From 416f14cf8882ca9b3ffae6918c83d1c0a56368a7 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 19 Dec 2023 11:58:27 +0100 Subject: [PATCH 1/2] downgrade to python 3.11 in the tests --- .github/workflows/create-lint-wf.yml | 4 ++-- .github/workflows/create-test-lint-wf-template.yml | 4 ++-- .github/workflows/create-test-wf.yml | 4 ++-- .github/workflows/deploy-pypi.yml | 4 ++-- .github/workflows/fix-linting.yml | 4 ++-- .github/workflows/lint-code.yml | 6 +++--- .github/workflows/pytest.yml | 2 +- .github/workflows/sync.yml | 4 ++-- .github/workflows/tools-api-docs-dev.yml | 4 ++-- .github/workflows/tools-api-docs-release.yml | 4 ++-- README.md | 2 +- nf_core/pipeline-template/.github/workflows/linting.yml | 2 +- 12 files changed, 22 insertions(+), 22 deletions(-) diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index 2a692da799..57dbe86d65 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.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 3.12 + - name: Set up Python 3.11 uses: actions/setup-python@v4 with: - python-version: 3.12 + python-version: 3.11 - name: Install python dependencies run: | diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index b4d8aead9f..37cbf65c7d 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -36,10 +36,10 @@ jobs: - uses: actions/checkout@v4 name: Check out source-code repository - - name: Set up Python 3.12 + - name: Set up Python 3.11 uses: actions/setup-python@v4 with: - python-version: 3.12 + python-version: 3.11 - name: Install python dependencies run: | diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index e4779d0684..026b0a889b 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -29,10 +29,10 @@ jobs: - uses: actions/checkout@v4 name: Check out source-code repository - - name: Set up Python 3.12 + - name: Set up Python 3.11 uses: actions/setup-python@v4 with: - python-version: 3.12 + python-version: 3.11 - name: Install python dependencies run: | diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml index b847df9218..62c53508d8 100644 --- a/.github/workflows/deploy-pypi.yml +++ b/.github/workflows/deploy-pypi.yml @@ -16,10 +16,10 @@ jobs: - uses: actions/checkout@v4 name: Check out source-code repository - - name: Set up Python 3.12 + - name: Set up Python 3.11 uses: actions/setup-python@v4 with: - python-version: 3.12 + python-version: 3.11 - name: Install python dependencies run: | diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index d846151205..4184bc5e59 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -40,10 +40,10 @@ jobs: # Override to remove the default --check flag so that we make changes options: "--color" - - name: Set up Python 3.12 + - name: Set up Python 3.11 uses: actions/setup-python@v4 with: - python-version: 3.12 + python-version: 3.11 - name: python-isort uses: isort/isort-action@v1.0.0 with: diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml index 168fac653c..23972c56f6 100644 --- a/.github/workflows/lint-code.yml +++ b/.github/workflows/lint-code.yml @@ -80,10 +80,10 @@ jobs: - name: Check out source-code repository uses: actions/checkout@v4 - - name: Set up Python 3.12 + - name: Set up Python 3.11 uses: actions/setup-python@v4 with: - python-version: 3.12 + python-version: 3.11 - name: python-isort uses: isort/isort-action@v1.1.0 with: @@ -96,7 +96,7 @@ jobs: - uses: actions/checkout@v4 - uses: actions/setup-python@v4 with: - python-version: 3.12 + python-version: 3.11 cache: "pip" - name: Install dependencies diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 46ebe8e57d..b6f3592165 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -28,7 +28,7 @@ jobs: runs-on: ["ubuntu-latest"] strategy: matrix: - python-version: ["3.8", "3.12"] + python-version: ["3.8", "3.11"] runner: ["ubuntu-latest"] include: - python-version: "3.8" diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml index a5cb451dc7..94f8ee54e2 100644 --- a/.github/workflows/sync.yml +++ b/.github/workflows/sync.yml @@ -48,10 +48,10 @@ jobs: path: nf-core/${{ matrix.pipeline }} fetch-depth: "0" - - name: Set up Python 3.12 + - name: Set up Python 3.11 uses: actions/setup-python@v4 with: - python-version: 3.12 + python-version: 3.11 - name: Install python dependencies run: | diff --git a/.github/workflows/tools-api-docs-dev.yml b/.github/workflows/tools-api-docs-dev.yml index f6106bd8b5..51c25fa250 100644 --- a/.github/workflows/tools-api-docs-dev.yml +++ b/.github/workflows/tools-api-docs-dev.yml @@ -26,10 +26,10 @@ jobs: - name: Check out source-code repository uses: actions/checkout@v4 - - name: Set up Python 3.12 + - name: Set up Python 3.11 uses: actions/setup-python@v4 with: - python-version: 3.12 + python-version: 3.11 - name: Install python dependencies run: | diff --git a/.github/workflows/tools-api-docs-release.yml b/.github/workflows/tools-api-docs-release.yml index 412784c233..b0869190d9 100644 --- a/.github/workflows/tools-api-docs-release.yml +++ b/.github/workflows/tools-api-docs-release.yml @@ -21,10 +21,10 @@ jobs: - name: Check out source-code repository uses: actions/checkout@v4 - - name: Set up Python 3.12 + - name: Set up Python 3.11 uses: actions/setup-python@v4 with: - python-version: 3.12 + python-version: 3.11 - name: Install python dependencies run: | diff --git a/README.md b/README.md index 6a10e1f382..1efc968d2d 100644 --- a/README.md +++ b/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=3.12 nf-core nextflow +conda create --name nf-core python=3.11 nf-core nextflow conda activate nf-core ``` diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml index 64d1851f2e..94aa5278be 100644 --- a/nf_core/pipeline-template/.github/workflows/linting.yml +++ b/nf_core/pipeline-template/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.12" + python-version: "3.11" architecture: "x64" - name: Install dependencies From c273c72aafbe7abc19ad5a4e29e1b6616822566f Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 19 Dec 2023 11:59:00 +0100 Subject: [PATCH 2/2] update changelog --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b7365fa3f1..96afd50499 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -46,7 +46,6 @@ - Update `schema build` functionality to automatically update defaults which have changed in the `nextflow.config`([#2479](https://github.com/nf-core/tools/pull/2479)) - 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)). - Add mypy to pre-commit config for the tools repo ([#2545](https://github.com/nf-core/tools/pull/2545)) - Use Path objects for ComponentCreate and update the structure of components templates ([#2551](https://github.com/nf-core/tools/pull/2551)). - GitPod base image: swap tool installation back to `conda` from `mamba` ([#2566](https://github.com/nf-core/tools/pull/2566)).