New command line API functionality

.devcontainer/onCreateCommand.sh

@@ -6,4 +6,4 @@ pip install wheel
 pip install openvino-dev==2023.0.1 # [OPTIONAL] to generate optimized models for inference
 pip install mlcube_docker          # [OPTIONAL] to deploy GaNDLF models as MLCube-compliant Docker containers
 pip install medmnist==2.1.0
-pip install torch==2.1.2 torchvision==0.16.2 torchaudio==2.1.2 --index-url https://download.pytorch.org/whl/cpu
+pip install torch==2.2.1 torchvision==0.17.1 torchaudio==2.2.1 --index-url https://download.pytorch.org/whl/cpu

.devcontainer/postCreateCommand.sh

@@ -6,9 +6,9 @@
 # if runnning on a GPU machine, install the GPU version of pytorch
 if command -v nvidia-smi &> /dev/null
 then
-	pip install torch==2.1.2 torchvision==0.16.2 torchaudio==2.1.2 --index-url https://download.pytorch.org/whl/cu118
+	pip install torch==2.2.1 torchvision==0.17.1 torchaudio==2.2.1 --index-url https://download.pytorch.org/whl/cu118
 fi
 
 pip install -e .
-python ./gandlf_verifyInstall
+gandlf verify-install
 gzip -dk -r tutorials/classification_medmnist_notebook/medmnist/dataset

.github/ISSUE_TEMPLATE/---bug-report.md

@@ -25,7 +25,7 @@ If applicable, add images, screenshots or other relevant media to help explain y
 
 ### Environment information
 <!-- Put the output of the following command:
-python ./gandlf_debugInfo
+gandlf debug-info
 -->
 GaNDLF version, OS, and any other relevant information.
 

.github/ISSUE_TEMPLATE/--questions-help-support.md

@@ -13,7 +13,7 @@ https://mlcommons.github.io/GaNDLF/faq
 
 ### Environment information
 <!-- Put the output of the following command:
-python ./gandlf_debugInfo
+gandlf debug-info
 -->
 GaNDLF version, OS, and any other relevant information.
 

.github/workflows/codacy.yml

@@ -16,9 +16,7 @@ name: Codacy Security Scan
 on:
   push:
     branches: [ master ]
-  pull_request:
-    # The branches below must be a subset of the branches above
-    branches: [ master ]
+  pull_request: {}
 
 permissions:
   contents: read

.github/workflows/codeql-analysis.yml

@@ -14,9 +14,7 @@ name: "CodeQL"
 on:
   push:
     branches: [ master ]
-  pull_request:
-    # The branches below must be a subset of the branches above
-    branches: [ master ]
+  pull_request: {}
   schedule:
     - cron: '25 5 * * 2'
 

.github/workflows/devcontainer.yml

@@ -3,8 +3,7 @@ name: Dev-Container CI
 on:
   push:
     branches: [ master ]
-  pull_request:
-    branches: [ master ]
+  pull_request: {}
 
 jobs:
   dev-container-test:

.github/workflows/docker-image.yml

@@ -4,8 +4,7 @@ on:
   push:
     branches: [ master ]
     tags: [ '*.*.*' ]
-  pull_request:
-    branches: [ master ]
+  pull_request: {}
   workflow_dispatch:
     inputs:
       versionTag:

.github/workflows/mlcube-test.yml

@@ -1,39 +1,36 @@
-# This workflow will test gandlf_deploy for model and metrics MLCubes
+# This workflow will test gandlf deploy for model and metrics MLCubes
 
 name: MLCube-Test
 
 on:
   push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
-
+    branches: [master]
+  pull_request: {}
 
 jobs:
   test-deploy:
-
     runs-on: ubuntu-latest
 
     steps:
-    - name: Free space
-      run: |
-        df -h
-        sudo rm -rf /opt/ghc
-        sudo rm -rf "/usr/local/share/boost"
-        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
-        sudo rm -rf "$ANDROID_SDK_ROOT"
-        df -h
-    - name: Checkout
-      uses: actions/checkout@v3
-    
-    # Use changed-files-specific action to collect file changes.
-    # The following commented condition applied to a step will run that step only if non-docs files have changed.
-    # It should be applied to all functionality-related steps.
-    # if: steps.changed-files-specific.outputs.only_modified == 'false'
-    - name: Detect and screen file changes
-      id: changed-files-specific
-      uses: tj-actions/changed-files@v41
-      with:
+      - name: Free space
+        run: |
+          df -h
+          sudo rm -rf /opt/ghc
+          sudo rm -rf "/usr/local/share/boost"
+          sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+          sudo rm -rf "$ANDROID_SDK_ROOT"
+          df -h
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      # Use changed-files-specific action to collect file changes.
+      # The following commented condition applied to a step will run that step only if non-docs files have changed.
+      # It should be applied to all functionality-related steps.
+      # if: steps.changed-files-specific.outputs.only_modified == 'false'
+      - name: Detect and screen file changes
+        id: changed-files-specific
+        uses: tj-actions/changed-files@v41
+        with:
           files: |
             .github/*.md
             .github/ISSUE_TEMPLATE/*.md
@@ -46,37 +43,37 @@ jobs:
             LICENSE
             Dockerfile-*
 
-    - name: Summarize docs and non-docs modifications
-      run: |
-        echo "List of docs files that have changed: ${{ steps.changed-files-specific.outputs.all_modified_files }}"
-        echo "Changed non-docs files: ${{ steps.changed-files-specific.outputs.other_modified_files }}"
-    
-    # This second step is unnecessary but highly recommended because
-    # It will cache database and saves time re-downloading it if database isn't stale.
-    - name: Cache pip
-      uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-
-    - name: Set up Python 3.9
-      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
-      uses: actions/setup-python@v4
-      with:
-        python-version: 3.9
-    - name: Install dependencies and package
-      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
-      run: |
-        sudo apt-get update
-        sudo apt-get install libvips libvips-tools -y
-        python -m pip install --upgrade pip==24.0
-        python -m pip install wheel
-        python -m pip install openvino-dev==2023.0.1 mlcube_docker
-        pip install torch==2.1.2 torchvision==0.16.2 torchaudio==2.1.2 --index-url https://download.pytorch.org/whl/cpu
-        pip install -e .
-    - name: Run mlcube deploy tests
-      working-directory: ./testing
-      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
-      run: |
-        sh test_deploy.sh
+      - name: Summarize docs and non-docs modifications
+        run: |
+          echo "List of docs files that have changed: ${{ steps.changed-files-specific.outputs.all_modified_files }}"
+          echo "Changed non-docs files: ${{ steps.changed-files-specific.outputs.other_modified_files }}"
+
+      # This second step is unnecessary but highly recommended because
+      # It will cache database and saves time re-downloading it if database isn't stale.
+      - name: Cache pip
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+      - name: Set up Python 3.9
+        if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+      - name: Install dependencies and package
+        if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
+        run: |
+          sudo apt-get update
+          sudo apt-get install libvips libvips-tools -y
+          python -m pip install --upgrade pip==24.0
+          python -m pip install wheel
+          python -m pip install openvino-dev==2023.0.1 mlcube_docker
+          pip install torch==2.2.1 torchvision==0.17.1 torchaudio==2.2.1 --index-url https://download.pytorch.org/whl/cpu
+          pip install -e .
+      - name: Run mlcube deploy tests
+        working-directory: ./testing
+        if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
+        run: |
+          sh test_deploy.sh

.github/workflows/openfl-test.yml

@@ -5,36 +5,33 @@ name: OpenFL-Test
 
 on:
   push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
-
+    branches: [master]
+  pull_request: {}
 
 jobs:
   openfl-test:
-
     runs-on: ubuntu-latest
 
     steps:
-    - name: Free space
-      run: |
-        df -h
-        sudo rm -rf /opt/ghc
-        sudo rm -rf "/usr/local/share/boost"
-        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
-        sudo rm -rf "$ANDROID_SDK_ROOT"
-        df -h
-    - name: Checkout
-      uses: actions/checkout@v3
-    
-    # Use changed-files-specific action to collect file changes.
-    # The following commented condition applied to a step will run that step only if non-docs files have changed.
-    # It should be applied to all functionality-related steps.
-    # if: steps.changed-files-specific.outputs.only_modified == 'false'
-    - name: Detect and screen file changes
-      id: changed-files-specific
-      uses: tj-actions/changed-files@v41
-      with:
+      - name: Free space
+        run: |
+          df -h
+          sudo rm -rf /opt/ghc
+          sudo rm -rf "/usr/local/share/boost"
+          sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+          sudo rm -rf "$ANDROID_SDK_ROOT"
+          df -h
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      # Use changed-files-specific action to collect file changes.
+      # The following commented condition applied to a step will run that step only if non-docs files have changed.
+      # It should be applied to all functionality-related steps.
+      # if: steps.changed-files-specific.outputs.only_modified == 'false'
+      - name: Detect and screen file changes
+        id: changed-files-specific
+        uses: tj-actions/changed-files@v41
+        with:
           files: |
             .github/*.md
             .github/ISSUE_TEMPLATE/*.md
@@ -47,59 +44,60 @@ jobs:
             LICENSE
             Dockerfile-*
 
-    - name: Summarize docs and non-docs modifications
-      run: |
-        echo "List of docs files that have changed: ${{ steps.changed-files-specific.outputs.all_modified_files }}"
-        echo "Changed non-docs files: ${{ steps.changed-files-specific.outputs.other_modified_files }}"
-
-    # This second step is unnecessary but highly recommended because
-    # It will cache database and saves time re-downloading it if database isn't stale.
-    - name: Cache pip
-      uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-
-    - name: Set up Python 3.9
-      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
-      uses: actions/setup-python@v4
-      with:
-        python-version: 3.9
-    - name: Install dependencies and package
-      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
-      run: |
-        sudo apt-get update
-        sudo apt-get install libvips libvips-tools -y
-        python -m pip install --upgrade pip==24.0
-        python -m pip install wheel
-        pip install torch==2.1.2 torchvision==0.16.2 torchaudio==2.1.2 --index-url https://download.pytorch.org/whl/cpu
-        pip install -e .
-    - name: Run generic unit tests to download data and construct CSVs
-      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
-      run: |
-        pytest --cov=. --cov-report=xml -k "prepare_data_for_ci"
-    # openfl tests start here
-    - name: Run OpenFL tests
-      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
-      run: |
-        echo "Removing onnx because of protobuf version conflict"
-        pip uninstall onnx -y
-        echo "Installing OpenFL"
-        git clone --depth=1 https://github.com/securefederatedai/openfl.git
-        cd openfl
-        git fetch --tags
-        # echo "Checkout the latest OpenFL tag"
-        # latestTag=$(git describe --tags "$(git rev-list --tags --max-count=1)")
-        # git checkout $latestTag
-        # sed -i -e 's/protobuf==3.19.6/protobuf/g' setup.py ## this should NOT be there
-        pip install -e .
-        cd ..
-        echo "Copying files to appropriate directories and updated headers"
-        head -n 1 testing/data/train_2d_rad_segmentation.csv > /home/runner/work/GaNDLF/GaNDLF/openfl/valid.csv
-        tail -n +9 testing/data/train_2d_rad_segmentation.csv >> /home/runner/work/GaNDLF/GaNDLF/openfl/valid.csv
-        head -n 8 testing/data/train_2d_rad_segmentation.csv > /home/runner/work/GaNDLF/GaNDLF/openfl/train.csv
-        sed -i 's/# n_channels: 3/num_channels: 3/g' testing/config_segmentation.yaml
-        config_to_use=$(pwd)/testing/config_segmentation.yaml
-        cd openfl
-        python -m tests.github.test_gandlf --template gandlf_seg_test --fed_workspace aggregator --col1 one --col2 two --rounds-to-train 1 --gandlf_config $config_to_use
+      - name: Summarize docs and non-docs modifications
+        run: |
+          echo "List of docs files that have changed: ${{ steps.changed-files-specific.outputs.all_modified_files }}"
+          echo "Changed non-docs files: ${{ steps.changed-files-specific.outputs.other_modified_files }}"
+
+      # This second step is unnecessary but highly recommended because
+      # It will cache database and saves time re-downloading it if database isn't stale.
+      - name: Cache pip
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+      - name: Set up Python 3.9
+        if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+      - name: Install dependencies and package
+        if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
+        run: |
+          sudo apt-get update
+          sudo apt-get install libvips libvips-tools -y
+          python -m pip install --upgrade pip==24.0
+          python -m pip install wheel
+          pip install torch==2.2.1 torchvision==0.17.1 torchaudio==2.2.1 --index-url https://download.pytorch.org/whl/cpu
+          pip install -e .
+      - name: Run generic unit tests to download data and construct CSVs
+        if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
+        run: |
+          pytest --cov=. --cov-report=xml -k "prepare_data_for_ci"
+      # openfl tests start here
+      - name: Run OpenFL tests
+        if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
+        run: |
+          echo "Removing onnx because of protobuf version conflict"
+          pip uninstall onnx -y
+          echo "Installing OpenFL"
+          git clone --depth=1 https://github.com/securefederatedai/openfl.git
+          cd openfl
+          git fetch --tags
+          # echo "Checkout the latest OpenFL tag"
+          # latestTag=$(git describe --tags "$(git rev-list --tags --max-count=1)")
+          # git checkout $latestTag
+          # sed -i -e 's/protobuf==3.19.6/protobuf/g' setup.py ## this should NOT be there
+          pip install -e .
+          cd ..
+          echo "Copying files to appropriate directories and updated headers"
+          head -n 1 testing/data/train_2d_rad_segmentation.csv > /home/runner/work/GaNDLF/GaNDLF/openfl/valid.csv
+          tail -n +9 testing/data/train_2d_rad_segmentation.csv >> /home/runner/work/GaNDLF/GaNDLF/openfl/valid.csv
+          head -n 8 testing/data/train_2d_rad_segmentation.csv > /home/runner/work/GaNDLF/GaNDLF/openfl/train.csv
+          sed -i 's/# n_channels: 3/num_channels: 3/g' testing/config_segmentation.yaml
+          config_to_use=$(pwd)/testing/config_segmentation.yaml
+          cd openfl
+          python -m tests.github.test_gandlf --template gandlf_seg_test --fed_workspace aggregator --col1 one --col2 two --rounds-to-train 1 --gandlf_config $config_to_use
+

.github/workflows/ossar-analysis.yml

@@ -6,9 +6,7 @@ name: OSSAR
 on:
   push:
     branches: [ master ]
-  pull_request:
-    # The branches below must be a subset of the branches above
-    branches: [ master ]
+  pull_request: {}
   schedule:
     - cron: '32 20 * * 3'