Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog,
and this project adheres to Semantic Versioning.

[3.4.1] 2025-07-02

Fixed

SpikeSortingLoader takes into account revisions
There is a specific test for spikeinterface CI in our integration tests

Release Note 3.4.0

features

Add revision as a kwarg to the spike sorting loader
Register bin files to flatiron
Ensure pre-existing compressed files are verified and registered
Only update relevant collections in update_collections
Update extended QC with task number prefix
Update trials extractors to handle clean first trial
Pin numpy to >=1.18,<=2.2 (numpy 2.3 is not compatible with numba)
oneibl.patcher.patch_dataset: revert from clobber to force
Ensure session paths are ALFPath instances
Update dataset QC
Handle None session path
Add options for SDSC and EC2 patchers
Use ALFPath objects in Task and DataHandler classes

Release Note 3.3.1

Bugfixes

SpikeSortingLoader: returns channels from 'electrodeSites' if available (it always was the intention...)

Release Note 3.3.0

features

ONE 3
Handle extraction of sessions where first Bpod trial missed on FPGA
Support for multi depth sessions by passing slices kwarg to suite2p fork
Selectively remove old FOV datasets in MesoscopePreprocess
Added starplot function
Improvements to LightningPose and SpikeSorting tasks

Bugfixes

Add back PROJECT_EXTRACTION_VERSION and TASK_VERSION to session JSON
Fix error in MesoscopeCompress when compressing multiply imaging bouts
Fix error in MesoscopeSync.setUp with remote location

Release Note 3.2.0

features

Add session delay info during registration of Bpod session
Add detailed criteria info to behaviour plots
Add column filtering, sorting and color-coding of values to metrics table of
task_qc_viewer

Bugfixes

Read in updated json keys from task settings to establish ready4recording
Handle extraction of sessions with dud spacers

Release Note 3.1.0

features

Add narrative during registration of Bpod session

Release Note 3.0.0

features

Support for py3.8 and 3.9 dropped
JobCreator Alyx task
Photometry sync task
Remove deprecated code, incl. iblatlas and brainbox/quality
Bugfix: badframes array dtype change int8 -> uint32
Brain wide map release information
Limited Numpy 2.0 and ONE 3.0 support

Release Note 2.40.0

features

iblsorter >= 1.9 sorting tasks with waveform extraction and channel sorting
s3 patcher prototype

2.40.1

Bugfix: ibllib.io.sess_params.merge_params supports tasks extractors key

2.40.2

Bugfix: badframes array dtype change int8 -> uint32

Release Note 2.39.0

features

register inputs without rename in registerSnapshots
iterate only plane folders in Suite2P
removed old pipeline

bugfixes

NeuromodulatorCW is a subclass of Advanced CW regarding debiasing
Behaviour QC: StimFreeze QC due to indexing errors, ITI duration and negative feedback delay for nogo trials
Camera QC fixes

2.39.1

Bugfix: brainbox.metrics.single_unit.quick_unit_metrics fix for indexing of n_spike_below2

2.39.2

Bugfix: routing of protocol to extractor through the project repository checks that the
target is indeed an extractor class.

Release Note 2.38.0

features

Support running large pipeline jobs within multiple python environments
Extraction and QC of of task pause periods
Register animated GIF snapshots and tiff images
Load waveforms low level changes in spike sorting loader
Loading of additional channel object attributes (qc labels) in spike sorting loader
Stimulus times now extracted in a more robust manner

bugfixes

Fix in training plots when no trials in block

Release Note 2.37.0

features

Add code in preparation for retirement of old training and ephys local server pipelines

bugfixes

Change handling of trials extraction of iblrigv8 sessions such that pregenerated session is not used

Release Note 2.36.0

features

Adding spike sorting iblsort task

Release Note 2.35.0

features

Adding LightningPose task

bugfixes

SessionLoader can now handle trials that are not in the alf collection
Extraction of trials from pre-generated sequences supports iblrigv8 keys

2.35.1

Ensure no REST cache used when searching sessions in IBLRegistationClient

2.35.2

Flag to allow session registration without water administrations
Support extraction of repNum for advancedChoiceWorld
Support matplotlib v3.9; min slidingRP version now 1.1.1

2.35.3

Use correct task for timeline acquisitions in make_pipeline

Release Note 2.34.0

features

Task assert_expected_input now take into account revisions
Camera qc and video motion now take into account dynamic pipeline folder

bugfixes

Typo in raw_ephys_data documentation
oneibl.register_datasets accounts for non existing sessions when checking protected dsets

2.34.1

Ensure mesoscope frame QC files are sorted before concatenating
Look for SESSION_TEMPLATE_ID key of task settings for extraction of pre-generated choice world sequences
Download required ap.meta files when building pipeline for task_qc command

Release Note 2.33.0

features

Datasets no longer registered by default if protected, need to force registration
Tasks now allows datasets to be registered before qc computation
Histology channel upload now reads in channel map from data when available

bugfixes

PostDLC tasks looks in alf folder for lick datasets

Release Notes 2.32

features

SDSC patcher automatically support revisions

other

Add extra key to alignment qc with manual resolution for channel upload

2.32.3

FpgaTrials supports alignment of Bpod datasets not part of trials object
Support chained protocols in BehaviourPlots task

2.32.4

Add support for variations of the biaseCW task in the json task description

2.32.5

Minor fixes to IBL registration client, including use of SESSION_END_TIME key

Release Notes 2.31

features

Training status uses new extractor map
Refactor neurodsp to ibldsp
ITI qc check for iblrig v8
Support habituationChoiceWorld extraction in iblrig v8.15.0

bugfixes

NP2 waveforms extracted with correct dtype
Sorted cluster ids in single unit metrics

Release Notes 2.30

features

Task QC viewer
Raw ephys data loading documentation

other

Pandas 3.0 support

Release Notes 2.29

features

Added raw data loaders and synchronisation tools in brainbox.io.one.SpikeSortingLoader, method ssl.raw_electrophysiology()

Release Notes 2.28

features

Added ibllib.pipes.dynamic_pipeline.get_trials_tasks function

bugfixes

Fix ibllib.io.extractors.ephys_fpga.extract_all for python 3.8

other

Change behavior qc to pass if number of trials > 400 (from start) can be found for which easy trial performance > 0.9

2.28.1

Typo in ibllib.pipes.video_tasks.EphysPostDLC class
ibllib.io.raw_data_loaders.patch_settings works with iblrigv8 settings files

2.28.2

Fix loading of personal projects extractor map

Release Notes 2.27

features

Add full video wheel motion alignment code to ibllib.io.extractors.video_motion module
Change FPGA camera extractor to attempt wheel alignment if audio alignment fails
Flexible FpgaTrials class allows subclassing for changes in hardware and task
Task QC thresholds depend on sound card
Extractor classes now return dicts instead of tuple
Support extraction of habituationChoiceWorld with FPGA
New IBLGlobusPatcher class allows safe and complete deletion of datasets

bugfixes

Fix numpy version dependent error in io.extractors.camera.attribute_times
Fix for habituationChoiceWorld stim off times occuring outside of trial intervals
Improvements to Timeline trials extractor, especially for valve open times
trainingPhaseChoiceWorld added to Bpod protocol extractor map fixture
Last trial of FPGA sessions now correctly extracted
Correct dynamic pipeline extraction of passive choice world trials

2.27.1

Correct handling of missing TTLs in FpgaTrialsHabituation

other

Removed deprecated pyschofit module
Deprecated oneibl.globus module in favour of one.remote.globus
Deprecated qc.task_extractors in favour of behaviour pipeline tasks

Release Notes 2.26

features

Deprecate ibllib.atlas. Code now contained in package iblatlas

bugfixes

2.26.1

fix typo in criterion_ephys where lapse high for 0.8 blocks only passed when non-zero.

Release Notes 2.25

features

Training status pipeline now compatible with dynamic pipeline
Dynamic DLC task using description file
Full photometry lookup table

bugfixes

fix for untrainable, unbiasable don't repopulate if already exists

2.25.1

relax assertion on Neuropixel channel mappings to allow for personal projects

2.25.2

listing of all collections does not skip repeat task protocols anymore for copy/extraction

Release Notes 2.23

Release Notes 2.23.1 2023-06-15

features

split swanson areas

bugfixes

trainig plots
fix datahandler on SDSC for ONEv2

Release Notes 2.23.0 2023-05-19

quiescence period extraction
ONEv2 requirement

Release Notes 2.22

Release Notes 2.22.3 2023-05-03

same as 2.22.2 (I messed up the release sorry)

Release Notes 2.22.2 2023-05-03

bugfixes

training plots

features

can change download path for atlas

Release Notes 2.22.1 2023-05-02

bugfixes

use session path in training status task

Release Notes 2.22.0

features

trials extractors support omissions trials from neuromodulator tasks
SpikeSortingLoader and EphysSessionLoader utils functions to load re...

What's Changed

Docs by @mayofaulkner in #809
update wf extractions args in SpikeSorting task by @chris-langfield in #807
SpikeSortingLoader.raw_waveforms() by @chris-langfield in #823
Force dynamic by @k1o0 in #813
Remove old pipeline by @k1o0 in #840
Aggregate trials by @k1o0 in #843
Aggregate training by @k1o0 in #844
Docs by @mayofaulkner in #847
Camera fixes by @mayofaulkner in #849
Mesoscope preprocess class by @k1o0 in #851
Mesoscope preprocess class by @k1o0 in #855
AlyxClient instead of ONE in report_health by @k1o0 in #856
Qc fixes by @oliche in #852
iterate only plane folders in suite2p dir by @k1o0 in #860
Register inputs without rename in RegisterSnapshots by @k1o0 in #861
neuromodulatorCW it a subclass of advancedCW by @oliche in #859

Full Changelog: 2.38.0...2.39.0

Releases: int-brain-lab/ibllib

3.4.1

Changelog

[3.4.1] 2025-07-02

Fixed

Release Note 3.4.0

features

Release Note 3.3.1

Bugfixes

Release Note 3.3.0

features

Bugfixes

Release Note 3.2.0

features

Bugfixes

Release Note 3.1.0

features

Release Note 3.0.0

features

Release Note 2.40.0

features

2.40.1

2.40.2

Release Note 2.39.0

features

bugfixes

2.39.1

2.39.2

Release Note 2.38.0

features

bugfixes

Release Note 2.37.0

features

bugfixes

Release Note 2.36.0

features

Release Note 2.35.0

features

bugfixes

2.35.1

2.35.2

2.35.3

Release Note 2.34.0

features

bugfixes

2.34.1

Release Note 2.33.0

features

bugfixes

Release Notes 2.32

features

other

2.32.3

2.32.4

2.32.5

Release Notes 2.31

features

bugfixes

Release Notes 2.30

features

other

Release Notes 2.29

features

Release Notes 2.28

features

bugfixes

other

2.28.1

2.28.2

Release Notes 2.27

features

bugfixes

2.27.1

other

Release Notes 2.26

features

bugfixes

2.26.1

Release Notes 2.25

features