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Merge commit 'v1.10.0-35-g5f7004819' (master) into enh-project-datasettype
* commit 'v1.10.0-35-g5f7004819': (218 commits) Include entity-less "scans.json" into an example of inheritance principle (#1945) fix(checks): Enforce timing mutual exclusions on BOLD/ASL data only (#1969) refactor contributing (#1965) [pre-commit.ci] pre-commit autoupdate (#1967) [SCHEMA] Allow physio files for anat datatype (#1961) [pre-commit.ci] pre-commit autoupdate Add an empty line in hope to get table rendered properly in "Ordering rules" section (#1953) schema: add check for duplicate READMEs (#1952) [MAINT] switch bidsschematools to pyproject.toml (#1948) fix(schema): Disable TaskName check for channels and markers files Permit and warn on task/acquisition/run for electrodes and coordsystems [FIX] Allow (but discourage) task entity for coordsystem.json fix(schema): Limit MRI metadata checks to NIfTIs fix: Only check for sorted times in arrays py3.13 (#1947) [pre-commit.ci] pre-commit autoupdate (#1946) [FIX] Update changelog links to avoid redirects (#1944) [ENH] Update DWI suffixes to include most common scanner derivatives (#1864) [pre-commit.ci] pre-commit autoupdate [MAINT] Update Release_Protocol.md ...
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‎.all-contributorsrc‎

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@@ -274,6 +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": [
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"doc"
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],
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"login": "arianna_sala",
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"name": "Arianna Sala",
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"profile": "https://www.coma.uliege.be/people/arianna-sala/"
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},
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{
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"avatar_url": [
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"https://avatars.githubusercontent.com/u/118582?v=4"
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},
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{
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"contributions": [
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"doc"
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"doc",
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"code",
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"test"
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],
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"login": "benjamin_dichter",
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"name": "Benjamin Dichter"
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"name": "Benjamin Dichter",
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"profile": "https://bendichter.com/"
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},
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{
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"contributions": [
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{
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"avatar_url": "https://avatars.githubusercontent.com/u/6051303?v=4",
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"contributions": [
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"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"
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"profile": "https://mikkelsenlab.weill.cornell.edu/"
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},
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{
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"contributions": [
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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"
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"login": "samuel_garcia",
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"name": "Samuel Garcia"
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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": "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"
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"login": "viacovella",
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"name": "Vittorio Iacovella"
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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": "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"

‎.github/workflows/changelog_generator.yml‎

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git add ${{ github.workspace }}/src/CHANGES.md
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git commit -m "[DOC] Auto-generated changelog entry"
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- name: Create Pull Request
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uses: peter-evans/create-pull-request@v6
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uses: peter-evans/create-pull-request@v7
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with:
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token: ${{ secrets.GITHUB_TOKEN }}
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branch: changelog_generator_update

‎.github/workflows/publish_schema.yml‎

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name: "Publish schema"
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on:
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push:
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branches:
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- "master"
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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defaults:
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run:
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shell: bash
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env:
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GIT_AUTHOR_NAME: BIDS CI
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GIT_AUTHOR_EMAIL: [email protected]
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GIT_COMMITTER_NAME: BIDS CI
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GIT_COMMITTER_EMAIL: [email protected]
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permissions:
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contents: write
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id-token: write
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jobs:
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publish:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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filter: "blob:none"
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- uses: actions/setup-python@v5
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with:
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python-version: 3
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- name: Install bidsschematools
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run: |
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pip install --upgrade tools/schemacode
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git clean -fxd tools/schemacode
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- name: Checkout jsr-dist
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run: |
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git checkout -t origin/jsr-dist
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- name: Regenerate schema
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run: bst export > schema.json
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- name: Regenerate context types
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run: |
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jq .meta.context schema.json \
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| npx quicktype --src-lang schema --lang ts -t Context --just-types \
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> context.ts
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- name: Regenerate metaschema types
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run: |
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# Name the file schema so the type will be named Schema
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bst export-metaschema > /tmp/schema.json
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npx --package=json-schema-to-typescript json2ts --unknownAny /tmp/schema.json > metaschema.ts
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- name: Determine next version
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run: |
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BASE=$( jq -r .schema_version schema.json )
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if [[ "$BASE" =~ ^[0-9]*.[0-9]*.[0-9]*$ ]]; then
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# Release, so unconditionally update version
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VERSION=$BASE
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jq ".version = \"$VERSION\"" jsr.json > tmp.json && mv tmp.json jsr.json
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else
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DENOVER=$( jq -r .version jsr.json )
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# Get the reference of the latest commit to touch the schema directory
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HASH=$( git log -n 1 --pretty=%h $REF -- src/schema )
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if [[ $DENOVER =~ ^"$BASE".[0-9] ]]; then
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PREFIX=${DENOVER%+*}
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let SERIAL=1+${PREFIX#$BASE.}
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else
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SERIAL=1
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fi
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VERSION="$BASE.$SERIAL+$HASH"
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fi
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echo VERSION=$VERSION | tee -a $GITHUB_ENV
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env:
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REF: ${{ github.ref }}
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- name: Check for changes, set version and commit
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run: |
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if ! git diff -s --exit-code; then
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jq ".version = \"$VERSION\"" jsr.json > tmp.json && mv tmp.json jsr.json
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git add jsr.json schema.json context.ts metaschema.ts
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git commit -m "Update schema JSR distribution"
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git push
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fi
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- name: Publish to JSR
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if: success()
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run: |
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npx jsr publish

‎.github/workflows/schemacode_ci.yml‎

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- name: "Install build dependencies"
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run: pip install --upgrade build twine
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- name: "Install test dependencies on tag"
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run: pip install --upgrade tools/schemacode[test]
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run: pip install --upgrade tools/schemacode[all]
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if: ${{ startsWith(github.ref, 'refs/tags/schema-') }}
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- name: "Build archive on tag"
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fail-fast: false
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matrix:
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os: ["ubuntu-latest"]
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python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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include:
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- os: macos-latest
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python-version: 3

‎.mailmap‎

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Ezequiel Mikulan <[email protected]>
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Guillaume Flandin <[email protected]>
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Dimitri Papadopoulos Orfanos <[email protected]>

‎.pre-commit-config.yaml‎

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exclude: 'tools/schemacode/bidsschematools/tests/data/broken_dataset_description.json'
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.6.0
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rev: v5.0.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-json
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- id: check-toml
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- id: check-ast
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- id: check-added-large-files
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- id: check-case-conflict
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- repo: https://github.com/python-jsonschema/check-jsonschema
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rev: 0.29.4
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hooks:
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- id: check-dependabot
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- id: check-github-workflows
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args: ["--verbose"]
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- id: check-metaschema
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files: src/metaschema.json
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- id: check-readthedocs
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files: readthedocs.yml
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- repo: https://github.com/psf/black
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rev: 24.4.2
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rev: 24.10.0
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- id: black
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- repo: https://github.com/pyCQA/flake8
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rev: 7.1.1
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- id: flake8
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args: [--config=tools/schemacode/setup.cfg]
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args: [--config=tools/schemacode/.flake8]
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: v4.0.0-alpha.8
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hooks:
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args: [-f=standard, -c=.yamllint.yml]
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- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
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rev: v2.14.0
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hooks:
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- id: pretty-format-toml
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args: [--autofix, --indent, '4', --no-sort]
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- repo: https://github.com/codespell-project/codespell
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- id: codespell
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v1.12.1
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- types-tabulate
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- types-jsonschema
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- jsonschema
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- httpx
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args: ["tools/schemacode/bidsschematools"]
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pass_filenames: false
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- repo: https://github.com/koalaman/shellcheck-precommit

‎.tributors‎

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"name": "Anthony Galassi",
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"orcid": "0000-0001-6550-4574"
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},
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"arianna_sala": {
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"affiliation": "université de Liège, Belgium",
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"blog": "https://www.coma.uliege.be/people/arianna-sala/",
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"contributions": [
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"doc"
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],
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"email": "[email protected]",
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"name": "Arianna Sala",
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"orcid": "0000-0001-8121-0891"
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},
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"arokem": {
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"affiliation": "University of Washington, Psychology, Seattle, WA, 98107, United States of America",
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"blog": "https://arokem.org/",
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"publish_email": true
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},
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"benjamin_dichter": {
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"affiliation": "CatalystNeuro",
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"blog": "https://bendichter.com/",
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"code",
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"test"
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"name": "Benjamin Dichter"
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"email": "[email protected]",
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"github": "bendichter",
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"name": "Benjamin Dichter",
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"orcid": "0000-0001-5725-6910"
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},
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"benjamin_gagl": {
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"affiliation": "University of Vienna",
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"name": "Marie-Hélène Bourget"
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},
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"markmikkelsen": {
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"affiliation": "Weill Cornell Medicine, Department of Radiology, New York, NY, 10021, USA",
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"blog": "https://vivo.weill.cornell.edu/display/cwid-mam4041",
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"affiliation": "Weill Cornell Medicine",
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"blog": "https://mikkelsenlab.weill.cornell.edu/",
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"contributions": [
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"data",
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"review"
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],
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"email": "[email protected]",
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"github": "markmikkelsen",
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"orcid": "0000-0002-0349-3782",
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"publish_email": true
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],
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"name": "Nicole C. Swann"
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"nbeliy": {
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"affiliation": "University of Liege (Liege, Belgium)",
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"contributions": [
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],
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"email": "[email protected]",
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"github": "nbeliy",
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"name": "Nikita Beliy",
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"orcid": "0009-0002-0830-3279"
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},
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"nima_bigdely_shamlo": {
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],
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"name": "Samuel Garcia"
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"SamGuay": {
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"affiliation": "Université de Montréal, Montreal, Québec, CA",
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"contributions": [
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"doc"
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],
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"email": "[email protected]",
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"github": "SamGuay",
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"name": "Samuel Guay",
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"orcid": "0000-0001-6990-839X"
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},
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"snastase": {
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"affiliation": "Princeton University",
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"blog": "https://snastase.github.io/",
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"name": "Vittorio Iacovella",
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"orcid": "0000-0002-0853-1573"
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},
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"viviana_siless": {
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"affiliation": "Business School, Universidad Torcuato di Tella",
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"contributions": [
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"doc"
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],
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"email": "[email protected]",
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"name": "Viviana Siless"
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},
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"vladimir_litvak": {
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"affiliation": "UCL Queen Square Institute of Neurology",
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"contributions": [

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