Pybids Versions Save

Python tools for querying and manipulating BIDS datasets.

0.16.4

5 months ago

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

9 months ago

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

Full Changelog: https://github.com/bids-standard/pybids/compare/0.16.2...0.16.3

0.16.2

9 months ago

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

9 months ago

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

1 year ago

DOI

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: https://github.com/bids-standard/pybids/compare/0.15.6...0.16.0

0.15.6

1 year ago

DOI

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

Full Changelog: https://github.com/bids-standard/pybids/compare/0.15.5...0.15.6

0.15.5

1 year ago

DOI

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: https://github.com/bids-standard/pybids/compare/0.15.4...0.15.5

0.15.3

1 year ago

DOI

What's Changed

New Contributors

Full Changelog: https://github.com/bids-standard/pybids/compare/0.15.2...0.15.3

0.15.2

1 year ago

DOI

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

Full Changelog: https://github.com/bids-standard/pybids/compare/0.15.1...0.15.2

0.15.1

2 years ago

DOI

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: https://github.com/bids-standard/pybids/compare/0.15.0...0.15.1