first commit

.github/workflows/build_and_publish.yaml

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+name: Build and Publish Docker Images
+
+on:
+  push:
+    branches:
+        - main
+    paths:
+        - '*/**'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        app_dir:
+          - voluseg
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Docker Builder
+        uses: docker/setup-buildx-action@v2
+
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+        #   username: YOUR_GITHUB_USERNAME # Replace with your GitHub username
+        #   password: ${{ secrets.GHCR_PAT }} # Use the PAT secret
+
+      - name: Pip install dendro
+        run: |
+          python -m pip install --upgrade pip
+          git clone https://github.com/magland/dendro.git
+          cd dendro/python
+          git pull
+          pip install .
+
+      - name: Generate Spec File
+        run: |
+          cd ${{ matrix.app_dir }}
+          chmod +x main.py
+          dendro make-app-spec-file --app-dir . --spec-output-file spec.json
+
+      - name: Build and push
+        run: |
+          docker build -f ${{ matrix.app_dir }}/Dockerfile -t ghcr.io/catalystneuro/dendro-${{ matrix.app_dir }}:latest .
+          docker push ghcr.io/catalystneuro/dendro-${{ matrix.app_dir }}:latest
+
+      - name: Commit files
+        run: |
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          GIT_STATUS=$(git status -s)
+          [[ ! -z "$GIT_STATUS" ]] && git add ${{ matrix.app_dir }}/spec.json && git commit -m "update spec.json" -a || echo "No changes to commit"
+
+      - name: Push changes
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ github.ref }}

voluseg/Dockerfile

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+FROM ghcr.io/mikarubi/voluseg/voluseg:docs
+
+USER root
+
+# Install git
+RUN apt-get update && apt-get install -y git
+
+# Install dendro from github
+RUN mkdir -p /src
+WORKDIR /src
+RUN git clone https://github.com/magland/dendro \
+    && cd dendro \
+    && cd python \
+    && pip install -e .
+
+# Install lindi
+RUN pip install lindi
+
+# Install pynwb
+RUN pip install pynwb
+
+# Copy files into the container
+COPY *.py /app/
+
+# Set the working directory
+WORKDIR /app

voluseg/VolusegProcessor.py

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+from dendro.sdk import ProcessorBase, BaseModel, Field, InputFile, OutputFile
+
+
+class VolusegContext(BaseModel):
+    input: InputFile = Field(description='Input NWB file in .nwb or .nwb.lindi.tar format')
+    output: OutputFile = Field(description='Output embedding in .lindi.tar format')
+    # units_path: str = Field(description='Path to the units table in the NWB file', default='units')
+    # max_iterations: int = Field(description='Maximum number of iterations', default=1000)
+    # batch_size: int = Field(description='Batch size', default=1000)
+    # bin_size_msec: float = Field(description='Bin size in milliseconds', default=20)
+    # output_dimensions: int = Field(description='Output dimensions', default=10)
+
+
+class VolusegProcessor(ProcessorBase):
+    name = 'voluseg_processor'
+    description = 'Run Voluseg for volumetric segmentation.'
+    label = 'voluseg_processor'
+    image = 'catalystneuro/dendro-voluseg:0.1.0'
+    executable = '/app/main.py'
+    attributes = {}
+
+    @staticmethod
+    def run(
+        context: VolusegContext
+    ):
+        pass

voluseg/main.py

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+from dendro.sdk import App
+from VolusegProcessor import VolusegProcessor
+
+app = App(
+    app_name='voluseg',
+    description='Voluseg processors'
+)
+
+app.add_processor(VolusegProcessor)
+
+
+if __name__ == '__main__':
+    app.run()