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

0.14.1

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 #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 allow python -m bids to run CLI (#794)

Full Changelog: 0.14.0...0.14.1

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)