Add workflow to build and deploy documentation (#1347)

Author: fepegar

.github/workflows/docs.yml

@@ -0,0 +1,86 @@
+name: Documentation
+
+on:
+  push:
+
+permissions:
+  contents: write
+
+concurrency:
+  group: docs-${{ github.ref }}
+  cancel-in-progress: false
+
+env:
+  FORCE_COLOR: 1
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Install dependencies
+        run: uv sync --group doc
+
+      - name: Install just
+        uses: extractions/setup-just@v3
+
+      - name: Restore TorchIO cached data
+        id: cache-torchio-data-restore
+        uses: actions/cache/restore@v4
+        with:
+          path: ~/.cache/torchio
+          key: ${{ runner.os }}-torchio-data
+
+      - name: Build docs
+        run: just build-docs
+
+      - name: Save TorchIO cached data
+        if: steps.cache-torchio-data-restore.outputs.cache-hit != 'true'
+        id: cache-torchio-data-save
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/torchio
+          key: ${{ steps.cache-torchio-data-restore.outputs.cache-primary-key }}
+
+      # Uploade to smokeshow if not on main branch
+      - name: Upload docs to smokeshow
+        if: github.ref != 'refs/heads/main'
+        run: |
+          rm ./docs/build/html/_images/*.gif
+          rm ./docs/build/html/_images/*.png
+          uvx smokeshow upload ./docs/build/html
+
+      # Upload to GitHub Pages if on main branch
+      - name: Upload artifacts using actions/upload-pages-artifact
+        if: github.ref == 'refs/heads/main'
+        id: deployment
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./docs/build/html
+
+  deploy:
+    if: github.ref == 'refs/heads/main'
+
+    needs: build
+
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      pages: write # to deploy to Pages
+      id-token: write # to verify the deployment originates from an appropriate source
+
+    runs-on: ubuntu-latest
+
+    # Deploy to the github-pages environment
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

docs/source/data/image.rst

@@ -41,6 +41,7 @@ structure.
 
 
 .. autoclass:: ScalarImage
+    :members:
 
 .. autoclass:: LabelMap
 

pyproject.toml

@@ -75,6 +75,7 @@ dev = [
     "pre-commit-uv==4.1.4",
 ]
 doc = [
+    "distinctipy==1.3.4",
     "einops==0.8.0",
     "furo==2024.8.6",
     "matplotlib==3.9.4",

src/torchio/transforms/preprocessing/spatial/to_canonical.py

@@ -22,6 +22,3 @@ class ToCanonical(ToOrientation):
 
     .. _NiBabel docs about image orientation: https://nipy.org/nibabel/image_orientation.html
     """
-
-    def __init__(self, **kwargs):
-        super().__init__('RAS', **kwargs)