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

0.16.3

Release Notes

Bug-fix release in the 0.16.x series.

This release resolves a regression introduced in 0.16.2 when JSON sidecar files contain null values.

What's Changed

• FIX: Drop JSON sidecar fields with null values during metadata indexing by @effigies in #1016

Full Changelog: 0.16.2...0.16.3

0.16.2

Release Notes

Bug-fix and performance release in the 0.16.x series. Notably, indexing is now significantly faster (2-2.5x).

CHANGES

• ENH: Speed up indexing by bulk committing to database (#1013) @adelavega
• Include indexer in add_derivatives call (#1009) @wasciutto
• Bump bids-examples from 8550641 to 75968b9 (#1008) @dependabot
• Bump bids-examples from e96b702 to 8550641 (#1007) @dependabot
• Bump bids-examples from d8455af to e96b702 (#1005) @dependabot
• Bump bids-examples from bc36231 to d8455af (#1003) @dependabot
• CI: Use OIDC publishing instead of tokens (#1001) @effigies

0.16.1

Release Notes

CHANGES

• REL: 0.16.1 (#998) @effigies
• MNT, DOC: fix imports in documentation scripts (#980) @DimitriPapadopoulos
• FIX: Improve parsing of suffix/extension in non-BIDS files (#997) @effigies
• MNT: update zenodo (#995) @DimitriPapadopoulos
• CI: Update Python version for doc/sdist/wheel tests (#996) @effigies
• ENH: Support use of Query enums in filter lists (#994) @pvandyken

0.16.0

Release Notes

New feature release in the 0.16.x series.

What's Changed

• FIX: Adapt to SQLAlchemy 1.4+ (#985)
• FIX: Fill na with zero for VIF (#976)
• ENH: Only warn if missing values not explicitly set (#977)
• ENH: Create run reports of whole graph / create HTML reports (#918)
• ENH: Speed up Sparse to Dense BIDSVariable conversion (#969)
• ENH: Update config to support motion and nirs modalities (#965)
• REF: Add derivative subdatasets in a less ad hoc fashion (#954)
• MNT: Update minimum dependencies, add CI job to test them (#987)
• MNT: Drop jinja2/markupsafe constraints (#986)
• MNT: Fix ruff issue E712 (#981)
• MNT: A few Python3 updates (#971)
• MNT: Drop Python 3.7 EOL (#974)
• MNT: Fix repeat-word typo (#968)
• MNT: Update vendored inflect to 5.6.2 (#961)
• MNT: Fix flake8 issues found by ruff (#955)
• MNT: Remove (large) unused PNG from doc directory (#962)
• MNT: http:// → https:// (#960)
• MNT: Update git submodules (#964)
• CI: Drop codecov PyPI package and appveyor config (#979)
• CI: Add Python 3.11 (#975)
• CI: Replace custom update_submodules action with dependabot action (#967)
• CI: fix errors caused by changes in examples (#963)
• CI: Update parameters to gh-action-pypi-publish (#957)

Full Changelog: 0.15.6...0.16.0

0.15.6

Release Notes

Bug-fix release in 0.15.x series.

What's Changed

• FIX: Exclude non-Hashables from set in .get(return_type='id') (#948)
• FIX: Broken pattern matching (#936)
• FIX: Coerce oversampling parameter in convolution to int (#929)
• FIX: Allowing custom BIDS configuration files for derivative datasets (#922)
• FIX: Address change in default pandas grouping behavior (#917)
• ENH: Speed up BIDSLayout.get(return_type='id', ...) (#942)
• ENH: Update default anat filename patterns in config (#933)
• DOC: Make clear how to ignore folders (#945)
• DOC: Fix tutorial link in README (#944)
• DOC: Mention conda installation in README (#928)
• MNT: Update git submodules (#946 + #943 + #932)
• MNT: Move package metadata to pyproject.toml, unvendor versioneer (#907)
• MNT: Bump formulaic max version constraint to include 0.5.x (#916)

New Contributors

• @sanjayankur31 made their first contribution in #916
• @thewilliamdrew made their first contribution in #922
• @sarthakpati made their first contribution in #928

Full Changelog: 0.15.5...0.15.6

0.15.5

Release Notes

Bug-fix release in 0.15.x series.

What's Changed

• FIX: Use kwargs for DataFrame.pivot() (#913)
• ENH: Add transformation history to BIDSStatsModelsNodeOutput (#905)
• ENH: Update examples, add to sphinx, and convert to .md (#908)
• ENH: More helpful __repr__ in modeling (#906)
• MNT: Update git submodules (#911)
• MNT: Bump peter-evans/create-pull-request from 3 to 4 (#904)
• CI: Automatically update GitHub Actions in the future (#903)

Full Changelog: 0.15.4...0.15.5

0.15.3

What's Changed

• FIX: Test and update sync_kwargs class variable on transformations by @jdkent in (#891)
• FIX: Filtering of DM columns by @adelavega in (#892)
• ENH: Enable using participants.tsv, scans.tsv & session.tsv values as grouping variables by @adelavega in (#894)
• REF: Rename incoming single contrast column to intercept by @adelavega in (#886)
• DOC: Update references to nistats with references to nilearn in docs by @alexisthual in (#882)
• TST: some sort of QA for derivatives' default_path_patterns by @GalBenZvi in (#879)
• MNT: Codespell errors by @effigies in (#885)
• CI: Update actions versions by @effigies in (#897)

New Contributors

• @GalBenZvi made their first contribution in #879
• @alexisthual made their first contribution in #882

Full Changelog: 0.15.2...0.15.3

0.15.2

Release Notes

Bug-fix release in 0.15.x series.

Changes

• FIX: Synchronize kwargs in transformations, e.g., in Assign (#836)
• FIX: Add HRF derivatives to variable collection when created (#838)
• FIX: Interpolate derivative pipeline name in error message (#847)
• FIX: Match only within relative path when indexer is validating (#859)
• FIX: Rename intercept in DummyContrast (#866)
• FIX: Add variables to correct Node in load_tsv_variables (#872)
• FIX: Repair variable IO so scans.tsv is found (#869)
• FIX: Restore automodel functionality (#853)
• FIX: Allow pybids layout --derivatives to be a boolean flag or accept a path (#848)
• ENH: Add default path patterns to derivatives.json (#605)
• ENH: Rename statsmodels contrasts if they cannot be uniquely identified downstream (#861)
• ENH: Make intercept-only first level models throw a NotImplementedError (#854)
• ENH: Update config to support microscopy, qMRI, PET, ASL (#840)
• TEST: Add bids-examples submodule and bids_examples pytest fixture (#842)
• TEST: Add tests for default path patterns (#846)
• TEST: Update bids-examples and remove expected failing tests (#845)
• MNT: Update git submodules (#874)
• MNT: Add workflow top automatically update submodule (#870)
• MNT: Remove deprecated no dot config (#841)
• CI: Upgrade several GitHub actions to v3 (#867)
• CI: Add cron jobs to avoid sneaky failures during low activity periods (#860)

New Contributors

• @jmumford made their first contribution in #869
• @arovai made their first contribution in #847

Full Changelog: 0.15.1...0.15.2

0.15.1

Release Notes

Bug-fix release in the 0.15.x series.

Changes

• RF/FIX: Decompose filter construction for special queries and lists (#826)
• ENH: Relax group_by rules, allowing any entity to be used (#829)
• MNT: Replace deprecated DataFrame.append call (#833)
• DOC: Fresh rerun of entire pybids_tutorial.ipynb (#832)

Full Changelog: 0.15.0...0.15.1