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Recent Releases of bids-validator

bids-validator - 2.0.11

Fixed

  • Docker build workflow should now run correctly on releases.

What's Changed

  • chore(ci): Fix actions/checkout invocation for tags by @effigies in https://github.com/bids-standard/bids-validator/pull/245

Full Changelog: https://github.com/bids-standard/bids-validator/compare/2.0.10...2.0.11

- TypeScript
Published by effigies 6 months ago

bids-validator - 2.0.10

Added

  • Added a FAQ to the user guide. (#215)

Changed

  • Improved handling of TSV columns with sidecar definitions. "Format", "Minimum" and "Maximum" keys are now supported.

  • --datasetTypes and --blacklistModalities options now accept a string array (--datasetTypes raw,derivative) and can be combined.

Fixed

  • A crash in the web validator prevented validation from taking place.

Infrastructure

Pull requests merged

  • fix: Use string[] options for datasetTypes and blacklistModalities by @nellh in https://github.com/bids-standard/bids-validator/pull/238
  • chore: Reenable DockerHub pushes by @effigies in https://github.com/bids-standard/bids-validator/pull/237
  • doc: Add FAQ by @effigies in https://github.com/bids-standard/bids-validator/pull/233
  • rf: Throw more issue-like objects in loading functions by @effigies in https://github.com/bids-standard/bids-validator/pull/236
  • feat: Unify schema and sidecar-defined column validation by @effigies in https://github.com/bids-standard/bids-validator/pull/234
  • fix: Do not crash on missing datasetTypes option by @effigies in https://github.com/bids-standard/bids-validator/pull/244

Full Changelog: https://github.com/bids-standard/bids-validator/compare/2.0.9...2.0.10

- TypeScript
Published by effigies 6 months ago

bids-validator - 2.0.9

Added

  • Display version in web app

  • The --datasetTypes flag accepts a list of DatasetTypes, allowing applications to restrict the datasets they accept.

Changed

  • Upgraded to BIDS schema version 1.0.13.

  • Raise error when JSON files are parsed and their root value is anything other than an object

PRs

  • chore: Bump schema version by @effigies in https://github.com/bids-standard/bids-validator/pull/223
  • chore(deps): Bump hed-validator dependency to 4.1.4 by @happy5214 in https://github.com/bids-standard/bids-validator/pull/220
  • chore: Update BIDS schema, relax to ~version by @effigies in https://github.com/bids-standard/bids-validator/pull/230
  • Raise error when json files are parsed and their root value is an array instead of object. by @rwblair in https://github.com/bids-standard/bids-validator/pull/225
  • feat: Display version in web app by @effigies in https://github.com/bids-standard/bids-validator/pull/208
  • fix: Revert to HED validator 4.0 by @effigies in https://github.com/bids-standard/bids-validator/pull/232
  • feat: Add DatasetType passlist to allow applications to limit support by @effigies in https://github.com/bids-standard/bids-validator/pull/235

Full Changelog: https://github.com/bids-standard/bids-validator/compare/2.0.8...2.0.9

- TypeScript
Published by rwblair 6 months ago

bids-validator - 2.0.8

Added

  • Support multi-inheritance for associated files. This will allow for multiple electrodes.tsv files, distinguished by the space- entity. (#206)

- TypeScript
Published by rwblair 7 months ago

bids-validator - 2.0.7

Changed

  • Handle TSV schema rules with missing or n/a values for additional_columns.

Full Changelog: https://github.com/bids-standard/bids-validator/compare/2.0.6...2.0.7

- TypeScript
Published by effigies 9 months ago

bids-validator - 2.0.6

Added

  • Explain the issue data fields in the documentation. (#199)

Changed

  • Validator now returns exit code 16 instead of 1 for validation of a dataset with errors.

  • Rely on schema.meta.associations to load context associations instead of relying on list maintained in validator.

Fixed

  • Sidecar checks are skipped for text files that should not have sidecars. This resolves a problem in derivative datasets, where BIDS specifies a RECOMMENDED field of Description in all derivative files. ([#202])

Full Changelog: https://github.com/bids-standard/bids-validator/compare/2.0.5...2.0.6

- TypeScript
Published by rwblair 9 months ago

bids-validator - 2.0.5

A hot-fix release that adds missing entries to the 2.0.4 changelog and fixes publication to PyPI.

Full Changelog: https://github.com/bids-standard/bids-validator/compare/2.0.4...2.0.5

- TypeScript
Published by effigies 11 months ago

bids-validator - 2.0.4

Added

  • Validate directory names names according to schema.rules.directories entries. Use rules to identify "opaque" directories whose contents are unspecified by BIDS.

What's Changed

  • chore: Bump @std/assert >= 1.0.8 by @effigies in https://github.com/bids-standard/bids-validator/pull/169
  • feat: Report field descriptions for missing or invalid metadata by @effigies in https://github.com/bids-standard/bids-validator/pull/177
  • chore: Compile Deno validator and package in wheels for PyPI by @effigies in https://github.com/bids-standard/bids-validator/pull/186
  • chore(wheel): Fetch version from deno.json by @effigies in https://github.com/bids-standard/bids-validator/pull/187
  • feat: Validate directories, do not recurse into schema-declared opaque dirs by @rwblair in https://github.com/bids-standard/bids-validator/pull/180
  • Rewrite HED code for version 4.0.0 of hed-validator by @happy5214 in https://github.com/bids-standard/bids-validator/pull/173
  • chore: Bump dependencies and autoformat by @effigies in https://github.com/bids-standard/bids-validator/pull/189
  • Add scrive for #180 and workflow to check for changes in changelog.d by @rwblair in https://github.com/bids-standard/bids-validator/pull/188

Full Changelog: https://github.com/bids-standard/bids-validator/compare/2.0.3...2.0.4

- TypeScript
Published by rwblair 11 months ago

bids-validator - 2.0.3

What's Changed

Fixed

  • Subject detection in participants.tsv and phenotype/ directories has been restored, enabling checks that were deactivated by the missing data. (#162)

  • Skip HED tests if schema cannot be loaded. This was exhibiting as a HED_ERROR with "cannot read property null". (#160)

  • TSV_INCORRECT_VALUE_TYPE* error messages now indicate that a match failed, instead of confusingly claim success. (#165)

  • Correct Uint8Array / DataView usage for TypeScript 5.7 (#170)

  • Prevent AJV logs from contaminating output (#166)

New Contributors

  • @dominikwelke made their first contribution in https://github.com/bids-standard/bids-validator/pull/165

Full Changelog: https://github.com/bids-standard/bids-validator/compare/2.0.2...2.0.3

- TypeScript
Published by effigies 12 months ago

bids-validator - 2.0.2

What's Changed

Added

  • Enable glob-style wildcards for location field in configuration files. (#134)

Changed

  • Ensure HED schemas are loaded only once, improving efficiency. (#156)

  • Change the output of the intersects() function in the expression language to return the intersection, if non-empty. Corresponds to https://github.com/bids-standard/bids-specification/pull/2044. (#150)

  • Update to BIDS schema version 1.0.1 (BIDSVersion 1.10.0) (#152)

  • Limit TSV validation to first 1000 rows by default, adding the --max-rows flag to control this behavior. (#139)

Fixed

  • TSV files may now have columns named set, clear, delete, keys, or value. These were previously masked by the methods on the data structure representing columns. (#155)

  • Improve handling of .bidsignore files in the web validator. Ignores matching directories but not the files they contained could fail to match. (#113)

  • Resolve issue with parsing headers of NIfTI files with large extensions. Fixes issue 126.

Infrastructure

  • Adopting scriv for changelog management.

New Contributors

  • @bpinsard made their first contribution in https://github.com/bids-standard/bids-validator/pull/134
  • @VisLab made their first contribution in https://github.com/bids-standard/bids-validator/pull/156

Full Changelog: https://github.com/bids-standard/bids-validator/compare/2.0.1...2.0.2

- TypeScript
Published by effigies about 1 year ago

bids-validator - 2.0.1

Release notes

Bug-fix release in the 2.0.x series.

Added

  • --prune flag prunes sourcedata and derivatives directories before walking them. Time and memory savings can be significant, at the cost of underestimates of dataset size. (#124)

Fixed

  • Improve handling of .bidsignore files in the web validator. Ignores matching directories but not the files they contained could fail to match. (#113)

  • Resolve issue with parsing headers of NIfTI files with large extensions. Fixes issue 126.

Infrastructure

  • Adopting scriv for changelog management.

Merged pull requests

  • fix: Restore legacy/ subdirectory, redirecting to legacy-validator by @effigies in https://github.com/bids-standard/bids-validator/pull/108
  • rf(filetree): Uniformize bidsignore reading between web, CLI and test functions by @effigies in https://github.com/bids-standard/bids-validator/pull/113
  • test: Check that bidsignored files are accepted in scans.tsv by @effigies in https://github.com/bids-standard/bids-validator/pull/114
  • doc: Adopt scriv as a changelog manager by @effigies in https://github.com/bids-standard/bids-validator/pull/116
  • fix: Truncate NIfTI header data to avoid extensions by @effigies in https://github.com/bids-standard/bids-validator/pull/127
  • chore: Bump @bids/schema v1.0.0 by @effigies in https://github.com/bids-standard/bids-validator/pull/128
  • feat: Add --prune option to prevent walking subtrees by @effigies in https://github.com/bids-standard/bids-validator/pull/124
  • Fix bst call for compiling schema by @tstoeter in https://github.com/bids-standard/bids-validator/pull/119
  • Fill in URLs in the README.md by @yarikoptic in https://github.com/bids-standard/bids-validator/pull/120
  • doc: Conform README and docs/index by @effigies in https://github.com/bids-standard/bids-validator/pull/130

New Contributors

  • @tstoeter made their first contribution in https://github.com/bids-standard/bids-validator/pull/119
  • @yarikoptic made their first contribution in https://github.com/bids-standard/bids-validator/pull/120

Full Changelog: https://github.com/bids-standard/bids-validator/compare/2.0.0...2.0.1

- TypeScript
Published by effigies about 1 year ago

bids-validator - 2.0.0

Release notes

This is the second major release of the BIDS Validator.

The validator has been rewritten from scratch to interpret the BIDS Schema. This new validator

A development version of the validator may be accessed at https://bids-standard.github.io/bids-validator/dev/. While we encourage testing of features in the upcoming release of BIDS, note that any feature may be reverted until BIDS is released. Use the stable validator to validate against the most recent release of BIDS.

This release includes an updated documentation site at https://bids-validator.readthedocs.io/en/latest/.

For more details on this release, see the announcement on the BIDS Blog.

Features

  • Validation of BIDS Derivatives datasets, including opt-in recursive validation of BIDS Derivatives datasets discovered in derivatives/ subdirectories.
  • Support for BIDS-MRS, introduced in BIDS 1.10.0.
  • Consistent application of the inheritance principle
  • Consistent type-checking of JSON sidecar fields and TSV column entries
  • Consistent warning of missing RECOMMENDED metadata.

- TypeScript
Published by effigies over 1 year ago