Changelog¶

Version 0.7.0 (September, 2018)¶

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).

NEW FEATURES:

File metadata is now searchable (use BIDSLayout.search_metadata())
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.

MINOR IMPROVEMENTS AND BUG FIXES:

Specifying ‘derivatives’ in a paths specification now automatically includes ‘bids’ (#246)
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)
Fix sum transformation
Improved test coverage

Hotfix release:

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.kollekshuns: 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)

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

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

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

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

History as we know it begins here.