0.15.0

Release Notes

New feature release in the 0.15.x series.

Downstream tools should be aware of a potentially breaking, albeit long-demanded, change introduced in #819. Run indices are now stored so that the integers that come out retain any zero-padding that was found during parsing.

This release also introduces the bids.ext namespace package that allows independent packages to install modules in this namespace. This is an infrastructural change that will allow some components to be separately managed and follow a different development pace.

Changes

• FIX: Allow grouping by run and session when entities are undefined (#822)
• FIX: Clarify exception message (#806)
• FIX: Catch UnicodeDecodeErrors along with JSONDecodeErrors for better reporting (#796)
• FIX: Accept paths/strings for layout configuration files (#799)
• FIX: Small typo: repeated word in docstring (#793)
• ENH: Retain zero-padding in run entities while preserving integer queries and comparisons (#819)
• ENH: Add bids.ext namespace package for subpackages (#820)
• ENH: Handle wildcards in model X (#810)
• ENH: Implement automatic detection of derivative data (#805)
• ENH: Add new Query for optional entities (#809)
• ENH: Add main to allow python -m bids to run CLI (#794)
• REF: Improve modularization of bids.reports (#617)
• DOC: Link from sphinx documentation to notebook tutorials. (#797)
• MNT: Test on Python 3.10, various CI updates (#824)
• MNT: Avoid jinja2 v3 until nbconvert handles breakages (#823)

New Contributors

• @kousu made their first contribution in #791
• @jstaph made their first contribution in #806
• @pvandyken made their first contribution in #805

Full Changelog: 0.14.0...0.15.0

0.14.0

Release Notes

New feature release in the 0.14.x series.

This release includes a significant refactor of BIDS Statistical Models,
replacing the bids.analysis module with bids.modeling.

Changes to bids.layout are minimal, and we do not anticipate API breakage.

Changes

• FIX: LGTM.com warning: Implicit string concatenation in a list (#785)
• FIX: Take the intersection of variables and Model.X, ignoring missing variables (usually contrasts) (#764)
• FIX: Associate "is_metadata" with Tag, not Entity; and only return non-metadata entries for core Entities in get(return_type='id') (#749)
• FIX: Only include regressors if they are TSV (#752)
• FIX: ensure force_dense=True runs to_dense only on sparse variables (#745)
• FIX: get unique, with conflicting meta-data (#748)
• FIX: Clean up some deprecation and syntax warnings (#738)
• ENH: Add pybids upgrade command (#654)
• ENH: Add Lag transformation (#759)
• ENH: Use indirect transformations structure (#737)
• ENH: Add visualization for statsmodel graph (#742)
• ENH: Permit explicit intercept (1) in Contrasts and DummyContrasts (#743)
• ENH: Add meta-analysis model type (#731)
• ENH: Contrast type is now test (#733)
• REF: Use pathlib.Path internally when possible (#746)
• REF: Remove group_by from edges and add filter (#734)
• REF: Improved/refactored StatsModels module (#722)
• MNT: Make sure codespell skips .git when run locally (#787)
• MNT: LGTM.com recommendations (#786)
• MNT: Better codespell configuration (#782)
• MNT: Constrain formulaic version to 0.2.x . (#784)
• MNT: Update versioneer: 0.18 → 0.20 (#778)
• MNT: Add "codespell" tool to CI checks to catch typos sooner (#776)
• MNT: Disable bids-nodot mode (#769)
• MNT: Send codecov reports again (#766)
• MNT: Set minimum version to Python 3.6 (#739)

0.13.2

Release Notes

Bug-fix release in the 0.13 series.

CHANGES

• FIX/TEST: gunzip regressors.tsv.gz, allow timeseries.tsv as well (#767)
• FIX: run is required (#762)
• MNT: Patch 0.13.x maint branch (#763)

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)