Changelog

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.