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chore: Add Read the Docs configuration files and Sphinx documentation…
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# .readthedocs.yaml | ||
# Read the Docs configuration file | ||
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details | ||
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# Required | ||
version: 2 | ||
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# 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" | ||
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# Build documentation in the "docs/" directory with Sphinx | ||
sphinx: | ||
configuration: docs/source/conf.py | ||
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# Optionally build your docs in additional formats such as PDF and ePub | ||
# formats: | ||
# - epub | ||
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# 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 |
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# Minimal makefile for Sphinx documentation | ||
# | ||
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# 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 | ||
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# Put it first so that "make" without argument is like "make help". | ||
help: | ||
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) | ||
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.PHONY: help Makefile | ||
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# 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) |
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@ECHO OFF | ||
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pushd %~dp0 | ||
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REM Command file for Sphinx documentation | ||
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if "%SPHINXBUILD%" == "" ( | ||
set SPHINXBUILD=sphinx-build | ||
) | ||
set SOURCEDIR=source | ||
set BUILDDIR=build | ||
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%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 | ||
) | ||
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if "%1" == "" goto help | ||
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% | ||
goto end | ||
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:help | ||
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% | ||
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:end | ||
popd |
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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 |
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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 | ||
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import os | ||
import sys | ||
sys.path.insert(0, os.path.abspath("../../")) | ||
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# -- Project information ----------------------------------------------------- | ||
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information | ||
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project = 'PoseCheck' | ||
copyright = '2024' | ||
author = 'Charlie Harris' | ||
release = '1.2' | ||
github_username = 'cch1999' | ||
github_repository = 'posecheck' | ||
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# -- General configuration --------------------------------------------------- | ||
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration | ||
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extensions = [ | ||
'sphinx.ext.autodoc', | ||
'sphinx.ext.doctest', | ||
'sphinx.ext.extlinks', | ||
'sphinx.ext.mathjax', | ||
'sphinx.ext.viewcode', | ||
'sphinx.ext.napoleon', | ||
'sphinx.ext.intersphinx'] | ||
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templates_path = ['_templates'] | ||
exclude_patterns = [] | ||
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# -- Options for HTML output ------------------------------------------------- | ||
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output | ||
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html_theme = 'sphinx_rtd_theme' | ||
html_static_path = ['_static'] | ||
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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.'] |
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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 | ||
====================== | ||
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**Warning: this documentation is WIP** | ||
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PoseCheck is a python package for checking the quality of 3D molecules poses from molecular generative models. | ||
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Installation | ||
============ | ||
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Install from PyPI | ||
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:: | ||
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git clone https://github.com/cch1999/posecheck.git | ||
cd posecheck | ||
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pip install -e . | ||
pip install -r requirements.txt | ||
conda install -c mx reduce | ||
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Getting Started | ||
=============== | ||
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TODO | ||
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.. toctree:: | ||
:maxdepth: 2 | ||
:caption: Contents: | ||
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hight level API |