Merge pull request #341 from effigies/chore/pre-commit

effigies · web-flow · commit ec90c1963c6c · 2026-02-10T11:45:34.000-05:00
chore: Add pre-commit hooks
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,18 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: 3e8a8703264a2f4a69428a0aa4dcb512790b2c8c # v6.0.0
+    hooks:
+      - id: check-json
+      - id: check-toml
+      - id: check-yaml
+      - id: check-merge-conflict
+      - id: check-symlinks
+        exclude: tests/data/broken-symlink
+      - id: destroyed-symlinks
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+      - id: trailing-whitespace
+  - repo: https://github.com/nozaq/pre-commit-deno
+    rev: db9b2333832fdbbb36b9c36d252cd52c2f9d41dc # 0.1.0
+    hooks:
+      - id: deno-fmt
diff --git a/CITATION.cff b/CITATION.cff
@@ -46,7 +46,7 @@ authors:
     orcid: https://orcid.org/0000-0002-6533-2909
   - family-names: Gau
     given-names: Rémi
-    orcid: https://orcid.org/0000-0002-1535-9767  
+    orcid: https://orcid.org/0000-0002-1535-9767
   - family-names: Gorgolewski
     given-names: Krzysztof J.
     orcid: https://orcid.org/0000-0003-3321-7583
diff --git a/LICENSE b/LICENSE
@@ -17,4 +17,4 @@ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
 FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
 COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
 IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/changelog.d/20260116_101315_markiewicz_pre_commit.md b/changelog.d/20260116_101315_markiewicz_pre_commit.md
@@ -0,0 +1,5 @@
+### Infrastructure
+
+- Added a [pre-commit](https://pre-commit.com/) configuration for developers.
+  To enable, run `pre-commit install`. For speed, we recommend installing `pre-commit`
+  via `uv tool install pre-commit --with=pre-commit-uv`.
diff --git a/docs/validation-model/inheritance-principle.md b/docs/validation-model/inheritance-principle.md
@@ -20,7 +20,7 @@ The validator uses a "walk back" algorithm to find inherited files:
 ```python
 def walkBack(file, extension):
     fileParts = parsePath(file.path)
-    
+
     fileTree = file.parent
     while fileTree:
         for child in fileTree.children:
diff --git a/local-run b/local-run
@@ -1,4 +1,4 @@
-#!/usr/bin/env -S deno run --allow-read --allow-write --allow-env --allow-net --allow-run 
+#!/usr/bin/env -S deno run --allow-read --allow-write --allow-env --allow-net --allow-run
 // This script runs the local copy of the validator, intended as a development aid.
 // You generally should run `deno run -A jsr:@bids/validator`
 import './src/bids-validator.ts'
diff --git a/src/tests/bom-utf16.tsv b/src/tests/bom-utf16.tsv
diff --git a/src/tests/bom-utf8.json b/src/tests/bom-utf8.json
@@ -1,3 +1,3 @@
-﻿{
+{
   "example": "JSON for test suite"
 }
diff --git a/tests/data/broken_pet_example_3-pet_blood/participants.tsv b/tests/data/broken_pet_example_3-pet_blood/participants.tsv
@@ -1,2 +1,2 @@
 participant_id	sex
-sub-01	F
+sub-01	F
diff --git a/tests/data/broken_pet_example_3-pet_blood/sub-01/ses-01/pet/sub-01_ses-01_recording-manual_blood.tsv b/tests/data/broken_pet_example_3-pet_blood/sub-01/ses-01/pet/sub-01_ses-01_recording-manual_blood.tsv
@@ -30,4 +30,4 @@ time	plasma_radioactivity	metabolite_parent_fraction
 4800	8095.22519	0.10388412
 5400	7480.43763	n/a
 6000	7099.9559	0.09530672
-7200	6279.54565	n/a
+7200	6279.54565	n/a
diff --git a/tests/data/empty_files/participants.tsv b/tests/data/empty_files/participants.tsv
@@ -1,4 +1,3 @@
 participant_id	age	sex	dominant_hand
 sub-emptyroom	n/a	n/a	n/a
 sub-0001	25	Male	Right
-
diff --git a/tests/data/no_t1w/participants.tsv b/tests/data/no_t1w/participants.tsv
@@ -1,2 +1,2 @@
 participant_id	sex	age
-sub-01	M	25
+sub-01	M	25
diff --git a/tests/data/pet_blood_missing_tsv_column/participants.tsv b/tests/data/pet_blood_missing_tsv_column/participants.tsv
@@ -1,2 +1,2 @@
 participant_id	sex
-sub-01	F
+sub-01	F
diff --git a/tests/data/pet_blood_missing_tsv_column/sub-01/ses-01/pet/sub-01_ses-01_recording-manual_blood.tsv b/tests/data/pet_blood_missing_tsv_column/sub-01/ses-01/pet/sub-01_ses-01_recording-manual_blood.tsv
@@ -30,4 +30,4 @@ time	metabolite_parent_fraction
 4800	0.10388412
 5400	n/a
 6000	0.09530672
-7200	n/a
+7200	n/a
diff --git a/tests/data/symlinked_subject/participants.tsv b/tests/data/symlinked_subject/participants.tsv
@@ -1,2 +1,2 @@
 participant_id	sex	age
-sub-01	M	25
+sub-01	M	25
diff --git a/tests/data/valid_filenames/participants.tsv b/tests/data/valid_filenames/participants.tsv
@@ -1,2 +1,2 @@
 participant_id	sex	age
-sub-01	M	25
+sub-01	M	25
diff --git a/tests/data/valid_headers/.bidsignore b/tests/data/valid_headers/.bidsignore
@@ -1 +1 @@
-*_not_bids.txt
+*_not_bids.txt
diff --git a/tests/data/valid_headers/participants.tsv b/tests/data/valid_headers/participants.tsv
@@ -1,2 +1,2 @@
 participant_id	sex	age
-sub-01	M	25
+sub-01	M	25
diff --git a/web/src/Collapse.css b/web/src/Collapse.css
@@ -57,7 +57,7 @@ input[type='checkbox'] {
   .warning .lbl-toggle {
     background: #E69F00;
   }
-  
+
   .error .lbl-toggle {
     background: #D55E00;
   }

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,3 @@`
`1`		`-{`
	`1`	`+{`
`2`	`2`	`"example": "JSON for test suite"`
`3`	`3`	`}`
Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`participant_id sex`
`2`		`-sub-01 F`
	`2`	`+sub-01 F`