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Merge commit 'v1.10.0-35-g5f7004819' (master) into enh-project-datase…
…ttype * commit 'v1.10.0-35-g5f7004819': (218 commits) Include entity-less "scans.json" into an example of inheritance principle (bids-standard#1945) fix(checks): Enforce timing mutual exclusions on BOLD/ASL data only (bids-standard#1969) refactor contributing (bids-standard#1965) [pre-commit.ci] pre-commit autoupdate (bids-standard#1967) [SCHEMA] Allow physio files for anat datatype (bids-standard#1961) [pre-commit.ci] pre-commit autoupdate Add an empty line in hope to get table rendered properly in "Ordering rules" section (bids-standard#1953) schema: add check for duplicate READMEs (bids-standard#1952) [MAINT] switch bidsschematools to pyproject.toml (bids-standard#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 (bids-standard#1947) [pre-commit.ci] pre-commit autoupdate (bids-standard#1946) [FIX] Update changelog links to avoid redirects (bids-standard#1944) [ENH] Update DWI suffixes to include most common scanner derivatives (bids-standard#1864) [pre-commit.ci] pre-commit autoupdate [MAINT] Update Release_Protocol.md ...
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| name: "Publish schema" | ||
|
|
||
| on: | ||
| push: | ||
| branches: | ||
| - "master" | ||
|
|
||
| concurrency: | ||
| group: ${{ github.workflow }}-${{ github.ref }} | ||
| cancel-in-progress: true | ||
|
|
||
| defaults: | ||
| run: | ||
| shell: bash | ||
|
|
||
| env: | ||
| GIT_AUTHOR_NAME: BIDS CI | ||
| GIT_AUTHOR_EMAIL: [email protected] | ||
| GIT_COMMITTER_NAME: BIDS CI | ||
| GIT_COMMITTER_EMAIL: [email protected] | ||
|
|
||
| permissions: | ||
| contents: write | ||
| id-token: write | ||
|
|
||
| jobs: | ||
| publish: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
| filter: "blob:none" | ||
| - uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: 3 | ||
| - name: Install bidsschematools | ||
| run: | | ||
| pip install --upgrade tools/schemacode | ||
| git clean -fxd tools/schemacode | ||
| - name: Checkout jsr-dist | ||
| run: | | ||
| git checkout -t origin/jsr-dist | ||
| - name: Regenerate schema | ||
| run: bst export > schema.json | ||
| - name: Regenerate context types | ||
| run: | | ||
| jq .meta.context schema.json \ | ||
| | npx quicktype --src-lang schema --lang ts -t Context --just-types \ | ||
| > context.ts | ||
| - name: Regenerate metaschema types | ||
| run: | | ||
| # Name the file schema so the type will be named Schema | ||
| bst export-metaschema > /tmp/schema.json | ||
| npx --package=json-schema-to-typescript json2ts --unknownAny /tmp/schema.json > metaschema.ts | ||
| - name: Determine next version | ||
| run: | | ||
| BASE=$( jq -r .schema_version schema.json ) | ||
| if [[ "$BASE" =~ ^[0-9]*.[0-9]*.[0-9]*$ ]]; then | ||
| # Release, so unconditionally update version | ||
| VERSION=$BASE | ||
| jq ".version = \"$VERSION\"" jsr.json > tmp.json && mv tmp.json jsr.json | ||
| else | ||
| DENOVER=$( jq -r .version jsr.json ) | ||
| # Get the reference of the latest commit to touch the schema directory | ||
| HASH=$( git log -n 1 --pretty=%h $REF -- src/schema ) | ||
| if [[ $DENOVER =~ ^"$BASE".[0-9] ]]; then | ||
| PREFIX=${DENOVER%+*} | ||
| let SERIAL=1+${PREFIX#$BASE.} | ||
| else | ||
| SERIAL=1 | ||
| fi | ||
| VERSION="$BASE.$SERIAL+$HASH" | ||
| fi | ||
| echo VERSION=$VERSION | tee -a $GITHUB_ENV | ||
| env: | ||
| REF: ${{ github.ref }} | ||
| - name: Check for changes, set version and commit | ||
| run: | | ||
| if ! git diff -s --exit-code; then | ||
| jq ".version = \"$VERSION\"" jsr.json > tmp.json && mv tmp.json jsr.json | ||
| git add jsr.json schema.json context.ts metaschema.ts | ||
| git commit -m "Update schema JSR distribution" | ||
| git push | ||
| fi | ||
| - name: Publish to JSR | ||
| if: success() | ||
| run: | | ||
| npx jsr publish |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -64,3 +64,5 @@ Patrick Park <[email protected]> | |
| Ezequiel Mikulan <[email protected]> | ||
|
|
||
| Guillaume Flandin <[email protected]> | ||
|
|
||
| Dimitri Papadopoulos Orfanos <[email protected]> | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -244,6 +244,16 @@ | |
| "name": "Anthony Galassi", | ||
| "orcid": "0000-0001-6550-4574" | ||
| }, | ||
| "arianna_sala": { | ||
| "affiliation": "université de Liège, Belgium", | ||
| "blog": "https://www.coma.uliege.be/people/arianna-sala/", | ||
| "contributions": [ | ||
| "doc" | ||
| ], | ||
| "email": "[email protected]", | ||
| "name": "Arianna Sala", | ||
| "orcid": "0000-0001-8121-0891" | ||
| }, | ||
| "arokem": { | ||
| "affiliation": "University of Washington, Psychology, Seattle, WA, 98107, United States of America", | ||
| "blog": "https://arokem.org/", | ||
|
|
@@ -348,10 +358,17 @@ | |
| "publish_email": true | ||
| }, | ||
| "benjamin_dichter": { | ||
| "affiliation": "CatalystNeuro", | ||
| "blog": "https://bendichter.com/", | ||
| "contributions": [ | ||
| "doc" | ||
| "doc", | ||
| "code", | ||
| "test" | ||
| ], | ||
| "name": "Benjamin Dichter" | ||
| "email": "[email protected]", | ||
| "github": "bendichter", | ||
| "name": "Benjamin Dichter", | ||
| "orcid": "0000-0001-5725-6910" | ||
| }, | ||
| "benjamin_gagl": { | ||
| "affiliation": "University of Vienna", | ||
|
|
@@ -1941,12 +1958,16 @@ | |
| "name": "Marie-Hélène Bourget" | ||
| }, | ||
| "markmikkelsen": { | ||
| "affiliation": "Weill Cornell Medicine, Department of Radiology, New York, NY, 10021, USA", | ||
| "blog": "https://vivo.weill.cornell.edu/display/cwid-mam4041", | ||
| "affiliation": "Weill Cornell Medicine", | ||
| "blog": "https://mikkelsenlab.weill.cornell.edu/", | ||
| "contributions": [ | ||
| "doc" | ||
| "doc", | ||
| "code", | ||
| "data", | ||
| "review" | ||
| ], | ||
| "email": "[email protected]", | ||
| "github": "markmikkelsen", | ||
| "name": "Mark Mikkelsen", | ||
| "orcid": "0000-0002-0349-3782", | ||
| "publish_email": true | ||
|
|
@@ -2241,6 +2262,16 @@ | |
| ], | ||
| "name": "Nicole C. Swann" | ||
| }, | ||
| "nbeliy": { | ||
| "affiliation": "University of Liege (Liege, Belgium)", | ||
| "contributions": [ | ||
| "doc" | ||
| ], | ||
| "email": "[email protected]", | ||
| "github": "nbeliy", | ||
| "name": "Nikita Beliy", | ||
| "orcid": "0009-0002-0830-3279" | ||
| }, | ||
| "nima_bigdely_shamlo": { | ||
| "contributions": [ | ||
| "doc" | ||
|
|
@@ -2556,6 +2587,16 @@ | |
| ], | ||
| "name": "Samuel Garcia" | ||
| }, | ||
| "SamGuay": { | ||
| "affiliation": "Université de Montréal, Montreal, Québec, CA", | ||
| "contributions": [ | ||
| "doc" | ||
| ], | ||
| "email": "[email protected]", | ||
| "github": "SamGuay", | ||
| "name": "Samuel Guay", | ||
| "orcid": "0000-0001-6990-839X" | ||
| }, | ||
| "snastase": { | ||
| "affiliation": "Princeton University", | ||
| "blog": "https://snastase.github.io/", | ||
|
|
@@ -3005,6 +3046,14 @@ | |
| "name": "Vittorio Iacovella", | ||
| "orcid": "0000-0002-0853-1573" | ||
| }, | ||
| "viviana_siless": { | ||
| "affiliation": "Business School, Universidad Torcuato di Tella", | ||
| "contributions": [ | ||
| "doc" | ||
| ], | ||
| "email": "[email protected]", | ||
| "name": "Viviana Siless" | ||
| }, | ||
| "vladimir_litvak": { | ||
| "affiliation": "UCL Queen Square Institute of Neurology", | ||
| "contributions": [ | ||
|
|
||
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