Merge pull request #2 from birdday/docs

Initial Docs build.

.github/workflows/sphinx.yml

@@ -0,0 +1,60 @@
+name: "Sphinx: Render docs"
+
+on: push
+
+jobs:
+  build:
+    runs-on: macos-latest
+    permissions:
+      contents: write
+
+    env:
+      ETS_TOOLKIT: qt4
+      QT_API: "pyqt5"
+      TVTK_VERBOSE: "true"
+      VTK_PARSER_VERBOSE: "true"
+      PYTHONUNBUFFERED: "1"
+      USER: "github-pages"
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+      - name: Install Linux packages for Qt5/Qt6 support and start Xvfb
+        uses: pyvista/setup-headless-display-action@v3
+        with:
+          qt: true
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+      - name: Upgrade pip, install package, install requirements, build docs
+        run: |
+          pip install --upgrade pip
+          pip install -r ./docs/requirements.txt
+      - name: Install dependencies
+        run: |
+          set -exo pipefail
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install --upgrade pyqt5 numpy vtk pillow pytest pytest-timeout traits traitsui --only-binary="numpy,vtk"
+      - name: Install mayavi and tvtk
+        run: pip install mayavi
+      # - name: Test Mayavi package
+      #   run: pytest -v --timeout=10 mayavi
+      # - name: Test tvtk package
+      #   run: pytest -sv --timeout=60 tvtk
+      - name: Install Atomaton
+        run: pip install -e .
+      - name: Build Docs
+        run: sphinx-build docs ./docs/_build/html/
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: html-docs
+          path: docs/_build/html/
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        if: github.ref == 'refs/heads/master'
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/_build/html/

atomaton/visualize.py

@@ -1,5 +1,7 @@
 import imageio
-import mayavi.mlab as mlab
+import os
+if not (os.environ.get("USER") == "github-pages"):
+    import mayavi.mlab as mlab
 import numpy as np
 import matplotlib.cm
 

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)

docs/conf.py

@@ -0,0 +1,41 @@
+# 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
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here.
+import sys
+from pathlib import Path
+sys.path.insert(0, str(Path(__file__).resolve().parents[2]))
+import atomaton
+
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'Atomaton'
+copyright = '2024, Brian A. Day'
+author = 'Brian A. Day'
+release = '0.1.0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.duration',
+    'sphinx.ext.doctest',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'pydata_sphinx_theme'
+html_static_path = ['_static']

docs/index.rst

@@ -0,0 +1,38 @@
+.. Atomaton documentation master file, created by
+   sphinx-quickstart on Fri Feb  2 21:53:39 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Atomaton's documentation!
+====================================
+
+.. toctree::
+   :maxdepth: 10
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+
+
+Contents
+--------
+
+.. toctree::
+
+   usage
+   lammps
+   visualize
+
+Check out the :doc:`usage` section for further information, including how to
+:ref:`install <installation>` the project.
+
+Learn how to :ref:`view structures <visualization>` and generate movies!
+
+Integrate with :ref:`LAMMPS <lammps>`!

docs/lammps.rst

@@ -0,0 +1,12 @@
+LAMMPS
+======
+
+.. _lammps:
+
+LAMMPS Input File Generation: :mod:`atomaton.write_lammps_files` 
+----------------------------------------------------------------
+
+.. automodule:: atomaton.write_lammps_files
+   :members:
+   :undoc-members:
+   :show-inheritance:

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

docs/requirements.txt

@@ -0,0 +1,2 @@
+sphinx==7.4.7
+pydata-sphinx-theme

docs/usage.rst

@@ -0,0 +1,23 @@
+Usage
+=====
+
+.. _installation:
+
+Installation
+------------
+
+To use Atomaton, first install it using pip:
+
+.. code-block:: console
+
+   (.venv) $ pip install atomaton
+
+
+Analyzer: :mod:`atomaton.analyze` 
+--------------------------------------------
+
+.. automodule:: atomaton.analyze
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

docs/visualize.rst

@@ -0,0 +1,12 @@
+View structures
+=====
+
+.. _visualization:
+
+Visualizer: :mod:`atomaton.visualize` 
+--------------------------------------------
+
+.. automodule:: atomaton.visualize
+   :members:
+   :undoc-members:
+   :show-inheritance:

setup.py

@@ -10,6 +10,6 @@
     author_email="[email protected]",
     url="https://github.com/birdday/atomaton",
     packages=["atomaton"],
-    install_requires=["numpy", "ase", "vtk==9.2.6", "mayavi", "imageio", "pyqt5", ],
+    install_requires=["numpy", "ase", "vtk", "mayavi", "imageio", "PyQt6"],
     tests_require=["pytest"],
 )