Give Ruff a try

.github/CONTRIBUTING.md

@@ -73,7 +73,7 @@ any code does not adhere to isort formatting.
 
 ### 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 black, 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

@@ -47,12 +47,17 @@ jobs:
         with:
           version: ${{ matrix.NXF_VER }}
 
-      # Install the Prettier linting tools
+      # Install the Prettier & Ruff linting tools
       - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier
 
+      - name: Install Ruff
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+
       # Install the editorconfig linting tools
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -76,6 +81,9 @@ jobs:
       - 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')
 
+      - name: Run Ruff
+        run: ruff .
+
       # Update modules to the latest version
       - name: nf-core modules update
         run: nf-core --log-file log.txt modules update --dir nf-core-testpipeline --all --no-preview

.github/workflows/fix-linting.yml

@@ -42,11 +42,12 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.8
-      - 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 .
 
       - name: Commit & push changes
         run: |

.github/workflows/lint-code.yml

@@ -70,7 +70,7 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
 
-  isort:
+  ruff:
     runs-on: ubuntu-latest
     steps:
       - name: Check out source-code repository
@@ -80,8 +80,9 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.8
-      - name: python-isort
-        uses: isort/isort-action@v1.1.0
-        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 .

.github/workflows/pytest-frozen-ubuntu-20.04.yml

@@ -33,6 +33,7 @@ jobs:
 
       - name: Downgrade git to the Ubuntu official repository's version
         run: |
+          sudo apt update
           sudo apt remove git git-man
           sudo add-apt-repository --remove ppa:git-core/ppa
           sudo apt install git

.gitpod.yml

@@ -17,3 +17,4 @@ 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 (v0.0.239)

.pre-commit-config.yaml

@@ -3,11 +3,13 @@ repos:
     rev: 23.1.0
     hooks:
       - id: black
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
+        language_version: python3.9
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v2.7.1"
     hooks:
       - id: prettier
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: "v0.0.239"
+    hooks:
+      - id: ruff
+        args: [--fix]

CHANGELOG.md

@@ -10,6 +10,8 @@
 
 ### Linting
 
+- Add Ruff to lint library imports and python code ([#2174](https://github.com/nf-core/tools/pull/2174))
+
 ### Modules
 
 - Add an `--empty-template` option to create a module without TODO statements or examples ([#2175](https://github.com/nf-core/tools/pull/2175) & [#2177](https://github.com/nf-core/tools/pull/2177))

README.md

@@ -4,6 +4,7 @@
 [![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://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v1.json)](https://github.com/charliermarsh/ruff)
 [![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
 
 [![install with Bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/recipes/nf-core/README.html)

nf_core/components/components_utils.py

@@ -1,5 +1,4 @@
 import logging
-import os
 import re
 from pathlib import Path
 

nf_core/gitpod/gitpod.Dockerfile

@@ -43,6 +43,7 @@ RUN conda config --add channels defaults && \
     nf-test \
     black \
     prettier \
+    ruff \
     pytest-workflow && \
     mamba clean --all -f -y
 

nf_core/lint/actions_ci.py

@@ -1,5 +1,4 @@
 import os
-import re
 
 import yaml
 

nf_core/modules/test_yml_builder.py

@@ -26,7 +26,6 @@
 from nf_core.components.components_command import ComponentCommand
 
 from ..lint_utils import run_prettier_on_file
-from .modules_repo import ModulesRepo
 
 log = logging.getLogger(__name__)
 
@@ -294,7 +293,8 @@ def get_md5_sums(self, command, results_dir=None, results_dir_repeat=None):
                 if test_files[i].get("md5sum") and not test_files[i].get("md5sum") == test_files_repeat[i]["md5sum"]:
                     test_files[i].pop("md5sum")
                     test_files[i]["contains"] = [
-                        "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead "
+                        "# TODO nf-core: file md5sum was variable, please replace this text with a "
+                        + "string found in the file instead "
                     ]
 
         if len(test_files) == 0:

nf_core/pipeline-template/pyproject.toml

@@ -4,7 +4,16 @@
 line-length = 120
 target_version = ["py37", "py38", "py39", "py310"]
 
-[tool.isort]
-profile = "black"
-known_first_party = ["nf_core"]
-multi_line_output = 3
+[tool.ruff]
+select = [
+    # Pyflakes
+    "F401", # imported but unused
+    "F841", # Local variable is assigned to but never used
+    # isort
+    "I001"
+]
+line-length = 120
+target-version = "py37"
+
+[tool.ruff.isort]
+known-first-party = ["nf_core"]

pyproject.toml

@@ -16,7 +16,19 @@ markers = [
 testpaths = ["tests"]
 norecursedirs = [ ".*", "build", "dist", "*.egg", "data", "__pycache__", ".github", "nf_core", "docs"]
 
-[tool.isort]
-profile = "black"
-known_first_party = ["nf_core"]
-multi_line_output = 3
+[tool.ruff]
+select = [
+    # Pyflakes
+    "F401", # imported but unused
+    "F841", # Local variable is assigned to but never used
+    # isort
+    "I001"
+]
+line-length = 120
+target-version = "py37"
+
+[tool.ruff.isort]
+known-first-party = ["nf_core"]
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["E402", "F401"]

requirements-dev.txt

@@ -1,5 +1,5 @@
 black
-isort
+ruff
 myst_parser
 pytest-cov
 pytest-datafiles

tests/modules/create_test_yml.py

@@ -1,11 +1,10 @@
 import os
-from pathlib import Path
 
 import pytest
 
 import nf_core.modules
 
-from ..utils import GITLAB_DEFAULT_BRANCH, GITLAB_URL, with_temporary_folder
+from ..utils import with_temporary_folder
 
 
 @with_temporary_folder

tests/modules/lint.py

@@ -1,4 +1,3 @@
-import os
 from pathlib import Path
 
 import pytest

tests/modules/modules_test.py

@@ -1,5 +1,4 @@
 """Test the 'modules test' command which runs module pytests."""
-import os
 import shutil
 from pathlib import Path
 

tests/subworkflows/remove.py

@@ -1,7 +1,5 @@
 from pathlib import Path
 
-from rich.console import Console
-
 from nf_core.modules.modules_json import ModulesJson
 
 
@@ -18,7 +16,7 @@ def test_subworkflows_remove_subworkflow(self):
     bam_sort_stats_samtools_path = Path(subworkflow_path, "bam_sort_stats_samtools")
     bam_stats_samtools_path = Path(subworkflow_path, "bam_stats_samtools")
     samtools_index_path = Path(self.subworkflow_install.dir, "modules", "nf-core", "samtools", "index")
-    mod_json_obj = ModulesJson(self.pipeline_dir)
+    ModulesJson(self.pipeline_dir)
     mod_json_before = ModulesJson(self.pipeline_dir).get_modules_json()
     assert self.subworkflow_remove.remove("bam_sort_stats_samtools")
     mod_json_after = ModulesJson(self.pipeline_dir).get_modules_json()

tests/subworkflows/subworkflows_test.py

@@ -1,5 +1,4 @@
 """Test the 'subworkflows test' command which runs module pytests."""
-import os
 import shutil
 from pathlib import Path
 

tests/subworkflows/update.py

@@ -8,7 +8,6 @@
 import nf_core.utils
 from nf_core.modules.modules_json import ModulesJson
 from nf_core.modules.modules_repo import NF_CORE_MODULES_NAME, NF_CORE_MODULES_REMOTE
-from nf_core.modules.remove import ModuleRemove
 from nf_core.modules.update import ModuleUpdate
 from nf_core.subworkflows.update import SubworkflowUpdate
 

tests/test_download.py

@@ -1,7 +1,6 @@
 """Tests for the download subcommand of nf-core tools
 """
 
-import hashlib
 import os
 import shutil
 import tempfile
@@ -14,7 +13,7 @@
 import nf_core.utils
 from nf_core.download import DownloadWorkflow
 
-from .utils import with_temporary_file, with_temporary_folder
+from .utils import with_temporary_folder
 
 
 class DownloadTest(unittest.TestCase):

tests/test_lint.py

@@ -55,7 +55,7 @@ def test_run_linting_function(self):
 
         We don't really check any of this code as it's just a series of function calls
         and we're testing each of those individually. This is mostly to check for syntax errors."""
-        lint_obj = nf_core.lint.run_linting(self.test_pipeline_dir, False)
+        nf_core.lint.run_linting(self.test_pipeline_dir, False)
 
     def test_init_PipelineLint(self):
         """Simply create a PipelineLint object.

tests/test_schema.py

@@ -305,7 +305,7 @@ def test_build_schema(self):
         Build a new schema param from a pipeline
         Run code to ensure it doesn't crash. Individual functions tested separately.
         """
-        param = self.schema_obj.build_schema(self.template_dir, True, False, None)
+        self.schema_obj.build_schema(self.template_dir, True, False, None)
 
     @with_temporary_folder
     def test_build_schema_from_scratch(self, tmp_dir):
@@ -319,7 +319,7 @@ def test_build_schema_from_scratch(self, tmp_dir):
         shutil.copytree(self.template_dir, test_pipeline_dir)
         os.remove(os.path.join(test_pipeline_dir, "nextflow_schema.json"))
 
-        param = self.schema_obj.build_schema(test_pipeline_dir, True, False, None)
+        self.schema_obj.build_schema(test_pipeline_dir, True, False, None)
 
     @mock.patch("requests.post")
     def test_launch_web_builder_timeout(self, mock_post):

tests/test_subworkflows.py

@@ -30,7 +30,7 @@ def create_modules_repo_dummy(tmp_dir):
     with open(os.path.join(root_dir, ".nf-core.yml"), "w") as fh:
         fh.writelines(["repository_type: modules", "\n", "org_path: nf-core", "\n"])
 
-    with requests_mock.Mocker() as mock:
+    with requests_mock.Mocker():
         subworkflow_create = nf_core.subworkflows.SubworkflowCreate(root_dir, "test_subworkflow", "@author", True)
         subworkflow_create.create()