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 flexibleparse_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 whenmerge=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
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.kollekshuns
: Containers that facilitate aggregation and manipulation ofVariable
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.