Add required files for docs site: https://py-tes.readthedocs.io

.github/workflows/docs.yml

@@ -33,4 +33,5 @@ jobs:
               tes
 
       - name: Build docs
-        run: mkdocs build
+        run: mkdocs build && mkdocs gh-deploy --force
+

.readthedocs.yaml

@@ -0,0 +1,32 @@
+# .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"
+    # 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/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

@@ -0,0 +1,177 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from https://www.sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/Snakemake.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Snakemake.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/Snakemake"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Snakemake"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

docs/_static/custom.css

@@ -0,0 +1,91 @@
+.image-reference img {
+    display: inline;
+    background: none !important;
+}
+
+.image-reference {
+    border-bottom: none !important;
+}
+
+:root {
+    --color-links: #047857;
+    --color-brand: #047857;
+}
+
+#content {
+    overflow-x: auto;
+}
+
+.sticky.top-16 {
+    overflow: unset;
+  }
+
+/* Light theme styles (default) */
+body.dark-theme {
+    background-color: black !important;
+}
+
+/* Dark theme styles */
+body.light-theme {
+    background-color: blue !important;
+}
+
+pre.light-theme .kn { color: #2838b0 !important } /* Keyword.Namespace */
+pre.light-theme .kp { color: #2838b0 !important } /* Keyword.Pseudo */
+pre.light-theme .kr { color: #2838b0 !important } /* Keyword.Reserved */
+pre.light-theme .kt { color: #2838b0; font-style: italic !important } /* Keyword.Type */
+pre.light-theme .m { color: #444444 !important } /* Literal.Number */
+pre.light-theme .s { color: #b83838 !important } /* Literal.String */
+pre.light-theme .na { color: #388038 !important } /* Name.Attribute */
+pre.light-theme .nb { color: #388038 !important } /* Name.Builtin */
+pre.light-theme .nc { color: #287088 !important } /* Name.Class */
+pre.light-theme .no { color: #b85820 !important } /* Name.Constant */
+pre.light-theme .nd { color: #287088 !important } /* Name.Decorator */
+pre.light-theme .ni { color: #709030 !important } /* Name.Entity */
+pre.light-theme .ne { color: #908828 !important } /* Name.Exception */
+pre.light-theme .nf { color: #785840 !important } /* Name.Function */
+pre.light-theme .nl { color: #289870 !important } /* Name.Label */
+pre.light-theme .nn { color: #289870 !important } /* Name.Namespace */
+pre.light-theme .nt { color: #2838b0 !important } /* Name.Tag */
+pre.light-theme .nv { color: #b04040 !important } /* Name.Variable */
+pre.light-theme .ow { color: #a848a8 !important } /* Operator.Word */
+pre.light-theme .pm { color: #888888 !important } /* Punctuation.Marker */
+pre.light-theme .w { color: #a89028 !important } /* Text.Whitespace */
+pre.light-theme .mb { color: #444444 !important } /* Literal.Number.Bin */
+pre.light-theme .mf { color: #444444 !important } /* Literal.Number.Float */
+pre.light-theme .mh { color: #444444 !important } /* Literal.Number.Hex */
+pre.light-theme .mi { color: #444444 !important } /* Literal.Number.Integer */
+pre.light-theme .mo { color: #444444 !important } /* Literal.Number.Oct */
+pre.light-theme .sa { color: #444444 !important } /* Literal.String.Affix */
+pre.light-theme .sb { color: #b83838 !important } /* Literal.String.Backtick */
+pre.light-theme .sc { color: #a848a8 !important } /* Literal.String.Char */
+pre.light-theme .dl { color: #b85820 !important } /* Literal.String.Delimiter */
+pre.light-theme .sd { color: #b85820; font-style: italic !important } /* Literal.String.Doc */
+pre.light-theme .s2 { color: #b83838 !important } /* Literal.String.Double */
+pre.light-theme .se { color: #709030 !important } /* Literal.String.Escape */
+pre.light-theme .sh { color: #b83838 !important } /* Literal.String.Heredoc */
+pre.light-theme .si { color: #b83838; text-decoration: underline !important } /* Literal.String.Interpol */
+pre.light-theme .sx { color: #a848a8 !important } /* Literal.String.Other */
+pre.light-theme .sr { color: #a848a8 !important } /* Literal.String.Regex */
+pre.light-theme .s1 { color: #b83838 !important } /* Literal.String.Single */
+pre.light-theme .ss { color: #b83838 !important } /* Literal.String.Symbol */
+pre.light-theme .bp { color: #388038; font-style: italic !important } /* Name.Builtin.Pseudo */
+pre.light-theme .fm { color: #b85820 !important } /* Name.Function.Magic */
+pre.light-theme .vc { color: #b04040 !important } /* Name.Variable.Class */
+pre.light-theme .vg { color: #908828 !important } /* Name.Variable.Global */
+pre.light-theme .vi { color: #b04040 !important } /* Name.Variable.Instance */
+pre.light-theme .vm { color: #b85820 !important } /* Name.Variable.Magic */
+pre.light-theme .il { color: #444444 !important } /* Literal.Number.Integer.Long */
+pre.light-theme .n { color: #444444 !important } /* Misc */
+pre.light-theme .o { color: #444 !important } /* Misc */
+pre.light-theme .p { color: #444 !important } /* Misc */
+pre.light-theme .k { color: #a848a8 !important } /* Misc */
+pre.light-theme .kc { color: #2838b0 !important } /* Misc */
+pre.light-theme .go { color: #546E7A !important } /* Misc */
+pre.light-theme .go { color: #546E7A !important } /* Misc */
+pre.light-theme .c1 { color: #546E7A !important } /* Misc */
+pre.light-theme .copy { background: #BBB !important } /* Misc */
+
+
+.c1 { color: #EEFFFF !important } /* Misc */
+.go { color: #EEFFFF !important } /* Misc */

docs/_static/custom.js

@@ -0,0 +1,28 @@
+// Select the button using its class, assuming it's the only one with this class
+const nav = document.querySelector(".flex.items-center.space-x-1");
+console.log(nav);
+
+const themeToggleButton = nav.childNodes[3];
+console.log(themeToggleButton);
+
+mode = localStorage.getItem('darkMode');
+setTheme(mode);
+
+// Add an event listener to the button
+themeToggleButton.addEventListener('click', function() {
+    mode = mode === 'light' ? 'dark' : 'light'
+    setTheme(mode);
+});
+
+function setTheme(mode) {
+    var pres = document.body.getElementsByTagName("pre");
+    for (let pre of pres) {
+        if (mode === 'dark') {
+            pre.classList.add('dark-theme');
+            pre.classList.remove('light-theme');
+        } else {
+            pre.classList.add('light-theme');
+            pre.classList.remove('dark-theme');
+        }
+    }
+}