Files for setting up the github workflow/Docs were copied from MALA a…

…nd originally authored by Daniel Kotik

Co-authored-by: Daniel Kotik <d.kotik@hzdr.de>

.github/workflows/gh-pages.yml

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+name: docs
+
+on:
+  pull_request:
+    branches:
+      - master
+      - develop
+      - main
+  push:
+    branches:
+      - main
+      - develop
+
+jobs:
+  test-docstrings:
+    runs-on: ubuntu-18.04
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.8'
+
+      - name: Upgrade pip
+        run: python3 -m pip install --upgrade pip
+
+      - name: Install dependencies
+        run: pip install -qU pydocstyle
+
+      - name: Check docstrings
+        run: pydocstyle --convention=numpy malada
+
+  build-and-deploy-pages:
+    needs: test-docstrings
+    runs-on: ubuntu-18.04
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0  # 0 fetches complete history and tags
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.8'
+
+      - name: Upgrade pip
+        run: python3 -m pip install --upgrade pip
+
+      - name: Install dependencies
+        run: |
+          pip install -q -r docs/requirements.txt
+
+      - name: Build API and docs
+        run: |
+          sphinx-apidoc -o docs/source/api malada
+          sphinx-build -W --keep-going -b html -d docs/_build/doctrees docs/source docs/_build/html
+          mv -v docs/_build/html public
+
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./public

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)
+
+apidocs:
+	sphinx-apidoc -f -o source/api ../malada

docs/requirements.txt

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+docutils==0.16         # dependency of myst-parser; problems with 0.17.*
+sphinx==3.5.*
+sphinx_rtd_theme==0.5.*
+myst-parser==0.14.*
+sphinx-markdown-tables==0.0.15

docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import subprocess
+import sys
+# sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath('../../'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'Materials Learning Algorithms Data Acquisition (MALADA)'
+copyright = 'noneyet'
+
+author = 'L. Fiedler'
+
+# The version info for the project
+tag = subprocess.run(['git', 'describe', '--tags'], capture_output=True,
+                        text=True)
+version = tag.stdout.strip()
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'myst_parser',
+    'sphinx_markdown_tables',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.napoleon',
+#    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+]
+
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+
+autodoc_mock_imports = [
+    'ase',
+    'optuna',
+    'mpmath',
+    'torch',
+    'numpy',
+    'scipy',
+    'oapackage',
+    'matplotlib',
+    'horovod',
+    'lammps',
+    'total_energy',
+]
+
+autodoc_member_order = 'groupwise'
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = []
+
+html_context = {
+  'display_github': True,
+  'github_repo': 'mala-project/malada',
+  'github_version': 'develop',
+  'conf_py_path': '/docs/source/',
+}
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = "./img/logos/mala_vertical.png"
+
+# The name of an image file (relative to this directory) to use as a favicon of
+# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+html_favicon = "./img/logos/mala_favicon.png"
+
+# The suffix of source file names.
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.txt': 'markdown',
+    '.md': 'markdown',
+}