CI/STY: Fix spelling errors, update style check

.codespellrc

@@ -0,0 +1,6 @@
+[codespell]
+skip = .git,*.pdf,*.svg,*.html,dataset_description.json,*.bib
+# te - TE
+# Weill - name
+# reson - Reson. abbreviation in citation
+ignore-words-list = te,weill,reson

.github/workflows/style.yml

@@ -1,4 +1,4 @@
-name: Style check
+name: Style + spelling check
 
 on:
   push:
@@ -11,30 +11,27 @@ defaults:
   run:
     shell: bash
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 permissions:
   contents: read
 
 jobs:
-  build:
-    if: "!contains(github.event.head_commit.message, '[skip ci]')"
+  style:
+    runs-on: ubuntu-latest
+    steps:
+      - 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
-    strategy:
-      matrix:
-        python-version: ['3.11']
 
     steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 1  # Only fetch the latest commit
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        pip install black isort
-    - name: black code formatting check
-      run: |
-        black --check nibabies/
-    - name: isort formatting check
-      run: isort nibabies/ --check-only
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

CHANGES.md

@@ -36,9 +36,9 @@ Previous, *NiBabies* expected input from the `--derivatives` flag to be in T1w s
   * DKR: Add M-CRIB-S to Docker container (#283)
   * DKR: Update dependencies, split into multi-stage build
   * ENH: Add option to exclude projecting high variance voxels to surface (#278)
-  * ENH: Resample morphometrics to fsLR CIFTI-2 files when outputing CIFTIs (#279)
+  * ENH: Resample morphometrics to fsLR CIFTI-2 files when outputting CIFTIs (#279)
   * ENH: Add MCRIBReconAll as alternative surface reconstruction method (#283)
-  * ENH: Reorder anatomical processsing, run ANTs DenoiseImage on anatomicals (#286)
+  * ENH: Reorder anatomical processing, run ANTs DenoiseImage on anatomicals (#286)
   * ENH: Extract participant ages from BIDS sources, deprecate `--age-months` (#287)
   * ENH: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2star map estimation (#296)
   * ENH: Allow precomputed derivatives in T1w or T2w space (#305)

docs/community.md

@@ -1,6 +1,6 @@
 ## NiPreps Community
 
-Check out the [official NiPreps community page](https://www.nipreps.org/community/), where topics such as contributing, code of coduct, and licensing are outlined.
+Check out the [official NiPreps community page](https://www.nipreps.org/community/), where topics such as contributing, code of conduct, and licensing are outlined.
 
 
 ## NiBabies Coding Style

long_description.md

@@ -13,7 +13,7 @@ other challenges require a more specialized workflow. *NiBabies*, an open-source
 pipeline extending from fMRIPrep for infant structural and functional MRI
 preprocessing, aims to address this need.
 
-The workflow is built atop [Nipype](https://nipype.readthedocs.io) and encompases a large
+The workflow is built atop [Nipype](https://nipype.readthedocs.io) and encompasses a large
 set of tools from well-known neuroimaging packages, including
 [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/),
 [ANTs](https://stnava.github.io/ANTs/),

nibabies/cli/parser.py

@@ -14,7 +14,7 @@
 
 def _build_parser():
     """Build parser object."""
-    from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser, Action
+    from argparse import Action, ArgumentDefaultsHelpFormatter, ArgumentParser
     from functools import partial
     from pathlib import Path
 
@@ -300,7 +300,7 @@ def _slice_time_ref(value, parser):
         dest='verbose_count',
         action='count',
         default=0,
-        help='increases log verbosity for each occurence, debug level is -vvv',
+        help='increases log verbosity for each occurrence, debug level is -vvv',
     )
 
     g_subset = parser.add_argument_group('Options for performing only a subset of the workflow')

nibabies/cli/workflow.py

@@ -20,7 +20,7 @@ def build_workflow(config_file):
     from ..utils.misc import check_deps
     from ..workflows.base import init_nibabies_wf
 
-    # initalize config
+    # initialize config
     config.load(config_file)
     build_logger = config.loggers.workflow
 

nibabies/config.py

@@ -707,7 +707,7 @@ def _set_ants_seed():
 
 
 def _set_numpy_seed():
-    """NumPy's random seed is independant from Python's `random` module"""
+    """NumPy's random seed is independent from Python's `random` module"""
     import numpy as np
 
     val = random.randint(1, 65536)