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For memory sake, make unreadable stacks that discard test pulses #22

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For memory sake, make unreadable stacks that discard test pulses #22

wants to merge 252 commits into from

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outofculture
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  • tests
  • test data
  • version bump
  • this is already released

campagnola and others added 30 commits December 6, 2019 10:11
@campagnola
fix mies nwb handling if entire recording is nan
f57babd
@campagnola
miesnwb bugfix
ca595cd
@campagnola
different strategy for handling aborted sweeps
9e74b46
@campagnola
Merge branch 'master' of github.com:AllenInstitute/neuroanalysis
555e2c6
@campagnola
minor doc update
5aa7a9d
@campagnola
Better initial psp yoffset
53c1f85
@campagnola
use mode instead of mean for measuring baseline
bbe61c4
@campagnola
fix psp fit yoffset bounds
0d95197
@campagnola
fix previous commit to use baseline mode
d0fff45
@campagnola
Add fit_scale_offset for analytical minimization in simple cases
8f31c78 
Add tools for determining time constant changes with exponential devonvolution
Performance improvements
@campagnola
Merge branch 'master' of github.com:AllenInstitute/neuroanalysis
b176956
@meganbkratz
start neuroanalysis/data directory for data models
406336e
@meganbkratz
fixed imports for moving experiment.py into data/dataset.py
4c9088f 
(cherry picked from commit dff2ea5)
@meganbkratz
add find_noisy_square_pulse function for finding pulses in noisy data…
ec33a04 
… -- good for finding pulses in a trace of pockel cell voltage

(cherry picked from commit 0379a27)
@meganbkratz
import fix for moving into data directory
59c26f5 
(cherry picked from commit c55086e)
@meganbkratz
fixes for python3
6c55daa 
(cherry picked from commit 33ca40f)
@meganbkratz
Adjustments for using Dataset directly with a loader class (instead o…
056f421 
…f subclassing)

(cherry picked from commit 818c1e4)
@meganbkratz
moved loader file to here instead of optoanalysis
51f5c0c 
(cherry picked from commit 4873907)
@meganbkratz
bugfix
c13cc3f 
(cherry picked from commit 26e6829)
@meganbkratz
moved device_config to neuroanalysis
784788d 
(cherry picked from commit a55801d)
@meganbkratz
added pyqtgraph debug console
9c2372a 
(cherry picked from commit c58b76e)
@meganbkratz
change parent property so it doesn't need to be overwritten in subcla…
4aceda3 
…sses

(cherry picked from commit 0a5873f)
@meganbkratz
added loading for Stimuli
368e87e 
(cherry picked from commit d27b039)
@meganbkratz
device name lookup
fcc1f44 
(cherry picked from commit ae57e55)
@meganbkratz
added DatasetLoader abstract base class
86b84b0 
(cherry picked from commit ad0f474)
@meganbkratz
fix for find_noisy_square_pulses
e4bfb36 
(cherry picked from commit a206eb2)
@meganbkratz
documentation
df2f189 
(cherry picked from commit 056ddde)
@meganbkratz
remove baseline functions from PatchClampRecording; add nearest_test_…
25feeb0 
…pulse functionality to loader

(cherry picked from commit cd307d7)
@meganbkratz
added deprecation error to explain why recording.baseline_regions no …
310d0ab 
…longer works

(cherry picked from commit dd62549)
@meganbkratz
cleanup device_config system
d05f629 
(cherry picked from commit 11efd80)
outofculture and others added 29 commits August 30, 2024 13:21
@outofculture
add bath recording
18e90cd
@outofculture
version the test pulse save schema
59bd8de
@outofculture
allow TSeries to concat with each other
25d42f0
@outofculture
put stimulus in proper format for saving
17c5042
@outofculture
ignore warnings in both places exp_fit is used
5e6cba8
@outofculture
more warnings it is safe to ignore
59e9f4a
@outofculture
Refactor PatchClampTestPulse to not be a Recording
9e7ff14 
- has-a relationship with its recording is better
- refactor how save/load works to understand this better
@outofculture
3.10 compat for warnings
19435da
@outofculture
Recording.save
45cf943
@outofculture
share safety checks between save and copy
3500838
@outofculture
time vals will now be none to start with
5a19693
@campagnola
Merge pull request AllenInstitute#12 from outofculture/can-we-pass
cd8f9a5 
Make tests and get the analysis to pass them
@outofculture
oops - wrong arg order
8459f41
@outofculture
more references
1fd6fd2
@outofculture
version bump
e28b6d4
@outofculture
useful property for safe closing
819e704
@outofculture
bump again
d486f74
@campagnola
Create action for CI
14e07db
@outofculture
Merge branch 'master' of github.com:AllenInstitute/neuroanalysis
ba5582c
@campagnola
CI update
605a163
@campagnola
Update python-package-conda.yml
06a36a9
@outofculture
bad old test
f3ed0f6
@campagnola
Fix flake complaints
62bd49d
@outofculture
Merge remote-tracking branch 'origin/ci-did-it' into testable
25acad2
@campagnola
Merge pull request AllenInstitute#14 from outofculture/testable
5cec1b1 
remove bad test
@campagnola
Merge pull request AllenInstitute#13 from outofculture/verbump
d20a2ce 
Bump version
@outofculture
allow TestPulseStacks to be unreadable to save on memory
d21ba7d
@outofculture
version bump
50f1b52
@outofculture
test data update
b1ff943
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5 participants
@outofculture @campagnola @meganbkratz @tmchartrand @scseeman