run full test matrix only on PRs to the master branch,

.github/workflows/create-lint-wf.yml

@@ -31,10 +31,10 @@ jobs:
         name: Check out source-code repository
 
       # Set up nf-core/tools
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |

.github/workflows/create-test-lint-wf-template.yml

@@ -36,10 +36,10 @@ jobs:
       - uses: actions/checkout@v3
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |

.github/workflows/create-test-wf.yml

@@ -29,10 +29,10 @@ jobs:
       - uses: actions/checkout@v3
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |

.github/workflows/deploy-pypi.yml

@@ -16,10 +16,10 @@ jobs:
       - uses: actions/checkout@v3
         name: Check out source-code repository
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |

.github/workflows/fix-linting.yml

@@ -38,10 +38,10 @@ jobs:
           # Override to remove the default --check flag so that we make changes
           options: "--color"
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
       - name: python-isort
         uses: isort/[email protected]
         with:

.github/workflows/lint-code.yml

@@ -77,10 +77,10 @@ jobs:
       - name: Check out source-code repository
         uses: actions/checkout@v3
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
       - name: python-isort
         uses: isort/[email protected]
         with:
@@ -93,7 +93,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v3
         with:
-          python-version: 3.11
+          python-version: 3.12
           cache: "pip"
 
       - name: Install dependencies
@@ -132,7 +132,9 @@ jobs:
         with:
           max_tip: "60"
           sufficient_tip: "10"
+          mypy_config: "mypy.ini"
           enable_threshold_check: "true"
           enable_base_tip_check: "true"
           github_token: ${{ secrets.GITHUB_TOKEN }}
-        if: ${{ github.event_name == 'pull_request' && github.head_ref == 'dev' }}
+        # only run on PRs to dev branch or manual dispatch
+        if: ${{ github.event_name == 'pull_request' && github.head_ref == 'dev' }}  || github.event_name == 'workflow_dispatch'

.github/workflows/pytest.yml

@@ -28,12 +28,11 @@ jobs:
     runs-on: ${{ matrix.runner }}
     strategy:
       matrix:
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.8", "3.12"]
         runner: ["ubuntu-latest"]
         include:
           - runner: "ubuntu-20.04"
             python-version: "3.8"
-
     steps:
       - uses: actions/checkout@v3
         name: Check out source-code repository
@@ -43,6 +42,9 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
+        # run full test matrix only on PRs to the master branch
+        if: github.ref == 'refs/heads/master' || matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8'
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip -r requirements-dev.txt

.github/workflows/sync.yml

@@ -48,10 +48,10 @@ jobs:
           path: nf-core/${{ matrix.pipeline }}
           fetch-depth: "0"
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |

.github/workflows/tools-api-docs-dev.yml

@@ -26,10 +26,10 @@ jobs:
       - name: Check out source-code repository
         uses: actions/checkout@v3
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |

.github/workflows/tools-api-docs-release.yml

@@ -21,10 +21,10 @@ jobs:
       - name: Check out source-code repository
         uses: actions/checkout@v3
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |

CHANGELOG.md

@@ -29,6 +29,7 @@
 
 - Change testing framework for modules and subworkflows from pytest to nf-test ([#2490](https://github.com/nf-core/tools/pull/2490))
 - `bump_version` keeps now the indentation level of the updated version entries ([#2514](https://github.com/nf-core/tools/pull/2514))
+- Run tests with Python 3.12 ([#2522](https://github.com/nf-core/tools/pull/2522)).
 
 # [v2.10 - Nickel Ostrich](https://github.com/nf-core/tools/releases/tag/2.10) + [2023-09-25]
 

README.md

@@ -76,7 +76,7 @@ conda install nf-core
 Alternatively, you can create a new environment with both nf-core/tools and nextflow:
 
 ```bash
-conda create --name nf-core python=3.11 nf-core nextflow
+conda create --name nf-core python=3.12 nf-core nextflow
 conda activate nf-core
 ```
 

mypy.ini

@@ -0,0 +1,2 @@
+[mypy]
+warn_unused_configs = True

nf_core/pipeline-template/.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies