Commit bd26e345 authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

Merge branch '143-update-galaxy-to-25-1' into 'dev' 

Update Galaxy to 25.1

Closes #143

See merge request !133
parents e9033bd8 77f04489

.ci/minikube-test-setup/deployment.yaml

+1 −1
Original line number Diff line number Diff line
@@ -15,7 +15,7 @@ spec: 
        app.kubernetes.io/name: test

    spec:

      containers:

      - image: postgres:12

      - image: postgres:17

        name: postgres

        ports:

        - containerPort: 5432

.circleci/config.yml

+2 −2
Original line number Diff line number Diff line
@@ -15,7 +15,7 @@ variables: 
jobs:

  get_code:

    docker:

      - image: cimg/python:3.8

      - image: cimg/python:3.9

    <<: *set_workdir

    steps:

      # Replace standard code checkout with shallow clone to speed things up.
@@ -73,7 +73,7 @@ jobs: 
            - ~/repo

  validate_test_tools:

    docker:

      - image: cimg/python:3.8

      - image: cimg/python:3.9

    <<: *set_workdir

    steps:

      - *restore_repo_cache

.github/dependabot.yml

0 → 100644
+12 −0
Original line number Diff line number Diff line 
# To get started with Dependabot version updates, you'll need to specify which

# package ecosystems to update and where the package manifests are located.

# Please see the documentation for all configuration options:

# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file



version: 2

updates:

  # Enable version updates for GitHub Actions

  - package-ecosystem: "github-actions"

    directory: "/"

    schedule:

      interval: "weekly"

.github/workflows/api.yaml

+6 −10
Original line number Diff line number Diff line
@@ -31,11 +31,11 @@ jobs: 
    strategy:

      fail-fast: false

      matrix:

        python-version: ['3.8']

        python-version: ['3.9']

        chunk: [0, 1]

    services:

      postgres:

        image: postgres:13

        image: postgres:17

        env:

          POSTGRES_USER: postgres

          POSTGRES_PASSWORD: postgres
@@ -47,15 +47,11 @@ jobs: 
        run: |

          echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV

          echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV

      - uses: actions/checkout@v4

      - uses: actions/checkout@v5

        with:

          path: 'galaxy root'

      - uses: actions/setup-node@v4

        with:

          node-version: '18.12.1'

          cache: 'yarn'

          cache-dependency-path: 'galaxy root/client/yarn.lock'

      - uses: actions/setup-python@v5

          persist-credentials: false

      - uses: actions/setup-python@v6

        with:

          python-version: ${{ matrix.python-version }}

          cache: 'pip'
@@ -72,7 +68,7 @@ jobs: 
      - name: Run tests

        run: ./run_tests.sh --coverage --skip_flakey_fails -api lib/galaxy_test/api -- --num-shards=2 --shard-id=${{ matrix.chunk }}

        working-directory: 'galaxy root'

      - uses: codecov/codecov-action@v3

      - uses: codecov/codecov-action@v5

        with:

          flags: api

          working-directory: 'galaxy root'

.github/workflows/bioblend.yaml

+8 −6
Original line number Diff line number Diff line
@@ -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
@@ -32,18 +32,20 @@ jobs: 
      fail-fast: false

      matrix:

        tox_env: [py313]

        galaxy_python_version: ["3.8"]

        galaxy_python_version: ['3.9']

    steps:

      - name: Checkout Galaxy

        uses: actions/checkout@v4

        uses: actions/checkout@v5

        with:

          fetch-depth: 1

          path: galaxy

          persist-credentials: false

      - name: Checkout Bioblend

        uses: actions/checkout@v4

        uses: actions/checkout@v5

        with:

          repository: galaxyproject/bioblend

          path: bioblend

          persist-credentials: false

      - name: Cache pip dir

        uses: actions/cache@v4

        with:
@@ -53,7 +55,7 @@ jobs: 
        id: get_bioblend_python_version

        run: echo "bioblend_python_version=$(echo "${{ matrix.tox_env }}" | sed -e 's/^py\([3-9]\)\([0-9]\+\)/\1.\2/')" >> $GITHUB_OUTPUT

      - name: Set up Python for BioBlend

        uses: actions/setup-python@v5

        uses: actions/setup-python@v6

        with:

          python-version: ${{ steps.get_bioblend_python_version.outputs.bioblend_python_version }}

      - name: Install tox
@@ -61,7 +63,7 @@ jobs: 
          python3 -m pip install --upgrade pip setuptools

          python3 -m pip install 'tox>=1.8.0'

      - name: Set up Python for Galaxy

        uses: actions/setup-python@v5

        uses: actions/setup-python@v6

        with:

          python-version: ${{ matrix.galaxy_python_version }}

      - name: Run tests