4.0.0 planemo (#1430)

test: fix planemo tests under latest MPL
test: planemo test to galaxy version 26
ci: boost action runner versions

Author: WardDeb

.github/workflows/pypi.yml

@@ -1,33 +1,33 @@
 name: pypi upload
 
 on:
-  create:
-    tags:
-    - '*'
+    create:
+        tags:
+            - "*"
 
 defaults:
-  run:
-    shell: bash -l {0}
+    run:
+        shell: bash -l {0}
 
 jobs:
-  pypi:
-    if: ${{ startsWith(github.ref, 'refs/tags/') }}
-    name: upload to pypi
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:
-        python-version: '3.12'
-        cache: 'pip'
-    - name: build
-      run: |
-        pip install .[actions]
-        rm -f dist/*
-        python -m build
-    - name: upload
-      env:
-        TWINE_USERNAME: "__token__"
-        TWINE_PASSWORD: ${{ secrets.pypi_password }}
-      run: |
-        twine upload dist/*
+    pypi:
+        if: ${{ startsWith(github.ref, 'refs/tags/') }}
+        name: upload to pypi
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v7
+            - uses: actions/setup-python@v6
+              with:
+                  python-version: "3.12"
+                  cache: "pip"
+            - name: build
+              run: |
+                  pip install .[actions]
+                  rm -f dist/*
+                  python -m build
+            - name: upload
+              env:
+                  TWINE_USERNAME: "__token__"
+                  TWINE_PASSWORD: ${{ secrets.pypi_password }}
+              run: |
+                  twine upload dist/*

.github/workflows/test_planemo.yml

@@ -2,59 +2,59 @@ name: tests_planemo
 on: [push, pull_request, workflow_dispatch]
 
 env:
-  GALAXY_BRANCH: release_24.1
+    GALAXY_BRANCH: release_26.0
 
 defaults:
-  run:
-    shell: bash -l {0}
+    run:
+        shell: bash -l {0}
 
 jobs:
-  planemo_test:
-    name: Planemo test
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        chunk: [1, 2, 3]
-    steps:
-    - uses: actions/checkout@v4
-    - uses: conda-incubator/setup-miniconda@v3
-      with:
-        miniconda-version: "latest"
-        auto-activate-base: true
-        python-version: "3.12"
-    - name: get samtools
-      run: |
-        conda install -c conda-forge -c bioconda samtools
-    - name: pip install
-      run: |
-        pip install .[actions]
-    - name: planemo
-      run: |
-        ./.planemo.sh ${{ matrix.chunk }} ${{ env.GALAXY_BRANCH }}
-    - uses: actions/upload-artifact@v4
-      with:
-        name: 'Tool test output ${{ matrix.chunk }}'
-        path: upload
-  planemo_combine_outputs:
-    name: Combine chunked test results
-    needs: planemo_test
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/download-artifact@v4
-      with:
-        path: artifacts
-    - name: Combine outputs
-      uses: galaxyproject/planemo-ci-action@v1
-      id: combine
-      with:
-        mode: combine
-        html-report: true
-    - uses: actions/upload-artifact@v4
-      with:
-        name: 'All tool test results'
-        path: upload
-    - name: Check outputs
-      uses: galaxyproject/planemo-ci-action@v1
-      id: check
-      with:
-        mode: check
+    planemo_test:
+        name: Planemo test
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                chunk: [1, 2, 3]
+        steps:
+            - uses: actions/checkout@v7
+            - uses: conda-incubator/setup-miniconda@v4
+              with:
+                  miniconda-version: "latest"
+                  auto-activate-base: true
+                  python-version: "3.12"
+            - name: get samtools
+              run: |
+                  conda install -c conda-forge -c bioconda samtools
+            - name: pip install
+              run: |
+                  pip install .[actions]
+            - name: planemo
+              run: |
+                  ./.planemo.sh ${{ matrix.chunk }} ${{ env.GALAXY_BRANCH }}
+            - uses: actions/upload-artifact@v7
+              with:
+                  name: "Tool test output ${{ matrix.chunk }}"
+                  path: upload
+    planemo_combine_outputs:
+        name: Combine chunked test results
+        needs: planemo_test
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/download-artifact@v8
+              with:
+                  path: artifacts
+            - name: Combine outputs
+              uses: galaxyproject/planemo-ci-action@v1
+              id: combine
+              with:
+                  mode: combine
+                  html-report: true
+            - uses: actions/upload-artifact@v7
+              with:
+                  name: "All tool test results"
+                  path: upload
+            - name: Check outputs
+              uses: galaxyproject/planemo-ci-action@v1
+              id: check
+              with:
+                  mode: check