int-brain-lab / ibllib / 7121692968188028

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Iblrigv8 (#641)

* small atlas fix

* Prepare experiment takes in an optional device id parameter

* typo

* session_params: session creation creates stub in local and remote

* Create stubs logging

* copy ephys: update prints to logger and option to transfer single sessions

* transfer ephys data logging and compatibility dynamic pipeline

* Actually we don't want a status flag

* fixing some lies in the type hints

* bugfix get collection: yaml can interpret some keys as datestrings

* un bon patch bien dégueulasse

* Fix training CW extraction v8

* add atlas test and add temporary requirement for widefield package

* add optional task_collection arg to compute training status

* skimage deprecated in favour of scikit-image

* typo

* training status computation compatible with chained protocols

* Dynamic pipeline training status

* finish merge

* add some logging to the jobs on server - make sure each run is separate

* fix training_status task failing in training pipeline integration

* dynamic pipeline lookups for specific subtask with sync suffix if not found

* TaskQC no longer saves to disk; use get_bpod_extractor

* training status task: do not raise on extraction error

* Auto stash before checking out "origin/iblrigv8"

stop training regression when two protocols on same day

* fix for bpod camera extraction get correct collection

* don't pass into qc

* pop the task collection

* fix tests

* flake after merge

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Co-authored-by: Miles Wells <k1o0@5tk.co>
Co-authored-by: Mayo Faulkner <mayo.faulkner@ucl.ac.uk>

131 of 131 new or added lines in 15 files covered. (100.0%)

13307 of 20149 relevant lines covered (66.04%)

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