Sphinx-generated documentation

.github/workflows/compilation.yml

@@ -34,8 +34,8 @@ jobs:
 
       - name: Print Versions
         run: |
-          .github/workflows/pip-versions.sh      
-      
+          .github/workflows/pip-versions.sh
+
 
   centos-stream:
     runs-on: ubuntu-latest
@@ -60,8 +60,8 @@ jobs:
 
          - name: Print Versions
            run: |
-             .github/workflows/pip-versions.sh              
-             
+             .github/workflows/pip-versions.sh
+
 
 
   ubuntu:
@@ -88,7 +88,7 @@ jobs:
 
          - name: Print Versions
            run: |
-             .github/workflows/pip-versions.sh              
+             .github/workflows/pip-versions.sh
 
 
   conda:
@@ -120,7 +120,7 @@ jobs:
 
          - name: Print Versions
            run: |
-             .github/workflows/conda-versions.sh              
+             .github/workflows/conda-versions.sh
 
   mpich:
     runs-on: ubuntu-latest
@@ -145,4 +145,7 @@ jobs:
 
          - name: Print Versions
            run: |
-             .github/workflows/pip-versions.sh
+             .github/workflows/pip-versions.sh
+
+  build-docs:
+    uses: ./.github/workflows/docs-build.yml

.github/workflows/docs-build.yml

@@ -0,0 +1,42 @@
+on:
+  workflow_call:
+    inputs:
+      upload-artifact:
+        required: false
+        type: boolean
+        default: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: po3
+          channels: conda-forge,defaults
+          auto-update-conda: true
+          environment-file: docs-environment.yml
+
+      - name: Install PyORBIT3
+        shell: bash -l {0}
+        run: |
+          # @woodtp -- MPI isn't required to build docs and enabling it causes Sphinx to segfault.
+          conda activate po3
+          pip install --config-settings=setup-args="-DUSE_MPI='none'" .
+
+      - name: Build Documentation
+        shell: bash -l {0}
+        run: |
+          conda activate po3
+          cd doc
+          make html
+
+      - name: Upload artifact
+        if: ${{ inputs.upload-artifact }}
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: './doc/build/html'

.github/workflows/docs.yml

@@ -1,12 +1,9 @@
-# Simple workflow for deploying static content to GitHub Pages
 name: Deploy Documentation to Pages
 
 on:
-  # Runs on pushes targeting the default branch
   push:
     branches: ["main"]
 
-  # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
 # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
@@ -22,29 +19,18 @@ concurrency:
   cancel-in-progress: false
 
 jobs:
-  # Single deploy job since we're just deploying
+  build:
+    uses: ./.github/workflows/docs-build.yml
+    with:
+      upload-artifact: true
+
   deploy:
+    needs: build
+    runs-on: ubuntu-latest
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}
-    runs-on: ubuntu-latest
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          activate-environment: po3
-          environment-file: docs-environment.yml
-      - uses: ammaraskar/sphinx-action@master
-        with:
-          docs-folder: "doc/"
-      # - name: Setup Pages
-      #   uses: actions/configure-pages@v5
-      - name: Upload artifact
-        uses: actions/upload-pages-artifact@v3
-        with:
-          # Upload entire repository
-          path: './doc/build/html'
       - name: Deploy to GitHub Pages
         id: deployment
         uses: actions/deploy-pages@v4

.gitignore

@@ -9,3 +9,5 @@ PyORBIT.egg-info
 *.so
 .*.swp
 .eggs
+.venv
+_autosummary/

README.md

@@ -29,16 +29,16 @@ The following commands may require root access.
 
 <details>
   <summary> Click for Ubuntu-based distributions</summary>
-  
+
   ```bash
   apt-get update
   apt-get install -y  build-essential python3 libfftw3-dev python3-venv libpython3-dev pkg-config git
-  ```    
+  ```
 </details>
 
 <details>
   <summary> Click for Redhat-based distributions</summary>
-  
+
   ```bash
   dnf group install -y "Development Tools"
   dnf install -y python3-devel fftw3-devel
@@ -47,16 +47,18 @@ The following commands may require root access.
 
 <details>
   <summary> Click for Mac</summary>
-  
+
   Install Homebrew, make sure that  homebrew programs are in the **$PATH** (optional step in Homebrew installation)
+
   ```bash
   brew install pkg-config fftw
   ```
 </details>
-  
+
   #### Create Python virtual environment
   Make sure that you have the correct python version installed. We require python>3.9. <br>
   Create virtual environment.
+
   ```
   python3 -m venv .po3
   . .po3/bin/activate
@@ -70,6 +72,7 @@ The following commands may require root access.
 
 First of all make sure you have conda installed and development packages.<br>
 Development packages for Ubuntu:
+
 ```
 apt update -y
 apt install -y curl gpg git build-essential
@@ -87,18 +90,18 @@ pip install -U meson-python setuptools setuptools-scm
 
 ## 3. Build
 
-If you plan to modify PyORBIT's code, install it in editable mode. 
+If you plan to modify PyORBIT's code, install it in editable mode.
 You will NOT need to rebuild after modifications to the code. [Meson](MesonBuild.md) will rebuild as necessary on import.
 ```
 pip install --no-build-isolation --editable .
 ```
 
 Alternatively if you don't plan to modify PyORBIT's code
+
 ```
 pip install .
 ```
 
-
 ## 4. Run full SNS linac example
 
 Navigate to your **examples** directory and launch tracking of SNS linac.
@@ -116,9 +119,9 @@ pip install --config-settings=setup-args="-DUSE_MPI=none" .
 Above will build PyORBIT without MPI even if MPI is present. You can change that option to `mpich`, `ompi`, `none` or `auto` (default).<br>
 | MPI flavor            | Installation command |
 |---------------|--------------|
-| No MPI                                  | `pip install --config-settings=setup-args="-DUSE_MPI=none" .`       | 
-| The first found MPI installation if any | `pip install --config-settings=setup-args="-DUSE_MPI=auto" .`       | 
-| OpenMPI | `pip install --config-settings=setup-args="-DUSE_MPI=ompi" .`       | 
+| No MPI                                  | `pip install --config-settings=setup-args="-DUSE_MPI=none" .`       |
+| The first found MPI installation if any | `pip install --config-settings=setup-args="-DUSE_MPI=auto" .`       |
+| OpenMPI | `pip install --config-settings=setup-args="-DUSE_MPI=ompi" .`       |
 | MPICH | `pip install --config-settings=setup-args="-DUSE_MPI=mpich" .`       |
 
 Meson uses PKG_CONFIG to discover packages. It could be useful to help it to find your MPI installation:

doc/.gitignore

@@ -0,0 +1,2 @@
+_doxygen
+source/api

doc/Makefile

@@ -0,0 +1,24 @@
+# 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 clean
+
+# 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) $(O)
+
+clean:
+	rm -rf "$(SOURCEDIR)"/_doxygen "$(SOURCEDIR)"/api "$(SOURCEDIR)"/_autosummary
+	@$(SPHINXBUILD) -M clean "$(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/conf.py

@@ -0,0 +1,78 @@
+# 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
+
+# -- Path setup --------------------------------------------------------------
+import sys
+from pathlib import Path
+
+sys.path.insert(0, str(Path(__file__).parent.parent / "py/"))
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "PyORBIT3"
+copyright = "2025, PyORBIT Collaboration"
+author = "PyORBIT Collaboration"
+release = "v3.0.1"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.coverage",
+    "sphinx.ext.todo",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx_copybutton",
+    "myst_parser",
+    "breathe",
+    "exhale",
+]
+
+napoleon_numpy_docstring = True
+autosummary_imported_members = True
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+# -- Breathe and Exhale Options ---------------------------------------------------------
+breathe_projects = {
+    "PyORBIT3": "./_doxygen/xml",
+}
+breathe_default_project = "PyORBIT3"
+
+doxyfile = "\n".join(
+    [
+        "INPUT = ../../src",
+        "EXCLUDE_PATTERNS = *wrap* *_init.cc",
+        "PREDEFINED += DOXYGEN_SHOULD_SKIP_THIS",
+        'PREDEFINED += PyObject_HEAD="PyObject ob_base;"',
+    ]
+)
+
+exhale_args = {
+    "containmentFolder": "./api",
+    "rootFileName": "pyorbit_root.rst",
+    "doxygenStripFromPath": "..",
+    "rootFileTitle": "PyORBIT3 C++ API",
+    "createTreeView": True,
+    "exhaleExecutesDoxygen": True,
+    "exhaleDoxygenStdin": doxyfile,
+}
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "pydata_sphinx_theme"
+html_static_path = ["_static"]
+html_show_source_link = True
+html_theme_options = {
+    "github_url": "https://github.com/PyORBIT-Collaboration/PyORBIT3",
+    "logo": {
+        "text": "PyORBIT3",
+    },
+}