Switch to ruff for formatting

.codespellrc

@@ -0,0 +1,8 @@
+[codespell]
+skip = .git,*.pdf,*.svg,*.html,dataset_description.json,*.gii,*.json
+# te - TE
+# Weill - name
+# reson - Reson. abbreviation in citation
+# DNE: acronym for does not exist
+# fo: acronym for file object
+ignore-words-list = te,weill,reson,DNE,fo

.github/workflows/lint.yml

@@ -1,26 +1,38 @@
-name: Linters
+name: Contribution checks
 
 on:
-  - push
-  - pull_request
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+defaults:
+  run:
+    shell: bash
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
 
 jobs:
-  lint:
+  style:
     runs-on: ubuntu-latest
     steps:
-    - name: Set up environment
-      uses: actions/checkout@v4
-      with:  # no need for the history
-        fetch-depth: 1
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.9'
-    - name: Install dependencies
-      run: |
-        pip install flake8 flake8-absolute-import flake8-black flake8-docstrings \
-        flake8-isort flake8-pyproject flake8-unused-arguments \
-        flake8-use-fstring pep8-naming \
-        codespell tomli
-    - name: Run linters
-      run: python -m flake8 cubids
+      - uses: actions/checkout@v4
+      - run: pipx run ruff check .
+      - run: pipx run ruff format --diff .
+
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

cubids/cubids.py

@@ -709,11 +709,11 @@ def copy_exemplars(self, exemplars_dir, exemplars_tsv, min_group_size):
         ----------
         exemplars_dir : :obj:`str`
             path to the directory that will contain one subject
-            from each Acqusition Group (*_AcqGrouping.tsv)
+            from each Acquisition Group (*_AcqGrouping.tsv)
             example path: /Users/Covitz/tsvs/CCNP_Acq_Groups/
         exemplars_tsv : :obj:`str`
             path to the .tsv file that lists one subject
-            from each Acqusition Group (*_AcqGrouping.tsv
+            from each Acquisition Group (*_AcqGrouping.tsv
             from the cubids-group output)
             example path: /Users/Covitz/tsvs/CCNP_Acq_Grouping.tsv
         min_group_size : :obj:`int`
@@ -923,7 +923,7 @@ def get_nifti_associations(self, nifti):
             A list of paths to files associated with the given NIfTI file, excluding
             the NIfTI file itself.
         """
-        # get all assocation files of a nifti image
+        # get all association files of a nifti image
         no_ext_file = str(nifti).split("/")[-1].split(".")[0]
         associations = []
         for path in Path(self.path).rglob(f"sub-*/**/{no_ext_file}.*"):

cubids/workflows.py

@@ -396,7 +396,7 @@ def copy_exemplars(
     if use_datalad:
         if not bod.is_datalad_clean():
             raise Exception(
-                "Untracked changes. Need to save " + str(bids_dir) + " before coyping exemplars"
+                "Untracked changes. Need to save " + str(bids_dir) + " before copying exemplars"
             )
     bod.copy_exemplars(
         str(exemplars_dir),

docs/example.rst

@@ -185,8 +185,8 @@ BIDS validation
     but can be slowed down by extremely large datasets.
 
 .. warning::
-    For internetless use cases, please see dedicated section of the `Installation page 
-    <https://cubids.readthedocs.io/en/latest/installation.html>`_ on how to download a local version 
+    For internetless use cases, please see dedicated section of the `Installation page
+    <https://cubids.readthedocs.io/en/latest/installation.html>`_ on how to download a local version
     of the validator.
 
     After that, you will need to add ``--local-validator`` option to the command string above.
@@ -216,7 +216,7 @@ To do this, we run the ``cubids purge`` command.
 ``cubids purge`` requires as input a list of files to cleanly "purge" from the dataset.
 You can create this file in any text editor,
 as long as it is saved as plain text ``.txt``.
-When specifying files in this text file, 
+When specifying files in this text file,
 always use relative paths starting from your BIDS directory.
 For this example, we created the following file:
 
@@ -321,7 +321,7 @@ based on acquisition fields such as dimension and voxel sizes, number of volumes
 
 While ``v0_validation.tsv`` identified all the BIDS validation errors present in the dataset,
 it did not identify any potential issues that might be present within the sidecars' metadata.
-Below, we see insances of missing metadata fields in a handful of sidecars,
+Below, we see instances of missing metadata fields in a handful of sidecars,
 which may impact successful execution of BIDS Apps.
 
 .. csv-table:: v0_summary.tsv

pyproject.toml

@@ -56,19 +56,10 @@ doc = [
 tests = [
     "codespell",
     "coverage",
-    "flake8",
-    "flake8-absolute-import",
-    "flake8-black",
-    "flake8-docstrings",
-    "flake8-isort",
-    "flake8-pyproject",
-    "flake8-unused-arguments",
-    "flake8-use-fstring",
-    "flake8-warnings",
     "niworkflows",
-    "pep8-naming",
     "pytest",
     "pytest-cov",
+    "ruff ~= 0.9.2",
     "tomli",
 ]
 maint = [
@@ -122,50 +113,55 @@ version-file = "cubids/_version.py"
 # Developer tool configurations
 #
 
+# Disable black
 [tool.black]
+exclude = ".*"
+
+[tool.ruff]
 line-length = 99
-target-version = ['py38']
-include = '\.pyi?$'
-exclude = '''
-(
-  /(
-      \.eggs         # exclude a few common directories in the
-    | \.git          # root of the project
-    | \.github
-    | \.hg
-    | \.pytest_cache
-    | _build
-    | build
-    | dist
-  )/
-  | versioneer.py
-  | cubids/_version.py
-)
-'''
-
-[tool.isort]
-profile = "black"
-multi_line_output = 3
-src_paths = ["isort", "test"]
-known_local_folder = ["cubids"]
-
-[tool.flake8]
-max-line-length = "99"
-doctests = "False"
-exclude = [
-    "*build/",
-    "cubids/_version.py",
-    "cubids/_warnings.py",
-    "cubids/config.py",
-    "cubids/data/",
-    "cubids/tests/",
+
+[tool.ruff.lint]
+extend-select = [
+  "F",
+  "E",
+  "W",
+  "I",
+  "UP",
+  "YTT",
+  "S",
+  "BLE",
+  "B",
+  "A",
+  # "CPY",
+  "C4",
+  "DTZ",
+  "T10",
+  # "EM",
+  "EXE",
+  "FA",
+  "ISC",
+  "ICN",
+  "PT",
+  "Q",
 ]
-ignore = ["D107", "E203", "E402", "E722", "W503", "N803", "N806", "N815"]
-per-file-ignores = [
-    "**/__init__.py : F401",
-    "docs/conf.py : E265",
+ignore = [
+  "S105",
+  "S311",  # We are not using random for cryptographic purposes
+  "ISC001",
+  "S603",
 ]
 
+[tool.ruff.lint.flake8-quotes]
+inline-quotes = "single"
+
+[tool.ruff.lint.extend-per-file-ignores]
+"*/test_*.py" = ["S101"]
+"docs/conf.py" = ["A001"]
+"docs/sphinxext/github_link.py" = ["BLE001"]
+
+[tool.ruff.format]
+quote-style = "single"
+
 [tool.pytest.ini_options]
 addopts = ["--doctest-modules"]
 

tox.ini

@@ -0,0 +1,102 @@
+[tox]
+requires =
+  tox>=4
+envlist =
+  py3{10,11,12}-latest
+  py310-min
+  py3{10,11,12}-pre
+skip_missing_interpreters = true
+
+# Configuration that allows us to split tests across GitHub runners effectively
+[gh-actions]
+python =
+  3.10: py310
+  3.11: py311
+  3.12: py312
+
+[gh-actions:env]
+DEPENDS =
+  min: min
+  latest: latest
+  pre: pre
+
+[testenv]
+description = Pytest with coverage
+labels = test
+pip_pre =
+  pre: true
+pass_env =
+  # getpass.getuser() sources for Windows:
+  LOGNAME
+  USER
+  LNAME
+  USERNAME
+  # Pass user color preferences through
+  PY_COLORS
+  FORCE_COLOR
+  NO_COLOR
+  CLICOLOR
+  CLICOLOR_FORCE
+  PYTHON_GIL
+extras = test
+setenv =
+  pre: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
+
+commands =
+  pytest --cov-report term-missing --durations=20 --durations-min=1.0 {posargs:-n auto}
+
+[testenv:style]
+description = Check our style guide
+labels = check
+deps =
+  ruff
+skip_install = true
+commands =
+  ruff check --diff
+  ruff format --diff
+
+[testenv:style-fix]
+description = Auto-apply style guide to the extent possible
+labels = pre-release
+deps =
+  ruff
+skip_install = true
+commands =
+  ruff check --fix
+  ruff format
+  ruff check --select ISC001
+
+[testenv:spellcheck]
+description = Check spelling
+labels = check
+deps =
+  codespell[toml]
+skip_install = true
+commands =
+  codespell . {posargs}
+
+[testenv:build{,-strict}]
+labels =
+  check
+  pre-release
+deps =
+  build
+  twine
+skip_install = true
+set_env =
+  # Ignore specific known warnings:
+  # https://github.com/pypa/pip/issues/11684
+  # https://github.com/pypa/pip/issues/12243
+  strict: PYTHONWARNINGS=error,once:pkg_resources is deprecated as an API.:DeprecationWarning:pip._internal.metadata.importlib._envs,once:Unimplemented abstract methods {'locate_file'}:DeprecationWarning:pip._internal.metadata.importlib._dists
+commands =
+  python -m build
+  python -m twine check dist/*
+
+[testenv:publish]
+depends = build
+labels = release
+deps =
+  twine
+skip_install = true
+commands =
+  python -m twine upload dist/*