docs: basic sphinx docs

.github/workflows/docs.yml

@@ -0,0 +1,102 @@
+name: Docs
+
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Build docs
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v5
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+
+    - name: Install Python dependencies
+      run: |
+        python -m pip install uv
+        uv pip --quiet install --system --upgrade ".[docs,test]"
+        uv pip install --system yq
+        python -m pip list
+
+    - name: Install apt-get dependencies
+      run: |
+        sudo apt-get update
+        # Ubuntu 22.04's pandoc is too old (2.9.2.x), so install manually
+        # until the ubuntu-latest updates.
+        curl --silent --location --remote-name https://github.com/jgm/pandoc/releases/download/3.1.6.2/pandoc-3.1.6.2-1-amd64.deb
+        sudo apt-get install ./pandoc-*amd64.deb
+
+    - name: Check docstrings
+      run: |
+        # ignore D107 missing comment for __init__, since starting from 1.0.0 there are no more __init__ functions
+        pydocstyle --select=D100,D101,D102,D103,D104,D105,D106 src/pylhe/
+
+    - name: Verify CITATION.cff schema
+      run: |
+        jsonschema <(curl -sL "https://citation-file-format.github.io/1.2.0/schema.json") --instance <(cat CITATION.cff | yq)
+
+    - name: Check for broken links
+      run: |
+        pushd docs
+        make linkcheck
+        # Don't ship the linkcheck
+        rm -r build/linkcheck
+        popd
+
+    - name: Build docs
+      run: |
+        pushd docs
+        make html
+
+    - name: Fix permissions if needed
+      run: |
+        chmod -c -R +rX "docs/build/html/" | while read line; do
+          echo "::warning title=Invalid file permissions automatically fixed::$line"
+        done
+
+    - name: Upload artifact
+      uses: actions/upload-pages-artifact@v3
+      with:
+        path: 'docs/build/html'
+
+  deploy:
+    name: Deploy docs to GitHub Pages
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    needs: build
+    # Set permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+    permissions:
+      contents: read
+      pages: write
+      id-token: write
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Setup Pages
+      uses: actions/configure-pages@v5
+
+    - name: Deploy to GitHub Pages
+      id: deployment
+      uses: actions/deploy-pages@v4

.gitignore

@@ -30,3 +30,7 @@ config.rst
 .pytest_cache
 htmlcov
 .benchmarks
+
+docs/source/_autosummary
+docs/source/examples/*.lhe
+docs/source/examples/*.lhe.gz

.readthedocs.yaml

@@ -0,0 +1,29 @@
+# .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 version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  apt_packages:
+    - curl
+    - jq
+  jobs:
+    post_create_environment:
+      - pip install uv
+    post_install:
+      # VIRTUAL_ENV needs to be set manually for now.
+      # See https://github.com/readthedocs/readthedocs.org/pull/11152/
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install '.[docs]'
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF and ePub
+formats: all

README.md

@@ -1,6 +1,6 @@
 # pylhe: Python LHE interface
 
-<img src="https://raw.githubusercontent.com/scikit-hep/pylhe/main/docs/_static/img/pylhe-logo.png" alt="pylhe logo" width="250"/>
+<img src="https://raw.githubusercontent.com/scikit-hep/pylhe/main/docs/source/_static/img/pylhe-logo.png" alt="pylhe logo" width="250"/>
 
 [![GitHub Project](https://img.shields.io/badge/GitHub--blue?style=social&logo=GitHub)](https://github.com/scikit-hep/pylhe)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1217031.svg)](https://doi.org/10.5281/zenodo.1217031)
@@ -75,7 +75,7 @@ event.graph.render(filename="test", format="pdf", cleanup=True)
 
 ### Writing
 
-For a full example see [write](examples/write_monte_carlo_example.ipynb) or [filter](examples/filter_events_example.ipynb).
+For a full example see [write](examples/03_write_monte_carlo_example.ipynb) or [filter](examples/02_filter_events_example.ipynb).
 The values in the sketch below are intentionally left empty since they depend on the use-case.
 The data structure of `pylhe` is:
 
@@ -159,6 +159,20 @@ The preferred BibTeX entry for citation of `pylhe` is
 }
 ```
 
+`pylhe` has been referenced in:
+
+* [Constraints on the trilinear and quartic Higgs couplings from triple Higgs production at the LHC and beyond](https://inspirehep.net/literature/2734125) (2023)
+* [BSM reach of four-top production at the LHC](https://inspirehep.net/literature/2633019) (2023)
+* [Probing compressed higgsinos with forward protons at the LHC](https://inspirehep.net/literature/2140007) (2023)
+* [FLArE up dark sectors with EM form factors at the LHC Forward Physics Facility](https://inspirehep.net/literature/2085195) (2022)
+* [Probing Neutrino-Portal Dark Matter at the Forward Physics Facility](https://inspirehep.net/literature/1966337) (2021)
+* [Looking forward to test the KOTO anomaly with FASER](https://inspirehep.net/literature/1801897) (2020)
+* [Probing Light Gauge Bosons in Tau Neutrino Experiments](https://inspirehep.net/literature/1794757) (2020)
+* [Benchmarking simplified template cross sections in WH production](https://inspirehep.net/literature/1750323) (2019)
+* [MadMiner: Machine learning-based inference for particle physics](https://inspirehep.net/literature/1746275) (2019)
+* [Search Strategy for Sleptons and Dark Matter Using the LHC as a Photon Collider](https://inspirehep.net/literature/1703804) (2018)
+
+
 ## Contributors
 
 We hereby acknowledge the contributors that made this project possible ([emoji key](https://allcontributors.org/docs/en/emoji-key)):

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     = 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)

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=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

docs/source/_templates/as_module.rst

@@ -0,0 +1,15 @@
+:mod:`{{fullname}}`
+======================
+
+.. currentmodule:: {{fullname}}
+
+
+.. automodule:: {{fullname}}
+   :members:
+
+   .. autosummary::
+   {% for element in functions %}
+      {{element}}
+   {% endfor %}
+
+   .. rubric:: Functions

docs/source/_templates/custom-class-template.rst

@@ -0,0 +1,33 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :show-inheritance:
+   :inherited-members:
+
+   {% block methods %}
+   .. automethod:: __init__
+
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+      :nosignatures:
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

docs/source/_templates/custom-module-template.rst

@@ -0,0 +1,52 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module Attributes
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :template: custom-class-template.rst
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

docs/source/conf.py

@@ -0,0 +1,58 @@
+# 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
+import os
+import re
+from datetime import datetime
+
+# we use toml to read pyproject.toml
+# the python provided toml parser does not support older python versions
+import toml
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+try:
+    info = toml.load("../../pyproject.toml")
+except FileNotFoundError:
+    info = toml.load("pyproject.toml")
+project = info["project"]["name"]
+current_year = datetime.now().year
+copyright = f"{current_year}, The Scikit-HEP admins"
+# Handle multiple authors
+authors_list = info.get("authors", [])
+author_names = [a.get("name", "") for a in authors_list if "name" in a]
+author = ", ".join(author_names)
+version = re.sub("^", "", os.popen("git describe --tags").read().strip())
+rst_epilog = f""".. |project| replace:: {project} \n\n"""
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "myst_nb",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.todo",
+    "sphinx.ext.doctest",
+    "sphinx_math_dollar",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.coverage",
+]
+nb_execution_mode = "off"
+templates_path = ["_templates"]
+exclude_patterns = []
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
+
+# Patterns of URLs to ignore
+linkcheck_ignore = [
+    # Currently, down or blocking
+    r"https?://allcontributors\.org/.*",
+]