use two-stage image with micromamba for cells

.github/workflows/make-flavor.yaml

@@ -21,12 +21,21 @@ on:
         required: true
 
 jobs:
-  build-naavre-cell:
+  build-naavre-cell-build:
     uses: ./.github/workflows/build-image.yaml
     with:
-      dockerfile: naavre-cell.Dockerfile
+      dockerfile: naavre-cell-build.Dockerfile
       flavor_dir: './flavors/${{ inputs.flavor_name }}'
-      image_name: naavre-cell-${{ inputs.flavor_name }}
+      image_name: naavre-cell-build-${{ inputs.flavor_name }}
+      image_repo: ${{ inputs.image_repo }}
+      image_version: ${{ inputs.image_version }}
+
+  build-naavre-cell-runtime:
+    uses: ./.github/workflows/build-image.yaml
+    with:
+      dockerfile: naavre-cell-runtime.Dockerfile
+      flavor_dir: './flavors/${{ inputs.flavor_name }}'
+      image_name: naavre-cell-runtime-${{ inputs.flavor_name }}
       image_repo: ${{ inputs.image_repo }}
       image_version: ${{ inputs.image_version }}
 
@@ -42,17 +51,26 @@ jobs:
 
   test:
     uses: ./.github/workflows/test-naavre-cell.yaml
-    needs: [build-naavre-cell]
+    needs: [build-naavre-cell-build, build-naavre-cell-runtime]
     with:
-      image_name: naavre-cell-${{ inputs.flavor_name }}
+      image_name_build: naavre-cell-build-${{ inputs.flavor_name }}
+      image_name_runtime: naavre-cell-runtime-${{ inputs.flavor_name }}
       image_repo: ${{ inputs.image_repo }}
       tests_dir: './flavors/${{ inputs.flavor_name }}/tests/'
 
-  push-naavre-cell:
+  push-naavre-cell-build:
+    uses: ./.github/workflows/push-image.yaml
+    needs: [build-naavre-cell-build, test]
+    with:
+      image_name: naavre-cell-build-${{ inputs.flavor_name }}
+      image_repo: ${{ inputs.image_repo }}
+    if: ${{ github.event_name == 'release' }}
+
+  push-naavre-cell-runtime:
     uses: ./.github/workflows/push-image.yaml
-    needs: [build-naavre-cell, test]
+    needs: [build-naavre-cell-runtime, test]
     with:
-      image_name: naavre-cell-${{ inputs.flavor_name }}
+      image_name: naavre-cell-runtime-${{ inputs.flavor_name }}
       image_repo: ${{ inputs.image_repo }}
     if: ${{ github.event_name == 'release' }}
 

.github/workflows/test-naavre-cell.yaml

@@ -3,8 +3,12 @@ name: Test cell base image
 on:
   workflow_call:
     inputs:
-      image_name:
-        description: 'Docker image name'
+      image_name_build:
+        description: 'Docker image name for build stage'
+        type: string
+        required: true
+      image_name_runtime:
+        description: 'Docker image name for runtime stage'
         type: string
         required: true
       image_repo:
@@ -35,6 +39,21 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build docker
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: docker/cell-test.Dockerfile
+          build-args: |
+            BUILD_IMAGE=${{ inputs.image_name_build }}
+            RUNTIME_IMAGE=${{ inputs.image_name_runtime }}
+          tags: cell_test
+          cache-from: type=gha
+          cache-to: type=gha,mode=min
+
       - name: Run tests
         run: |
-          docker run -v ${{ inputs.tests_dir }}:/tests/ ${{ inputs.image_repo }}/${{ inputs.image_name }} /bin/sh /tests/tests.sh
+          docker run -v ${{ inputs.tests_dir }}:/tests/ cell_test /bin/sh /tests/tests.sh

docker/cell-test.Dockerfile

@@ -0,0 +1,22 @@
+ARG BUILD_IMAGE
+ARG RUNTIME_IMAGE
+
+FROM ${BUILD_IMAGE} AS build
+# When building actual cells, extra dependencies are installed here:
+# COPY environment.yaml .
+# RUN micromamba install -y -n venv -f environment.yaml
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+USER root
+RUN conda-pack -p /opt/conda/envs/venv -o /tmp/env.tar && \
+    mkdir /venv && \
+    cd /venv && \
+    tar xf /tmp/env.tar && \
+    rm /tmp/env.tar
+RUN /venv/bin/conda-unpack
+
+FROM ${RUNTIME_IMAGE} AS runtime
+COPY --from=build /venv /venv
+WORKDIR /app
+# When building actual cells, we copy files to the cell. In the tests, we use a
+# volume mount
+# COPY my-task-name.R .

docker/naavre-cell-build.Dockerfile

@@ -0,0 +1,6 @@
+FROM mambaorg/micromamba:1.5.6
+RUN micromamba install -y -n base -c conda-forge conda-pack
+ARG CONDA_ENV_FILE
+COPY ${CONDA_ENV_FILE} environment.yaml
+RUN micromamba create -y -f environment.yaml && \
+    micromamba clean --all --yes

docker/naavre-cell-runtime.Dockerfile

@@ -0,0 +1 @@
+FROM ubuntu:24.04