Merge pull request #10 from calico/sphinx-doc

add sphinx doc

.github/workflows/documentation.yml

@@ -0,0 +1,38 @@
+name: Baskerville Docs
+
+on:
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash
+
+permissions:
+  contents: write
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v3
+
+      - name: Install dependencies
+        run: |
+          cd ${{ github.workspace }}/src/docs
+          pip install -r requirements.txt
+      - name: Sphinx build
+        run: |
+          cd ${{ github.workspace }}/src/docs/source
+          rm -f *.rst make.bat
+          cd ${{ github.workspace }}/src
+          sphinx-apidoc -F -a -o docs/source baskerville
+          cd ${{ github.workspace }}/src/docs
+          make html
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ${{ github.workspace }}/src/docs/build/html
+          force_orphan: true

setup.cfg

@@ -35,6 +35,7 @@ install_requires =
     seaborn~=0.12.2
     scikit-learn~=1.2.2
     scipy~=1.9.1
+    sphinx~=7.2.6
     statsmodels~=0.13.5
     tabulate~=0.8.10
     tensorflow==2.13.0

src/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     = source
+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)

src/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=source
+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

src/docs/requirements.txt

@@ -0,0 +1,4 @@
+sphinx 
+sphinx_rtd_theme 
+python-dotenv
+google

src/docs/source/baskerville.helpers.rst

@@ -0,0 +1,19 @@
+baskerville.helpers Subpackages of helpers for the Baskerville package.
+==============================================================================
+
+Submodules
+----------
+
+baskerville.helpers.gcs_utils module
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.helpers.gcs_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.helpers.utils module
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.helpers.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:

src/docs/source/baskerville.rst

@@ -0,0 +1,98 @@
+baskerville package
+===================
+
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   baskerville.helpers
+   baskerville.scripts
+
+Submodules
+----------
+
+baskerville.bed module
+~~~~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: baskerville.bed
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.blocks module
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: baskerville.blocks
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.dataset module
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. automodule:: baskerville.dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.dna module
+~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.dna
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+baskerville.gene module
+~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.gene
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.layers module
+~~~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.layers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.metrics module
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.metrics
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.seqnn module
+~~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.seqnn
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.snps module
+~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.snps
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.trainer module
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.trainer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.vcf module
+~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.vcf
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+

src/docs/source/baskerville.scripts.rst

@@ -0,0 +1,53 @@
+baskerville.scripts Subpackages of scripts for the Baskerville project.
+=============================================================
+
+"""
+This package contains scripts for the Baskerville project
+that are not part of the main codebase.
+
+"""
+Submodules
+==========
+
+baskerville.scripts.hound_eval_spec module
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.scripts.hound_eval_spec
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.scripts.hound_eval module
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.scripts.hound_eval
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.scripts.hound_predbed module
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.scripts.hound_predbed
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+baskerville.scripts.hound_snp module
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.scripts.hound_snp
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.scripts.hound_snp_slurm module
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.scripts.hound_snp_slurm
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.scripts.hound_train module
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. automodule:: baskerville.scripts.hound_train
+   :members:
+   :undoc-members:
+   :show-inheritance:

src/docs/source/conf.py

@@ -0,0 +1,38 @@
+# 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
+import os
+import sys
+
+# This root should be where docs folder is visible.
+sys.path.insert(0, os.path.abspath("../.."))
+sys.setrecursionlimit(1500)
+
+project = "baskerville"
+copyright = "2023, David Kelly"
+author = "David Kelly"
+release = "0.0.1"
+
+# -- 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 = []
+
+
+# -- 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"]

src/docs/source/index.rst

@@ -0,0 +1,16 @@
+Welcome to baskerville's documentation!
+=======================================
+
+.. toctree::
+   :maxdepth: 4
+   :caption: Contents:
+
+   baskerville
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`