0.13.1

Release Notes

Bug-fix release in the 0.13 series. With thanks to Lea Waller for contributions.

CHANGES

• ENH: Improve get performance (#723)
• STY: Fix typos identified by codespell (#720)
• TEST: dataset-level model spec retrieval (#693)

0.13

Release Notes

Minor new feature and bugfix release in the 0.13 series.

CHANGES

Version 0.13 (April 14, 2021)

FIX: Resample to n_vols for sampling_rate == 'TR' (#713)
FIX: Lazily load metadata, skip when missing data files are missing sidecars (#711)
FIX: Ensure indicator matrix is boolean when indexing in Split transformation (#710)
FIX: Correctly pair metadata file when creating association records (#699)
FIX: Resolve side-effects of new testfile in #682 (#695)
FIX: BIDSLayout -- TypeError: unhashable type: 'dict' (#682)
ENH: Add res/den entities to derivatives.json (#709)
ENH: Update datatypes (#708)
ENH: add more informative validation error message for dataset_description.json (#705)
ENH: Add flip, inv, mt, and part entities (#688)
CI: Run packaging tests on main repository only (#696)
CI: Migrate to GH actions (#691)

0.12.3

Release Notes

Minor new feature and bugfix release in the 0.12.x series.

CHANGES

• FIX: Require aligned input for logical operations (#649) @adelavega
• ENH: Incremental variable loading in Step setup (#672) @tyarkoni

0.12.2

Release Notes

Bug-fix release in 0.12.x series.

Changes

• FIX: Support nibabel < 3 when calculating time series length (#669)
• FIX: Sanitize single derivative Path passed to BIDSLayout (#665)
• FIX: Force UTF-8 encoding in _index_metadata (#663)
• FIX: Explicitly convert to HTML when testing tutorial (nbconvert 6.0 breakage) (#664)

0.12.0

Release Notes

New feature release for the 0.12.x series.

This release includes significant speedups for BIDSLayout creation and improves handling of GIFTI and CIFTI-2 derivative files.

Changes

• FIX: Remove need to eager load associations (#642)
• ENH: Fetch number of time points from NIfTI, GIFTI or CIFTI-2 (#637)
• ENH: Catch any NIfTI/GIFTI (incl. CIFTI-2) files as BIDSImageFiles (#638)

0.11.1

Release Notes

Bug-fix release in the 0.11.x series

With thanks to Mathias Goncalves for finding and fixing the issue.

Changes

• FIX: Preserve get logic when using custom config (#636)

0.11.0

Release Notes

New feature release in the 0.11.x series.

One significant change in this PR is to add the configuration option extension_initial_dot.
Setting to True will adopt the future default behavior of returning extension entities with
an initial dot (.).

Other notable changes include a significant refactoring of the Analysis module, and a number of
small improvements to error reporting that should add up to simpler debugging for users and
developers.

Changes

• FIX: Post-fix And and Or transformations with underscore (#628)
• FIX: made _validate_file work on Windows (#627)
• FIX: Scale transformation fails if passed constant input. (#614)
• FIX: Certain queries involving multiple layouts are very slow (#616)
• FIX: Bug in get() when passing enums as extensions (#612)
• FIX: Bug in BIDSDataFile.get_df() (#611)
• FIX: Make entity assertions Python 3.5-safe (#606)
• FIX: BIDSLayout.build_path to respect absolute_paths. (#580)
• ENH: Adds OS-level file copying instead of reading/writing via Python (#613)
• ENH: Add explicit warning message when users pass in filters as a dictionary keyword (#623)
• ENH: Introduce PyBIDS exceptions (#615)
• ENH: Add example bids and derivatives dataset_description.json strings to error messages (#620)
• ENH: Improved handling of invalid filters (#610)
• ENH: Add method to generate report from list of files (#607)
• ENH: Pass kwargs from BIDSImageFile.get_image() to nibabel.load (#601)
• ENH: Model spec module and associated utilities (#548)
• ENH: Add BIDSMetadata dictionary to report file with missing metadata (#593)
• RF: Add extension_initial_dot config option to transition to extension entity with initial dot (#629)
• MNT: Automatically deploy docs (#598)
• CI: Drop --pre check for Python 3.5 (#621)
• CI: Test on Python 3.8 (#594)

0.10.2

Release Notes

Bug fix release in the 0.10.x series.

Changes

• FIX: Add Replace as exception to recursive JSON conversion (#589)

0.10.1

Release Notes

Bug fix release in the 0.10.x series.

This release just makes available some of the latest minor fixes and improvements.

Changes

• FIX: Replace os.path.sep with fwdslash because bids validator hardcodes fwd (#582)
• FIX: Refactor of build_path and inner machinery (#574)
• FIX: Domain entity, and slow __repr__ (#569)
• FIX: "strict" helptext in BIDSLayout.write_contents_to_file (#566)
• FIX: typos in helpstrings and comments (#564)
• FIX: Correct term "caret" to "angle bracket" in helpstrings (#565)
• ENH: Extend build_path to generate lists of files (#576)
• ENH: Add one parametric test of BIDSLayout.build_path (#577)
• ENH: Enable partial metadata indexing (#560)
• ENH: Upscale to collection sampling rate prior to resampling (#568)
• ENH: Calculate default sampling rate for SparseRunVariable.to_dense (#571)
• MNT: Add .vscode (for Visual Studio Code) to .gitignore (#562)
• MNT: Ignore pip-wheel-metadata (#581)
• DOC: Remove Python 2 support statement, now that v0.10.0 has dropped it (#561)

0.10.0

Release Notes

New feature release in the 0.10.x series.

This release removes Python 2 support.

Changes

• ENH: Helpful error for db argument mismatch, and add classmethod load_from_db (#547)
• ENH: Add Resample transformation (#373)
• ENH: Save BIDSLayout + Derivatives to folder (with init arguments) (#540)
• ENH: Adds support for NONE and ANY query Enums (#542)
• ENH: Transformation-related improvements (#541)
• ENH: FEMA contrasts (#520)
• STY: Minor PEP8 Fixes (#545)
• MNT: Various (#543)
• MNT: Remove Python 2.7 support (#524)
• CI: Configure Circle Artifact Redirector (#544)