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Develop #685

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Dec 13, 2023
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270fdd4
Deprecate globus module
k1o0 Aug 30, 2023
0e60893
Use ONE Globus in patcher
k1o0 Sep 6, 2023
d97ccd1
Add delete_dataset method
k1o0 Sep 6, 2023
64e72f3
Delete S3 files
k1o0 Sep 11, 2023
1889e7c
Bump ONE version
k1o0 Sep 15, 2023
7d811e0
full session wheel alignment
mayofaulkner Sep 25, 2023
3deb565
Merge branch 'release/2.26' into develop
mayofaulkner Sep 25, 2023
8511bb6
Merge branch 'develop' into globusDeprecation
k1o0 Sep 26, 2023
f77bb4a
add video wheel alignment to fpga camera extraction
mayofaulkner Sep 26, 2023
e5b71cf
report server health to data repo not lab
mayofaulkner Sep 26, 2023
a8850a2
circular imports
mayofaulkner Sep 26, 2023
976b4b0
Merge branch 'develop' into wheel_alignment
mayofaulkner Sep 26, 2023
5c59536
upload plot to alyx
mayofaulkner Sep 27, 2023
3cd2ca8
remove circular imports
mayofaulkner Sep 27, 2023
935c0c7
Density gain option (#652)
chris-langfield Oct 4, 2023
6bc95d2
doc probe geometry
GaelleChapuis Oct 6, 2023
a497411
sync extension optional; reduce logging clutter
k1o0 Oct 6, 2023
6c04956
flake8
k1o0 Oct 6, 2023
68fb8cd
Task qc extractor refactor (#649)
k1o0 Oct 6, 2023
3d8a626
Merge branch 'develop' into globusDeprecation
k1o0 Oct 6, 2023
7d5bfc1
Merge branch 'develop' into wheel_alignment
mayofaulkner Oct 9, 2023
b567a3c
remove behavior flag, infer from files
mayofaulkner Oct 10, 2023
69972c3
restrict to left and right cameras
mayofaulkner Oct 10, 2023
659efcf
fix glob pattern
mayofaulkner Oct 10, 2023
2a66a13
authenticate alyx
mayofaulkner Oct 10, 2023
fbaea40
Merge pull request #651 from int-brain-lab/wheel_alignment
mayofaulkner Oct 10, 2023
04733ac
save figure with label name
mayofaulkner Oct 10, 2023
9acbf8e
Merge remote-tracking branch 'origin/develop' into docs
GaelleChapuis Oct 11, 2023
10007ec
close figure and change processes
mayofaulkner Oct 11, 2023
c8d6556
doc strings to wheel alignment module
mayofaulkner Oct 11, 2023
c6b0784
Mesoscope brain location (#656)
k1o0 Oct 11, 2023
2803838
Merge branch 'master' into develop
k1o0 Oct 11, 2023
6e59101
change nprocess
mayofaulkner Oct 11, 2023
65aa9a4
Merge branch 'develop' into wheel_alignment
mayofaulkner Oct 11, 2023
3bdaf87
Merge pull request #661 from int-brain-lab/wheel_alignment
mayofaulkner Oct 11, 2023
c9d7127
better logging and release notes
mayofaulkner Oct 12, 2023
bfa88e5
Merge pull request #662 from int-brain-lab/wheel_alignment
mayofaulkner Oct 12, 2023
5f97c0b
Move url2uri to ONE
k1o0 Oct 17, 2023
c8de86f
Merge remote-tracking branch 'origin/develop' into docs
GaelleChapuis Oct 18, 2023
eab63da
mpciROIs.uuids (#663)
k1o0 Oct 18, 2023
f8b7ad2
raw audio spectrogram example
GaelleChapuis Oct 18, 2023
bc52877
Merge branch 'develop' into globusDeprecation
k1o0 Oct 18, 2023
183a68d
fix from brainbox.io.one import load_channel_locations
GaelleChapuis Oct 18, 2023
21233e3
fix the docs
mayofaulkner Oct 19, 2023
e761f67
Test GlobusPatcher
k1o0 Oct 23, 2023
5a46c63
Merge branch 'develop' into globusDeprecation
k1o0 Oct 23, 2023
154d4cd
Moved Mayo's examples to tasks.py module
k1o0 Oct 23, 2023
7277c78
Merge branch 'globusDeprecation' of https://github.com/int-brain-lab/…
k1o0 Oct 23, 2023
148c4c2
Ensure paths are str in GlobusPatcher; ignore tmin, tmax if no trials…
k1o0 Oct 23, 2023
47b5eff
remove deprecated psychofit module; fix tests
k1o0 Oct 24, 2023
eb41a31
doc raw data probe geometry
GaelleChapuis Oct 24, 2023
f76e29d
local coordinates not existing as a key
GaelleChapuis Oct 24, 2023
1712805
Merge pull request #660 from int-brain-lab/docs
GaelleChapuis Oct 24, 2023
276bfea
Add device_sound key to v7 settings; QC bugfix and test
k1o0 Oct 25, 2023
c9850ec
sdsc load data possible by monkey patching alfio in brainbox.io.one
oliche Oct 19, 2023
94fdbda
Merge pull request #664 from int-brain-lab/uuidFilenames
oliche Oct 25, 2023
166c4c5
bump ONE version
k1o0 Nov 2, 2023
e7ed533
use packaging instead of pkg_resources; use IBLRIG_VERSION instead of…
k1o0 Nov 3, 2023
06d65ea
QC notes and test fix
k1o0 Nov 6, 2023
262bb75
Extend globus module deprecation
k1o0 Nov 6, 2023
036d6ea
Issue #666
k1o0 Nov 15, 2023
0159729
FpgaTrials refactor and FpgaHabituationTrials subclass
k1o0 Nov 17, 2023
822f183
Auto stash before merge of "develop" and "origin/develop"
mayofaulkner Nov 28, 2023
dd7b087
training status to run on SDSC
juhuntenburg Nov 28, 2023
def1353
training status - only extract bpod data, don't run qc and don't sync
mayofaulkner Nov 30, 2023
d229498
Remove test reference to module constant
k1o0 Dec 5, 2023
cb9bc9d
when no spacer take last ttl as end time
mayofaulkner Dec 6, 2023
3a02da2
improve logging
mayofaulkner Dec 6, 2023
8aff0ad
mesoscope trials extractor refactor; fix attribute_times numpy versio…
k1o0 Dec 8, 2023
6b1416c
Build trials after syncing Bpod clock
k1o0 Dec 8, 2023
bac2374
Include wheel in Bpod trials dict passed to FpgaTrials
k1o0 Dec 8, 2023
ba2553d
Add more fields to qc extractor
k1o0 Dec 8, 2023
e0cac72
Merge pull request #673 from int-brain-lab/HabituationNidq
k1o0 Dec 8, 2023
cfbefba
Merge branch 'probe_plot_fix' into passive_fix
mayofaulkner Dec 11, 2023
30d1d78
Merge branch 'develop' into passive_fix
mayofaulkner Dec 11, 2023
c848cea
Merge branch 'develop' into TrainingTaskQC
k1o0 Dec 11, 2023
f3f057c
flake
k1o0 Dec 11, 2023
6075d57
Merge pull request #681 from int-brain-lab/passive_fix
mayofaulkner Dec 11, 2023
d31d7d1
Merge branch 'develop' into globusDeprecation
k1o0 Dec 11, 2023
74e57b8
Merge branch 'develop' into globusDeprecation
k1o0 Dec 11, 2023
f5290b0
Skip phase distribution check; handle NaNs in stim move before go cue
k1o0 Dec 11, 2023
0ca5082
use get_bpod_event_times
k1o0 Dec 11, 2023
beda422
Merge pull request #665 from int-brain-lab/TrainingTaskQC
k1o0 Dec 11, 2023
b31d14e
Increase default protocol period
k1o0 Dec 12, 2023
da365e6
Merge branch 'develop' into globusDeprecation
k1o0 Dec 12, 2023
49ad5a3
Test new extractor methods
k1o0 Dec 12, 2023
48cfcd0
Move test_ephys_trials tests to test_ephys_fpga; remove old functions
k1o0 Dec 12, 2023
276603e
Added trainingPhaseChoiceWorld to task protocol extractor map; fix ty…
k1o0 Dec 12, 2023
f617813
remove prepare_experiment
k1o0 Dec 12, 2023
9e38c64
Merge pull request #647 from int-brain-lab/globusDeprecation
k1o0 Dec 12, 2023
bb1a851
Merge pull request #684 from int-brain-lab/removeOldFunctions
k1o0 Dec 13, 2023
ebc9774
Release notes
k1o0 Dec 13, 2023
9fbc0f2
randomise session for histology
mayofaulkner Dec 13, 2023
8454d8d
randomise all seeds
mayofaulkner Dec 13, 2023
8c944d2
Merge pull request #687 from int-brain-lab/random_sessions_for_tests
mayofaulkner Dec 13, 2023
7c2a821
Update release notes; remove unused time date range function
k1o0 Dec 13, 2023
934f9da
Remove double import; delete session notes first on teardown
k1o0 Dec 13, 2023
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2 changes: 1 addition & 1 deletion .flake8
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[flake8]
max-line-length = 130
ignore = W504, W503, E266
ignore = W504, W503, E266, D, BLK
exclude =
.git,
__pycache__,
Expand Down
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ __pycache__
python/scratch
.idea/*
.vscode/
*.code-workspace
*checkpoint.ipynb
build/
venv/
Expand Down
306 changes: 0 additions & 306 deletions brainbox/behavior/pyschofit.py

This file was deleted.

6 changes: 3 additions & 3 deletions brainbox/behavior/training.py
Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,6 @@
from one.api import ONE
from one.alf.io import AlfBunch
from one.alf.exceptions import ALFObjectNotFound

import psychofit as psy

_logger = logging.getLogger('ibllib')
Expand Down Expand Up @@ -83,15 +82,16 @@ class TrainingStatus(IntFlag):
... assert TrainingStatus[status.upper()] in ~TrainingStatus.FAILED, 'Subject untrained'
... assert TrainingStatus[status.upper()] in TrainingStatus.TRAINED ^ TrainingStatus.READY

# Get the next training status
Get the next training status

>>> next(member for member in sorted(TrainingStatus) if member > TrainingStatus[status.upper()])
<TrainingStatus.READY4RECORDING: 128>

Notes
-----
- ~TrainingStatus.TRAINED means any status but trained 1a or trained 1b.
- A subject may acheive both TRAINED_1A and TRAINED_1B within a single session, therefore it
is possible to have skipped the TRAINED_1A session status.
is possible to have skipped the TRAINED_1A session status.
"""
UNTRAINABLE = auto()
UNBIASABLE = auto()
Expand Down
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