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Merge remote-tracking branch 'bids-standard/master' into mgp/allow-desc-in-segmentations
2 parents 1866012 + 6a40161 commit 91c4bff

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Lines changed: 8952 additions & 3914 deletions

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.all-contributorsrc

Lines changed: 97 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -192,6 +192,13 @@
192192
"login": "ali_khan",
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"name": "Ali Khan"
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},
195+
{
196+
"contributions": [
197+
"tool"
198+
],
199+
"login": "alizee_wickenheiser",
200+
"name": "Alizee Wickenheiser"
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},
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{
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"contributions": [
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"userTesting"
@@ -267,6 +274,14 @@
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"name": "Anthony Galassi",
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"profile": "https://github.com/bendhouseart"
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},
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{
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"contributions": [
279+
"doc"
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],
281+
"login": "arianna_sala",
282+
"name": "Arianna Sala",
283+
"profile": "https://www.coma.uliege.be/people/arianna-sala/"
284+
},
270285
{
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"avatar_url": [
272287
"https://avatars.githubusercontent.com/u/118582?v=4"
@@ -376,10 +391,13 @@
376391
},
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{
378393
"contributions": [
379-
"doc"
394+
"doc",
395+
"code",
396+
"test"
380397
],
381398
"login": "benjamin_dichter",
382-
"name": "Benjamin Dichter"
399+
"name": "Benjamin Dichter",
400+
"profile": "https://bendichter.com/"
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},
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{
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"contributions": [
@@ -443,6 +461,14 @@
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"login": "carlo_miniussi",
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"name": "Carlo Miniussi"
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},
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{
465+
"contributions": [
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"data",
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"tool"
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],
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"login": "cecile_madjar",
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"name": "Cecile Madjar"
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},
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{
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"contributions": [
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"doc"
@@ -1002,7 +1028,8 @@
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"tool",
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"eventOrganizing",
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"fundingFinding",
1005-
"infra"
1031+
"infra",
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"talk"
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],
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"login": "francopestilli",
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"name": "Franco Pestilli",
@@ -1461,6 +1488,13 @@
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"name": "Jeanette Mumford",
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"profile": "https://jeanettemumford.org/"
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},
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{
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"contributions": [
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"tool"
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],
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"login": "jefferson_casimir",
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"name": "Jefferson Casimir"
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},
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{
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"contributions": [
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"doc"
@@ -1799,6 +1833,13 @@
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"name": "Kurt Schilling",
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"profile": "https://github.com/schillkg"
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},
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{
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"contributions": [
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"tool"
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],
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"login": "laetitia_fesselier",
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"name": "Laetitia Fesselier"
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},
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{
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"contributions": [
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"financial"
@@ -1969,11 +2010,14 @@
19692010
{
19702011
"avatar_url": "https://avatars.githubusercontent.com/u/6051303?v=4",
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"contributions": [
1972-
"doc"
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"doc",
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"code",
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"data",
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"review"
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],
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"login": "markmikkelsen",
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"name": "Mark Mikkelsen",
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"profile": "https://vivo.weill.cornell.edu/display/cwid-mam4041"
2020+
"profile": "https://mikkelsenlab.weill.cornell.edu/"
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},
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{
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"contributions": [
@@ -2273,6 +2317,13 @@
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"login": "nicole_c_swann",
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"name": "Nicole C. Swann"
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},
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{
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"contributions": [
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"doc"
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],
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"login": "nbeliy",
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"name": "Nikita Beliy"
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},
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{
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"contributions": [
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"doc"
@@ -2606,6 +2657,13 @@
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"login": "samuel_garcia",
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"name": "Samuel Garcia"
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},
2660+
{
2661+
"contributions": [
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"doc"
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],
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"login": "SamGuay",
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"name": "Samuel Guay"
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},
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{
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"avatar_url": [
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"https://avatars.githubusercontent.com/u/3496566?v=4"
@@ -2728,6 +2786,17 @@
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"login": "stephan_bickel",
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"name": "Stephan Bickel"
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},
2789+
{
2790+
"contributions": [
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"bug",
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"code",
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"question",
2794+
"tool",
2795+
"userTesting"
2796+
],
2797+
"login": "smeisler",
2798+
"name": "Steven Meisler"
2799+
},
27312800
{
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"avatar_url": "https://avatars.githubusercontent.com/u/11152799?v=4",
27332802
"contributions": [
@@ -2987,6 +3056,14 @@
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"name": "Tristan Glatard",
29883057
"profile": "https://github.com/glatard"
29893058
},
3059+
{
3060+
"contributions": [
3061+
"data",
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"tool"
3063+
],
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"login": "tyler_collins",
3065+
"name": "Tyler Collins"
3066+
},
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{
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"contributions": [
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"doc"
@@ -3030,6 +3107,13 @@
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"login": "viacovella",
30313108
"name": "Vittorio Iacovella"
30323109
},
3110+
{
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"contributions": [
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"doc"
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],
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"login": "viviana_siless",
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"name": "Viviana Siless"
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},
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{
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"contributions": [
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"doc"
@@ -3091,7 +3175,14 @@
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"tool",
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"question",
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"bug",
3094-
"code"
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"code",
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"data",
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"fundingFinding",
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"ideas",
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"plugin",
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"review",
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"userTesting",
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"infra"
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],
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"login": "yarikoptic",
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"name": "Yaroslav O. Halchenko",

.circleci/config.yml

Lines changed: 4 additions & 124 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@ version: 2.1
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jobs:
33
build_docs:
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docker:
5-
- image: cimg/python:3.8
5+
- image: cimg/python:3.12-node
66
steps:
77
# checkout code to default ~/project
88
- checkout
@@ -21,14 +21,15 @@ jobs:
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- persist_to_workspace:
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# the mkdocs build outputs are in ~/project/site
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root: ~/project
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paths: site
24+
paths:
25+
- site
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- store_artifacts:
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path: ~/project/site/
2728
destination: dev_docs
2829

2930
check_links:
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docker:
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- image: cimg/python:3.8
32+
- image: cimg/python:3.12
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steps:
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# checkout code to default ~/project
3435
- checkout
@@ -92,132 +93,11 @@ jobs:
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- store_artifacts:
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path: bids-spec.pdf
9495

95-
# Automatically generate a changelog since migration from Google Docs to GitHub
96-
github_changelog_generator:
97-
docker:
98-
- image: ferrarimarco/github-changelog-generator:1.14.3
99-
steps:
100-
- setup_remote_docker:
101-
version: 18.06.0-ce
102-
# checkout code to default ~/project
103-
- checkout
104-
- run:
105-
name: Build changelog
106-
# $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI
107-
command: |
108-
mkdir ~/changelog_build
109-
git status
110-
if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
111-
github_changelog_generator \
112-
--exclude-tags-regex "^(?!v).*?$" \
113-
--user bids-standard \
114-
--project bids-specification \
115-
--token ${CHANGE_TOKEN} \
116-
--output ~/changelog_build/CHANGES.md \
117-
--base ~/project/src/pregh-changes.md \
118-
--header-label "# Changelog" \
119-
--release-branch master \
120-
--no-issues \
121-
--no-filter-by-milestone \
122-
--no-compare-link \
123-
--pr-label "" \
124-
--enhancement-label "" \
125-
--bugs-label "" \
126-
--exclude-labels "exclude-from-changelog"
127-
cat ~/changelog_build/CHANGES.md
128-
else
129-
echo "Commit or Release, do nothing"
130-
fi
131-
- persist_to_workspace:
132-
# raw generated changelog in ~/changelog_build/CHANGES.md
133-
root: ~/.
134-
paths: changelog_build
135-
136-
# Lint and fix the auto generated changes.md file
137-
lint_generated_changelog:
138-
docker:
139-
- image: cimg/node:lts
140-
steps:
141-
# checkout code to default ~/project
142-
- checkout
143-
- attach_workspace:
144-
# the freshly built CHANGES.md will be in ~/changelog_build/CHANGES.md
145-
at: ~/.
146-
- run:
147-
name: install remark and extensions
148-
command: npm install `cat npm-requirements.txt`
149-
- run:
150-
name: remark on autogenerated CHANGES.md
151-
# format changelog, then use sed to change * to -, then lint changelog
152-
command: |
153-
git status
154-
if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
155-
head -n 100 ~/changelog_build/CHANGES.md
156-
npx remark-cli ~/changelog_build/CHANGES.md --rc-path ~/project/.remarkrc --output ~/changelog_build/CHANGES.md
157-
head -n 100 ~/changelog_build/CHANGES.md
158-
sed -i 's/* /- /' ~/changelog_build/CHANGES.md
159-
head -n 100 ~/changelog_build/CHANGES.md
160-
npx remark-cli ~/changelog_build/CHANGES.md --frail --rc-path ~/project/.remarkrc
161-
else
162-
echo "Commit or Release, do nothing"
163-
fi
164-
- persist_to_workspace:
165-
# linted and fixed changelog in ~/changelog_build/CHANGES.md
166-
root: ~/.
167-
paths: changelog_build
168-
169-
# Push built changelog to repo
170-
commit_generated_changelog:
171-
docker:
172-
- image: cimg/base:stable
173-
steps:
174-
- setup_remote_docker:
175-
version: 17.11.0-ce
176-
# checkout code to default ~/project
177-
- checkout
178-
- attach_workspace:
179-
# fixed+linted changelog in ~/changelog_build/CHANGES.md
180-
at: ~/.
181-
- deploy:
182-
name: Changelog deployment
183-
# $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI
184-
command: |
185-
if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
186-
mv ~/changelog_build/CHANGES.md ~/project/src/CHANGES.md
187-
merge_message=$(git log -1 | grep Merge | grep "pull")
188-
PR_number=$(echo $merge_message | cut -d ' ' -f 4)
189-
git config credential.helper 'cache --timeout=120'
190-
git config user.email "bids.maintenance@gmail.com"
191-
git config user.name "bids-maintenance"
192-
git add ~/project/src/CHANGES.md
193-
git commit -m "[DOC] Auto-generate changelog entry for PR ${PR_number}"
194-
git push https://${CHANGE_TOKEN}@github.com/bids-standard/bids-specification.git master
195-
else
196-
echo "Commit or Release, do nothing"
197-
fi
198-
19996
workflows:
200-
version: 2
20197
search_build:
20298
jobs:
20399
- build_docs
204100
- check_links:
205101
requires:
206102
- build_docs
207-
- github_changelog_generator:
208-
filters:
209-
branches:
210-
only: master
211-
- lint_generated_changelog:
212-
requires:
213-
- github_changelog_generator
214-
filters:
215-
branches:
216-
only: master
217-
- commit_generated_changelog:
218-
requires:
219-
- lint_generated_changelog
220-
filters:
221-
branches:
222-
only: master
223103
- build_docs_pdf

.codespellrc

Lines changed: 1 addition & 1 deletion
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@@ -1,6 +1,6 @@
11
[codespell]
22
skip = *.js,*.svg,*.eps,.git,node_modules,env,venv,.mypy_cache,package-lock.json,CITATION.cff,tools/new_contributors.tsv,./tools/schemacode/docs/build
3-
ignore-words-list = fo,te,als,Acknowledgements,acknowledgements,weill,bu,winn
3+
ignore-words-list = fo,te,als,Acknowledgements,acknowledgements,weill,bu,winn,manuel
44
builtin = clear,rare,en-GB_to_en-US
55
# this overloads default dictionaries and I have not yet figured out
66
# how to have multiple https://github.com/codespell-project/codespell/issues/2727

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