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Template: Update python to 3.12 #2805

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Mar 19, 2024
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4 changes: 2 additions & 2 deletions .github/ISSUE_TEMPLATE/bug_report.yml
Original file line number Diff line number Diff line change
@@ -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)_
6 changes: 3 additions & 3 deletions .github/workflows/changelog.yml
Original file line number Diff line number Diff line change
@@ -38,7 +38,7 @@ jobs:

- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
with:
python-version: "3.11"
python-version: "3.12"

- name: Install packages
run: |
@@ -64,10 +64,10 @@ 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
4 changes: 2 additions & 2 deletions .github/workflows/create-lint-wf.yml
Original file line number Diff line number Diff line change
@@ -52,10 +52,10 @@ 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
4 changes: 2 additions & 2 deletions .github/workflows/create-test-lint-wf-template.yml
Original file line number Diff line number Diff line change
@@ -64,10 +64,10 @@ 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: |
4 changes: 2 additions & 2 deletions .github/workflows/create-test-wf.yml
Original file line number Diff line number Diff line change
@@ -51,10 +51,10 @@ 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: |
4 changes: 2 additions & 2 deletions .github/workflows/deploy-pypi.yml
Original file line number Diff line number Diff line change
@@ -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: |
2 changes: 1 addition & 1 deletion .github/workflows/fix-linting.yml
Original file line number Diff line number Diff line change
@@ -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
4 changes: 2 additions & 2 deletions .github/workflows/lint-code.yml
Original file line number Diff line number Diff line change
@@ -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
6 changes: 3 additions & 3 deletions .github/workflows/pytest.yml
Original file line number Diff line number Diff line change
@@ -40,7 +40,7 @@ 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"
@@ -159,12 +159,12 @@ 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
4 changes: 2 additions & 2 deletions .github/workflows/sync.yml
Original file line number Diff line number Diff line change
@@ -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: |
1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -10,6 +10,7 @@
- Add fallback to `download_pipeline.yml` in case the pipeline does not support stub runs ([#2846](https://github.com/nf-core/tools/pull/2846))
- Set topic variable correctly in the mastodon announcement ([#2848](https://github.com/nf-core/tools/pull/2848))
- Add a cleanup action to `download_pipeline.yml` to fix failures caused by inadequate storage space on the runner ([#2849](https://github.com/nf-core/tools/pull/2849))
- Update python to 3.12 ([#2805](https://github.com/nf-core/tools/pull/2805))

### Linting

6 changes: 3 additions & 3 deletions Dockerfile
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
FROM python:3.11-slim@sha256:a2eb07f336e4f194358382611b4fea136c632b40baa6314cb27a366deeaf0144
LABEL authors="phil.ewels@scilifelab.se,erik.danielsson@scilifelab.se" \
description="Docker image containing requirements for the nfcore tools"
FROM python:3.12-slim
LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
description="Docker image containing requirements for nf-core/tools"

# Do not pick up python packages from $HOME
ENV PYTHONNUSERSITE=1
2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
@@ -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
```

Original file line number Diff line number Diff line change
@@ -37,7 +37,7 @@ 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:
Original file line number Diff line number Diff line change
@@ -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
6 changes: 3 additions & 3 deletions nf_core/pipeline-template/.github/workflows/linting.yml
Original file line number Diff line number Diff line change
@@ -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