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@yarikoptic yarikoptic released this 02 Jun 12:51
· 3 commits to main since this release
v0.1.0
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Learn about vigilant mode.

v0.1.0 (Mon Jun 01 2026)

Initial public alpha release of bids-utils — a Python library and CLI for
structural manipulation of BIDS datasets, designed to be schema-driven
(via bidsschematools) and VCS-aware (plain git, git-annex, and
DataLad).

🚀 What's in 0.1.0

  • CLI commands: rename, migrate, subject-rename, session-rename,
    remove-subject, remove-session, remove-run, merge, split,
    aggregate-metadata, segregate-metadata, audit-metadata, completion.
  • Library API: every CLI command maps to a public Python function with
    OperationResult return values; suitable for scripted pipelines.
  • Migration engine: applies BIDS 1.x intra-major deprecation rules
    (BasedOn/RawSources → Sources, ScanDate → _scans.tsv acq_time,
    DCOffsetCorrection → SoftwareFilters, AcquisitionDuration →
    FrameAcquisitionDuration, deprecated coordinate-system labels, etc.) at
    safe / advisory / non-auto-fixable tiers, with a schema-coverage
    audit (migrate --audit) so missing rules surface as drift.
  • VCS integration: detects DataLad → git-annex → git → plain
    filesystem; uses git mv (or the annex equivalent) for moves; preserves
    locked-annexed-symlink semantics during renames; configurable
    --annexed={error,get,skip,skip-warning} policy for fetched content.
  • Observability: --dry-run=overview|detailed, --json output mode,
    exit codes (0 success / 1 partial / 2 refused), and per-source Change
    entries in batch operations.
  • Test infrastructure: per-test git worktree fixture pattern over the
    bids-examples clone, plus an adversarial-suffix injection helper for
    heudiconv __dup-NN / +mine / --crap / _test source filenames.
    Mutating sweeps validate against the BIDS validator pre- and
    post-operation across ~1700 cases.

⚠ Known limitations

  • The rename --set / edit-filename split (FR-039 / FR-040, atomic-batch
    glob input per FR-043) is specified but not yet implemented —
    scheduled for 0.2.0. Use rename --set key=value FILE (current form) for
    entity edits until then.
  • BIDS 2.0 migration is scaffolding-only — concrete rules are stubs.
  • Performance optimization for >1000-subject datasets is unverified
    (SC-003 deferred).

Authors: 1

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