v3.0 beta

[3.0β]

Important

This is a pre-release and may not be stable

This version drops support for python 3.9 and below, and ONE is now in remote mode by default.
Also adds a new ALFPath class to replace alf path functions and now returns UUID objects instead of str.

Modified

• supports python >= 3.10 only
• OneAlyx uses remote mode by default, instead of auto
• OneAlyx.search now updates the cache tables in remote mode as paginated sessions are accessed
• datasets table file_size column nullable by default
• one.alf.io.save_metadata now returns the saved filepath
• paths returned by One methods and functions in one.alf.io are now ALFPath instances
• bugfix: one.alf.path.full_path_parts didn't always raise when invalid path passed
• one.alf.path module containing ALFPath class
• ALF cache table generation has lower memory footprint
• setup in silent mode now uses defaults if base url matches default one
• bugfix: error downloading from http server with keep_uuids=True
• one.alf.spec.readableALF and one.alf.spec._dromedary preserve plural acronyms, e.g. 'ROIs'
• UUID objects returned by to_eid, search, and search_insertions instead of str
• LazyId objects now handled correctly by One converter methods
• LazyId object only returned when greater than 1 page of results
• OneAlyx.search_insertions now updates local cache with query results
• bugfix: OneAlyx.list_datasets behaves the same as One.list_datasets w.r.t. revisions and default datasets
• default REST cache expiry reduced from 24 hours to 5 minutes

Added

• one.alf.cache.remove_cache_table_files and One._remove_cache_table_files for deleting cache table files
• one.alf.cache.EMPTY_DATASETS_FRAME and EMPTY_SESSION_FRAME vars for table column, index, and dtype template
• pyproject.toml replaces deprecated setup file
• one.alf.exceptions.InvalidALF exception
• one.params.delete_params
• One._search_insertions for offline query of insertions when cache table present

Removed

• setup.py
• one.alf.files; use one.alf.path instead
• one.alf.io.remove_uuid_file
• one.alf.io.remove_uuid_recursive
• one.util.ensure_list; use iblutil.util.ensure_list instead
• one.remote.globus.create_globus_client; use one.remote.globus.Globus class instead

v2.11.1

[2.11.1]

Modified

• HOTFIX: consistent behaviour in OneAlyx.list_datasets when keep_eid_index == True

v2.11.0

[2.11.0]

This version deprecates one.alf.files in preperation for replacing with one.alf.path in version 3.

Modified

• one.alf.files has been deprecated and moved to one.alf.path

v2.10.1

[2.10.1]

Modified

• prompt user to strip quotation marks if used during ONE setup
• indicate when downloading from S3
• added 'keep_eid_index' kwarg to One.list_datasets which will return the data frame with the eid index level reinstated
• HOTFIX: include Subject/lab part in destination path when downloading from S3

v2.10.0

[2.10.0]

This version fixes issues with Alyx authentication in silent mode, and improves behaviour of loading revisions.

Modified

• sub-collections no longer captured when filtering with filename that starts with wildcard in wildcard mode
• bugfix of spurious error raised when loading dataset with a revision provided
• default_revisions_only parameter in One.list_datasets filters non-default datasets
• permit data frame input to One.load_datasets and load precise relative paths provided (instead of default revisions)
• redundent session_path column has been dropped from the datasets cache table
• bugfix in one.params.setup: suggest previous cache dir if available instead of always the default
• bugfix in one.params.setup: remove all extrenuous parameters (i.e. TOKEN) when running setup in silent mode
• warn user to reauthenticate when password is None in silent mode
• always force authentication when password passed, even when token cached
• bugfix: negative indexing of paginated response objects now functions correctly
• deprecate one.util.ensure_list; moved to iblutil.util.ensure_list

Added

• one.alf.exceptions.ALFWarning category allows users to filter warnings relating to mixed revisions

v2.9.1

[2.9.1]

Modified

• HOTFIX: When downloading cache only authenticate Alyx when necessary
• HOTFIX: Ensure http data server URL does not end in slash
• HOTFIX: Handle public aggregate dataset relative paths
• HOTFIX: No longer warns in silent mode when no param conflicts present
• Explicit kwargs in load_* methods to avoid user confusion (e.g. no 'namespace' kwarg for load_dataset)

v2.9.0

[2.9.0]

This version adds a couple of new ALF functions.

Added

• one.alf.io.find_variants allows one to find similar datasets on disk, such as revisions
• one.alf.files.without_revision returns a file path without the revision folder

Modified

• one.alf.files.add_uuid_string will now replace a UUID in a filename if one already present.

v2.8.1

[2.8.1]

Modified

• HOTFIX: fix error when sizing npz objects in alf.io.load_object

v2.8.0

[2.8.0]

This version of ONE adds support for loading .npz files.

Modified

• one.alf.io.load_file_content loads npz files and returns only array if single compressed array with default name of 'arr_0'.
• log warning when instantiating RegistrationClient with AlyxClient REST cache active
• bugfix in load_collection when one or more files missing

v2.7.0

[2.7.0]

This version of ONE adds support for Alyx 2.0.0 and pandas 3.0.0 with dataset QC filters. This version no longer supports 'data' search filter.

Added

• support for Alyx v2.0.0
• support for pandas v3.0.0
• one.alf.spec.QC enumeration
• ONE_HTTP_DL_THREADS environment variable allows user to specify maximum number of threads to use
• RegistrationClient.check_protected_files method to determine which datasets are protected on Alyx before registration
• github workflow for releasing to PyPi

Modified

• support 'qc' category field in dataset cache table
• One.search supports ´dataset_qc_lte` filter
• One.list_datasets supports ´dataset_qc_lteandignore_qc_not_set` filters
• one.alf.io.iter_sessions pattern arg to make more performant

Removed

• One.search no longer supports 'data' filter: kwarg must be 'dataset'