From 98b7da08d9c49b1090719c543dcb90e25fcca108 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 28 Feb 2024 14:22:32 +0100 Subject: [PATCH 1/2] upgrade to python 3.12 --- .github/ISSUE_TEMPLATE/bug_report.yml | 4 ++-- .github/workflows/changelog.yml | 6 +++--- .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 | 2 +- .github/workflows/lint-code.yml | 4 ++-- .github/workflows/pytest.yml | 6 +++--- .github/workflows/sync.yml | 4 ++-- Dockerfile | 2 +- README.md | 2 +- .../.github/workflows/download_pipeline.yml | 2 +- nf_core/pipeline-template/.github/workflows/fix-linting.yml | 2 +- nf_core/pipeline-template/.github/workflows/linting.yml | 6 +++--- 15 files changed, 28 insertions(+), 28 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 8fdd2bd7e1..5043b37acc 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -37,5 +37,5 @@ body: * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ * OS _(eg. CentOS Linux, macOS, Linux Mint)_ - * Version of nf-core/tools _(eg. 1.1, 1.5, 1.8.2)_ - * Python version _(eg. 3.10, 3.11)_ + * Version of nf-core/tools _(eg. 1.10, 1.12.1, 1.13)_ + * Python version _(eg. 3.11, 3.12)_ diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml index 6316d62f33..88d0be2eb1 100644 --- a/.github/workflows/changelog.yml +++ b/.github/workflows/changelog.yml @@ -36,7 +36,7 @@ jobs: - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: - python-version: "3.11" + python-version: "3.12" - name: Install packages run: | @@ -62,10 +62,10 @@ jobs: git diff --exit-code ${GITHUB_WORKSPACE}/CHANGELOG.md || echo "changed=YES" >> $GITHUB_ENV echo "File changed: ${{ env.changed }}" - - name: Set up Python 3.11 + - name: Set up Python 3.12 uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: - python-version: 3.11 + python-version: "3.12" cache: "pip" - name: Install pre-commit diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index e69229c051..0162dc6ec0 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -49,10 +49,10 @@ 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@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: - python-version: 3.11 + python-version: "3.12" cache: pip - name: Install python dependencies diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 6f27236462..3f1bc362f3 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -61,10 +61,10 @@ jobs: - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 name: Check out source-code repository - - name: Set up Python 3.11 + - name: Set up Python 3.12 uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: - python-version: 3.11 + python-version: "3.12" - name: Install python dependencies run: | diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml index 0166931be7..e82faae592 100644 --- a/.github/workflows/create-test-wf.yml +++ b/.github/workflows/create-test-wf.yml @@ -48,10 +48,10 @@ jobs: - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 name: Check out source-code repository - - name: Set up Python 3.11 + - name: Set up Python 3.12 uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: - python-version: 3.11 + python-version: "3.12" - name: Install python dependencies run: | diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml index e53d2f2f5a..ca698dad1f 100644 --- a/.github/workflows/deploy-pypi.yml +++ b/.github/workflows/deploy-pypi.yml @@ -16,10 +16,10 @@ jobs: - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 name: Check out source-code repository - - name: Set up Python 3.11 + - name: Set up Python 3.12 uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: - python-version: 3.11 + python-version: "3.12" - name: Install python dependencies run: | diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 95a03c70fe..3e6c4d4ef6 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -34,7 +34,7 @@ jobs: # Install and run pre-commit - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: - python-version: 3.11 + python-version: "3.12" - name: Install pre-commit run: pip install pre-commit diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml index 8ed52a0582..53151a8989 100644 --- a/.github/workflows/lint-code.yml +++ b/.github/workflows/lint-code.yml @@ -20,10 +20,10 @@ jobs: steps: - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - - name: Set up Python 3.11 + - name: Set up Python 3.12 uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: - python-version: 3.11 + python-version: "3.12" cache: "pip" - name: Install pre-commit diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 5faeef49da..c749458dbe 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -38,7 +38,7 @@ jobs: runs-on: "ubuntu-latest" strategy: matrix: - python-version: ["3.8", "3.11"] + python-version: ["3.8", "3.12"] runner: ["ubuntu-latest"] include: - python-version: "3.8" @@ -173,12 +173,12 @@ jobs: cd pytest - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - - name: Set up Python 3.11 + - name: Set up Python 3.12 uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 env: AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/ with: - python-version: 3.11 + python-version: "3.12" cache: "pip" - name: Install dependencies diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml index d89e255bfb..14eb589360 100644 --- a/.github/workflows/sync.yml +++ b/.github/workflows/sync.yml @@ -56,10 +56,10 @@ 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@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: - python-version: 3.11 + python-version: "3.12" - name: Install python dependencies run: | diff --git a/Dockerfile b/Dockerfile index 62431be140..6ca7e9a67f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.11-slim@sha256:ce81dc539f0aedc9114cae640f8352fad83d37461c24a3615b01f081d0c0583a +FROM python:3.12-slim LABEL authors="phil.ewels@scilifelab.se,erik.danielsson@scilifelab.se" \ description="Docker image containing requirements for the nfcore tools" diff --git a/README.md b/README.md index cf0b01d210..833fad626f 100644 --- a/README.md +++ b/README.md @@ -82,7 +82,7 @@ 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 ``` diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index 20b811ab2b..4017fbdc2d 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -32,7 +32,7 @@ jobs: - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: - python-version: "3.11" + python-version: "3.12" architecture: "x64" - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 with: diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.github/workflows/fix-linting.yml index 28e6605b96..e976b9f09c 100644 --- a/nf_core/pipeline-template/.github/workflows/fix-linting.yml +++ b/nf_core/pipeline-template/.github/workflows/fix-linting.yml @@ -34,7 +34,7 @@ jobs: # Install and run pre-commit - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: - python-version: 3.11 + python-version: "3.12" - name: Install pre-commit run: pip install pre-commit diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml index 3ec259b5ed..ea740d15a3 100644 --- a/nf_core/pipeline-template/.github/workflows/linting.yml +++ b/nf_core/pipeline-template/.github/workflows/linting.yml @@ -16,10 +16,10 @@ jobs: steps: - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - - name: Set up Python 3.11 + - name: Set up Python 3.12 uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: - python-version: 3.11 + python-version: "3.12" cache: "pip" - name: Install pre-commit @@ -39,7 +39,7 @@ jobs: - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: - python-version: "3.11" + python-version: "3.12" architecture: "x64" - name: Install dependencies From ecc697ea8c98fddf3e0b0ab0d424916f88848a98 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 28 Feb 2024 13:27:11 +0000 Subject: [PATCH 2/2] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3fe084d81a..7c6be5ca44 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,7 @@ ### Template - Remove obsolete editor settings in `devcontainer.json` and `gitpod.yml` ([#2795](https://github.com/nf-core/tools/pull/2795)) +- Update python to 3.12 ([#2805](https://github.com/nf-core/tools/pull/2805)) ### Linting