730 retinal oct rpd segmentation

.github/workflows/premerge-cpu.yml

@@ -16,29 +16,70 @@ 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 # 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: Initialize Conda for shell integration
+      shell: bash
+      run: |
+        conda init bash
+        eval "$(conda shell.bash hook)"
+
     - name: cache weekly timestamp
-      id: pip-cache
+      id: pip-cache-ts
       run: |
-        echo "::set-output name=datew::$(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: Run check script
+      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'

ci/run_premerge_cpu.sh

@@ -30,6 +30,12 @@ elif [[ $# -gt 1 ]]; then
     exit 1
 fi
 
+# Bunles that requires special python version
+declare -A bundle_python_versions=(
+    ["retinalOCT_RPD_segmentation"]="3.9"
+)
+DEFAULT_PYTHON_VERSION_FOR_VENV="3.10"
+
 # Usually, CPU test is required, but for some bundles that are too large to run in Github Actions, we can exclude them.
 exclude_test_list=("maisi_ct_generative")
 is_excluded() {
@@ -41,22 +47,23 @@ is_excluded() {
     return 1 # Return false (1) if not excluded
 }
 
+install_common_deps_in_activated_env() {
+    python -m pip install --upgrade pip wheel
+    python -m pip install --upgrade setuptools
+    python -m pip install jsonschema gdown pyyaml parameterized fire
+    export PYTHONPATH=$PWD
+}
+
 init_venv() {
     if [ ! -d "model_zoo_venv" ]; then  # Check if the venv directory does not exist
         echo "initializing pip environment"
         python -m venv model_zoo_venv
         source model_zoo_venv/bin/activate
-        pip install --upgrade pip wheel
-        pip install --upgrade setuptools
-        pip install jsonschema gdown pyyaml parameterized fire
-        export PYTHONPATH=$PWD
+        install_common_deps_in_activated_env
     else
         echo "Virtual environment model_zoo_venv already exists. Activating..."
         source model_zoo_venv/bin/activate
-        pip install --upgrade pip wheel
-        pip install --upgrade setuptools
-        pip install jsonschema gdown pyyaml parameterized fire
-        export PYTHONPATH=$PWD
+        install_common_deps_in_activated_env
     fi
 }
 
@@ -70,6 +77,42 @@ remove_venv() {
     fi
 }
 
+init_conda_env() {
+    local python_version_to_create="$1"
+    local bundle_identifier="$2"
+    local conda_env_name="conda_env_${bundle_identifier}"
+
+    # Always source conda.sh to ensure conda activate is available
+    if [ -n "$CONDA_EXE" ] && [ -f "$(dirname "$CONDA_EXE")/../etc/profile.d/conda.sh" ]; then
+        source "$(dirname "$CONDA_EXE")/../etc/profile.d/conda.sh"
+    elif [ -n "$MINICONDA_PATH_0" ] && [ -f "$MINICONDA_PATH_0/etc/profile.d/conda.sh" ]; then
+        source "$MINICONDA_PATH_0/etc/profile.d/conda.sh"
+    else
+        echo "Warning: Could not reliably source conda.sh for Conda activation."
+    fi
+
+    if conda env list | grep -q "^${conda_env_name}[[:space:]]"; then
+        echo "Conda env '$conda_env_name' already exists. Removing for a clean start..."
+        conda env remove -n "$conda_env_name" -y
+    fi
+
+    conda create -n "$conda_env_name" python="$python_version_to_create" -y
+    conda activate "$conda_env_name"
+    install_common_deps_in_activated_env
+    conda deactivate 2>/dev/null || true
+}
+
+remove_conda_env() {
+    local conda_env_name_to_remove="$1"
+    if [ -z "$conda_env_name_to_remove" ]; then
+        echo "Warning: No Conda env name provided to remove_conda_env."
+        return
+    fi
+    echo "Deactivating and removing Conda environment: $conda_env_name_to_remove"
+    conda deactivate 2>/dev/null || true
+    conda env remove -n "$conda_env_name_to_remove" -y
+}
+
 verify_bundle() {
     for dir in /opt/hostedtoolcache/*; do
         if [[ $dir != "/opt/hostedtoolcache/Python" ]]; then
@@ -106,15 +149,36 @@ verify_bundle() {
                     else
                         include_pre_release=""
                     fi
-                    init_venv
+                    # determine if conda env should be used for the bundle
+                    active_conda_env_for_bundle=""
+                    required_python_version="${bundle_python_versions[$bundle]}"
+                    use_conda_for_bundle=false
+                    if [[ -n "$required_python_version" && "$required_python_version" != "$DEFAULT_PYTHON_VERSION_FOR_VENV" ]]
+                    then
+                        use_conda_for_bundle=true
+                    fi
+                    if $use_conda_for_bundle
+                    then
+                        init_conda_env "$required_python_version" "$bundle"
+                        active_conda_env_for_bundle="conda_env_${bundle}"
+                        conda activate "$active_conda_env_for_bundle"
+                    else
+                        init_venv
+                    fi
                     # Check if the requirements file exists and is not empty
                     if [ -s "$requirements_file" ]; then
                         echo "install required libraries for bundle: $bundle"
                         pip install $include_pre_release -r "$requirements_file"
                     fi
                     # verify bundle
                     python $(pwd)/ci/verify_bundle.py -b "$bundle" -m "min"  # min tests on cpu
-                    remove_venv
+                    # cleanup
+                    if $use_conda_for_bundle
+                    then
+                        remove_conda_env "$active_conda_env_for_bundle"
+                    else
+                        remove_venv
+                    fi
                 fi
             done
         else

ci/run_premerge_gpu.sh

@@ -29,22 +29,28 @@ if [[ $# -gt 1 ]]; then
     exit 1
 fi
 
+declare -A bundle_python_versions=(
+    ["retinalOCT_RPD_segmentation"]="3.9"
+)
+DEFAULT_PYTHON_VERSION_FOR_VENV="3.10"
+
+install_common_deps_in_activated_env() {
+    python -m pip install --upgrade pip wheel
+    python -m pip install --upgrade setuptools
+    python -m pip install jsonschema gdown pyyaml parameterized fire
+    export PYTHONPATH=$PWD
+}
+
 init_venv() {
     if [ ! -d "model_zoo_venv" ]; then  # Check if the venv directory does not exist
         echo "initializing pip environment"
         python -m venv model_zoo_venv
         source model_zoo_venv/bin/activate
-        pip install --upgrade pip wheel
-        pip install --upgrade setuptools
-        pip install jsonschema gdown pyyaml parameterized fire
-        export PYTHONPATH=$PWD
+        install_common_deps_in_activated_env
     else
         echo "Virtual environment model_zoo_venv already exists. Activating..."
         source model_zoo_venv/bin/activate
-        pip install --upgrade pip wheel
-        pip install --upgrade setuptools
-        pip install jsonschema gdown pyyaml parameterized fire
-        export PYTHONPATH=$PWD
+        install_common_deps_in_activated_env
     fi
 }
 
@@ -58,6 +64,42 @@ remove_venv() {
     fi
 }
 
+init_conda_env() {
+    local python_version_to_create="$1"
+    local bundle_identifier="$2"
+    local conda_env_name="conda_env_${bundle_identifier}"
+
+    # Always source conda.sh to ensure conda activate is available
+    if [ -n "$CONDA_EXE" ] && [ -f "$(dirname "$CONDA_EXE")/../etc/profile.d/conda.sh" ]; then
+        source "$(dirname "$CONDA_EXE")/../etc/profile.d/conda.sh"
+    elif [ -n "$MINICONDA_PATH_0" ] && [ -f "$MINICONDA_PATH_0/etc/profile.d/conda.sh" ]; then
+        source "$MINICONDA_PATH_0/etc/profile.d/conda.sh"
+    else
+        echo "Warning: Could not reliably source conda.sh for Conda activation."
+    fi
+
+    if conda env list | grep -q "^${conda_env_name}[[:space:]]"; then
+        echo "Conda env '$conda_env_name' already exists. Removing for a clean start..."
+        conda env remove -n "$conda_env_name" -y
+    fi
+
+    conda create -n "$conda_env_name" python="$python_version_to_create" -y
+    conda activate "$conda_env_name"
+    install_common_deps_in_activated_env
+    conda deactivate 2>/dev/null || true
+}
+
+remove_conda_env() {
+    local conda_env_name_to_remove="$1"
+    if [ -z "$conda_env_name_to_remove" ]; then
+        echo "Warning: No Conda env name provided to remove_conda_env."
+        return
+    fi
+    echo "Deactivating and removing Conda environment: $conda_env_name_to_remove"
+    conda deactivate 2>/dev/null || true
+    conda env remove -n "$conda_env_name_to_remove" -y
+}
+
 verify_bundle() {
     echo 'Run verify bundle...'
     head_ref=$(git rev-parse HEAD)
@@ -82,7 +124,22 @@ verify_bundle() {
             else
                 include_pre_release=""
             fi
-            init_venv
+            # determine if conda env should be used for the bundle
+            active_conda_env_for_bundle=""
+            required_python_version="${bundle_python_versions[$bundle]}"
+            use_conda_for_bundle=false
+            if [[ -n "$required_python_version" && "$required_python_version" != "$DEFAULT_PYTHON_VERSION_FOR_VENV" ]]
+            then
+                use_conda_for_bundle=true
+            fi
+            if $use_conda_for_bundle
+            then
+                init_conda_env "$required_python_version" "$bundle"
+                active_conda_env_for_bundle="conda_env_${bundle}"
+                conda activate "$active_conda_env_for_bundle"
+            else
+                init_venv
+            fi
             # Check if the requirements file exists and is not empty
             if [ -s "$requirements_file" ]; then
                 echo "install required libraries for bundle: $bundle"
@@ -101,7 +158,13 @@ verify_bundle() {
                 test_cmd="torchrun $(pwd)/ci/unit_tests/runner.py --b \"$bundle\" --dist True"
             fi
             eval $test_cmd
-            remove_venv
+            # cleanup
+            if $use_conda_for_bundle
+            then
+                remove_conda_env "$active_conda_env_for_bundle"
+            else
+                remove_venv
+            fi
         done
         else
             echo "this pull request does not change any bundles, skip verify."

ci/run_regular_tests_cpu.sh

@@ -30,8 +30,7 @@ elif [[ $# -gt 1 ]]; then
     exit 1
 fi
 
-# Usually, CPU test is required, but for some bundles that are too large to run in Github Actions, we can exclude them.
-exclude_test_list=("maisi_ct_generative")
+exclude_test_list=("maisi_ct_generative" "retinalOCT_RPD_segmentation")
 is_excluded() {
     for item in "${exclude_test_list[@]}"; do  # Use exclude_test_list here
         if [ "$1" == "$item" ]; then