0.21.0

Release notes

New feature release in the 0.21.x series.

This release fixes compatibility with univeral_pathlib 0.3. The following dependencies have been updated to new minimum versions:

• Python 3.10
• NumPy 1.24
• SciPy 1.10
• NiBabel 5.0
• Pandas 2.0

Changes

• FIX: UPath protocol mismatch (#1183)
• MNT: Drop Python 3.9 support (#1184)

Full Changelog: 0.20.0...0.21.0

0.20.0

Release notes

New feature release in the 0.20.x series.

This release finalizes some deprecations that were started in the 0.7 and 0.14 series. In particular, passing indexer arguments to BIDSLayout and disabling absolute_paths mode in BIDSLayout() or BIDSLayout.get() will now error. To adjust indexing behavior, create an explicit BIDSLayoutIndexer() and pass BIDSLayout(..., indexer=indexer). To access relative paths, use the BIDSFile.relative_path property on BIDSLayout.get() return values.

Changes

• FIX: Check for attribute that can be absent before assigning (#1165)
• FIX: Accommodate deprecations in the upcoming Pandas 3 release (#1173)
• FIX: Repaired convolution issue that arises when onset values are repeated (#1133)
• ENH: StatsModels: Add invalid_inputs parameter to allow dropping of missing data columns to run nodes (#1145)
• ENH: Add missing root-level path patterns (#1169)
• ENH: Parse seg- entities from dseg or probseg files (#1172)
• DOC: Update link to derivatives config file (#1132)
• MNT: Address warnings produced by pybids and dependencies (#1136)
• MNT: Lock test environment, update with dependabot (#1134)

New Contributors

• @emmanuel-ferdman made their first contribution in #1132
• @coryshain made their first contribution in #1145

Full Changelog: 0.19.0...0.20.0

0.19.0

Release notes

New feature release in the 0.19.x series.

This release adds plus signs to labels and suffixes, anticipating the release of BIDS 1.10.1 or 1.11.0 (whichever is next). Until the BIDS specification is updated and the bidsschematools package containing the updated schema is published, files with + will not validate, but can still be indexed with BIDSLayout(..., validate=False).

Several small fixes resolving issues with BIDS Stats Models are included, and complex JSON metadata (lists and objects) will now play more nicely with contexts where they need to be hashed.

Changes

• FIX: Catch StopIteration on directory walk (#1124)
• FIX: Ensure dotfiles are always filtered (#1123)
• FIX: Copy entities dict before modifying run variable type (#1120)
• FIX: Allow numpy arrays to treat PaddedInt like int (#1119)
• FIX: Make lists and dicts hashable (#1112)
• ENH: Allow plus signs in labels (#1117)
• MNT: Remove formulaic upper bound (#1121)
• MNT: Use tox-uv to ease lower bound checking, test on Python 3.13 (#1109)

Full Changelog: 0.18.1...0.19.0

0.18.1

Release notes

Bug-fix release in the 0.18.x series.

0.18.0 was missing package data, which went unnoticed because the workflow to publish to PyPI was also broken. These have been fixed, and we no longer alter global logging state.

With thanks to Fede Raimondo for the contribution.

Changes

• FIX: Install package data (#1108)
• FIX: Remove calls to root logger basicConfig (#1106)
• MNT: Upload attested package to (test) PyPI (#1110)

New Contributors

• @fraimondo made their first contribution in #1106

Full Changelog: 0.18.0...0.18.1

0.18.0

Release notes

New feature release in the 0.18.x series.

No actual new features, but this version moves test data out of the
installed distribution and ratchets its dependencies on Python and
the Scientific Python stack, justifying a minor release.

Changes

• FIX: Improve compatibility with cloud paths (#1094)
• MNT: Transition to src/ layout (#1099)
• MNT: Update minimum Python (3.9) and dependencies (SPEC 0 + 1yr) (#1092)
• MNT: Update test for BIDS-MRS (#1089)

Full Changelog: 0.17.2...0.18.0

0.17.2

Release Notes

Bug-fix release in the 0.17.x series.

Changes

• BUG: symlink dirs treated as files during indexing by @cookpa in #1087

New Contributors

• @cookpa made their first contribution in #1087

Full Changelog: 0.17.1...0.17.2

0.17.1

Release Notes

Bug-fix release in the 0.17.x series.

Mostly quiets down warnings generated by more recent versions of Pandas.

Changes

• FIX: Create indices with object dtype (#1084)
• MNT: Transfer validation tests to bids validator (#1081)

Full Changelog: 0.17.0...0.17.1

0.17.0

Release notes

Feature release in the 0.17.0 series.

This release includes experimental support for MRS (BEP22) datasets and universal_pathlib.

Changes

• ENH: pathlib -> universal_pathlib to enable cloud (and other filesystem) support (#1074)
• ENH: Add MRS entities, path patterns (#1075)
• STY: No parentheses after assert (#1065)
• MNT: Bump bids-examples from 47c4da1 to 401f4cf (#1073)
• MNT: Fix typo newly found by codespell (#1066)

Full Changelog: 0.16.5...0.17.0

0.16.5

Release notes

Bug-fix release in the 0.16.x series.

This release includes minor fixes, but reworks the testing infrastructure and resolves Python 3.12 incompatibilities.

What's Changed

• FIX: Handle FileNotFoundError in BIDSLayout init when is_derivative=True and validate=False (#1049)
• FIX: Add dwi root sbref, missing dwi entities to path patterns (#1059)
• ENH: Update indexer to treat .zarr as files not dirs (#1046)
• DOC: Deal with several warnings and errors in the doc build (#1061)
• TST: Add bids-examples tests to cover ieeg, eeg, dwi (#1060)
• MNT: Add Python 3.12 support (#1057)
• MNT: Use tox to simplify testing environment setup (#1055)
• MNT: Bump codecov/codecov-action from 3 to 4 (#1041)
• MNT: Bump bids-examples from 1a000d6 to eff47f1 (#1039)
• MNT: Bump bids-examples from b6e5234 to 1a000d6 (#1038)
• MNT: Bump actions/upload-artifact from 3 to 4 (#1037)
• MNT: Bump actions/setup-python from 4 to 5 (#1036)

New Contributors

• @bpinsard made their first contribution in #1059
• @akhanf made their first contribution in #1046
• @alperkent made their first contribution in #1049

Full Changelog: 0.16.4...0.16.5

0.16.4

Release Notes

Bug-fix release in the 0.16.x series.

This release resolves a bug likely introduced in 0.9.0 (when PyBIDS started using SQL), in which boolean metadata fields with values of False were read in as True.

CHANGES

• REL: 0.16.4 (#1035) @tsalo
• FIX: Ensure values of boolean metadata fields are preserved (#1034) @tsalo
• Build(deps): Bump bids-examples from 064db11 to b6e5234 (#1031) @dependabot
• [STY] pacify codespell (#1029) @Remi-Gau
• Build(deps): Bump bids-examples from d039879 to 064db11 (#1028) @dependabot
• Build(deps): Bump bids-examples from bfcc5c6 to d039879 (#1027) @dependabot
• Bump bids-examples from 502c917 to bfcc5c6 (#1026) @dependabot
• Bump bids-examples from 1c30c6e to 502c917 (#1025) @dependabot
• Bump actions/checkout from 3 to 4 (#1024) @dependabot
• Clearer BIDSValidation error message (#1023) @pierre-nedelec
• Bump bids-examples from e857597 to 1c30c6e (#1021) @dependabot
• Bump bids-examples from c557d1f to e857597 (#1019) @dependabot
• [FIX] update config for PET tracer entity (#1018) @Remi-Gau
• Bump bids-examples from 75968b9 to c557d1f (#1011) @dependabot