Changelog

Version 0.16.4 (November 30, 2023)

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.

  • FIX: Ensure values of boolean metadata fields are preserved (#1034)

  • FIX: update config for PET tracer entity (#1018)

  • ENH: Clearer BIDSValidation error message (#1023)

  • STY: pacify codespell (#1029)

  • CI: Build(deps): Bump bids-examples from 064db11 to b6e5234 (#1031)

  • CI: Build(deps): Bump bids-examples from d039879 to 064db11 (#1028)

  • CI: Build(deps): Bump bids-examples from bfcc5c6 to d039879 (#1027)

  • CI: Bump bids-examples from 502c917 to bfcc5c6 (#1026)

  • CI: Bump bids-examples from 1c30c6e to 502c917 (#1025)

  • CI: Bump bids-examples from e857597 to 1c30c6e (#1021)

  • CI: Bump bids-examples from c557d1f to e857597 (#1019)

  • CI: Bump bids-examples from 75968b9 to c557d1f (#1011)

  • CI: Bump actions/checkout from 3 to 4 (#1024)

Version 0.16.3 (August 16, 2023)

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.

  • FIX: Drop JSON sidecar fields with null values during metadata indexing (#1016)

Version 0.16.2 (August 11, 2023)

Bug-fix and performance release in the 0.16.x series. Notably, indexing is now significantly faster (2-2.5x).

  • ENH: Speed up indexing by bulk committing to database (#1013)

  • Include indexer in add_derivatives call (#1009)

  • Bump bids-examples from 8550641 to 75968b9 (#1008)

  • Bump bids-examples from e96b702 to 8550641 (#1007)

  • Bump bids-examples from d8455af to e96b702 (#1005)

  • Bump bids-examples from bc36231 to d8455af (#1003)

  • CI: Use OIDC publishing instead of tokens (#1001)

Version 0.16.1 (May 01, 2023)

Bug-fix release in the 0.16.x series.

  • FIX: Improve parsing of suffix/extension in non-BIDS files (#997)

  • FIX: Support use of Query enums in filter lists (#994)

  • MNT: Clean up imports in documentation scripts (#980)

  • MNT: update zenodo (#995)

  • CI: Update Python version for doc/sdist/wheel tests (#996)

Version 0.16.0 (April 26, 2023)

New feature release in the 0.16.x series.

  • 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)

Version 0.15.6 (February 28, 2023)

Bug-fix release in 0.15.x series.

  • 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)

Version 0.15.5 (November 07, 2022)

Bug-fix release in 0.15.x series.

  • 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)

Version 0.15.4 (October 08, 2022)

Bug-fix release in 0.15.x series.

  • FIX: Use ‘contrasts’ in DummyContrasts, not ‘condition_list’ (#902)

  • FIX: Transformations: sync_kwargs, for non-list arguments, listify by variable length (#901)

  • CI: Update actions versions (#899)

Version 0.15.3 (September 12, 2022)

Bug-fix release in 0.15.x series.

  • FIX: Test and update sync_kwargs class variable on transformations (#891)

  • FIX: Filtering of DM columns (#892)

  • ENH: Enable using participants.tsv, scans.tsv & session.tsv values as grouping variables (#894)

  • REF: Rename incoming single contrast column to intercept (#886)

  • DOC: Update references to nistats with references to nilearn in docs (#882)

  • TST: some sort of QA for derivatives’ default_path_patterns (#879)

  • MNT: Update git submodules (#887)

  • MNT: Codespell errors (#885)

  • MNT: Update git submodules (#884)

  • MNT: Update git submodules (#883)

  • CI: Update actions versions (#897)

Version 0.15.2 (July 25, 2022)

Bug-fix release in 0.15.x series.

  • 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)

Version 0.15.1 (April 04, 2022)

Bug-fix release in the 0.15.x series.

  • 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)

Version 0.15.0 (March 28, 2022)

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.

  • 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)

Version 0.14.1 (March 29, 2022)

Bug-fix release in the 0.14.x series.

  • RF/FIX: Decompose filter construction for special queries and lists (#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)

Version 0.14.0 (November 09, 2021)

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.

  • 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)

Version 0.13.2 (August 20, 2021)

Bug-fix release in the 0.13 series.

  • 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)

Version 0.13.1 (May 21, 2021)

Bug-fix release in the 0.13 series.

  • ENH: Improve get performance (#723)

  • STY: Fix typos identified by codespell (#720)

  • TEST: dataset-level model spec retrieval (#693)

Version 0.13 (April 14, 2021)

New feature release in the 0.13 series.

  • 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)

Version 0.12.4 (November 10, 2020)

Bug-fix release in the 0.12.x series.

  • FIX: Do not error when popping missing scan_length (#679)

Version 0.12.3 (October 23, 2020)

  • FIX: Require aligned input for logical operations (#649)

  • ENH: Incremental variable loading in Step setup (#672)

Version 0.12.2 (October 09, 2020)

Bug-fix release in 0.12.x series.

  • 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)

Version 0.12.1 (September 09, 2020)

  • FIX: drop obsolete test (#652)

  • FIX: Convolve zero-duration (impulse) events when variable contains multiple events (#645)

  • ENH: Add CLI to PyBIDS (#650)

  • ENH: Add relpath attribute to BIDSFile and associated refactoring (#647)

  • DOC: Add example for using parse_file_entities from bids.layout (#639)

  • MNT: Remove deprecated database_file argument to BIDSLayout (#644)

Version 0.12.0 (August 04, 2020)

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.

  • 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)

Version 0.11.1 (July 02, 2020)

Bug-fix release in the 0.11.x series

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

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

Version 0.11.0 (June 29, 2020)

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.

  • 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)

Version 0.10.2 (February 26, 2020)

Bug fix release in the 0.10.x series.

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

Version 0.10.1 (February 10, 2020)

Bug fix release in the 0.10.x series.

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

  • 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)

Version 0.10.0 (December 03, 2019)

New feature release in the 0.10.x series.

This release removes Python 2 support.

  • 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)

Version 0.9.5 (November 6, 2019)

Bug fix release in the 0.9.x series.

Final planned release with Python 2 support.

  • FIX: Filter before downsampling (#529)

  • FIX: Copy input dict in replace_entities; Typos in default_path_patterns (#517)

  • FIX: Use string dtype for all entities when using regex search (#511)

  • FIX: Update Sphinx docs for 2.2 (#507)

  • ENH: Enable automatic derivative database caching (#523)

  • ENH: Raise ValueError if BIDSLayout.build_path fails to match any pattern (#508)

  • RF: Subclass analysis Node from object (#528)

  • DOC: Unify docstring format (#499)

  • DOC: Auto-generate stubs (#513)

  • STY: .sql is a misleading extension to sqlite files (#531)

  • STY: General cleanups (#526, #527)

Version 0.9.4 (September 20, 2019)

Bug fix release in the 0.9.x series.

  • FIX: Ignore default_ignore paths by default (#495)

  • FIX: Filter and sort on scalar metadata in get_nodes() (#488)

  • FIX: Automatically sanitize dtype of get() arguments (#492)

  • FIX: Check that default_path_patterns is not None before using in build_path (#485)

  • FIX: Add CBV and phase modalities to func datatype path pattern (#479)

  • FIX: Drop bold suffix constraint from echo entity (#477)

  • ENH: Enforce dtypes on spec-defined columns when reading in DFs (#494)

  • ENH: Validate built paths (#496)

  • ENH: Update contrast enhancing agent query name (ceagent) (#497)

  • DOC: Add citation information to README (#493)

  • DOC: Improve wording in Python notebook example comment (#484)

  • DOC: Finish sentence in Python Notebook example documentation (#483)

  • DOC: Add JOSS Badge (#472)

  • STY: Apply syntax highlight to Python notebook example doc (#482)

  • MAINT: Move setup configuration to setup.cfg (#448)

  • MAINT: Additional Zenodo metadata (#470)

  • MAINT/CI: Use extras_require to declare dependencies for tests (#471)

Version 0.9.3 (August 7, 2019)

This version includes a number of minor fixes and improvements, one of which breaks the existing API (by renaming two entities; see #464). Changes include:

  • FIX: Avoid DB collisions for redundant entities (#468)

  • FIX: Minor changes to entity names in core spec (#464)

  • FIX: Make bids.reports work properly with .nii images (#463)

  • CI: Execute notebook in Travis (#461)

  • ENH: More sensible repr for Tag model (#467)

Version 0.9.2 (July 12, 2019)

This version includes a number of minor fixes and improvements. EEG files are better handled, and BIDSLayout and BIDSFile play more nicely with Path-like objects.

With thanks to new contributor Cecile Madjar.

  • FIX: Instantiate ignore/force_index after root validation (#457)

  • FIX: Restore <entity>=None query returning files lacking the entity (#458)

  • ENH: Add BIDSJSONFile (#444)

  • ENH: Add BIDSFile.__fspath__ to work with pathlib (#449)

  • ENH: Add eeg datatype to layout config (#455)

  • RF: Remove unused kwargs to BIDSFile (#443)

  • DOC: Improve docstring consistency, style (#443)

  • DOC: Address final JOSS review (#453)

  • STY: PEP8 Fixes (#456)

  • MAINT: Set name explicitly in setup.py (#450)

Version 0.9.1 (May 24, 2019)

Hotfix release:

  • Fixed package deployment issues (#446)

  • Updated author list (#447)

Thanks to new contributors Erin Dickie, Chadwick Boulay and Johannes Wennberg.

Version 0.9.0 (May 21, 2019)

Version 0.9 replaces the native Python backend with a SQLite database managed via SQLAlchemy. The layout module has been refactored (again), but API changes are minimal. This release also adds many new features and closes a number of open issues.

API CHANGES/DEPRECATIONS:

  • The extensions argument has now been banished forever; instead, use extension, which is now defined as a first-class entity. The former will continue to work until at least the 0.11 release (closes #404).

  • Relatedly, values for extension should no longer include a leading ., though this should also continue to work for the time being.

  • The BIDSLayout init argument index_associated has been removed as the various other filtering/indexing options mean there is longer a good reason for users to manipulate this.

  • bids.layout.MetadataIndex no longer exists. It’s unlikely that anyone will notice this.

  • BIDSLayout.get_metadata() no longer takes additional entities as optional keyword arguments (they weren’t necessary for anything).

  • Direct access to most BIDSFile properties is discouraged, and in one case is broken in 0.9 (for .metadata, which was unavoidable, because it’s reserved by SQLAlchemy). Instead, users should use getters (get_metadata, get_image, get_df, etc.) whenever possible.

NEW FUNCTIONALITY:

  • All file and metadata indexing and querying is now supported by a relational (SQLite) database (see #422). While this has few API implications, the efficiency of many operations is improved, and complex user-generated queries can now be performed via the SQLAlchemy .session stored in each BIDSLayout.

  • Adds .save() method to the BIDSLayout that saves the current SQLite DB to the specified location. Conversely, passing a filename as database_file at init will use the specified store instead of re-indexing all files. This eliminates the need for a pickling strategy (#435).

  • Related to the above, the BIDSLayout init adds a reset_database argument that forces reindexing even if a database_file is specified.

  • The BIDSLayout has a new index_metadata flag that controls whether or not the contents of JSON metadata files are indexed.

  • Added metadata flag to BIDSLayout.to_df() that controls whether or not metadata columns are included in the returned pandas DataFrame (#232).

  • Added get_entities() method to BIDSLayout that allows retrieval of all Entity instances available within a specified scope (#346).

  • Adds drop_invalid_filters argument to BIDSLayout.get(), enabling users to (optionally) ensure that invalid filters don’t clobber all search results (#402).

  • BIDSFile instances now have a get_associations() method that returns associated files (see #431).

  • The BIDSFile class has been split into a hierarchy, with BIDSImageFile and BIDSDataFile subclasses. The former adds a get_image() method (returns a NiBabel image); the latter adds a get_df() method (returns a pandas DF). All BIDSFile instances now also have a get_entities() method.

BUG FIXES AND OTHER MINOR CHANGES:

  • Metadata key/value pairs and file entities are now treated identically, eliminating a source of ambiguity in search (see #398).

  • Metadata no longer bleeds between raw and derivatives directories unless explicitly specified (see #383).

  • BIDSLayout.get_collections() no longer drops user-added columns (#273).

  • Various minor fixes/improvements/changes to tests.

  • The tutorial Jupyter notebook has been fixed and updated to reflect the latest changes.

Version 0.8.0 (February 15, 2019)

Version 0.8 refactors much of the layout module. It drops the grabbit dependency, overhauls the file indexing process, and features a number of other improvements. However, changes to the public API are very minimal, and in the vast majority of cases, 0.8 should be a drop-in replacement for 0.7.*.

API-BREAKING CHANGES:

  • Changes to (rarely-used) BIDSLayout initialization arguments:

    • include and exclude have been replaced with ignore and force_index. Paths passed to ignore will be ignored from indexing; paths passed to force_index will be forcibly indexed even if they are otherwise BIDS-non-compliant. force_index takes precedence over ignore.

  • Most querying/selection methods add a new scope argument that controls scope of querying (e.g., 'raw', 'derivatives', 'all', etc.). In some cases this replaces the more limited derivatives argument.

  • No more domains: with the grabbit removal (see below), the notion of a 'domain' has been removed. This should impact few users, but those who need to restrict indexing or querying to specific parts of a BIDS project should be able to use the scope argument more effectively.

OTHER CHANGES:

  • FIX: Path indexing issues in get_file() (#379)

  • FIX: Duplicate file returns under certain conditions (#350)

  • FIX: Pass new variable args as kwargs in split() (#386) @effigies

  • TEST: Update naming conventions for synthetic dataset (#385) @effigies

  • REF: The grabbit package is no longer a dependency; as a result, much of the functionality from grabbit has been ported over to pybids.

  • REF: Required functionality from six and inflect is now bundled with pybids in bids.external, minimizing external dependencies.

  • REF: Core modules have been reorganized. Key data structures and containers (e.g., BIDSFile, Entity, etc.) are now in a new bids.layout.core module.

  • REF: A new Config class has been introduced to house the information found in bids.json and other layout configuration files.

  • REF: The file-indexing process has been completely refactored. A new hierarchy of BIDSNode objects has been introduced. While this has no real impact on the public API, and isn’t really intended for public consumption yet, it will in future make it easier for users to work with BIDS projects in a tree-like way, while also laying the basis for a more sensible approach to reading and accessing associated BIDS data (e.g., .tsv files).

  • MNT: All invocations of pd.read_table have been replaced with read_csv.

Version 0.7.1 (February 01, 2019)

This is a bug fix release in the 0.7 series. The primary API change is improved handling of Path objects.

  • FIX: Path validation (#342)

  • FIX: Ensure consistent entities at all levels (#326)

  • FIX: Edge case where a resampled column was too-long-by-one (#365)

  • FIX: Use BIDS metadata for TR over nii header (#357)

  • FIX: Add check for run_info to be a list, pass run_info in correct position. (#353)

  • FIX: If sampling_rate is 'auto', set to first rate of DenseRunVariables (#351)

  • FIX: Get the absolute path of the test data directory (#347)

  • FIX: Update reports to be 0.7-compatible (#341)

  • ENH: Rename sr variable to more intuitive interval (#366)

  • ENH: Support pathlib.Path and other str-castable types (#307)

  • MNT: Updates link to derivative config file in notebook (#344)

  • MNT: Add bids-validator dependency (#363)

  • MNT: Require pandas >= 0.23.0 (#348)

  • MNT: Bump grabbit version (#338)

  • CI: Ignore OSX Python 3.5 failures (#372)

  • CI: Build with Python 3.7 on Travis, deploy on 3.6 (#337)

Version 0.7.0 (January 10, 2019)

This is a major, API-breaking release. It introduces a large number of new features, bug fixes, and improvements.

API-BREAKING CHANGES:

  • A number of entities (or keywords) have been renamed to align more closely with the BIDS specification documents: * ‘type’ becomes ‘suffix’ * ‘modality’ becomes ‘datatype’ * ‘acq’ is removed (use ‘acquisition’) * ‘mod’ becomes ‘modality’

  • The following directories are no longer indexed by default: derivatives/, code/, stimuli/, models/, sourcedata/. They must be explicitly included using the ‘include’ initialization argument.

  • The grabbids module has been renamed to layout and BIDSLayout.py and BIDSvalidator.py are now layout.py and validation.py, respectively.

  • The BIDS validator is now enabled by default at layout initialization (i.e., validate=True)

  • The exclude initialization argument has been removed.

  • BIDSLayout.parse_entities utility has been removed (use the more flexible parse_file_entities).

  • Calls to .get() now return BIDSFile objects, rather than namedtuples, by default (#281). The BIDSFile API has been tweaked to ensure backwards incompatibility in nearly all cases.

  • Naming conventions throughout the codebase have been updated to ensure consistency with the BIDS specs. This is most salient in the analysis module, where snake_case has been replaced with CamelCase throughout.

NEW FEATURES:

  • File metadata (i.e., in JSON sidecars) is now searchable by default, and behaves just like native BIDS entities (e.g., metadata keys can be passed as arguments to .get() calls)

  • A new BIDSFile wrapper provides easy access to .metadata and .image

  • HRF convolution is now supported via bundling of nistats’ hemodynamic_models module; convolution is handled via the convolve_HRF transformation.

  • Named config paths that customize how projects are processed can be added at run-time (#313)

  • Preliminary support for BIDS-Derivatives RC1 (mainly core keywords)

MINOR IMPROVEMENTS AND BUG FIXES:

  • Specifying ‘derivatives’ in a path specification now automatically includes ‘bids’ (#246)

  • Zenodo DOIs are now minted with new releases (#308)

  • Variable loading via load_variables can now be done incrementally

  • Expanded and improved path-building via layout.build_path()

  • get_collections no longer breaks when merge=True and the list is empty (#202)

  • Layout initialization no longer fails when validate=True (#222)

  • The auto_contrasts field in the modeling tools now complies with the BIDS-Model spec (#234)

  • Printing a BIDSFile now provides more useful information, including path (#298)

  • Resample design matrix to 1/TR by default (#309)

  • Fix the Sum transformation

  • Ensure that resampling works properly when a sampling rate is passed to get_design_matrix (#297)

  • Propagate derivative entities into top-level dynamic getters (#306)

  • Deprecated get_header call in nibabel removed (#300)

  • Fix bug in entity indexing for BIDSVariableCollection (#319)

  • Exclude modules with heavy dependencies from root namespace for performance reasons (#321)

  • Fix bug that caused in-place updating of input selectors in Analysis objects (#323)

  • Add a DropNA transformation (#325)

  • Add a get_tr() method to BIDSLayout (#327)

  • Add entity hints when calling get() with a target argument (#328)

  • Improved test coverage

Version 0.6.5 (August 21, 2018)

  • FIX: Do not drop rows of NaNs (#217) @adelavega

  • FIX: Declare run as having integer type (#236) @effigies

  • ENH: MEG support (#229) @jasmainak

  • REF: rename grabbids to layout, closes #228 (#230) @ltirrell

  • DOC: add .get_collection examples to tutorial (#219) @Shotgunosine

  • DOC: Fix link in README to point to documentation (#223) @KirstieJane

  • DOC: Add binder link for tutorial (#225) @KirstieJane

  • MAINT: Restore “analysis” installation extra (#218) @yarikoptic

  • MAINT: Do not import tests in __init__.py (#226) @tyarkoni

Version 0.5.1 (March 9, 2018)

Hotfix release:

  • Includes data files omitted from 0.5.0 release.

  • Improves testing of installation.

Version 0.5.0 (March 6, 2018)

This is a major release that introduces the following features:

  • A new bids.variables module that adds the following submodules: * bids.variables.entities.py: Classes for representing BIDS hierarchies as a graph-like structure. * bids.variables.variables.py: Classes and functions for representing and manipulating non-imaging data read from BIDS projects (e.g., fMRI events, densely-sampled physiological measures, etc.). * bids.variables.io.py: Tools for loading variable data from BIDS projects. * bids.variables.collections: Containers that facilitate aggregation and manipulation of Variable classes.

  • Extensions to the BIDSLayout class that make it easy to retrieve data/variables from the project (i.e., Layout.get_collections)

  • A new auto_model utility that generates simple BIDS-Model specifications from BIDS projects (thanks to @Shotgunosine)

  • A new reports module that generates methods sections from metadata in BIDS projects (thanks to @tsalo)

  • Experimental support for copying/writing out files in a BIDS-compliant way

  • Expand bids.json config file to include missing entity definitions

  • Ability to parse files without updating the Layout index

  • Updated grabbids module to reflect grabbit changes that now allow many-to-many mapping of configurations to folders

  • Too many other minor improvements and bug fixes to list (when you’re very lazy, even a small amount of work is too much)

Version 0.4.2 (November 16, 2017)

We did some minor stuff, but we were drunk again and couldn’t read our handwriting on the napkin the next morning.

Version 0.4.1 (November 3, 2017)

We did some minor stuff, and we didn’t think it was important enough to document.

Version 0.4.0 (November 1, 2017)

We did some stuff, but other stuff was happening in the news, and we were too distracted to write things down.

Version 0.3.0 (August 11, 2017)

We did some stuff, but we were drunk and forgot to write it down.

Version 0.2.1 (June 8, 2017)

History as we know it begins here.