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Iblrigv8 #438

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ac1a6ab
Update tools.py
bimac Aug 13, 2024
9b1ef12
add pytest annotations to ci
bimac Aug 13, 2024
8666e4d
Update documentation.yaml
bimac Aug 13, 2024
b9a05f0
Update documentation.yaml
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08e8c10
update pre-commit
bimac Aug 14, 2024
8d97a60
attempt at unpinning qt
bimac Aug 14, 2024
09800e3
revert ...
bimac Aug 14, 2024
18f2279
work on read-me and documentation
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bda31ee
Update frame2ttl.py
bimac Aug 14, 2024
b82ad4f
order past session found by latest first
oliche Aug 16, 2024
0ef65b7
bump version number and changelog
oliche Aug 16, 2024
a49725b
Add matplotlib as an explicit dependency > 3.9.2
oliche Aug 16, 2024
5f0cb5a
Merge pull request #708 from int-brain-lab/hotfix-getinfo
oliche Aug 16, 2024
a6e489e
Merge branch 'iblrigv8' into iblrigv8dev
bimac Aug 16, 2024
169cf71
update dependencies
bimac Aug 16, 2024
022f068
Merge pull request #706 from int-brain-lab/iblrigv8dev
bimac Aug 16, 2024
06772c4
exclude tests from coverage
bimac Aug 16, 2024
bed113b
validation: check for unexpected input events
bimac Aug 20, 2024
684d576
validator for Frame2TTL
bimac Aug 20, 2024
6efe34f
Update hardware_validation.py
bimac Aug 20, 2024
67896ea
Update hardware_validation.py
bimac Aug 20, 2024
8d93d16
Update hardware_validation.py
bimac Aug 20, 2024
1341522
some refinements to hardware validators
bimac Aug 21, 2024
f4bdc7c
prepare release
bimac Aug 21, 2024
e3baed0
run all validators
bimac Aug 21, 2024
6ffcbad
Update test_hardware_validation.py
bimac Aug 21, 2024
db04546
Merge pull request #709 from int-brain-lab/iblrigv8dev
bimac Aug 21, 2024
72e5005
Update documentation.yaml
bimac Aug 21, 2024
98867da
Update pyproject.toml
bimac Aug 21, 2024
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Update pyproject.toml
bimac Aug 21, 2024
8df0cd5
remove scripts
bimac Aug 21, 2024
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Update pyproject.toml
bimac Aug 21, 2024
610957a
replace pdf document with a link
bimac Aug 21, 2024
811eaa8
add call_git method
bimac Aug 21, 2024
e610416
start work on get_lab_location_dict()
bimac Aug 22, 2024
40c85a6
Update tools.py
bimac Aug 22, 2024
de97284
Update tools.py
bimac Aug 22, 2024
28ac26f
work on documentation
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f7c0371
Merge branch 'iblrigv8dev' of github.com:int-brain-lab/iblrig into ib…
bimac Aug 22, 2024
910dfb4
Update tools.py
bimac Aug 22, 2024
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Update release.yaml
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work on github actions
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bimac Aug 22, 2024
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bimac Aug 22, 2024
251f060
Update release.yaml
bimac Aug 22, 2024
8d101ea
Update release.yaml
bimac Aug 22, 2024
0b203af
attempt to fix PDF build
bimac Aug 22, 2024
9906730
Update conf.py
bimac Aug 22, 2024
9617731
attempt to fix PDF build #2
bimac Aug 22, 2024
c466d54
attempt to fix PDF build #3
bimac Aug 22, 2024
2cde750
support for sphinx_simplepdf
bimac Aug 23, 2024
3db037e
Update release.yaml
bimac Aug 23, 2024
6442468
Merge branch 'iblrigv8dev' of github.com:int-brain-lab/iblrig into ib…
bimac Aug 23, 2024
0e2b9ec
Update release.yaml
bimac Aug 23, 2024
a888fe7
Update release.yaml
bimac Aug 23, 2024
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Update release.yaml
bimac Aug 23, 2024
eb66b01
Update release.yaml
bimac Aug 23, 2024
7a97dee
prepare release
bimac Aug 23, 2024
61e6f7d
further simplifications with regards to calling git
bimac Aug 23, 2024
75246e0
Update version_management.py
bimac Aug 23, 2024
acf21f2
make get_changelog() more robust
bimac Aug 23, 2024
222cebb
try and log state machine pybpod crashed state
oliche Aug 23, 2024
18aba4e
upload hardware information to Alyx
bimac Aug 23, 2024
6c60326
ruff
bimac Aug 23, 2024
b48ce36
Update wizard.py
bimac Aug 23, 2024
41cead2
Update base_choice_world.py
bimac Aug 23, 2024
4d13517
Update base_choice_world.py
bimac Aug 23, 2024
870dff3
Update CHANGELOG.md
bimac Aug 23, 2024
b07f1f4
Merge branch 'iblrigv8dev' of github.com:int-brain-lab/iblrig into ib…
bimac Aug 23, 2024
ad41db2
Merge pull request #710 from int-brain-lab/iblrigv8dev
bimac Aug 26, 2024
91f1550
Update release.yaml
bimac Aug 26, 2024
017dc7c
Update release.yaml
bimac Aug 26, 2024
04baddc
Create validate_hifi.py
bimac Aug 26, 2024
1d5591b
Update release.yaml
bimac Aug 26, 2024
eaf3516
add changelog / version info
bimac Aug 26, 2024
dd1af77
Update CHANGELOG.md
bimac Aug 26, 2024
f26ed87
Update faq.rst
bimac Aug 26, 2024
599c9ed
Merge branch 'iblrigv8dev' of github.com:int-brain-lab/iblrig into ib…
bimac Aug 26, 2024
14a471e
document states in get_state_machine_trial()
bimac Aug 27, 2024
7606f28
Merge branch 'iblrigv8dev' of https://github.com/int-brain-lab/iblrig…
bimac Aug 27, 2024
fe5c2c2
add QObjects for handling Alyx
bimac Aug 28, 2024
110cbf4
add documentation
bimac Aug 28, 2024
5ce2e10
Update tools.py
bimac Aug 28, 2024
955823c
Update tools.py
bimac Aug 28, 2024
3011ba2
add StatefulButton
bimac Aug 29, 2024
3cb4a89
Update tools.py
bimac Aug 29, 2024
ddd83aa
validate trialdata
bimac Aug 30, 2024
89d13b3
Update pydantic_definitions.py
bimac Aug 30, 2024
54b9c91
Update base_choice_world.py
bimac Aug 30, 2024
0d55122
Update pydantic_definitions.py
bimac Aug 30, 2024
947df85
class method for creating empty dataframe based on pydantic model
bimac Aug 30, 2024
d6c6b95
Finish implementation of trial_data check
bimac Aug 31, 2024
6226a4d
Update pydantic_definitions.py
bimac Aug 31, 2024
b6f43ba
place TrialDataModels with session classes
bimac Aug 31, 2024
b20bd36
work on documentation
bimac Sep 2, 2024
4fdd124
repair CI
bimac Sep 2, 2024
dca9248
simplify use of TrialDataModel
bimac Sep 2, 2024
dd2301d
minor fix
bimac Sep 3, 2024
0c9f77d
make protocol_name an abstract property of BaseSession
bimac Sep 3, 2024
770d435
do not cache subjects and projects
bimac Sep 3, 2024
768a1fa
Update base_tasks.py
bimac Sep 3, 2024
0ad4f6f
minor changes to base_tasks (protocol, abstract properties)
bimac Sep 3, 2024
3371657
Update custom-module-template.rst
bimac Sep 3, 2024
9552658
add `TrialDataModel` for all session types in `base_choice_world`
bimac Sep 3, 2024
1d178bc
Update reference_write_your_own_task.rst
bimac Sep 3, 2024
33d26bc
Merge branch 'iblrigv8dev' of github.com:int-brain-lab/iblrig into ib…
bimac Sep 3, 2024
f37a84b
add private submodules of iblrig_tasks to API reference
bimac Sep 3, 2024
75932fa
add TrialDataModel to NeuroModulatorChoiceWorld
bimac Sep 4, 2024
b39fd8e
EphysCW: actually use pregenerated data from parquet
bimac Sep 4, 2024
71e9be0
Update base_choice_world.py
bimac Sep 4, 2024
6c6684f
correct trial fixtures for ephysChoiceWorld
bimac Sep 4, 2024
e20c8bc
simplify overriding of trial parameters in draw_next_trial_info
bimac Sep 4, 2024
b0a17e9
minor update to documentation
bimac Sep 10, 2024
3d014f2
prepare release
bimac Sep 10, 2024
b9334f3
use dict for passing extra log items in show_trial_log
bimac Sep 10, 2024
a93837d
Update CHANGELOG.md
bimac Sep 10, 2024
f4abec1
Update CHANGELOG.md
bimac Sep 10, 2024
1842d95
Merge branch 'iblrigv8' into iblrigv8dev
bimac Sep 10, 2024
a946a6f
Merge pull request #711 from int-brain-lab/iblrigv8dev
bimac Sep 10, 2024
20c166d
install PortAudio for doc action (needed for API documentation)
bimac Sep 10, 2024
91430d7
Update documentation.yaml
bimac Sep 10, 2024
7f5e4e4
change UI workflow for appending a session
bimac Sep 11, 2024
cb5eb44
ruff
bimac Sep 11, 2024
e890e64
only offer append when MAIN_SYNC == False
bimac Sep 13, 2024
37330f3
Update base_choice_world.py
bimac Sep 13, 2024
2a6ca62
add test for passiveCW fixtures
bimac Sep 16, 2024
eee1f18
add ks-test
bimac Sep 17, 2024
aa43391
Update test_passive_choice_world.py
bimac Sep 18, 2024
3f38c46
Update test_passive_choice_world.py
bimac Sep 18, 2024
01e088a
Update test_passive_choice_world.py
bimac Sep 18, 2024
adc1ba0
Video QC: change log level from WARNING to INFO if less than 0.1% of …
bimac Sep 19, 2024
ca4ce3a
Use restricted quadratic fit when converting reward volume to valve o…
bimac Sep 23, 2024
73b6a53
valve calibration: plot shows value down to 0 ms opening time
bimac Sep 23, 2024
d7e21f8
unit test for valve
bimac Sep 23, 2024
84c77d6
TrainingCW: add `signed_contrast` to trials_table definition
bimac Sep 23, 2024
7cba05e
Merge branch 'iblrigv8dev' of https://github.com/int-brain-lab/iblrig…
bimac Sep 23, 2024
7a7f45b
Merge pull request #716 from int-brain-lab/iblrigv8dev
bimac Sep 23, 2024
5c2021e
fix: make Frame2TTL validation more robust
bimac Sep 27, 2024
646ec93
Merge pull request #722 from int-brain-lab/iblrigv8dev
bimac Sep 27, 2024
8e3ece3
add pyqt dependency
bimac Oct 1, 2024
dc3d164
update to iblqt 0.1.1
bimac Oct 1, 2024
5ef3d09
Doc for placing mouse onto previous Training Phase
GaelleChapuis Oct 3, 2024
a23ddb7
Developper documentation building update
GaelleChapuis Oct 3, 2024
d89bb2c
HOTFIX resolves #379
k1o0 Oct 4, 2024
66051a9
SIM910 / SIM300
bimac Oct 4, 2024
8e4cc6b
more yoda / fix test / changelog
bimac Oct 4, 2024
c190239
Merge pull request #723 from int-brain-lab/hotfix/8.24.3
bimac Oct 4, 2024
d585cdc
prepare release
bimac Oct 4, 2024
0f4a573
Merge pull request #724 from int-brain-lab/iblrigv8dev
bimac Oct 4, 2024
6ed03da
WIP fibrephotometry
oliche Jun 20, 2024
c472fa3
WIP photometry copiers / starters
oliche Jun 20, 2024
ccbb381
Start photometry workflow
oliche Jun 24, 2024
e728df5
photometry: start bonsai workflow script
oliche Jun 28, 2024
1360ce6
minimal set of parameters to start a photometry session
oliche Sep 17, 2024
32c9ecc
add the default bonsai path relative to home
oliche Sep 17, 2024
5f98134
debug arguement
oliche Sep 17, 2024
a309c94
bonsai executable
oliche Sep 17, 2024
63f1cb9
add documentation
oliche Sep 17, 2024
e577630
WIP copier photometry
oliche Oct 11, 2024
bcc789d
save changes to the bonsai workflow
Oct 11, 2024
732116c
add argument parser
bimac Oct 11, 2024
d49a24b
Merge branch 'photometry' of github.com:int-brain-lab/iblrig into pho…
bimac Oct 11, 2024
7e1eaf1
start_photometry_task_cmd
oliche Oct 11, 2024
e8c9f42
Replace np.NaN with np.nan
bimac Oct 14, 2024
f65da20
Update base_choice_world.py
bimac Oct 14, 2024
aafc830
Update .gitignore
bimac Oct 16, 2024
93cff54
log session version
bimac Oct 17, 2024
2ada996
fixing typo
bimac Oct 17, 2024
800ad29
correct gain for rotary encoder thresholds in trainingChoiceWorld
bimac Oct 17, 2024
5cd11df
update requirements
bimac Oct 17, 2024
b4c9bbb
version number / changelog
bimac Oct 18, 2024
aa6e047
remove patch_old_params function
k1o0 Oct 18, 2024
eda5b5b
Fix passive test
k1o0 Oct 18, 2024
d1d3578
Merge pull request #729 from int-brain-lab/remove_old_pipeline
bimac Oct 18, 2024
8805fbe
Update CHANGELOG.md
bimac Oct 18, 2024
64347f2
move stimulus_gain() to RotaryEncoderMixin
bimac Oct 18, 2024
a0c9806
Update hardware.py
bimac Oct 18, 2024
ed3569d
Update base_tasks.py
bimac Oct 18, 2024
a7f4e46
Update hardware.py
bimac Oct 18, 2024
f53a195
Merge branch 'iblrigv8' into iblrigv8dev
bimac Oct 18, 2024
9801a3e
fix CI
bimac Oct 18, 2024
60403a3
Merge pull request #730 from int-brain-lab/iblrigv8dev
bimac Oct 18, 2024
714218d
Update CHANGELOG.md
bimac Oct 18, 2024
57f2df4
fix: visual stimulus not showing for first trial
bimac Oct 18, 2024
6491e9f
Merge pull request #732 from int-brain-lab/iblrigv8dev
bimac Oct 18, 2024
761e827
add property getters for feedback delays
bimac Oct 21, 2024
0e0bc83
Merge pull request #733 from int-brain-lab/iblrigv8dev
bimac Oct 21, 2024
8649207
fix debiasing
bimac Oct 24, 2024
90cc171
ruff
bimac Oct 24, 2024
6671d7b
Merge pull request #734 from int-brain-lab/iblrigv8dev
bimac Oct 24, 2024
cc037ef
add methods for converting bpod data into a dataframe
bimac Oct 25, 2024
aa4a827
add methods for converting state timing to dataframe
bimac Oct 27, 2024
b4bc6ab
combine methods for getting trials data and event data as dataframes
bimac Oct 27, 2024
34e8fda
WIP fibrephotometry
oliche Jun 20, 2024
259e380
WIP photometry copiers / starters
oliche Jun 20, 2024
ac18ce8
Start photometry workflow
oliche Jun 24, 2024
6ca90f2
photometry: start bonsai workflow script
oliche Jun 28, 2024
abd161b
minimal set of parameters to start a photometry session
oliche Sep 17, 2024
0e9120f
add the default bonsai path relative to home
oliche Sep 17, 2024
e3d02b8
debug arguement
oliche Sep 17, 2024
649a192
bonsai executable
oliche Sep 17, 2024
545152e
add documentation
oliche Sep 17, 2024
14a2205
WIP copier photometry
oliche Oct 11, 2024
3c2b4f5
add argument parser
bimac Oct 11, 2024
5a5d939
save changes to the bonsai workflow
Oct 11, 2024
fdcf2f6
start_photometry_task_cmd
oliche Oct 11, 2024
9fc2755
wip photometry UCL extraction
oliche Nov 8, 2024
cff3a9e
neurophotometrics copier init/copy collections
oliche Nov 10, 2024
4746be5
completed copy for UCL neurophotometrics
oliche Nov 11, 2024
aa44044
Merge branch 'iblrigv8' into photometry
bimac Nov 11, 2024
ff9366e
Merge branch 'photometry' of github.com:int-brain-lab/iblrig into pho…
bimac Nov 11, 2024
db9cd24
Update test_neurophotometrics.py
bimac Nov 11, 2024
347c705
make sure the description starts with device name
oliche Nov 11, 2024
6da07ff
update dependencies / add pandera
bimac Nov 12, 2024
3c43c88
fix tests
oliche Nov 12, 2024
e05594e
pin to numpy < 2.0
bimac Nov 12, 2024
7938783
Replace tkinter dialogs with CLI input prompt
bimac Nov 12, 2024
55e3dc6
one.alf.files -> one.alf.path
k1o0 Nov 1, 2024
5b0f763
Merge pull request #735 from int-brain-lab/alfFilesDeprecation
k1o0 Nov 13, 2024
0095512
use TimedeltaIndex and drop 'Time' column
bimac Nov 13, 2024
686361e
propagate state-names using ffill
bimac Nov 13, 2024
3d8eaa5
Merge branch 'iblrigv8dev' into photometry
bimac Nov 15, 2024
79d9084
Merge pull request #737 from int-brain-lab/photometry
bimac Nov 15, 2024
5c1e6eb
Merge branch 'online-plots' into iblrigv8dev
bimac Nov 15, 2024
1b7c889
Merge branch 'online-plots' into iblrigv8dev
bimac Nov 15, 2024
5ad937d
prepare release
bimac Nov 15, 2024
51f0ef2
Merge pull request #740 from int-brain-lab/iblrigv8dev
bimac Nov 15, 2024
e2552fe
added test for photometry copier
grg2rsr Nov 20, 2024
07dc869
remove static_vars() and get_detailed_version_string()
bimac Nov 22, 2024
ff36cdf
update ruff
bimac Nov 22, 2024
0da0752
add photometry documentation
oliche Nov 25, 2024
a1c21c9
oh non, le typo
oliche Nov 25, 2024
25d5ce2
rename menu item for getting v7 training status
bimac Dec 2, 2024
578bff8
ruff
grg2rsr Dec 2, 2024
f6e4952
Merge branch 'iblrigv8dev' into photometry_copier_test
bimac Dec 4, 2024
1f2d6e5
add narrative logic
bimac Dec 5, 2024
bd68568
Merge pull request #741 from int-brain-lab/photometry_copier_test
grg2rsr Dec 5, 2024
925051b
finish implementation of narrative editor
bimac Dec 5, 2024
c6a954a
write narrative at end of session
bimac Dec 5, 2024
02ec009
avoid non-necessary write operations
bimac Dec 5, 2024
b4e37a2
Merge pull request #748 from int-brain-lab/feat/narrative
bimac Dec 5, 2024
c913c8f
prepare release
bimac Dec 5, 2024
e45c923
Update test_gui.py
bimac Dec 5, 2024
7c3efd3
Update test_gui.py
bimac Dec 5, 2024
215c99f
Merge pull request #742 from int-brain-lab/iblrigv8dev
bimac Dec 5, 2024
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Update CHANGELOG.md
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bimac committed Oct 18, 2024

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commit 8805fbe0a87c1de63ebe9018a1786ff2875d8f9f
1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -9,6 +9,7 @@ Changelog
8.24.3
------
* fix: create the `raw_ephys_data` folder even if there are no probes (when running behavior sessions on ephys rig)
* fix: replace `np.NaN` with `np.nan`
* move some Qt related code to `iblqt` repository

8.24.2