Merge pull request NHERI-SimCenter#70 from ioannis-vm/docs

Introduce documentation pages.

.github/workflows/build_docs.yaml

@@ -0,0 +1,31 @@
+name: Build and deploy documentation
+on:
+  push:
+    branches:
+      - docs
+jobs:
+  build-docs:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.10']
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc
+          python -m pip install -e .[development]
+      - name: Build docs
+        run: cd doc && make html
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./doc/build/html

.github/workflows/docs_check.yaml

@@ -0,0 +1,32 @@
+name: Check for Sphinx Warnings
+
+on:
+  pull_request:
+    paths:
+      - "doc/**"
+      - "**/*.rst"
+      - ".github/workflows/docs_check.yaml"
+      - "setup.py"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out the repository
+      uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.x'
+
+    - name: Install dependencies
+      run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc
+          python -m pip install -e .[development]
+
+    - name: Check for Sphinx warnings
+      run: |
+        sphinx-build -M html ./doc/source ./doc/_build --fail-on-warning

doc/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)

doc/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

doc/source/_extensions/latest_citation.py

@@ -0,0 +1,56 @@
+# noqa: INP001, CPY001, D100
+import requests
+from docutils import nodes
+from docutils.parsers.rst import Directive
+
+
+class LatestCitationDirective(Directive):  # noqa: D101
+    def run(self):  # noqa: ANN201, D102
+        citation_text, bibtex_text = self.get_latest_zenodo_citation()
+
+        # Create nodes for the standard citation and BibTeX
+        citation_node = nodes.paragraph(text=citation_text)
+        bibtex_node = nodes.literal_block(text=bibtex_text, language='bibtex')
+
+        return [citation_node, bibtex_node]
+
+    def get_latest_zenodo_citation(self):  # noqa: PLR6301, ANN201, D102
+        url = 'https://zenodo.org/api/records/?q=conceptdoi:10.5281/zenodo.2558557&sort=mostrecent'
+        try:
+            response = requests.get(url)  # noqa: S113
+        except requests.exceptions.ConnectionError:
+            return '(No Connection)', ''
+        data = response.json()
+        latest_record = data['hits']['hits'][0]
+        authors = [
+            author['name'] for author in latest_record['metadata']['creators']
+        ]
+        combine_chars = [', '] * (len(authors) - 2) + [', and ']
+        author_str = authors[0]
+        for author, combine_char in zip(authors[1::], combine_chars):
+            author_str += combine_char + author
+        title = latest_record['metadata']['title'].split(': ')[0]
+        version = latest_record['metadata']['version']
+        doi = latest_record['metadata']['doi']
+        year = latest_record['metadata']['publication_date'][:4]
+        month = latest_record['metadata']['publication_date'][5:7]  # noqa: F841
+        publisher = 'Zenodo'
+
+        # Standard citation
+        citation_text = f'{author_str} ({year}) {title}. DOI:{doi}'
+
+        # BibTeX citation
+        bibtex_text = f"""@software{{{author_str.replace(" ", "_").replace(",", "").replace("_and_", "_").lower()}_{year}_{doi.split('.')[-1]},
+  author       = {{{" and ".join(authors)}}},
+  title        = {{{title}}},
+  year         = {year},
+  publisher    = {{{publisher}}},
+  version      = {{{version}}},
+  doi          = {{{doi}}},
+}}"""
+
+        return citation_text, bibtex_text
+
+
+def setup(app):  # noqa: ANN201, D103, ANN001
+    app.add_directive('latest-citation', LatestCitationDirective)

doc/source/_static/css/custom.css

@@ -0,0 +1,33 @@
+wy-nav-content {
+    max-width: none;
+}
+
+
+.math {
+    text-align: left;
+}
+
+.eqno {
+    float: right;
+}
+
+
+#div.wy-side-scroll{
+#	background:#cb463f;
+#}
+
+div.wy-menu.wy-menu-vertical > .caption {
+	 color: #cb463f;
+}
+
+# LIGHT BLUE  background:#0099ff
+# BLUE: background:#0B619C
+# ADAM RED: background:#cb463f;
+
+span.caption.caption-text{
+	color: #000000;
+}
+
+td{
+	white-space: normal !important;
+}