redo ci

.github/workflows/ci_deploy_docker.yaml

@@ -0,0 +1,68 @@
+
+name: ci_deploy_docker
+
+on:
+  # Also run when the pull request merges  (which generates a push)
+  # So that we can tag the docker image appropriately.
+  push:
+    tags: [ 'v*.*.*' ]
+
+env:
+  IMAGE_NAME:  ${{ github.repository }}
+  REGISTRY: ghcr.io
+  TEST_TAG:  ${{ github.repository }}:test
+
+jobs:
+  deploy_docker:
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+    - name: Checkout branch
+      uses: actions/checkout@v4
+
+    - name: Build the Docker image
+      id: build
+      uses: docker/build-push-action@v5
+      with:
+        load: true
+        tags: ${{ env.TEST_TAG }}
+
+    # run the test on the docker image
+    - name: Run tests in docker image
+      run: >
+        docker run
+        --ipc=host
+        ${{ env.TEST_TAG }}
+        python -m pytest ./test -s --log-cli-level DEBUG
+
+    # Login against a Docker registry except on PR
+    # https://github.com/docker/login-action
+    - name: Log into registry ${{ env.REGISTRY }}
+      uses: docker/login-action@v2
+      with:
+        registry: ${{ env.REGISTRY }}
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    # Extract metadata (tags, labels) for Docker
+    # https://github.com/docker/metadata-action
+    - name: Extract Docker metadata
+      id: meta
+      uses: docker/metadata-action@v5
+      with:
+        images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+    # Build an Docker image with Buildx (don't on PR)
+    # https://github.com/docker/build-push-action
+    - name: Build and push Docker image
+      id: build-and-push
+      uses: docker/build-push-action@v5
+      with:
+        context: .
+        push: true
+        tags: ${{ steps.meta.outputs.tags }}
+        labels: ${{ steps.meta.outputs.labels }}

.github/workflows/ci_pytest.yaml

@@ -0,0 +1,32 @@
+name: ci_pytest
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build_and_test:
+    runs-on: ubuntu-latest
+    permissions:
+        contents: read
+        packages: write
+
+    steps:
+      - name: Checkout branch
+        uses: actions/checkout@v4
+
+      # See https://github.com/marketplace/actions/setup-micromamba
+      - name: setup-micromamba
+        uses: mamba-org/[email protected]
+        with:
+          micromamba-version: '1.5.8-0'  # temporary fix as setup-mircomamba hangs with later mamba version
+          environment-file: environment.yml
+          environment-name: patchwork  # activate the environment
+          cache-environment: true
+          cache-downloads: true
+          generate-run-shell: true
+
+      - name: Run tests with pytest
+        shell: micromamba-shell {0}
+        run: python -m pytest ./test -s --log-cli-level DEBUG