Add GitHub Actions CI for unit tests

.github/workflows/test.yml

@@ -0,0 +1,71 @@
+name: ANTsPyNet Unit Tests
+
+on:
+  push:
+  pull_request:
+
+env:
+  USE_SOURCE_BUILD: false  # Set to 'false' to use PyPI version of ANTsPy
+
+jobs:
+  test:
+    name: Test on Python ${{ matrix.python-version }}
+    runs-on: ubuntu-22.04
+
+    strategy:
+      matrix:
+        python-version: [3.11]
+
+    steps:
+      - name: Checkout ANTsPyNet
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install build tools
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y cmake build-essential git
+
+      - name: Install ANTsPy (source or PyPI)
+        run: |
+          if [ "$USE_SOURCE_BUILD" = "true" ]; then
+            echo "🔧 Installing ANTsPy from GitHub source..."
+            git clone https://github.com/ANTsX/ANTsPy.git
+            pip install scikit-build-core pybind11 nanobind # 🔑 install build backend dependencies
+            pip install ./ANTsPy --no-build-isolation --no-deps
+          else
+            echo "📦 Installing ANTsPy from PyPI..."
+            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 .
+          sed -i '/antspyx==/d' requirements.txt
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+      - name: Pre-download ANTsXNet models and data
+        run: |
+          python download_all_data.py --strict
+
+      - name: Run tests (individually via pytest)
+        run: |
+          pip install pytest pytest-xdist pytest-forked psutil
+          for f in tests/test_*.py; do
+            echo "🔍 Running $f"
+            python -c "import psutil; print('Memory before:', psutil.virtual_memory().used // (1024*1024), 'MB')"
+            pytest -v -s --forked "$f" || exit 1
+            python -c "import psutil; print('Memory after :', psutil.virtual_memory().used // (1024*1024), 'MB')"
+          done

antspynet/utilities/get_pretrained_network.py

@@ -106,10 +106,6 @@ def switch_networks(argument):
             "ex5_coronal_weights": "https://figshare.com/ndownloader/files/42434193",
             "ex5_sagittal_weights": "https://figshare.com/ndownloader/files/42434202",
             "allen_brain_mask_weights" : "https://figshare.com/ndownloader/files/36999880",  #https://figshare.com/ndownloader/files/42481248
-            "allen_brain_leftright_coronal_mask_weights" : "",
-            "allen_cerebellum_coronal_mask_weights" : "",
-            "allen_cerebellum_sagittal_mask_weights" : "",
-            "allen_sr_weights" : "",
             "mouseMriBrainExtraction" : "https://figshare.com/ndownloader/files/44714947",
             "mouseT2wBrainExtraction3D" : "https://figshare.com/ndownloader/files/49188910",
             "mouseT2wBrainParcellation3DNick" : "https://figshare.com/ndownloader/files/44714944",
@@ -268,10 +264,6 @@ def switch_networks(argument):
                   "ex5_coronal_weights",
                   "ex5_sagittal_weights",
                   "allen_brain_mask_weights",
-                  "allen_brain_leftright_coronal_mask_weights",
-                  "allen_cerebellum_coronal_mask_weights",
-                  "allen_cerebellum_sagittal_mask_weights",
-                  "allen_sr_weights",
                   "mouseMriBrainExtraction",
                   "mouseT2wBrainExtraction3D",
                   "mouseT2wBrainParcellation3DNick",

download_all_data.py

@@ -0,0 +1,53 @@
+import antspynet
+import argparse
+import sys
+
+def download_all_data(strict=False):
+    print("Downloading data files from get_antsxnet_data...")
+    try:
+        data_keys = antspynet.get_antsxnet_data("show")
+        for key in data_keys:
+            if key == "show":
+                continue
+            try:
+                print(f"  ↳ Downloading data: {key}")
+                fpath = antspynet.get_antsxnet_data(key)
+                print(f"    ✓ Saved to: {fpath}")
+            except Exception as e:
+                print(f"    ✗ Failed to download {key}: {e}")
+                if strict:
+                    raise
+    except Exception as e:
+        print(f"✗ Failed to retrieve data keys: {e}")
+        if strict:
+            sys.exit(1)
+
+    print("\nDownloading model weights from get_pretrained_network...")
+    try:
+        model_keys = antspynet.get_pretrained_network("show")
+        for key in model_keys:
+            if key == "show":
+                continue
+            try:
+                print(f"  ↳ Downloading model: {key}")
+                fpath = antspynet.get_pretrained_network(key)
+                print(f"    ✓ Saved to: {fpath}")
+            except Exception as e:
+                print(f"    ✗ Failed to download {key}: {e}")
+                if strict:
+                    raise
+    except Exception as e:
+        print(f"✗ Failed to retrieve model keys: {e}")
+        if strict:
+            sys.exit(1)
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--strict", action="store_true", help="Exit on first failed download.")
+    args = parser.parse_args()
+
+    try:
+        download_all_data(strict=args.strict)
+    except Exception as e:
+        print(f"\nAborted due to error: {e}")
+        sys.exit(1)

pyproject.toml

@@ -23,7 +23,7 @@ dependencies = [
     "numpy",
     "tensorflow>=2.11,<=2.17",
 #    "keras<3",
-    "antspyx>=0.4.2",
+    "antspyx>=0.6.1",
     "scikit-learn",
     "requests",
     "statsmodels",