bench
+=================
+.. automodule:: med_bench
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+get_estimation
+--------
+
+.. automodule:: med_bench.get_estimation
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+get_simulated_data
+--------
+
+.. automodule:: med_bench.get_simulated_data
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+mediation
+--------
+
+.. automodule:: med_bench.mediation
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+utils
+--------
+
+.. automodule:: med_bench.utils.utils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+nuisances
+--------
+
+.. automodule:: med_bench.utils.nuisances
+    :members:
+    :undoc-members:
+    :show-inheritance:
+