Changelog¶
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
andexclude
have been replaced withignore
andforce_index
. Paths passed toignore
will be ignored from indexing; paths passed toforce_index
will be forcibly indexed even if they are otherwise BIDS-non-compliant.force_index
takes precedence overignore
.
- 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 limitedderivatives
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 thescope
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 newbids.layout.core
module. - REF: A new
Config
class has been introduced to house the information found inbids.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 withread_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, passrun_info
in correct position. (#353) - FIX: If
sampling_rate
is'auto'
, set to first rate ofDenseRunVariables
(#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 intuitiveinterval
(#366) - ENH: Support
pathlib.Path
and otherstr
-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 flexibleparse_file_entities
).- Calls to
.get()
now returnBIDSFile
objects, rather than namedtuples, by default (#281). TheBIDSFile
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 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)
- 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 toBIDSLayout
(#327) - Add entity hints when calling
get()
with atarget
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.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.