add docs + gh pages deploy

.github/workflows/build_docs.yml

@@ -0,0 +1,51 @@
+name: Build documentation
+
+on:
+  # only run on PRs, not on pushes to main
+  # (this is handled by deploy_docs.yml)
+  pull_request:
+
+  workflow_call:
+    inputs:
+      artifact_name:
+        description: "Name of the artifact to upload"
+        required: false
+        type: string
+
+jobs:
+  test-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Install system requirements
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc
+
+      - name: Setup Python environment
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: Install doc requirements
+        run: |
+          pip install jax[cpu]
+          pip install .
+          pip install -r docs/requirements.txt
+
+      - name: Build docs
+        run: |
+          cd docs
+          export SPHINXOPTS="-W"  # treat warnings as errors
+          make html
+
+      - name: Upload HTML files
+        uses: actions/upload-artifact@v3
+        if: ${{ inputs.artifact_name }}
+        with:
+          name: ${{ inputs.artifact_name }}
+          path: docs/build/html
+          if-no-files-found: error

.github/workflows/deploy_docs.yml

@@ -0,0 +1,48 @@
+name: Deploy docs to GitHub Pages
+
+on:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  build-docs:
+    uses: ./.github/workflows/build_docs.yml
+    with:
+      artifact_name: exponax-docs-html
+
+  deploy:
+    needs: [build-docs]
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Pages
+        uses: actions/configure-pages@v2
+
+      - name: Download HTML doc artifact
+        uses: actions/download-artifact@v3
+        with:
+          name: exponax-docs-html
+          path: docs_build
+
+      - name: Upload pages artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: docs_build
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v1

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     = .
+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) -c .

docs/conf.py

@@ -0,0 +1,49 @@
+# 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
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import re
+
+from exponax import __version__  # noqa: E402
+
+project = "exponax"
+copyright = "2024, The exponax Team"
+author = "The exponax Team"
+
+# The short X.Y version
+parsed_version = re.match(r"(\d+\.\d+\.\d+)", __version__)
+if parsed_version:
+    version = parsed_version.group(1)
+else:
+    version = "0.0.0"
+
+# The full version, including alpha/beta/rc tags
+release = __version__
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+]
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("http://docs.scipy.org/doc/numpy/", None),
+}
+
+templates_path = []
+exclude_patterns = ["build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "alabaster"
+html_static_path = ["static"]

docs/index.rst

@@ -0,0 +1,6 @@
+API documentation
+=================
+
+.. automodule:: exponax
+   :members:
+   :undoc-members:

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=.
+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/requirements.txt

@@ -0,0 +1 @@
+sphinx==7.0.1

exponax/__init__.py

@@ -14,6 +14,8 @@
     wrap_bc,
 )
 
+__version__ = "0.1.0"
+
 __all__ = [
     "BaseStepper",
     "ForcedStepper",

exponax/_utils.py

@@ -29,7 +29,7 @@ def make_grid(
         - `domain_extent`: The extent of the domain in each spatial dimension.
         - `num_points`: The number of points in each spatial dimension.
         - `full`: Whether to include the right boundary point in the grid.
-          Default: `False`. The right point is redundant for periodic boundary
+            Default: `False`. The right point is redundant for periodic boundary
             conditions and is not considered a degree of freedom. Use this
             option, for example, if you need a full grid for plotting.
         - `zero_centered`: Whether to center the grid around zero. Default:
@@ -38,8 +38,7 @@ def make_grid(
         - `indexing`: The indexing convention to use. Default: `'ij'`.
 
     **Returns:**
-        - `grid`: The grid in the spatial domain. Shape: `(num_spatial_dims,
-            ..., num_points)`.
+        - `grid`: The grid in the spatial domain. Shape: `(num_spatial_dims, ..., num_points)`.
     """
     if full:
         grid_1d = jnp.linspace(0, domain_extent, num_points + 1, endpoint=True)
@@ -266,9 +265,9 @@ def stack_sub_trajectories(
             condition in the subtrajectories.
 
     **Returns:**
-        - `sub_trjs`: The stacked subtrajectories. Expected shape: `(n_stacks,
-            n, ...)`. `n_stacks` is the number of subtrajectories stacked
-            together, i.e., `n_timesteps - n + 1`.
+        - `sub_trjs`: The stacked subtrajectories. Expected shape: `(n_stacks, n, ...)`. 
+           `n_stacks` is the number of subtrajectories stacked together, i.e., 
+           `n_timesteps - n + 1`.
     """
     n_time_steps = [leaf.shape[0] for leaf in jtu.tree_leaves(trj)]