poldracklab · yarikoptic · Apr 9, 2024 · Apr 9, 2024 · Apr 9, 2024 · Apr 9, 2024
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,23 @@
+# Codespell configuration is within pyproject.toml
+---
+name: Codespell
+
+on:
+  push:
+    branches: [dev]
+  pull_request:
+    branches: [dev]
+
+permissions:
+  contents: read
+
+jobs:
+  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
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -22,3 +22,10 @@ repos:
     hooks:
       - id: pyupgrade
         exclude: ^(fitlins/_version.py|versioneer.py)
+  - repo: https://github.com/codespell-project/codespell
+    # Configuration for codespell is in pyproject.toml
+    rev: v2.2.6
+    hooks:
+    - id: codespell
+      additional_dependencies:
+      - tomli
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -157,7 +157,7 @@ Pull requests titles should begin with a descriptive prefix:
 * ``DOC``: new or updated documentation
 * ``STY``: style changes
 * ``REF``: refactoring existing code
-* ``CI``: updates to continous integration infrastructure
+* ``CI``: updates to continuous integration infrastructure
 * ``MAINT``: general maintenance
 
 For example: `[ENH] Support for naive thresholding`

diff --git a/docs/examples/models.rst b/docs/examples/models.rst
@@ -42,11 +42,11 @@ Dataset: https://openneuro.org/datasets/ds000030/versions/00016
 
 The balloon analog risk task (BART) is a risk-taking game where participants
 decide whether to inflate a balloon, risking explosion, or cash out.
-There are two trial types (``BALOON`` [*sic*] and ``CONTROL``), and three
+There are two trial types (``BALLOON`` [*sic*] and ``CONTROL``), and three
 possible actions (``ACCEPT``, ``CASHOUT``, ``EXPLODE``).
 
 In this model, we contrast responses to ``ACCEPT`` and ``EXPLODE`` actions
-in ``BALOON`` trials only.
+in ``BALLOON`` trials only.
 
 This model is similar to the word-pseudoword model above, but also demonstrates
 the use of the ``And`` transformation, that takes the logical and of two binary

diff --git a/docs/examples/reports.rst b/docs/examples/reports.rst
@@ -46,7 +46,7 @@ collinear regressor.
 
    Correlations between regressors are plotted.
    Bold black lines separate variables that are included in contrasts, or *variables
-   of interest*, and variables that are not, or *nuissance regressors*.
+   of interest*, and variables that are not, or *nuisance regressors*.
 
 Contrast matrices
 -----------------

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -149,7 +149,7 @@ For Windows users::
       singularityware/docker2singularity \
       poldracklab/fitlins:<VERSION>
 
-This image may now be transfered to your cluster.
+This image may now be transferred to your cluster.
 
 Running a Singularity image
 ---------------------------

diff --git a/examples/models/ds000030/models/model-001_smdl.json b/examples/models/ds000030/models/model-001_smdl.json
@@ -18,7 +18,7 @@
                 {
                     "Name": "And",
                     "Input": [
-                        "trial_type.BALOON",
+                        "trial_type.BALLOON",
                         "action.ACCEPT"
                     ],
                     "Output": [
@@ -28,7 +28,7 @@
                 {
                     "Name": "And",
                     "Input": [
-                        "trial_type.BALOON",
+                        "trial_type.BALLOON",
                         "action.EXPLODE"
                     ],
                     "Output": [

diff --git a/examples/notebooks/ds003_sample_analysis.ipynb b/examples/notebooks/ds003_sample_analysis.ipynb
@@ -5645,7 +5645,7 @@
     "rf_tb_img = image.load_img(rf_tb_path)\n",
     "rf_aw_img = image.load_img(rf_aw_path)\n",
     "\n",
-    "# subtract resuts to see dif\n",
+    "# subtract results to see dif\n",
     "dif_wp_dat = nl_wp_img.get_fdata() - rf_wp_img.get_fdata()\n",
     "dif_tb_dat = nl_tb_img.get_fdata() - rf_tb_img.get_fdata()\n",
     "dif_aw_dat = nl_aw_img.get_fdata() - rf_aw_img.get_fdata()\n",

diff --git a/fitlins/_version.py b/fitlins/_version.py
@@ -308,7 +308,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, runner=run_command):
         # TAG-NUM-gHEX
         mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
         if not mo:
-            # unparseable. Maybe git-describe is misbehaving?
+            # unparsable. Maybe git-describe is misbehaving?
             pieces["error"] = ("unable to parse git-describe output: '%s'"
                                % describe_out)
             return pieces

diff --git a/fitlins/interfaces/bids.py b/fitlins/interfaces/bids.py
@@ -206,7 +206,7 @@ class LoadBIDSModel(SimpleInterface):
         The collection of specs from each level. Each dict at individual levels
         contains the following keys:
             'contrasts'  : a list of ContrastInfo objects each unit of analysis.
-                A contrast specifiction is a list of contrast
+                A contrast specification is a list of contrast
                 dictionaries. Each dict has form:
                   {
                     'name': str,
@@ -224,7 +224,7 @@ class LoadBIDSModel(SimpleInterface):
             'X'  : The design matrix
             'model'  : The model part from the BIDS-StatsModels specification.
             'metadata' (only higher-levels): a parallel DataFrame with the same number of
-                rows as X that contains all known metadata variabes that vary on a row-by-row
+                rows as X that contains all known metadata variables that vary on a row-by-row
                 basis but aren't actually predictiors
 
     warnings : list of files

diff --git a/fitlins/tests/README.md b/fitlins/tests/README.md
@@ -1,6 +1,6 @@
 # Integration tests for the fitlins commandline
 
-The tests in this directory call fitlins from the commandline in order to compare outputs with known reference values. Refernce data can be obtained with datalad via:
+The tests in this directory call fitlins from the commandline in order to compare outputs with known reference values. Reference data can be obtained with datalad via:
 ```
 datalad install -r -s https://gin.g-node.org/shotgunosine/fitlins_tests
 datalad get fitlins_tests/ds003/ds003_fmriprep/sub-0{1,2,3}/func/*_space-MNI152NLin2009cAsym_desc-*.nii.gz \
@@ -20,5 +20,5 @@ pytest fitlins/fitlins/tests --bids-dir=${tests_dir}ds003/ds003_fmriprep/sourced
 
 The three tests are:
 - afni_smooth: AFNI estimator with 10mm isotropic smoothing added
-- afni_blurto: AFNI estimator blured to 5mm smoothness
+- afni_blurto: AFNI estimator blurred to 5mm smoothness
 - nistats_smooth: Nistats estimator with 10mm isotropic smoothing added
diff --git a/pyproject.toml b/pyproject.toml
@@ -6,3 +6,10 @@ line-length = 99
 target-version = ['py37']
 skip-string-normalization = true
 extend-exclude = '_version.py|versioneer.py'
+
+[tool.codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = '.git*,*.pdf,*.svg,venvs,versioneer.py,*.css,*.min.*,*.gii'
+check-hidden = true
+ignore-regex = '^\s*"image/\S+": ".*'
+# ignore-words-list = ''
diff --git a/tools/update_changes.sh b/tools/update_changes.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 #
 # Collects the pull-requests since the latest release and
-# aranges them in the CHANGES.txt file.
+# arranges them in the CHANGES.txt file.
 #
 # This is a script to be run before releasing a new version.
 #