Changelog¶
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, useextension
, 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 argumentindex_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 eachBIDSLayout
.Adds
.save()
method to theBIDSLayout
that saves the current SQLite DB to the specified location. Conversely, passing a filename asdatabase_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 areset_database
argument that forces reindexing even if adatabase_file
is specified.The
BIDSLayout
has a newindex_metadata
flag that controls whether or not the contents of JSON metadata files are indexed.Added
metadata
flag toBIDSLayout.to_df()
that controls whether or not metadata columns are included in the returned pandasDataFrame
(#232).Added
get_entities()
method toBIDSLayout
that allows retrieval of allEntity
instances available within a specified scope (#346).Adds
drop_invalid_filters
argument toBIDSLayout.get()
, enabling users to (optionally) ensure that invalid filters don’t clobber all search results (#402).BIDSFile
instances now have aget_associations()
method that returns associated files (see #431).The
BIDSFile
class has been split into a hierarchy, withBIDSImageFile
andBIDSDataFile
subclasses. The former adds aget_image()
method (returns a NiBabel image); the latter adds aget_df()
method (returns a pandas DF). AllBIDSFile
instances now also have aget_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
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 definitionsAbility 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.