Add ruff - Replace Black, isort and pyupgrade

.github/CONTRIBUTING.md

@@ -35,45 +35,28 @@ pip install -e .
 
 ## Code formatting
 
-### Black
+### Ruff
 
-All Python code in nf-core/tools must be passed through the [Black Python code formatter](https://black.readthedocs.io/en/stable/).
+All Python code in nf-core/tools must be passed through the [Ruff code linter and formatter](https://github.com/astral-sh/ruff).
 This ensures a harmonised code formatting style throughout the package, from all contributors.
 
-You can run Black on the command line (it's included in `requirements-dev.txt`) - eg. to run recursively on the whole repository:
+You can run Ruff on the command line (it's included in `requirements-dev.txt`) - eg. to run recursively on the whole repository:
 
 ```bash
-black .
+ruff format .
 ```
 
-Alternatively, Black has [integrations for most common editors](https://black.readthedocs.io/en/stable/editor_integration.html)
+Alternatively, Ruff has [integrations for most common editors](https://github.com/astral-sh/ruff-lsp) and VSCode(https://github.com/astral-sh/ruff-vscode)
 to automatically format code when you hit save.
-You can also set it up to run when you [make a commit](https://black.readthedocs.io/en/stable/version_control_integration.html).
 
 There is an automated CI check that runs when you open a pull-request to nf-core/tools that will fail if
-any code does not adhere to Black formatting.
+any code does not adhere to Ruff formatting.
 
-### isort
-
-All Python code must also be passed through [isort](https://pycqa.github.io/isort/index.html).
-This ensures a harmonised imports throughout the package, from all contributors.
-
-To run isort on the command line recursively on the whole repository you can use:
-
-```bash
-isort .
-```
-
-isort also has [plugins for most common editors](https://github.com/pycqa/isort/wiki/isort-Plugins)
-to automatically format code when you hit save.
-Or [version control integration](https://pycqa.github.io/isort/docs/configuration/pre-commit.html) to set it up to run when you make a commit.
-
-There is an automated CI check that runs when you open a pull-request to nf-core/tools that will fail if
-any code does not adhere to isort formatting.
+Ruff has been adopted for linting and formatting in replacement of Black, isort (for imports) and pyupgrade. It also includes Flake8.
 
 ### pre-commit hooks
 
-This repository comes with [pre-commit](https://pre-commit.com/) hooks for black, isort and Prettier. pre-commit automatically runs checks before a commit is committed into the git history. If all checks pass, the commit is made, if files are changed by the pre-commit hooks, the user is informed and has to stage the changes and attempt the commit again.
+This repository comes with [pre-commit](https://pre-commit.com/) hooks for ruff and Prettier. pre-commit automatically runs checks before a commit is committed into the git history. If all checks pass, the commit is made, if files are changed by the pre-commit hooks, the user is informed and has to stage the changes and attempt the commit again.
 
 You can use the pre-commit hooks if you like, but you don't have to. The CI on Github will run the same checks as the tools installed with pre-commit. If the pre-commit checks pass, then the same checks in the CI will pass, too.
 

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

@@ -55,6 +55,11 @@ jobs:
       - name: Install Prettier and editorconfig-checker
         run: npm install -g prettier editorconfig-checker
 
+      - name: Install ruff
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+
       # Build a pipeline from the template
       - name: nf-core create
         run: |
@@ -76,6 +81,10 @@ jobs:
       - name: Run Prettier --check
         run: prettier --check create-lint-wf/nf-core-testpipeline
 
+      - name: Run Ruff check
+        run: ruff check create-lint-wf/nf-core-testpipeline
+      - name: Run Ruff format
+        run: ruff format create-lint-wf/nf-core-testpipeline
       - name: Run ECLint check
         run: editorconfig-checker -exclude README.md $(find nf-core-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
         working-directory: create-lint-wf

.github/workflows/fix-linting.yml

@@ -34,21 +34,19 @@ 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:
           python-version: 3.11
-      - name: python-isort
-        uses: isort/isort-action@v1.0.0
-        with:
-          isortVersion: "latest"
-          requirementsFiles: "requirements.txt requirements-dev.txt"
+
+      - name: Install Ruff
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: Run Ruff
+        run: |
+          ruff check --fix .
+          ruff format .
 
       - name: Commit & push changes
         run: |

.github/workflows/lint-code.yml

@@ -44,52 +44,48 @@ jobs:
       - name: Run Prettier --check
         run: prettier --check ${GITHUB_WORKSPACE}
 
-  PythonBlack:
+  Ruff:
     runs-on: ["self-hosted"]
     steps:
-      - uses: actions/checkout@v4
+      - name: Check out source-code repository
+        uses: actions/checkout@v4
+
+      - 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 check
+        run: ruff check .
 
-      - name: Check code lints with Black
-        uses: psf/black@stable
+      - name: Run Ruff format
+        run: ruff format .
 
       # 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 check --fix .` and `ruff format .`
 
             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 }}
           allow-repeats: false
 
-  isort:
-    runs-on: ["self-hosted"]
-    steps:
-      - name: Check out source-code repository
-        uses: actions/checkout@v4
-
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.11
-      - name: python-isort
-        uses: isort/isort-action@v1.1.0
-        with:
-          isortVersion: "latest"
-          requirementsFiles: "requirements.txt requirements-dev.txt"
-
   static-type-check:
     runs-on: ["self-hosted"]
     steps:

.gitpod.yml

@@ -21,3 +21,4 @@ vscode:
     # - nextflow.nextflow                    # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
+    - charliermarsh.ruff # Code linter Ruff

.pre-commit-config.yaml

@@ -1,21 +1,14 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.1.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.9
     hooks:
-      - id: black
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
+      - id: ruff # linter
+        args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
+      - id: ruff-format # formatter
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v2.7.1"
     hooks:
       - id: prettier
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
-    hooks:
-      - id: pyupgrade
-        args: [--py38-plus]
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: "v1.7.1" # Use the sha / tag you want to point at
     hooks:

.prettierignore

@@ -6,3 +6,7 @@ testing
 nf_core/module-template/meta.yml
 nf_core/module-template/tests/tags.yml
 nf_core/subworkflow-template/tests/tags.yml
+# don't run on things handled by ruff
+*.py
+*.pyc
+

CHANGELOG.md

@@ -14,6 +14,8 @@
 
 ### General
 
+- Add Ruff linter and formatter replacing Black, isort and pyupgrade ([#2620](https://github.com/nf-core/tools/pull/2620))
+
 # [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]
 
 ### Template

README.md

@@ -2,9 +2,8 @@
 
 [![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)
-[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
+[![code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
 
 [![install with Bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/recipes/nf-core/README.html)
 [![install with PyPI](https://img.shields.io/badge/install%20with-PyPI-blue.svg)](https://pypi.org/project/nf-core/)

docs/api/_src/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #
@@ -16,9 +15,10 @@
 import sys
 from typing import Dict
 
-sys.path.insert(0, os.path.abspath("../../../nf_core"))
 import nf_core
 
+sys.path.insert(0, os.path.abspath("../../../nf_core"))
+
 # -- Project information -----------------------------------------------------
 
 project = "nf-core/tools"

nf_core/__main__.py

@@ -934,7 +934,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed,
     Test modules within a pipeline or a clone of the
     nf-core/modules repository.
     """
-    from nf_core.components.lint import LintException
+    from nf_core.components.lint import LintExceptionError
     from nf_core.modules import ModuleLint
 
     try:
@@ -960,7 +960,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed,
         )
         if len(module_lint.failed) > 0:
             sys.exit(1)
-    except LintException as e:
+    except LintExceptionError as e:
         log.error(e)
         sys.exit(1)
     except (UserWarning, LookupError) as e:
@@ -1020,7 +1020,7 @@ def bump_versions(ctx, tool, dir, all, show_all):
     the nf-core/modules repo.
     """
     from nf_core.modules.bump_versions import ModuleVersionBumper
-    from nf_core.modules.modules_utils import ModuleException
+    from nf_core.modules.modules_utils import ModuleExceptionError
 
     try:
         version_bumper = ModuleVersionBumper(
@@ -1030,7 +1030,7 @@ def bump_versions(ctx, tool, dir, all, show_all):
             ctx.obj["modules_repo_no_pull"],
         )
         version_bumper.bump_versions(module=tool, all_modules=all, show_uptodate=show_all)
-    except ModuleException as e:
+    except ModuleExceptionError as e:
         log.error(e)
         sys.exit(1)
     except (UserWarning, LookupError) as e:
@@ -1207,7 +1207,7 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo
     Test subworkflows within a pipeline or a clone of the
     nf-core/modules repository.
     """
-    from nf_core.components.lint import LintException
+    from nf_core.components.lint import LintExceptionError
     from nf_core.subworkflows import SubworkflowLint
 
     try:
@@ -1232,7 +1232,7 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo
         )
         if len(subworkflow_lint.failed) > 0:
             sys.exit(1)
-    except LintException as e:
+    except LintExceptionError as e:
         log.error(e)
         sys.exit(1)
     except (UserWarning, LookupError) as e:
@@ -1647,7 +1647,7 @@ def sync(dir, from_branch, pull_request, github_repository, username, template_y
     the pipeline. It is run automatically for all pipelines when ever a
     new release of [link=https://github.com/nf-core/tools]nf-core/tools[/link] (and the included template) is made.
     """
-    from nf_core.sync import PipelineSync, PullRequestException, SyncException
+    from nf_core.sync import PipelineSync, PullRequestExceptionError, SyncExceptionError
     from nf_core.utils import is_pipeline_directory
 
     # Check if pipeline directory contains necessary files
@@ -1657,7 +1657,7 @@ def sync(dir, from_branch, pull_request, github_repository, username, template_y
     sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml)
     try:
         sync_obj.sync()
-    except (SyncException, PullRequestException) as e:
+    except (SyncExceptionError, PullRequestExceptionError) as e:
         log.error(e)
         sys.exit(1)
 

nf_core/bump_version.py

@@ -68,7 +68,7 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
             [
                 (
                     f"/releases/tag/{current_version}",
-                    f"/tree/dev",
+                    "/tree/dev",
                 )
             ],
         )
@@ -78,7 +78,7 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None:
             pipeline_obj,
             [
                 (
-                    f"/tree/dev",
+                    "/tree/dev",
                     f"/releases/tag/{multiqc_new_version}",
                 )
             ],
@@ -187,7 +187,7 @@ def update_file_version(filename: Union[str, Path], pipeline_obj: Pipeline, patt
     fn = pipeline_obj._fp(filename)
     content = ""
     try:
-        with open(fn, "r") as fh:
+        with open(fn) as fh:
             content = fh.read()
     except FileNotFoundError:
         log.warning(f"File not found: '{fn}'")

nf_core/components/components_command.py

@@ -227,7 +227,7 @@ def check_patch_paths(self, patch_path: Path, module_name: str) -> None:
         if patch_path.exists():
             log.info(f"Modules {module_name} contains a patch file.")
             rewrite = False
-            with open(patch_path, "r") as fh:
+            with open(patch_path) as fh:
                 lines = fh.readlines()
                 for index, line in enumerate(lines):
                     # Check if there are old paths in the patch file and replace
@@ -264,7 +264,7 @@ def check_if_in_include_stmts(self, component_path: str) -> Dict[str, List[Dict[
         if self.repo_type == "pipeline":
             workflow_files = Path(self.dir, "workflows").glob("*.nf")
             for workflow_file in workflow_files:
-                with open(workflow_file, "r") as fh:
+                with open(workflow_file) as fh:
                     # Check if component path is in the file using mmap
                     with mmap.mmap(fh.fileno(), 0, access=mmap.ACCESS_READ) as s:
                         if s.find(component_path.encode()) != -1:

nf_core/components/components_utils.py

@@ -53,7 +53,7 @@ def get_repo_info(directory: str, use_prompt: Optional[bool] = True) -> Tuple[st
         raise UserWarning("Repository type could not be established")
 
     # Check if it's a valid answer
-    if not repo_type in ["pipeline", "modules"]:
+    if repo_type not in ["pipeline", "modules"]:
         raise UserWarning(f"Invalid repository type: '{repo_type}'")
 
     # Check for org if modules repo
@@ -138,7 +138,7 @@ def get_components_to_install(subworkflow_dir: str) -> Tuple[List[str], List[str
     """
     modules = []
     subworkflows = []
-    with open(Path(subworkflow_dir, "main.nf"), "r") as fh:
+    with open(Path(subworkflow_dir, "main.nf")) as fh:
         for line in fh:
             regex = re.compile(
                 r"include(?: *{ *)([a-zA-Z\_0-9]*)(?: *as *)?(?:[a-zA-Z\_0-9]*)?(?: *})(?: *from *)(?:'|\")(.*)(?:'|\")"