Merge branch 'dev' into collections-in-dataset-names

Author: bernt-matthias

.github/workflows/api.yaml

@@ -35,7 +35,7 @@ jobs:
         chunk: [0, 1]
     services:
       postgres:
-        image: postgres:13
+        image: postgres:17
         env:
           POSTGRES_USER: postgres
           POSTGRES_PASSWORD: postgres

.github/workflows/bioblend.yaml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     services:
       postgres:
-        image: postgres
+        image: postgres:17
         # Provide the password for postgres
         env:
           POSTGRES_PASSWORD: postgres

.github/workflows/check_test_class_names.yaml

@@ -25,6 +25,6 @@ jobs:
           cache: 'pip'
           cache-dependency-path: 'requirements.txt'
       - name: Install Python dependencies
-        run: pip install -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt
+        run: pip install -r requirements.txt -r lib/galaxy/dependencies/pinned-test-requirements.txt
       - name: Run tests
         run: .ci/check_test_class_names.sh

.github/workflows/cwl_conformance.yaml

@@ -31,7 +31,7 @@ jobs:
         conformance-version: ['cwl_conformance_v1_0'] #, 'cwl_conformance_v1_1', 'cwl_conformance_v1_2']
     services:
       postgres:
-        image: postgres:13
+        image: postgres:17
         env:
           POSTGRES_USER: postgres
           POSTGRES_PASSWORD: postgres

.github/workflows/db_indexes.yaml

@@ -25,7 +25,7 @@ jobs:
     strategy:
       matrix:
         db: ['postgresql', 'sqlite']
-        postgresql-version: ['13']
+        postgresql-version: ['17']
         python-version: ['3.9']
         include:
           - db: postgresql

.github/workflows/framework_tools.yaml

@@ -30,7 +30,7 @@ jobs:
         python-version: ['3.9']
     services:
       postgres:
-        image: postgres:13
+        image: postgres:17
         env:
           POSTGRES_USER: postgres
           POSTGRES_PASSWORD: postgres

.github/workflows/framework_workflows.yaml

@@ -29,7 +29,7 @@ jobs:
         python-version: ['3.9']
     services:
       postgres:
-        image: postgres:13
+        image: postgres:17
         env:
           POSTGRES_USER: postgres
           POSTGRES_PASSWORD: postgres

.github/workflows/integration.yaml

@@ -35,7 +35,7 @@ jobs:
         chunk: ['0', '1', '2', '3']
     services:
       postgres:
-        image: postgres:13
+        image: postgres:17
         env:
           POSTGRES_USER: postgres
           POSTGRES_PASSWORD: postgres

.github/workflows/integration_selenium.yaml

@@ -36,7 +36,7 @@ jobs:
         python-version: ['3.9']
     services:
       postgres:
-        image: postgres:13
+        image: postgres:17
         env:
           POSTGRES_USER: postgres
           POSTGRES_PASSWORD: postgres

.github/workflows/js_lint.yaml

@@ -35,45 +35,6 @@ jobs:
       - name: Run prettier checks
         run: yarn run format-check
         working-directory: client
-      # Run vue-tsc, compare with base, only fail if errors increased.
-      - name: Run vue-tsc on PR
-        id: current
+      - name: Run vue-tsc
         working-directory: client
-        run: |
-          # Run vue-tsc in a simulated TTY to capture the summary output.
-          script -q -c 'npx vue-tsc --noEmit' current.log 
-          # Extract the error count from the summary line; default to 0 if not found.
-          CURRENT_ERRORS=$(grep -oE 'Found [0-9]+ errors' current.log | head -1 | grep -oE '[0-9]+' || echo 0)
-          echo "Current vue-tsc errors: $CURRENT_ERRORS"
-          echo "current_errors=$CURRENT_ERRORS" >> $GITHUB_OUTPUT
-      # Check out the target base branch into a separate directory called "base".
-      - name: Checkout target base branch
-        uses: actions/checkout@v4
-        with:
-          ref: ${{ github.event.pull_request.base.ref }}
-      - run: yarn install --frozen-lockfile
-        working-directory: client
-      # Run vue-tsc on the base branch and capture its error count.
-      - name: Run vue-tsc on base branch
-        id: baseline
-        working-directory: client
-        run: |
-          # Run vue-tsc in a simulated TTY and save the output to baseline.log.
-          script -q -c 'npx vue-tsc --noEmit' baseline.log 
-          # Extract the error count from the summary line; default to 0 if not found.
-          BASE_ERRORS=$(grep -oE 'Found [0-9]+ errors' baseline.log | head -1 | grep -oE '[0-9]+' || echo 0)
-          echo "Baseline vue-tsc errors: $BASE_ERRORS"
-          echo "baseline_errors=$BASE_ERRORS" >> $GITHUB_OUTPUT
-      # Compare the error counts between the PR branch and the base branch.
-      - name: Compare vue-tsc error counts
-        run: |
-          CURRENT=${{ steps.current.outputs.current_errors }}
-          BASE=${{ steps.baseline.outputs.baseline_errors }}
-          echo "Current errors: ${CURRENT}"
-          echo "Baseline errors: ${BASE}"
-          if [ "$CURRENT" -gt "$BASE" ]; then
-            echo "vue-tsc error count increased from ${BASE} to ${CURRENT}. Failing the build."
-            exit 1
-          else
-            echo "vue-tsc error count did not increase."
-          fi
+        run: npx vue-tsc --noEmit