CI pipelines for Docker, testing, releases

.github/workflows/release.yaml

@@ -0,0 +1,93 @@
+name: Release (TestPyPI + Docker Hub)
+
+on:
+  release:
+    types: [created]
+
+permissions:
+  contents: read
+
+env:
+  PYTHON_VERSION: "3.12"
+  DOCKER_IMAGE: antsx/antspynet
+
+jobs:
+
+  tests:
+    uses: ./.github/workflows/test.yml
+
+  build-sdist:
+    name: Build sdist
+    needs: [tests]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "${{ env.PYTHON_VERSION }}"
+
+      - name: Build sdist
+        run: |
+          python -m pip install --upgrade pip build
+          python -m build --sdist --outdir dist
+
+      - name: Upload sdist artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-dist
+          path: dist/*
+
+  docker:
+    name: Build and push Docker image
+    needs: [tests]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Compute Docker tags from release
+        id: meta
+        run: |
+          # For a release-triggered workflow, GITHUB_REF_NAME is the tag name (e.g., v0.2.3)
+          echo "tag=${GITHUB_REF_NAME#v}" >> "$GITHUB_OUTPUT"
+
+      - name: Build and push
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: ./docker/Dockerfile
+          push: true
+          tags: |
+            ${{ env.DOCKER_IMAGE }}:${{ steps.meta.outputs.tag }}
+            ${{ env.DOCKER_IMAGE }}:latest
+
+  publish-testpypi:
+    name: Publish sdist to PyPI
+    runs-on: ubuntu-latest
+    needs:
+      - build-sdist
+      - docker
+    steps:
+      - name: Download sdist artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: python-dist
+          path: dist
+
+      - name: Publish to TestPyPI (API token)
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          skip-existing: true
+          verify-metadata: true

.github/workflows/test.yml

@@ -1,9 +1,8 @@
 name: ANTsPyNet Unit Tests
 
 on:
-  push:
-  pull_request:
-
+  workflow_call:
+  workflow_dispatch:
 env:
   USE_SOURCE_BUILD: false  # Set to 'false' to use PyPI version of ANTsPy
 
@@ -42,14 +41,6 @@ jobs:
             pip install antspyx
           fi
 
-      - name: Cache ANTsXNet model/data downloads
-        uses: actions/cache@v4
-        with:
-          path: ~/.keras/ANTsXNet
-          key: antsxnet-${{ runner.os }}-${{ hashFiles('**/download_all_data.py') }}
-          restore-keys: |
-            antsxnet-${{ runner.os }}-
-
       - name: Install ANTsPyNet and dependencies
         run: |
           pip install -e .

antspynet/utilities/get_antsxnet_data.py

@@ -66,19 +66,19 @@ def switch_data(argument):
             "biobank": "https://ndownloader.figshare.com/files/22429242",
             "croppedMni152": "https://ndownloader.figshare.com/files/22933754",
             "croppedMni152Priors": "https://ndownloader.figshare.com/files/27688437",
-            "deepFlashPriors": "https://figshare.com/ndownloader/files/31208272",
-            "deepFlashTemplateT1": "https://figshare.com/ndownloader/files/31207795",
-            "deepFlashTemplateT1SkullStripped": "https://figshare.com/ndownloader/files/31339867",
-            "deepFlashTemplateT2": "https://figshare.com/ndownloader/files/31207798",
-            "deepFlashTemplateT2SkullStripped": "https://figshare.com/ndownloader/files/31339870",
-            "deepFlashTemplate2T1SkullStripped": "https://figshare.com/ndownloader/files/46461451",
-            "deepFlashTemplate2Labels": "https://figshare.com/ndownloader/files/46461415",
+            "deepFlashPriors": "https://ndownloader.figshare.com/files/31208272",
+            "deepFlashTemplateT1": "https://ndownloader.figshare.com/files/31207795",
+            "deepFlashTemplateT1SkullStripped": "https://ndownloader.figshare.com/files/31339867",
+            "deepFlashTemplateT2": "https://ndownloader.figshare.com/files/31207798",
+            "deepFlashTemplateT2SkullStripped": "https://ndownloader.figshare.com/files/31339870",
+            "deepFlashTemplate2T1SkullStripped": "https://ndownloader.figshare.com/files/46461451",
+            "deepFlashTemplate2Labels": "https://ndownloader.figshare.com/files/46461415",
             "mprage_hippmapp3r": "https://ndownloader.figshare.com/files/24984689",
-            "protonLobePriors": "https://figshare.com/ndownloader/files/30678452",
+            "protonLobePriors": "https://ndownloader.figshare.com/files/30678452",
             "protonLungTemplate": "https://ndownloader.figshare.com/files/22707338",
             "ctLungTemplate": "https://ndownloader.figshare.com/files/22707335",
             "luna16LungPriors": "https://ndownloader.figshare.com/files/28253796",
-            "xrayLungPriors": "https://figshare.com/ndownloader/files/41965815",
+            "xrayLungPriors": "https://ndownloader.figshare.com/files/41965815",
             "priorDktLabels": "https://ndownloader.figshare.com/files/24139802",
             "S_template3": "https://ndownloader.figshare.com/files/22597175",
             "priorDeepFlashLeftLabels": "https://ndownloader.figshare.com/files/25422098",
@@ -90,34 +90,34 @@ def switch_data(argument):
             "nki": "https://ndownloader.figshare.com/files/25516355",
             "nki10": "https://ndownloader.figshare.com/files/25516346",
             "oasis": "https://ndownloader.figshare.com/files/25516352",
-            "magetTemplate": "https://figshare.com/ndownloader/files/41052572",
-            "magetTemplateBrainMask": "https://figshare.com/ndownloader/files/41052569",
-            "magetCerebellumTemplate": "https://figshare.com/ndownloader/files/41052581",
-            "magetCerebellumTemplatePriors": "https://figshare.com/ndownloader/files/41052578",
-            "magetCerebellumxTemplate0GenericAffine": "https://figshare.com/ndownloader/files/41052575",
-            "mraTemplate": "https://figshare.com/ndownloader/files/46406695",
-            "mraTemplateBrainMask": "https://figshare.com/ndownloader/files/46406698",
-            "mraTemplateVesselPrior": "https://figshare.com/ndownloader/files/46406713",
-            "hcpaT1Template": "https://figshare.com/ndownloader/files/54248318",
-            "hcpaT2Template": "https://figshare.com/ndownloader/files/54248324",
-            "hcpaFATemplate": "https://figshare.com/ndownloader/files/54248321",
-            "hcpyaT1Template": "https://figshare.com/ndownloader/files/46746142",
-            "hcpyaT2Template": "https://figshare.com/ndownloader/files/46746334",
-            "hcpyaFATemplate": "https://figshare.com/ndownloader/files/46746349",
-            "hcpyaTemplateBrainMask": "https://figshare.com/ndownloader/files/46746388",
-            "hcpyaTemplateBrainSegmentation": "https://figshare.com/ndownloader/files/46746367",
-            "hcpinterT1Template": "https://figshare.com/ndownloader/files/49372855",
-            "hcpinterT2Template": "https://figshare.com/ndownloader/files/49372849",
-            "hcpinterFATemplate": "https://figshare.com/ndownloader/files/49372858",
-            "hcpinterTemplateBrainMask": "https://figshare.com/ndownloader/files/49372861",
-            "hcpinterTemplateBrainSegmentation": "https://figshare.com/ndownloader/files/49372852",
-            "bsplineT2MouseTemplate": "https://figshare.com/ndownloader/files/44706247",
-            "bsplineT2MouseTemplateBrainMask": "https://figshare.com/ndownloader/files/44869285",
-            "DevCCF_P56_MRI-T2_50um": "https://figshare.com/ndownloader/files/44706244",
-            "DevCCF_P56_MRI-T2_50um_BrainParcellationNickMask": "https://figshare.com/ndownloader/files/44706238",
-            "DevCCF_P56_MRI-T2_50um_BrainParcellationTctMask": "https://figshare.com/ndownloader/files/47214532",
-            "DevCCF_P04_STPT_50um": "https://figshare.com/ndownloader/files/46711546",
-            "DevCCF_P04_STPT_50um_BrainParcellationJayMask": "https://figshare.com/ndownloader/files/46712656"
+            "magetTemplate": "https://ndownloader.figshare.com/files/41052572",
+            "magetTemplateBrainMask": "https://ndownloader.figshare.com/files/41052569",
+            "magetCerebellumTemplate": "https://ndownloader.figshare.com/files/41052581",
+            "magetCerebellumTemplatePriors": "https://ndownloader.figshare.com/files/41052578",
+            "magetCerebellumxTemplate0GenericAffine": "https://ndownloader.figshare.com/files/41052575",
+            "mraTemplate": "https://ndownloader.figshare.com/files/46406695",
+            "mraTemplateBrainMask": "https://ndownloader.figshare.com/files/46406698",
+            "mraTemplateVesselPrior": "https://ndownloader.figshare.com/files/46406713",
+            "hcpaT1Template": "https://ndownloader.figshare.com/files/54248318",
+            "hcpaT2Template": "https://ndownloader.figshare.com/files/54248324",
+            "hcpaFATemplate": "https://ndownloader.figshare.com/files/54248321",
+            "hcpyaT1Template": "https://ndownloader.figshare.com/files/46746142",
+            "hcpyaT2Template": "https://ndownloader.figshare.com/files/46746334",
+            "hcpyaFATemplate": "https://ndownloader.figshare.com/files/46746349",
+            "hcpyaTemplateBrainMask": "https://ndownloader.figshare.com/files/46746388",
+            "hcpyaTemplateBrainSegmentation": "https://ndownloader.figshare.com/files/46746367",
+            "hcpinterT1Template": "https://ndownloader.figshare.com/files/49372855",
+            "hcpinterT2Template": "https://ndownloader.figshare.com/files/49372849",
+            "hcpinterFATemplate": "https://ndownloader.figshare.com/files/49372858",
+            "hcpinterTemplateBrainMask": "https://ndownloader.figshare.com/files/49372861",
+            "hcpinterTemplateBrainSegmentation": "https://ndownloader.figshare.com/files/49372852",
+            "bsplineT2MouseTemplate": "https://ndownloader.figshare.com/files/44706247",
+            "bsplineT2MouseTemplateBrainMask": "https://ndownloader.figshare.com/files/44869285",
+            "DevCCF_P56_MRI-T2_50um": "https://ndownloader.figshare.com/files/44706244",
+            "DevCCF_P56_MRI-T2_50um_BrainParcellationNickMask": "https://ndownloader.figshare.com/files/44706238",
+            "DevCCF_P56_MRI-T2_50um_BrainParcellationTctMask": "https://ndownloader.figshare.com/files/47214532",
+            "DevCCF_P04_STPT_50um": "https://ndownloader.figshare.com/files/46711546",
+            "DevCCF_P04_STPT_50um_BrainParcellationJayMask": "https://ndownloader.figshare.com/files/46712656"
         }
         return(switcher.get(argument, "Invalid argument."))