ENH: Bump GitHub Actions versions

.github/workflows/build-test-publish.yml

@@ -1,28 +1,21 @@
-name: 'build-test-publish'
+name: "build-test-publish"
 
-on:
-  [push, pull_request]    
-
-environment:
-  name: pypi
-  url: https://pypi.org/p/<your-pypi-project-name>
-permissions:
-  id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+on: [push, pull_request]
 
 jobs:
   build_wheel:
     name: Build Python wheels
     runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
       - name: "Build pure Python wheels"
         run: |
           python -m pip wheel -w dist -e src/
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: wheel
           path: ./dist/itk_dreg-*.whl
@@ -33,51 +26,57 @@ jobs:
     needs:
       - build_wheel
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
-      with:
-        python-version: "3.11"
-    - name: Update pip
-      run: |
-        python -m pip install --upgrade pip
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Update pip
+        run: |
+          python -m pip install --upgrade pip
 
-    - name: "Install Dependencies"
-      shell: bash
-      run: |
-        python -m pip install flit
-        cd src
-        flit install --deps develop
+      - name: "Install Dependencies"
+        shell: bash
+        run: |
+          python -m pip install flit
+          cd src
+          flit install --deps develop
 
-    - name: Download Python Wheel Artifact
-      uses: actions/download-artifact@v3
-      with:
-        name: wheel
+      - name: Download Python Wheel Artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: wheel
 
-    - name: "Install itk_dreg from Wheel Artifact"
-      run: |
-        wheel_name_full=`(find . -name "itk_dreg-*.whl")`
-        python -m pip uninstall -y itk_dreg
-        python -m pip install ${wheel_name_full}
+      - name: "Install itk_dreg from Wheel Artifact"
+        run: |
+          wheel_name_full=`(find . -name "itk_dreg-*.whl")`
+          python -m pip uninstall -y itk_dreg
+          python -m pip install ${wheel_name_full}
 
-    - name: "Run Tests"
-      shell: bash
-      run: |
-        pytest ./test -vvv -s -k "not localcluster and not serialize_pairwise_result"
+      - name: "Run Tests"
+        shell: bash
+        run: |
+          pytest ./test -vvv -s -k "not localcluster and not serialize_pairwise_result"
 
   publish:
     needs:
       - build_wheel
       - pytest
     runs-on: ubuntu-22.04
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/itk-dreg
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+
     steps:
-    - name: Download Python Wheel Artifact
-      uses: actions/download-artifact@v3
-      with:
-        name: wheel
-        path: dist
+      - name: Download Python Wheel Artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: wheel
+          path: dist
 
-    - name: "Publish Python wheel to the Python Package Index"
-      uses: pypa/gh-action-pypi-publish@v1.8.10
-      with:
-        skip_existing: true
+      - name: "Publish Python wheel to the Python Package Index"
+        uses: pypa/gh-action-pypi-publish@v1.8.10
+        with:
+          skip_existing: true

.github/workflows/lint.yml

@@ -1,23 +1,22 @@
-name: 'lint'
+name: "lint"
 
-on:
-  [push, pull_request]
+on: [push, pull_request]
 
 jobs:
   ruff-check:
     name: "Lint with Ruff"
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3    
-    - uses: chartboost/ruff-action@v1
-      with:
-        src: "./src"
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
+        with:
+          src: "./src"
 
   black-autoformat:
     name: "Lint with Black"
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: psf/black@stable
-      with:
-        src: "./src"
+      - uses: actions/checkout@v4
+      - uses: psf/black@stable
+        with:
+          src: "./src"

.github/workflows/test-notebooks.yml

@@ -1,7 +1,6 @@
-name: 'test-notebooks'
+name: "test-notebooks"
 
-on:
-  [push, pull_request]
+on: [push, pull_request]
 
 env:
   aind-ccf-alignment-experiments-tag: 756e846d08b07fcffbc3c387216a59a9fa563fd6
@@ -11,32 +10,32 @@ jobs:
     name: "Test Jupyter Notebooks with PyTest"
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - uses: actions/setup-python@v4
-      with:
-        python-version: "3.11"
-    - name: Update pip
-      run: |
-        python -m pip install --upgrade pip
-    - name: Setup Graphviz
-      uses: ts-graphviz/setup-graphviz@v1
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Update pip
+        run: |
+          python -m pip install --upgrade pip
+      - name: Setup Graphviz
+        uses: ts-graphviz/setup-graphviz@v1
 
-    - name: "Install Dependencies Not Available on PyPI"
-      shell: bash
-      run: |
-        git clone https://github.com/AllenNeuralDynamics/aind-ccf-alignment-experiments.git
-        pushd aind-ccf-alignment-experiments
-        git checkout ${{ env.aind-ccf-alignment-experiments-tag }}
-        python -m pip install .
+      - name: "Install Dependencies Not Available on PyPI"
+        shell: bash
+        run: |
+          git clone https://github.com/AllenNeuralDynamics/aind-ccf-alignment-experiments.git
+          pushd aind-ccf-alignment-experiments
+          git checkout ${{ env.aind-ccf-alignment-experiments-tag }}
+          python -m pip install .
 
-    - name: "Install Dependencies with Flit"
-      shell: bash
-      run: |
-        python -m pip install flit
-        pushd src
-        flit install --extras all
+      - name: "Install Dependencies with Flit"
+        shell: bash
+        run: |
+          python -m pip install flit
+          pushd src
+          flit install --extras all
 
-    - name: "Run Tests"
-      shell: bash
-      run: |
-        pytest --nbmake --nbmake-timeout=30000 examples/*.ipynb -vvv -s -k "not LightsheetRegistration.ipynb"
+      - name: "Run Tests"
+        shell: bash
+        run: |
+          pytest --nbmake --nbmake-timeout=30000 examples/*.ipynb -vvv -s -k "not LightsheetRegistration.ipynb"

.gitignore

@@ -8,3 +8,4 @@ examples/mydask.png
 data/
 _build/
 tmp/
+docs/apidocs/

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)

docs/conf.py

@@ -0,0 +1,57 @@
+# 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
+
+from datetime import date
+import os
+
+project = 'itk-dreg'
+copyright = f'{date.today().year}, NumFOCUS'
+author = 'Insight Software Consortium'
+
+extensions = [
+    'sphinx.ext.autosummary',
+    'autodoc2',
+    'myst_parser',
+    'sphinx.ext.intersphinx',
+    'sphinx_copybutton',
+    'sphinxext.opengraph',
+    'sphinx_design',
+]
+
+myst_enable_extensions = ["colon_fence", "fieldlist"]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+autodoc2_packages = [
+    {
+        "path": "../src/itk_dreg",
+        "exclude_files": [],
+    },
+]
+autodoc2_render_plugin = "myst"
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3/", None),
+    "itkwasm": ("https://itkwasm.readthedocs.io/en/latest/", None),
+}
+
+html_theme = 'furo'
+html_static_path = ['_static']
+html_logo = "_static/logo.svg"
+html_favicon = "_static/favicon.png"
+html_title = f"{project}"
+html_baseurl = os.environ.get("SPHINX_BASE_URL", "")
+
+# Furo options
+html_theme_options = {
+    "top_of_page_button": "edit",
+    "source_repository": "https://github.com/InsightSoftwareConsortium/itk-dreg",
+    "source_branch": "main",
+    "source_directory": "docs",
+}