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* origin/master: (288 commits)
  chore(deps): bump codecov/codecov-action from 4 to 5 (#1989)
  chore: Bump schema post-dev version
  schema-0.11.3.post3
  chore(ci): Fix pytest call for make_archive
  chore: Remove excess test data from bidsschematools installation directories (#1985)
  feat(cli): Add tool for filename validation for use in pre-receive hooks (#1986)
  rm COC (#1979)
  chore: Bump schema post-dev version
  schema-0.11.3.post2
  Update CONTRIBUTING.md (#1978)
  fix(schema): Check SliceTiming length against SliceEncodingDirection
  fix(schema): Do not warn about missing events for task-noise
  fix(schema): Check for existence of stim_files in beh.tsv
  chore: Use GITHUB_REF(_NAME) correctly
  chore: Debug environment
  chore: Bump schema post-dev version
  schema-0.11.3.post1
  chore: Output version, set correct env var
  chore: Update publish_schema to publish post-releases
  fix(schema): Include changes to schema that do not modify spec
  ...

 Conflicts:
	mkdocs.yml
	src/schema/objects/columns.yaml
	src/schema/objects/metadata.yaml
	src/schema/objects/modalities.yaml
	src/schema/objects/suffixes.yaml
	src/schema/rules/modalities.yaml
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yarikoptic committed Nov 20, 2024
2 parents 2b9e757 + 6a40161 commit 6b11f54
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43 changes: 39 additions & 4 deletions .all-contributorsrc
Original file line number Diff line number Diff line change
Expand Up @@ -274,6 +274,14 @@
"name": "Anthony Galassi",
"profile": "https://github.com/bendhouseart"
},
{
"contributions": [
"doc"
],
"login": "arianna_sala",
"name": "Arianna Sala",
"profile": "https://www.coma.uliege.be/people/arianna-sala/"
},
{
"avatar_url": [
"https://avatars.githubusercontent.com/u/118582?v=4"
Expand Down Expand Up @@ -383,10 +391,13 @@
},
{
"contributions": [
"doc"
"doc",
"code",
"test"
],
"login": "benjamin_dichter",
"name": "Benjamin Dichter"
"name": "Benjamin Dichter",
"profile": "https://bendichter.com/"
},
{
"contributions": [
Expand Down Expand Up @@ -1999,11 +2010,14 @@
{
"avatar_url": "https://avatars.githubusercontent.com/u/6051303?v=4",
"contributions": [
"doc"
"doc",
"code",
"data",
"review"
],
"login": "markmikkelsen",
"name": "Mark Mikkelsen",
"profile": "https://vivo.weill.cornell.edu/display/cwid-mam4041"
"profile": "https://mikkelsenlab.weill.cornell.edu/"
},
{
"contributions": [
Expand Down Expand Up @@ -2303,6 +2317,13 @@
"login": "nicole_c_swann",
"name": "Nicole C. Swann"
},
{
"contributions": [
"doc"
],
"login": "nbeliy",
"name": "Nikita Beliy"
},
{
"contributions": [
"doc"
Expand Down Expand Up @@ -2636,6 +2657,13 @@
"login": "samuel_garcia",
"name": "Samuel Garcia"
},
{
"contributions": [
"doc"
],
"login": "SamGuay",
"name": "Samuel Guay"
},
{
"avatar_url": [
"https://avatars.githubusercontent.com/u/3496566?v=4"
Expand Down Expand Up @@ -3079,6 +3107,13 @@
"login": "viacovella",
"name": "Vittorio Iacovella"
},
{
"contributions": [
"doc"
],
"login": "viviana_siless",
"name": "Viviana Siless"
},
{
"contributions": [
"doc"
Expand Down
122 changes: 0 additions & 122 deletions .circleci/config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -93,133 +93,11 @@ jobs:
- store_artifacts:
path: bids-spec.pdf

# Automatically generate a changelog since migration from Google Docs to GitHub
github_changelog_generator:
docker:
- image: ferrarimarco/github-changelog-generator:1.14.3
steps:
- setup_remote_docker:
version: 18.06.0-ce
# checkout code to default ~/project
- checkout
- run:
name: Build changelog
# $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI
command: |
mkdir ~/changelog_build
git status
if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
github_changelog_generator \
--exclude-tags-regex "^(?!v).*?$" \
--user bids-standard \
--project bids-specification \
--token ${CHANGE_TOKEN} \
--output ~/changelog_build/CHANGES.md \
--base ~/project/src/pregh-changes.md \
--header-label "# Changelog" \
--release-branch master \
--no-issues \
--no-filter-by-milestone \
--no-compare-link \
--pr-label "" \
--enhancement-label "" \
--bugs-label "" \
--exclude-labels "exclude-from-changelog"
cat ~/changelog_build/CHANGES.md
else
echo "Commit or Release, do nothing"
fi
- persist_to_workspace:
# raw generated changelog in ~/changelog_build/CHANGES.md
root: ~/.
paths:
- changelog_build

# Lint and fix the auto generated changes.md file
lint_generated_changelog:
docker:
- image: cimg/node:lts
steps:
# checkout code to default ~/project
- checkout
- attach_workspace:
# the freshly built CHANGES.md will be in ~/changelog_build/CHANGES.md
at: ~/.
- run:
name: install remark and extensions
command: npm install `cat npm-requirements.txt`
- run:
name: remark on autogenerated CHANGES.md
# format changelog, then use sed to change * to -, then lint changelog
command: |
git status
if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
head -n 100 ~/changelog_build/CHANGES.md
npx remark-cli ~/changelog_build/CHANGES.md --rc-path ~/project/.remarkrc --output ~/changelog_build/CHANGES.md
head -n 100 ~/changelog_build/CHANGES.md
sed -i 's/* /- /' ~/changelog_build/CHANGES.md
head -n 100 ~/changelog_build/CHANGES.md
npx remark-cli ~/changelog_build/CHANGES.md --frail --rc-path ~/project/.remarkrc
else
echo "Commit or Release, do nothing"
fi
- persist_to_workspace:
# linted and fixed changelog in ~/changelog_build/CHANGES.md
root: ~/.
paths:
- changelog_build

# Push built changelog to repo
commit_generated_changelog:
docker:
- image: cimg/base:stable
steps:
- setup_remote_docker:
version: 17.11.0-ce
# checkout code to default ~/project
- checkout
- attach_workspace:
# fixed+linted changelog in ~/changelog_build/CHANGES.md
at: ~/.
- run:
name: Changelog deployment
# $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI
command: |
if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
mv ~/changelog_build/CHANGES.md ~/project/src/CHANGES.md
merge_message=$(git log -1 | grep Merge | grep "pull")
PR_number=$(echo $merge_message | cut -d ' ' -f 4)
git config credential.helper 'cache --timeout=120'
git config user.email "[email protected]"
git config user.name "bids-maintenance"
git add ~/project/src/CHANGES.md
git commit -m "[DOC] Auto-generate changelog entry for PR ${PR_number}"
git push https://${CHANGE_TOKEN}@github.com/bids-standard/bids-specification.git master
else
echo "Commit or Release, do nothing"
fi
workflows:
search_build:
jobs:
- build_docs
- check_links:
requires:
- build_docs
- github_changelog_generator:
filters:
branches:
only: master
- lint_generated_changelog:
requires:
- github_changelog_generator
filters:
branches:
only: master
- commit_generated_changelog:
requires:
- lint_generated_changelog
filters:
branches:
only: master
- build_docs_pdf
57 changes: 41 additions & 16 deletions .github/pull_request_template.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,27 +2,52 @@

See the [CONTRIBUTING](https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md) guide. Specifically:

- Please keep the title of your Pull Request (PR) short but informative - it will
appear in the changelog.
- Please keep the title of your Pull Request (PR) short but informative - it will appear in the changelog.
- If you do **not** want a PR to appear in the changelog, it must receive the `exclude-from-changelog` label.
- Please ensure your name is credited on our [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md).
To add your name, please edit our [Contributors wiki](https://github.com/bids-standard/bids-specification/wiki/Contributors) and add your name with the type of contribution.

- Please ensure your name is credited
on our [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md).
To add your name, please edit our [Contributors wiki](https://github.com/bids-standard/bids-specification/wiki/Contributors)
and add your name with the type of contribution.
For assistance, please tag @bids-standard/maintainers.

- Use one of the following prefixes in the title of your PR:
- `[ENH]` - enhancement of the specification that adds a new feature or
support for a new data type
- `[ENH]` - enhancement of the specification that adds a new feature or support for a new data type
- `[FIX]` - fix of a typo or language clarification
- `[INFRA]` - changes to the infrastructure automating the specification
release (for example building HTML docs)
- `[INFRA]` - changes to the infrastructure automating the specification release (for example building HTML docs)
- `[SCHEMA]` - changes to the BIDS schema and/or related code
- `[MISC]` - everything else including changes to the file listing
contributors
- If you are opening a PR to obtain early feedback, but the changes
are not ready to be merged (also known as a "Work in Progress" PR), please
use a [Draft PR](https://github.blog/2019-02-14-introducing-draft-pull-requests/).
- After opening the PR, our continuous integration services will automatically check your contribution for formatting errors and render a preview of the BIDS specification with your changes.
- `[MISC]` - everything else including changes to the file listing contributors

- If you are opening a PR to obtain early feedback,
but the changes are not ready to be merged (also known as a "Work in Progress" PR),
please use a [Draft PR](https://github.blog/2019-02-14-introducing-draft-pull-requests/).

- After opening the PR, our continuous integration services will automatically check your contribution
for formatting errors and render a preview of the BIDS specification with your changes.
To see the checks and preview, scroll down and click on the `show all checks` link.
From the list, select the `Details` link of the `ci/circleci: build_docs artifact` check to see the preview of the BIDS specification.
- If you are updating the schema *and* you need to subsequently make changes to the bidsschematools code (validation, tests, rendering), this means your PR probably introduces a compatibility breaking change and you should increment the minor version (the second number) in `bids-specification/src/schema/SCHEMA_VERSION`.
From the list:
- select the `Details` link of the `docs/readthedocs.org:bids-specification` check to see the HTML preview of the BIDS specification.
- select the `Details` link of the `Check the rendered PDF version here! ` check to see the PDF preview of the BIDS specification.

- If you are updating the schema *and* you need to subsequently make changes to the bidsschematools code (validation, tests, rendering),
this means your PR probably introduces a compatibility breaking change
and you should increment the minor version (the second number) in `bids-specification/src/schema/SCHEMA_VERSION`.

- If you are opening a PR for a BIDS extension proposal (BEP),
make sure that your top message contains the following notes

> [!Note]
>
> **We meet regularly to discuss this BEP**
>
> Next meeting: **insert date** on **URL to join**
>
> Communication channel on github repo / matrix / slack / discord : **insert URL to join**
>
> [!Tip]
>
> [**HTML preview of this BEP**](insert URL to HTML preview once available)
>
--- PLEASE READ AND DELETE THE TEXT ABOVE BEFORE OPENING THE PULL REQUEST ---
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