bids-standard/pybids: 0.7.0

Release notes

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