730 retinal oct rpd segmentation

.github/workflows/premerge-cpu.yml

@@ -16,29 +16,76 @@ jobs:
   premerge-cpu:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - name: Checkout code
+      uses: actions/checkout@v4
+
     - name: Set up Python 3.10
       uses: actions/setup-python@v4
       with:
-        python-version: 3.10.14
+        python-version: 3.10.14 # This will be the default Python
+
+    - name: Set up Miniconda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-update-conda: true
+        # The python-version here is for Conda's base, if activated.
+        # We set auto-activate-base to false, so actions/setup-python's version remains default.
+        python-version: 3.10.14 
+        auto-activate-base: false # Crucial: ensures the Python 3.10 from actions/setup-python is the default
+
     - name: cache weekly timestamp
-      id: pip-cache
+      id: pip-cache-ts
       run: |
-        echo "::set-output name=datew::$(date '+%Y-%V')"
-    - name: cache for pip
+        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
+
+    - name: Get pip cache directory
+      id: pip-cache-dir
+      # This runs using the default Python (3.10)
+      shell: bash 
+      run: echo "dir=$(python -m pip cache dir)" >> $GITHUB_OUTPUT
+
+    - name: Cache pip dependencies (for Python 3.10 global env)
+      uses: actions/cache@v4
+      id: cache-pip
+      with:
+        path: ${{ steps.pip-cache-dir.outputs.dir }}
+        key: ${{ runner.os }}-pip-3.10-${{ steps.pip-cache-ts.outputs.datew }}-${{ hashFiles('**/requirements.txt', '**/setup.py') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-3.10-${{ steps.pip-cache-ts.outputs.datew }}-
+
+    # Cache Conda packages (for environments your bash script might create)
+    # setup-miniconda action sets MINICONDA_PATH_0 environment variable
+    - name: Cache Conda packages
       uses: actions/cache@v4
-      id: cache
+      id: cache-conda
       with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
-    - name: Install dependencies
+        path: ${{ env.MINICONDA_PATH_0 }}/pkgs
+        key: ${{ runner.os }}-conda-pkgs-${{ steps.pip-cache-ts.outputs.datew }}-${{ hashFiles('**/environment*.yml', '**/requirements*.txt') }} # Adjust hashFiles as needed
+        restore-keys: |
+          ${{ runner.os }}-conda-pkgs-${{ steps.pip-cache-ts.outputs.datew }}-
+
+    - name: Install global Python dependencies (using Python 3.10)
+      shell: bash
       run: |
         python -m pip install --upgrade pip wheel
         python -m pip install --upgrade setuptools
-    - name: check
+
+    - name: Check environment
+      shell: bash
+      run: |
+        echo "Default Python version:"
+        python --version
+        echo "Conda executable path:"
+        command -v conda
+        conda info
+        # This ensures conda command is available, but the default python is still 3.10
+
+    - name: Run check script
+      # The shell: bash -el {0} can be helpful if conda init modified shell profiles
+      # and your script needs to `conda activate` sub-environments.
+      shell: bash -el {0} 
       run: |
         # clean up temporary files
         $(pwd)/runtests.sh --clean
         df -h
-        bash $(pwd)/ci/run_premerge_cpu.sh changed
-      shell: bash
+        bash $(pwd)/ci/run_premerge_cpu.sh

ci/bundle_custom_data.py

@@ -23,11 +23,16 @@
     "maisi_ct_generative",
     "cxr_image_synthesis_latent_diffusion_model",
     "brain_image_synthesis_latent_diffusion_model",
+    "retinalOCT_RPD_segmentation",
 ]
 
 # This list is used for our CI tests to determine whether a bundle contains the preferred files.
 # If a bundle does not have any of the preferred files, please add the bundle name into the list.
-exclude_verify_preferred_files_list = ["pediatric_abdominal_ct_segmentation", "maisi_ct_generative"]
+exclude_verify_preferred_files_list = [
+    "pediatric_abdominal_ct_segmentation",
+    "maisi_ct_generative",
+    "retinalOCT_RPD_segmentation",
+]
 
 # This list is used for our CI tests to determine whether a bundle needs to be tested with
 # the `verify_export_torchscript` function in `verify_bundle.py`.
@@ -47,6 +52,7 @@
     "mednist_ddpm",
     "cxr_image_synthesis_latent_diffusion_model",
     "brain_image_synthesis_latent_diffusion_model",
+    "retinalOCT_RPD_segmentation",
 ]
 
 # This list is used for our CI tests to determine whether a bundle needs to be tested after downloading
@@ -58,7 +64,9 @@
 # This dict is used for our CI tests to install required dependencies that cannot be installed by `pip install` directly.
 # If a bundle has this kind of dependencies, please add the bundle name (key), and the path of the install script (value)
 # into the dict.
-install_dependency_dict = {}
+install_dependency_dict = {
+    "retinalOCT_RPD_segmentation": "ci/install_scripts/install_retinalOCT_RPD_segmentation_dependency.sh"
+}
 
 # This list is used for our CI tests to determine whether a bundle supports TensorRT export. Related
 # test will be employed for bundles in the dict.

ci/get_bundle_requirements.py

@@ -19,6 +19,8 @@
 
 ALLOW_MONAI_RC = os.environ.get("ALLOW_MONAI_RC", "false").lower() in ("true", "1", "t", "y", "yes")
 
+special_dependencies_list = ["detectron2"]
+
 
 def increment_version(version):
     """
@@ -79,6 +81,8 @@ def get_requirements(bundle, models_path, requirements_file):
             if package_key in metadata.keys():
                 optional_dict = metadata[package_key]
                 for name, version in optional_dict.items():
+                    if name in special_dependencies_list:
+                        continue
                     libs.append(f"{name}=={version}")
 
         if len(libs) > 0:

ci/install_scripts/install_retinalOCT_RPD_segmentation_dependency.sh

@@ -0,0 +1,2 @@
+# ensure that using evironment with python==3.9
+python -m pip install 'git+https://github.com/facebookresearch/detectron2.git@65184fc057d4fab080a98564f6b60fae0b94edc4'