Merge pull request #10 from cch1999/docs

chore: Add Read the Docs configuration files and Sphinx documentation…

.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # myst_parser: "2.0.0"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+   - requirements: docs/requirements.txt

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     = 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)

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=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

docs/requirements.txt

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+# Defining the exact version will make sure things don't break
+sphinx==7.2.6
+sphinx_rtd_theme==2.0.0
+readthedocs-sphinx-search==0.3.2
+myst-parser==2.0.0
+mpytools>=0.0.9
+numpy
+matplotlib
+plotly
+ase
+rdkit
+py3Dmol
+IPython
+kaleido

docs/source/conf.py

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+# 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
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath("../../"))
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'PoseCheck'
+copyright = '2024'
+author = 'Charlie Harris'
+release = '1.2'
+github_username = 'cch1999'
+github_repository = 'posecheck'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+              'sphinx.ext.autodoc',
+              'sphinx.ext.doctest',
+              'sphinx.ext.extlinks',
+              'sphinx.ext.mathjax',
+              'sphinx.ext.viewcode',
+              'sphinx.ext.napoleon',
+              'sphinx.ext.intersphinx']
+
+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']
+
+source_suffix = '.rst'
+master_doc = 'index'
+# project = 'ASE'
+# copyright = f'{datetime.date.today().year}, ASE-developers'
+# templates_path = ['templates']
+exclude_patterns = ['build']
+# default_role = 'math'
+# pygments_style = 'sphinx'
+autoclass_content = 'both'
+modindex_common_prefix = ['mp.']

docs/source/index.rst

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+.. MolParse documentation master file, created by
+   sphinx-quickstart on Wed Mar 13 13:02:45 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+======================
+PoseCheck Documentation
+======================
+
+**Warning: this documentation is WIP**
+
+PoseCheck is a python package for checking the quality of 3D molecules poses from molecular generative models.
+
+Installation
+============
+
+Install from PyPI
+
+::
+
+   git clone https://github.com/cch1999/posecheck.git
+   cd posecheck
+
+   pip install -e .
+   pip install -r requirements.txt
+   conda install -c mx reduce
+
+Getting Started
+===============
+
+TODO
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   hight level API