Dev (#27)

* Adding digest_unanalyzed route + debug Operation being linked to Readset when ingesting transfer and GenPipes * Using project rather than project_name or project_id in routes - test 1 * Need to convert project_id from name_to_id from list of int into str * Adding a new attribute for experiment: nucleic_acid_type * Accepting metric without flag set * Allowing job_status being null if job hasn't been submitted * Skipping null job during ingesting genpipes as we don't want files not generated * Build and push Image. Dockefile to Containerfile * Release container with latest_release tag on gitub release (#26) * Tag image on quay on releases * Update pyproject.toml to fix enum error message --------- Co-authored-by: Paul Stretenowich <paul.stretenowich@mcgill.ca>
c3g · Jan 16, 2024 · a23d6f6 · a23d6f6
1 parent 8127c01
commit a23d6f6
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diff --git a/.github/workflows/build_image.yml b/.github/workflows/build_image.yml
@@ -0,0 +1,38 @@
+---
+name: Release
+on:
+    release:
+        types: [published]
+
+env:
+  REGISTRY_USER: c3genomics+github_pusher
+  IMAGE_REGISTRY: quay.io
+  REGISTRY_PASSWORD: ${{ secrets.QUAY_ROBOT_TOKEN }}
+  IMAGE: c3genomics/project_tracking
+  LATEST_RELEASE: latest_release
+
+jobs:
+  build:
+    name: Release image
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: set tag
+      run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
+    - name: pull release
+      run: |
+            # pull taged images and set to latest release
+            podman pull ${{ env.IMAGE_REGISTRY }}/${{ env.IMAGE }}:${{ env.RELEASE_VERSION }}
+            podman tag ${{ env.IMAGE_REGISTRY }}/${{ env.IMAGE }}:${{ env.RELEASE_VERSION }} \
+                ${{ env.IMAGE_REGISTRY }}/${{ env.IMAGE }}:${{ env.LATEST_RELEASE }}
+    - name: Push to repo
+      uses: redhat-actions/push-to-registry@v2
+      with:
+          username: ${{ env.REGISTRY_USER }}
+          password: ${{ env.REGISTRY_PASSWORD }}
+          registry: ${{ env.IMAGE_REGISTRY }}
+          image: ${{ env.IMAGE }}
+          tags: ${{ env.LATEST_RELEASE }}
+    - name: Print image url
+      run: echo "Image pushed to ${{ steps.push-to-repo.outputs.registry-paths }}"
+
diff --git a/.github/workflows/run_test.yml b/.github/workflows/run_test.yml
@@ -1,77 +1,71 @@
 ---
 name: Tests suite
 on:
-  pull_request:
-    types: [opened, synchronize, reopened]
-    branches:
-      - 'main'
-      - 'dev'
-  push:
-    branches:
-      - 'main'
-      - 'dev'
-
-    tags:
-      - '[0-9]+.[0-9]+.[0-9]+'
+    pull_request:
+        types: [opened, synchronize, reopened]
+        branches: ['main', 'dev']
+    push:
+        tags: '[0-9]+.[0-9]+.[0-9]+'
+        branches: ['main', 'dev']
 
 env:
-  REGISTRY_USER: c3genomics+github_pusher
-  IMAGE_REGISTRY: quay.io
-  REGISTRY_PASSWORD: ${{ secrets.QUAY_ROBOT_TOKEN }}
-  IMAGE: c3genomics/project_tracking
+    REGISTRY_USER: c3genomics+github_pusher
+    IMAGE_REGISTRY: quay.io
+    REGISTRY_PASSWORD: ${{ secrets.QUAY_ROBOT_TOKEN }}
+    IMAGE: c3genomics/project_tracking
 
 jobs:
-  test:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        python-version: ["3.11"]
-        os: [ubuntu-latest, macos-latest]
+    test:
+        runs-on: ${{ matrix.os }}
+        strategy:
+            matrix:
+                python-version: ["3.11"]
+                os: [ubuntu-latest, macos-latest]
 
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .[tests] flake8
-      - name: Lint with flake8
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-            # exit-zero treats all errors as warnings. The GitHub editor is
-            # 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 \
-          --max-line-length=127 --statistics
-      - name: Test with pytest
-        run: |
-          pytest -v
-  build:
-    needs: test
-    if: startsWith(github.ref, 'refs/tags')
-    name: Build image
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3
-    - name: set tag
-      run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
-    - name: Buildah Action
-      uses: redhat-actions/buildah-build@v2
-      with:
-        image: ${{ env.IMAGE_REGISTRY }}/${{ env.IMAGE }}
-        tags: ${{ env.RELEASE_VERSION }} latest_release
-        containerfiles: ./Containerfile
-    - name: Push to repo
-      uses: redhat-actions/push-to-registry@v2
-      with:
-          username: ${{ env.REGISTRY_USER }}
-          password: ${{ env.REGISTRY_PASSWORD }}
-          registry: ${{ env.IMAGE_REGISTRY }}
-          image: ${{ env.IMAGE }}
-          tags: ${{ env.RELEASE_VERSION }} latest_release
-    - name: Print image url
-      run: echo "Image pushed to ${{ steps.push-to-repo.outputs.registry-paths }}"
-      
+        steps:
+        - uses: actions/checkout@v3
+        - name: Set up Python ${{ matrix.python-version }}
+          uses: actions/setup-python@v4
+          with:
+              python-version: ${{ matrix.python-version }}
+        - name: Install dependencies
+          run: |
+              python -m pip install --upgrade pip
+              pip install .[tests] flake8
+        - name: Lint with flake8
+          run: |
+              # stop the build if there are Python syntax errors or undefined names
+              flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+                # exit-zero treats all errors as warnings. The GitHub editor is
+                # 127 chars wide
+              flake8 . --count --exit-zero --max-complexity=10 \
+              --max-line-length=127 --statistics
+        - name: Test with pytest
+          run: |
+              pytest -v
+    build:
+        needs: test
+        if: startsWith(github.ref, 'refs/tags')
+        name: Build image
+        runs-on: ubuntu-latest
+        steps:
+        - uses: actions/checkout@v3
+        - name: set tag
+          run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
+        - name: Buildah Action
+          uses: redhat-actions/buildah-build@v2
+          with:
+              image: ${{ env.IMAGE_REGISTRY }}/${{ env.IMAGE }}
+              tags: ${{ env.RELEASE_VERSION }}
+              containerfiles: ./Containerfile
+        - name: Push to repo
+          uses: redhat-actions/push-to-registry@v2
+          with:
+              username: ${{ env.REGISTRY_USER }}
+              password: ${{ env.REGISTRY_PASSWORD }}
+              registry: ${{ env.IMAGE_REGISTRY }}
+              image: ${{ env.IMAGE }}
+              tags: ${{ env.RELEASE_VERSION }}
+        - name: Print image url
+          run: echo "Image pushed to  ${{ env.IMAGE_REGISTRY }}/${{ env.IMAGE }}:${{ env.RELEASE_VERSION }}"
+