WIP: automated package and publish of MAP

.github/workflows/publish_map.yml

@@ -0,0 +1,59 @@
+# Workflow to publish TotalSegmentator-AIDE MAP on GHCR
+
+name: Build and package MAP
+
+on:
+  push:
+    branches: ['24_publish_map']
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest ]
+        python-version: [ '3.10' ]
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install Python packages
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest pytest-cov
+        pip install -r app/app_requirements.txt
+
+    - name: Display installed pip packages
+      run: |
+        pip list
+
+    - name: Free disk space
+      run: |
+        df -h
+        sudo swapoff -a
+        sudo rm -rf /swapfile /usr/share/dotnet /usr/local/lib/android /opt/ghc
+        sudo apt clean
+        docker rmi $(docker image ls -aq)
+        df -h
+
+    - name: Package MAP & test MAP end-to-end
+      run: |
+        monai-deploy package app --base nvcr.io/nvidia/pytorch:22.08-py3 --tag map-init:temp -l DEBUG
+        docker images
+        docker build --build-arg INIT_CONTAINER=map-init:temp -t map-final:temp app
+        docker images
+        monai-deploy run map tests/data/rtstructwriter/dcm tests/data/output
+        ls tests/data/output
+        if test -f "tests/data/output/output-rt-struct.dcm"; then echo "Output RT Struct exists."; fi

app/Dockerfile

@@ -1,5 +1,7 @@
+ARG INIT_CONTAINER
+
 # Use initial MAP for build
-FROM ghcr.io/gstt-csc/totalsegmentator-aide/map-init:0.1.2 AS build
+FROM $INIT_CONTAINER AS build
 
 # Add dcm2niix to MAP
 WORKDIR /bin

app/app.py

@@ -9,15 +9,21 @@
 # Tom Roberts ([email protected] / [email protected])
 
 import logging
+from pathlib import Path
 
+import monai.deploy.core as md
 from monai.deploy.core import Application, resource
 
 from operators.dcm2nii_operator import Dcm2NiiOperator
 from operators.rtstructwriter_operator import RTStructWriterOperator
 from operators.totalsegmentator_operator import TotalSegmentatorOperator
 
+requirements_file = (
+    Path(__file__).resolve().parent / "app_requirements.txt"
+)
 
 @resource(cpu=1, gpu=1, memory="32Gi")
+@md.env(pip_packages=requirements_file.as_posix())
 class TotalSegmentatorApp(Application):
     """
     TotalSegmentator - segmentation of 104 anatomical structures in CT images.

app/app_requirements.txt

@@ -0,0 +1,7 @@
+torch
+monai-deploy-app-sdk
+highdicom
+nibabel
+monai
+rt_utils
+typeguard~=2.12.1  # known issue in monai-deploy-app-sdk https://github.com/Project-MONAI/monai-deploy-app-sdk/issues/410

requirements-map-init.txt

@@ -0,0 +1,2 @@
+numpy<1.21.0
+protobuf<3.20