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Merged
mayofaulkner merged 97 commits into from
Feb 14, 2023
Merged

Chained protocols #557

mayofaulkner merged 97 commits into from
Feb 14, 2023

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@k1o0
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@k1o0 k1o0 commented Jan 19, 2023 •
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Release 2.21

Release Notes 2.21.0 2023-02-13

features

  • support for multiple task protocols within a session
  • extract protocol period from spacer signals
  • function for changing subject, collection, number or date in a settings file
  • function to retrieve task protocol number from experiment description
  • dataset type validation supports null filename patterns
  • oneibl.registration uses one.registration client as superclass
  • experiment description files are created and registered in legacy pipelines
  • QC sign-off keys are added to session JSON field
  • class-based note template API for attaching session notes for QC sign-offs
  • protocol and procedures now taken from experiment description file
  • handle truncated first spacer in passive extraction
  • fix the Perirhinal area layer color in Allen Atlas
  • fix region volume computation
  • vectorised swanson flatmap
  • brainbox trial ITI loader

k1o0 and others added 30 commits November 22, 2022 11:41
@k1o0
WIP
a42ba6c
@k1o0
Merge branch 'develop' of https://github.com/int-brain-lab/ibllib int…
7c3f201 
…o develop
@k1o0
Merge branch 'develop' into chainedProtocols
3de9755
@k1o0
extractors arg in exp description
c2e65dd
@k1o0
Merge remote-tracking branch 'origin/develop' into chainedProtocols
5f7637c
@k1o0
WIP
5953eea
@k1o0
Merge branch 'develop' into chainedProtocols
4f68585
@k1o0
WIP
b9f6bf8
@k1o0
Task number in task name
d0f66fb
@mayofaulkner
211a467 
add task collections
@mayofaulkner
more task collections
f67fb84
@mayofaulkner
5aa526e 
protocol number argument
@juhuntenburg
Fix tests
3a922b2
@juhuntenburg
get task number
dc0190c
@k1o0
Extract spacers
56d1d56
@k1o0
Merge branch 'chainedProtocols' of https://github.com/int-brain-lab/i…
9671348 
…bllib into chainedProtocols
@k1o0
Extract ephys behaviour using protocol number
44fad65
@juhuntenburg
Chained test and tests passing
618a97d
@juhuntenburg
Merge remote-tracking branch 'origin/chainedProtocols' into chainedPr…
39c1c20 
…otocols
@k1o0
Protocol number arg in ephys_passive
b9564a0
@juhuntenburg
Merge remote-tracking branch 'origin/chainedProtocols' into chainedPr…
17ec890 
…otocols
@mayofaulkner
Auto stash before merge of "chainedProtocols" and "origin/chainedProt…
39d4037 
…ocols"

fixes to wheel extraction
@k1o0
protocol_number only passed if collection startwith raw_task_data
8a98f36
@k1o0
Merge branch 'chainedProtocols' of https://github.com/int-brain-lab/i…
398b03d 
…bllib into chainedProtocols
@k1o0
number -> protocol_number
739b96f
@mayofaulkner
d0af8a2 
register session with project and procedures from experiment description file
@k1o0
minor fixes
28afae2
@juhuntenburg
Small fixes
16f7c92
@k1o0
Sign off checklist keys in ExperimentDescriptionRegisterRaw
e7c24e9
@k1o0
Allow custom sign off keys for certian devices
654131e
mayofaulkner and others added 28 commits February 7, 2023 14:56
@mayofaulkner
bd54831 
svg options for all plots
@GaelleChapuis
tmax instead of overall end time
58ae644
@GaelleChapuis
a8231eb 
tmax taken as end of f2ttl if none
@mayofaulkner
032f713 
flake :|
@k1o0
Patch settings function
fc3eb39
@oliche
fix region volume computation
4bdfd79
@k1o0
trial ITI loader
e5f24a3
@k1o0
Merge branch 'chainedProtocols' of https://github.com/int-brain-lab/i…
73a0c45 
…bllib into chainedProtocols
@oliche
fix the Perirhinal area layer color in Allen Atlas
c571c14
@oliche
Merge branch 'chainedProtocols' of https://github.com/int-brain-lab/i…
078eac4 
…bllib into chainedProtocols
@GaelleChapuis
passing thresh as var
790603f
@GaelleChapuis
WIP bugfix for guido
80c499b
@GaelleChapuis
WIP
369d97e
@GaelleChapuis
7c32214 
WIP use conv to find max, then search for middle of spacer backward
@GaelleChapuis
d69ca6e 
Guido's session fix
@GaelleChapuis
9bec6b8 
Submit final code
@GaelleChapuis
int
a302836
@k1o0
flake
5c163e2
@mayofaulkner
de8f9e4 
Streamer option not to convert to volts
@k1o0
Merge pull request #568 from int-brain-lab/swanson_vector
a0d84d9 
Swanson vector
@mayofaulkner
8c7e266 
fix race condition tests
@mayofaulkner
f7b24f9 
fix more tests
@mayofaulkner
Merge pull request #569 from int-brain-lab/swanson_vector
0e9f201 
Swanson vector
@mayofaulkner
Auto stash before checking out "origin/chainedProtocols"
599c3c6 
mock lab for registration, random probe names
@mayofaulkner
cd880a5 
proper patch
@mayofaulkner
db54547 
make eid string
@mayofaulkner
53c1100 
new session for ntoes
@mayofaulkner
bd70121 
new session for notes test
@mayofaulkner mayofaulkner merged commit 7af131f into develop Feb 14, 2023
@k1o0 k1o0 deleted the chainedProtocols branch May 11, 2023 09:56
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6 participants

@k1o0 @mayofaulkner @juhuntenburg @oliche @GaelleChapuis