Overhaul sphinx docs

.github/workflows/documentation.yml

@@ -14,17 +14,19 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v6
-    - name: Set up Python 3.10
+    - name: Set up Python 3.12
       uses: actions/setup-python@v6
       with:
-        python-version: '3.10'
+        python-version: '3.12'
     - name: Install dependencies
       run: |
         pip install .[develop]
     - name: Build the docs
       run: |
         sphinx-apidoc -f -o docs/source pisa
         cd docs && make html
+      env:
+        SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ github.token }}
     - name: Deploy to gh pages
       uses: peaceiris/actions-gh-pages@v4
       with:

INSTALL.md

@@ -216,16 +216,22 @@ Support for all of these comes pre-packaged or as `conda`/`mamba`-installable pa
     `sudo apt install git`
   * it is already installed on IceCube's Cobalt nodes
 
-Required Python modules whose installation is taken care of by pip are specified in [setup.py](setup.py).
+Required Python modules whose installation is taken care of by pip are specified in [setup.py](https://github.com/icecube/pisa/blob/master/setup.py).
 
 ### Optional Dependencies
 
 Some of the following optional dependencies must be installed manually prior to installing PISA, and some will be installed automatically by pip, and this seems to vary from system to system. Therefore you can first try to run the installation, and just install whatever pip says it needed, or just use apt, pip, or conda/mamba to install the below before running the PISA installation.
 
 * [emcee](https://github.com/dfm/emcee) Required for MCMC sampling functionality in the `llh_client`& `llh_server` utils modules and the `analysis` module.
+* [Furo Sphinx Theme](https://pradyunsg.me/furo/) Sphinx extension HTML theme. (Required to compile PISA's documentation.)
+  * Installed alongside PISA if you specify option `['develop']` to `pip`
 * [GLoBES wrapper](https://github.com/atrettin/GLoBES_wrapper) Required for `osc.globes` service.
 * [LeptonWeighter](https://github.com/icecube/leptonweighter) Required for `data.licloader_weighter` service.
+* [linkify-it-py](https://github.com/tsutsu3/linkify-it-py) MyST-Parser extension for converting bare URLs into hyperlinks. (Required to compile PISA's documentation.)
+  * Installed alongside PISA if you specify option `['develop']` to `pip`
 * [MCEq](https://github.com/mceq-project/MCEq) Required for `create_barr_sys_tables_mceq.py` script.
+* [MyST-NB](https://myst-nb.readthedocs.io/) Sphinx extension for compiling markdown and jupyter notebooks. (Required to compile PISA's documentation.)
+  * Installed alongside PISA if you specify option `['develop']` to `pip`
 * [nuSQuiDS](https://github.com/arguelles/nuSQuIDS) Required for `osc.nusquids` service.
 * [OpenMP](https://openmp.org) Intra-process parallelization to accelerate code on on multi-core/multi-CPU computers.
   * Available from your compiler: gcc supports OpenMP 4.0 and Clang >= 3.8.0 supports OpenMP 3.1. Either version of OpenMP should work, but Clang has yet to be tested for its OpenMP support.
@@ -234,25 +240,25 @@ Some of the following optional dependencies must be installed manually prior to
   * Installed alongside PISA if you specify option `['develop']` to `pip`
 * [Pytest](https://docs.pytest.org/) Python testing framework. Used by a couple unit tests.
   * Installed alongside PISA if you specify option `['develop']` to `pip`
-* [recommonmark](http://recommonmark.readthedocs.io/en/latest/) Translator to allow markdown docs/docstrings to be used; plugin for Sphinx. (Required to compile PISA's documentation.)
-  * Installed alongside PISA if you specify option `['develop']` to `pip`
 * [ROOT >= 6.12.04 with PyROOT](https://root.cern.ch) Required for `absorption.earth_absorption` service, and to read ROOT cross section files in the `crossSections` utils module. Due to a bug in ROOT's Python support (documented here https://github.com/IceCubeOpenSource/pisa/issues/430), you need at least version 6.12.04 of ROOT.
-* [Sphinx >= 1.3](https://www.sphinx-doc.org)
+* [Sphinx >= 1.3](https://www.sphinx-doc.org) Documentation generator. (Required to compile PISA's documentation.)
   * Installed alongside PISA if you specify option `['develop']` to `pip`
-* [Read the Docs Sphinx Theme](https://github.com/readthedocs/sphinx_rtd_theme)
+* [Sphinx Github Changelog](https://sphinx-github-changelog.readthedocs.io) Sphinx extension for building a changelog from GitHub releases. (Required to compile PISA's documentation.)
   * Installed alongside PISA if you specify option `['develop']` to `pip`
 * [versioneer](https://github.com/python-versioneer/python-versioneer) Automatically get versions from git and make these embeddable and usable in code. Note that the install process is unique since it first places `versioneer.py` in the PISA root directory, and then updates source files within the repository to provide static and dynamic version info.
   * Installed alongside PISA if you specify option `['develop']` to `pip`
-* [black](https://github.com/psf/black) Format your Python code, _automatically_, with typically very nice results!
 
 ### Compile the documentation
 
-In case you installed the optional "develop" dependencies, you can compile a (new) version of the documentation to html via
+In case you installed the optional "develop" dependencies, you can compile a (new) version of the documentation to html locally. Be aware that the above Sphinx Github Changelog extension requires authentication using a GitHub API token.
+If you don't have a suitable personal access token yet, generate one with a public-repo scope and assign it to the `GITHUB_TOKEN` environment variable before running `make` below.
+
+In case code structure has changed, regenerate the source files that document all of PISA's (sub-)packages and modules by executing
 ```bash
 cd $PISA && sphinx-apidoc -f -o docs/source pisa
 ```
 
-In case code structure has changed, rebuild the API documentation by executing
+Finally, rebuild the HTML documentation by executing
 ```bash
 cd $PISA/docs && make html
 ```

LICENSE

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright (c) 2014-2025 The IceCube Collaboration
+   Copyright (c) 2014-2026 The IceCube Collaboration
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

README.md

@@ -15,7 +15,7 @@
 
 PISA is a software written to analyze the results (or expected results) of an experiment based on Monte Carlo (MC) simulation.
 
-In particular, PISA was written by and for the IceCube Collaboration for analyses employing the [IceCube Neutrino Observatory](https://icecube.wisc.edu/), including the [DeepCore](https://arxiv.org/abs/1109.6096) and the planned [Upgrade](https://arxiv.org/abs/2307.15295) low-energy in-fill arrays.
+In particular, PISA was written by and for the IceCube Collaboration for analyses employing the [IceCube Neutrino Observatory](https://icecube.wisc.edu/), including the [DeepCore](https://arxiv.org/abs/1109.6096) and the [Upgrade](https://arxiv.org/abs/2509.13066) low-energy in-fill arrays.
 
 > [!NOTE]
 > However, any experiment can make use of PISA for analyzing expected and actual results.

docs/Makefile

@@ -1,216 +1,21 @@
-# Makefile for Sphinx documentation
+# Minimal makefile for Sphinx documentation
 #
 
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-PAPER         =
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+# ubuntu-latest provides 4 CPUs (https://docs.github.com/en/actions/reference/runners/github-hosted-runners#standard-github-hosted-runners-for-public-repositories)
+SPHINXOPTS    ?= -v -j 4
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
 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 http://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) source
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
-
-.PHONY: help
+# Put it first so that "make" without argument is like "make help".
 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 "  applehelp  to make an Apple Help Book"
-	@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)"
-	@echo "  coverage   to run coverage check of the documentation (if enabled)"
-
-.PHONY: clean
-clean:
-	rm -rf $(BUILDDIR)/*
-
-.PHONY: html
-html:
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-.PHONY: dirhtml
-dirhtml:
-	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
-	@echo
-	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
-
-.PHONY: singlehtml
-singlehtml:
-	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
-	@echo
-	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
-
-.PHONY: pickle
-pickle:
-	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
-	@echo
-	@echo "Build finished; now you can process the pickle files."
-
-.PHONY: json
-json:
-	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
-	@echo
-	@echo "Build finished; now you can process the JSON files."
-
-.PHONY: htmlhelp
-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."
-
-.PHONY: qthelp
-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/PISA.qhcp"
-	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/PISA.qhc"
-
-.PHONY: applehelp
-applehelp:
-	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
-	@echo
-	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
-	@echo "N.B. You won't be able to view it unless you put it in" \
-	      "~/Library/Documentation/Help or install it in your application" \
-	      "bundle."
-
-.PHONY: devhelp
-devhelp:
-	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
-	@echo
-	@echo "Build finished."
-	@echo "To view the help file:"
-	@echo "# mkdir -p $$HOME/.local/share/devhelp/PISA"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/PISA"
-	@echo "# devhelp"
-
-.PHONY: epub
-epub:
-	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
-	@echo
-	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
-
-.PHONY: latex
-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)."
-
-.PHONY: latexpdf
-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."
-
-.PHONY: latexpdfja
-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."
-
-.PHONY: text
-text:
-	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
-	@echo
-	@echo "Build finished. The text files are in $(BUILDDIR)/text."
-
-.PHONY: man
-man:
-	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
-	@echo
-	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
-
-.PHONY: texinfo
-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)."
-
-.PHONY: info
-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."
-
-.PHONY: gettext
-gettext:
-	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
-	@echo
-	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
-
-.PHONY: changes
-changes:
-	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
-	@echo
-	@echo "The overview file is in $(BUILDDIR)/changes."
-
-.PHONY: linkcheck
-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."
-
-.PHONY: doctest
-doctest:
-	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
-	@echo "Testing of doctests in the sources finished, look at the " \
-	      "results in $(BUILDDIR)/doctest/output.txt."
-
-.PHONY: coverage
-coverage:
-	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
-	@echo "Testing of coverage in the sources finished, look at the " \
-	      "results in $(BUILDDIR)/coverage/python.txt."
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-.PHONY: xml
-xml:
-	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
-	@echo
-	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+.PHONY: help Makefile
 
-.PHONY: pseudoxml
-pseudoxml:
-	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
-	@echo
-	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
+# 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/source/_static/custom.css

@@ -0,0 +1,3 @@
+.sidebar-brand-text {
+  font-size: 0.8rem !important; /* reduce sidebar title font size to some visually pleasing fraction */
+}

docs/source/changelog.rst

@@ -0,0 +1,6 @@
+=========
+Changelog
+=========
+
+.. changelog::
+   :github: https://github.com/icecube/pisa/releases/