Pybids Versions Save
Python tools for querying and manipulating BIDS datasets.
0.14.1
2 years ago
Release Notes
Bug-fix release in the 0.14.x series.
Changes
- RF/FIX: Decompose filter construction for special queries and lists by @effigies in https://github.com/bids-standard/pybids/pull/826
Includes the following back-ports from 0.15.0:
- FIX: Clarify exception message (#806)
- FIX: Catch UnicodeDecodeErrors along with JSONDecodeErrors for better reporting (#796)
- FIX: Accept paths/strings for layout configuration files (#799)
- ENH: Add
__main__to allowpython -m bidsto run CLI (#794)
Full Changelog: https://github.com/bids-standard/pybids/compare/0.14.0...0.14.1
0.15.0
2 years ago
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
Queryfor optional entities (#809) - ENH: Add main to allow
python -m bidsto 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 https://github.com/bids-standard/pybids/pull/791
- @jstaph made their first contribution in https://github.com/bids-standard/pybids/pull/806
- @pvandyken made their first contribution in https://github.com/bids-standard/pybids/pull/805
Full Changelog: https://github.com/bids-standard/pybids/compare/0.14.0...0.15.0
0.14.0
2 years ago
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 upgradecommand (#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
2 years ago
0.13.1
3 years ago
0.13
3 years agoRelease 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
3 years ago0.12.2
3 years ago
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
3 years ago
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)
