Merge remote-tracking branch 'origin/master'

# Conflicts: # fuji_server/controllers/fair_check.py # fuji_server/evaluators/fair_evaluator_minimal_metadata.py # fuji_server/evaluators/fair_evaluator_searchable.py # fuji_server/harvester/metadata_harvester.py
pangaea-data-publisher · Sep 28, 2023 · 4348d30 · 4348d30
2 parents 73623a1 + 2db47f8
commit 4348d30
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -1,7 +1,14 @@
 version: 2
 updates:
   - package-ecosystem: github-actions
-    directory: "/"
+    directory: /
+    schedule:
+      interval: monthly
+  - package-ecosystem: pip
+    directory: /
+    schedule:
+      interval: monthly
+  - package-ecosystem: docker
+    directory: /
     schedule:
       interval: monthly
-    target-branch: master
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -24,7 +24,7 @@ jobs:
   # docs:
   #   runs-on: ubuntu-22.04
   #   steps:
-  #   - uses: actions/checkout@v3
+  #   - uses: actions/checkout@v4
   #   - name: Set up Python 3.11
   #     uses: actions/setup-python@v4
   #     with:
@@ -50,16 +50,16 @@ jobs:
   lint:
     runs-on: ubuntu-22.04
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Cache python dependencies
       uses: actions/cache@v3
       with:
         path: |
           ~/.cache/pip
           ~/.cache/pre-commit
-        key: pip-lint-${{ hashFiles('.pre-commit-config.yaml', 'pyproject.toml') }}
+        key: lint-${{ hashFiles('.pre-commit-config.yaml', 'pyproject.toml') }}
         restore-keys: |
-          pip-lint-
+          lint-
     - name: Set up Python 3.11
       uses: actions/setup-python@v4
       with:
@@ -71,30 +71,45 @@ jobs:
 
   tests:
     runs-on: ubuntu-22.04
-    strategy:
-      matrix:
-        python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
-    - name: Cache python dependencies
-      uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: pip-tests-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}
-        restore-keys: |
-          pip-tests-${{ matrix.python-version }}-
-    - name: Set up Python ${{ matrix.python-version }}
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
       uses: actions/setup-python@v4
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: '3.11'
+        cache: pip
     - name: Install python dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip install hatch
-
-    # TODO: remove, once dependencies are updated
-    - run: hatch run python -m pip list
-    - run: hatch run python -m pip list --outdated
+        python -m pip install --upgrade hatch
 
     - name: Run test suite with coverage
-      run: hatch run cov
+      run: hatch run cov-ci
+
+    - name: Upload coverage reports
+      uses: actions/upload-artifact@v3
+      with:
+        name: coverage
+        retention-days: 1
+        path: |
+          junit.xml
+          pytest-coverage.txt
+
+  coverage:
+    runs-on: ubuntu-22.04
+    needs: tests
+    permissions:
+      contents: read
+      pull-requests: write
+    steps:
+    - name: Download coverage reports
+      uses: actions/download-artifact@v3
+      with:
+        name: coverage
+    # Ref: https://github.com/MishaKav/pytest-coverage-comment
+    - name: Add coverage comment
+      uses: MishaKav/[email protected]
+      with:
+        title: Coverage
+        pytest-coverage-path: pytest-coverage.txt
+        junitxml-path: junit.xml
diff --git a/.github/workflows/publish-docker.yml b/.github/workflows/publish-docker.yml
@@ -5,13 +5,13 @@ on:
   push:
     # Publish `master` as Docker `latest` image.
     branches:
-      - master
+    - master
     # Publish `v1.2.3` tags as releases?
     # tags:
     #   - v*
   release:
     types:
-      - created
+    - created
 
 env:
   DOCKER_BUILDKIT: 1
@@ -25,35 +25,35 @@ jobs:
 
     steps:
 
-      - run: docker --version
-      - run: docker buildx version
+    - run: docker --version
+    - run: docker buildx version
 
-      - uses: actions/checkout@v3
+    - uses: actions/checkout@v3
 
-      - name: Build image
-        run: docker build . --file Dockerfile --tag $IMAGE_NAME
+    - name: Build image
+      run: docker build . --file Dockerfile --tag $IMAGE_NAME
 
-      - name: Log into GitHub Container Registry
-        run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login https://ghcr.io -u ${{ github.actor }} --password-stdin
+    - name: Log into GitHub Container Registry
+      run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login https://ghcr.io -u ${{ github.actor }} --password-stdin
 
-      - name: Push image to GitHub Container Registry
-        run: |
-          IMAGE_ID=ghcr.io/${{ github.repository_owner }}/$IMAGE_NAME
+    - name: Push image to GitHub Container Registry
+      run: |
+        IMAGE_ID=ghcr.io/${{ github.repository_owner }}/$IMAGE_NAME
 
-          # Change all uppercase to lowercase
-          IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
+        # Change all uppercase to lowercase
+        IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
 
-          # Strip git ref prefix from version
-          VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
+        # Strip git ref prefix from version
+        VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
 
-          # Strip "v" prefix from tag name
-          [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
+        # Strip "v" prefix from tag name
+        [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
 
-          # Use Docker `latest` tag convention
-          [ "$VERSION" == "master" ] && VERSION=latest
+        # Use Docker `latest` tag convention
+        [ "$VERSION" == "master" ] && VERSION=latest
 
-          echo IMAGE_ID=$IMAGE_ID
-          echo VERSION=$VERSION
+        echo IMAGE_ID=$IMAGE_ID
+        echo VERSION=$VERSION
 
-          docker tag $IMAGE_NAME $IMAGE_ID:$VERSION
-          docker push $IMAGE_ID:$VERSION
+        docker tag $IMAGE_NAME $IMAGE_ID:$VERSION
+        docker push $IMAGE_ID:$VERSION
diff --git a/.gitignore b/.gitignore
@@ -76,6 +76,8 @@ nosetests.xml
 coverage.xml
 *,cover
 .hypothesis/
+junit.xml
+pytest-coverage.txt
 
 # Translations
 *.mo
@@ -184,3 +186,6 @@ Temporary Items
 *.el
 # # Jetbrains PyCharm Project folder:
 .idea/
+
+# Ruff
+.ruff_cache
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,7 +3,6 @@ repos:
   rev: v4.4.0
   hooks:
   - id: end-of-file-fixer
-    exclude_types: [json, text]
   - id: mixed-line-ending
     types: [python]
   - id: trailing-whitespace
@@ -12,6 +11,8 @@ repos:
   - id: check-json
   - id: pretty-format-json
     args: [--autofix]
+  - id: file-contents-sorter
+    files: ^fuji_server\/data\/.*.txt$
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
   rev: v2.10.0
   hooks:

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -1,17 +1,17 @@
-version: "3.3"
+version: '3.3'
 services:
   fujirest:
-    image: "ghcr.io/pangaea-data-publisher/fuji:latest"
+    image: ghcr.io/pangaea-data-publisher/fuji:latest
     ports:
-      - "1071:1071"
+    - 1071:1071
     environment:
-      - ENABLE_CORS=true
+    - ENABLE_CORS=true
 
   notebook:
-    image: "jupyter/minimal-notebook:latest"
+    image: jupyter/minimal-notebook:latest
     environment:
-      - JUPYTER_ENABLE_LAB=yes
+    - JUPYTER_ENABLE_LAB=yes
     volumes:
-      - .:/home/jovyan/work
+    - .:/home/jovyan/work
     ports:
-      - "8888:8888"
+    - 8888:8888