Draft Pull Request to Visualize all the changes - #1

Draft

tabedzki wants to merge 276 commits into

BrainCOGS:mainfrom

This pull request is big! We're only showing the most recent 250 commits

Commits on Feb 3, 2023

bugfix
sidhulyalkar
committed
ce14098
change si related table names
sidhulyalkar
committed
7c836f1
bugfix
sidhulyalkar
committed
dd63664

Commits on Feb 4, 2023

update initial comment
sidhulyalkar
committed
54888ed
Merge branch 'datajoint:main' into modular_spikeinterface
sidhulyalkar
authored
50a4f6c

Commits on Feb 9, 2023

Commits on Feb 11, 2023

sglx preprocessing modifications
sidhulyalkar
committed
f0b7497

Commits on Feb 13, 2023

sglx testing progress
sidhulyalkar
committed
13fe31c

Commits on Feb 15, 2023

wip parametrize preprocessing
sidhulyalkar
committed
d41c7f3

Commits on Feb 18, 2023

post processing waveform extractor extensions
sidhulyalkar
committed
109a71a
post processing waveform extractor extensions
sidhulyalkar
committed
1febd7e

Commits on Feb 20, 2023

Fix data loading bug related to cluster_groups and KSLabel df key
sidhulyalkar
committed
a478e06

Commits on Feb 22, 2023

waveform extraction wip
sidhulyalkar
committed
634761d

Commits on Feb 23, 2023

modification to handle spike interface waveforms
sidhulyalkar
committed
ff0dfee
adjust post processing
sidhulyalkar
committed
cb31229

Commits on Mar 6, 2023

bugfix in postprocessing definition
sidhulyalkar
committed
6098421

Commits on Mar 8, 2023

add SI ibl destriping and catGT implementations
sidhulyalkar
committed
6006464
remove preprocess params list
sidhulyalkar
committed
c050875
preprocessing changes
sidhulyalkar
committed
4ea56c0

Commits on May 15, 2023

Merge branch 'datajoint:main' into modular_spikeinterface
sidhulyalkar
authored
1e74457
Update requirements.txt
sidhulyalkar
authored
0a87579

Commits on Jun 13, 2023

Merge branch 'datajoint:main' into modular_spikeinterface
sidhulyalkar
authored
fb71cea

Commits on Jun 14, 2023

fix spikeglx stream loading
sidhulyalkar
committed
22f1f65

Commits on Aug 3, 2023

Merge branch 'modular_spikeinterface' of https://github.com/sidhulyalkar/element-array-ephys into si
JaerongA
committed
5a0f624

Commits on Oct 10, 2023

Merge branch 'datajoint:main' into si
JaerongA
authored
1a46369

Commits on Oct 11, 2023

Commits on Oct 13, 2023

modify key_source in PreProcessing
JaerongA
committed
7836a8b

Commits on Dec 14, 2023

feat: :sparkles: improve to_probeinterface
JaerongA
committed
6bee166

Commits on Dec 15, 2023

create preprocessing.py
JaerongA
committed
9ae6b44
add SI_SORTERS , SI_READERS
JaerongA
committed
9d5eee6
feat: :art: si_clustering.PreProcessing
JaerongA
committed
1fceb90

Commits on Dec 20, 2023

feat: :art: si_clustering.SIClustering
JaerongA
committed
df8ed74
feat: :sparkles: add PostProcessing table & clean up
JaerongA
committed
2ed337b

Commits on Jan 3, 2024

fix: :bug: fix input/output data directory
JaerongA
committed
f6e3e46
check for presence of recording file
JaerongA
committed
e1c0d68
fix: :bug: fix path & typo
JaerongA
committed
653e7e8

Commits on Jan 5, 2024

code review
ttngu207
authored
8c25bd2
Merge pull request #4 from ttngu207/spike-interface-patch-1
JaerongA
authored
1084aae

Commits on Jan 10, 2024

Minor fixes
kushalbakshi
committed
fd5e9fa

Commits on Feb 1, 2024

feat: :sparkles: modify QualityMetrics make function
JaerongA
committed
90d1ba4

Commits on Feb 6, 2024

update si_spike_sorting.PreProcessing make function
JaerongA
committed
cacefac

Commits on Feb 7, 2024

update SIClustering make function
JaerongA
committed
f98e1ed
update PostProcessing make function
JaerongA
committed
7a060ef
feat: :sparkles: add n.a. to ClusterQualityLabel
JaerongA
committed
6daf0c5
extract all waveforms
JaerongA
committed
e41ff1d

Commits on Feb 8, 2024

Commits on Feb 12, 2024

update WaveformSet ingestion
JaerongA
committed
b01c36c

Commits on Feb 13, 2024

Update element_array_ephys/ephys_no_curation.py

JaerongA
and
kushalbakshi
authored
853b66f
Update element_array_ephys/ephys_no_curation.py

JaerongA
and
kushalbakshi
authored
67ebf4e
Update element_array_ephys/ephys_no_curation.py

JaerongA
and
kushalbakshi
authored
5fe6043
ci: run test only on the main branch
JaerongA
committed
ac08163
Merge remote-tracking branch 'upstream/datajoint-spikeinterface' into datajoint-spikeinterface
JaerongA
committed
545aa92
build: :heavy_plus_sign: add spikingcircus dependencies
JaerongA
committed
e95331c
refactor: fix typo & black formatting
JaerongA
committed
be5135e

Commits on Feb 15, 2024

feat: :sparkles: add EphysRecording.Channel part table
JaerongA
committed
4b6fc0e

Commits on Feb 16, 2024

fix: :bug: fix get_logger missing error
JaerongA
committed
4802511
fix typo & remove sorter_name
JaerongA
committed
bca67b3
feat: :sparkles: add memoized_result implementation in SIClustering
JaerongA
committed
1faa8f2
create a folder for storing recording pickle object
JaerongA
committed
58f3a44
install element_interface from datajoint upstream
JaerongA
committed
4fcea51
add required_key for parameters
JaerongA
committed
4f0e020
set recording channel info
JaerongA
committed
83e7a16
fix loading preprocessor
JaerongA
committed
1d18a39
make all output dir non-sharable
JaerongA
committed
b0a863f

Commits on Feb 19, 2024

refactor & accept changes from code review
JaerongA
committed
7d28351
remove memoized_result for testing
JaerongA
committed
95f5286

Commits on Feb 20, 2024

build: :heavy_plus_sign: add element-interface to required packages
JaerongA
committed
a7ebb9a

Commits on Feb 21, 2024

update pre-commit with the latest hooks
JaerongA
committed
134ff54

Commits on Feb 27, 2024

build: :heavy_plus_sign: Add numba as required package
JaerongA
committed
7972426
adjust extract_waveforms parameters
JaerongA
committed
ed11526

Commits on Feb 29, 2024

refactor: :recycle: update the output dir for CuratedClustering
JaerongA
committed
bab86b7
feat: :sparkles: add quality label mapping
JaerongA
committed
0898ce5

Commits on Mar 1, 2024

feat: :sparkles: Ingest EphysRecording.Channel
JaerongA
committed
727af24
get channel to electrode mapping in CuratedClustering
JaerongA
committed
1df41ea
refactor: :recycle: Fix metrics directory in QualityMetrics
JaerongA
committed
417219f
feat: :sparkles: replace get_neuropixels_channel2electrode_map with channel_info
JaerongA
committed
f70ae4e
fix CuratedClustering make function
JaerongA
committed
0ccbec9
improve try except logic
JaerongA
committed
86bb8d7
docs: :memo: update comments in ephys_no_curation
JaerongA
committed
673faed
refactor: :recycle: improve if else block in EphysRecording
JaerongA
committed
8ab4c58
feat: :sparkles: Update WaveformSet make function
JaerongA
committed
226142b

Commits on Mar 5, 2024

refactor: :fire: remove & get_neuropixels_channel2electrode_map and generate_electrode_config
JaerongA
committed
ea39839
Update element_array_ephys/ephys_no_curation.py

JaerongA
and
ttngu207
authored
5bfe201
add generate_electrode_config_name
JaerongA
committed
1d80584

Commits on Mar 7, 2024

refactor: :recycle: change sorter_name
JaerongA
committed
88ce139

Commits on Mar 8, 2024

address review comments for generate_electrode_config_entry
JaerongA
committed
7eaefa4
Merge pull request #179 from JaerongA/datajoint-spikeinterface
Thinh Nguyen
authored
90b81e3

Commits on Mar 11, 2024

Commits on Mar 12, 2024

Commits on Apr 4, 2024

Merge remote-tracking branch 'upstream/datajoint-spikeinterface' into datajoint-spikeinterface
ttngu207
committed
aff15bf

Commits on Apr 17, 2024

feat: save spike interface results with relative path
ttngu207
committed
67a1ffc

Commits on Apr 18, 2024

Merge branch 'datajoint:main' into main
kushalbakshi
authored
41e4d6d

Commits on Apr 26, 2024

fix(spikeglx): bugfix loading spikeglx data
ttngu207
authored
d44dbaa
Merge remote-tracking branch 'upstream/datajoint-spikeinterface' into datajoint-spikeinterface
ttngu207
committed
1819cbc
fix: bugfix inserting `ElectrodeConfig`
ttngu207
committed
d86928b
Merge pull request #186 from ttngu207/datajoint-spikeinterface
MilagrosMarin
authored
6a6e7b7
feat(spikesorting): save to phy and generate report
ttngu207
committed
f8ffd77
chore: cleanup init
ttngu207
committed
7309082
fix: update channel-electrode mapping
ttngu207
committed
d778b1e
feat: test spikeinterface for spikeglx data
ttngu207
committed
015341c

Commits on Apr 29, 2024

Commits on May 7, 2024

Refactor Quality Metrics Logic + blackformatting
MilagrosMarin
committed
93895a9

Commits on May 8, 2024

Commits on May 9, 2024

update `postprocessing` logic
MilagrosMarin
committed
403d1df

Commits on May 14, 2024

Merge remote-tracking branch 'upstream/datajoint-spikeinterface' into datajoint-spikeinterface
ttngu207
committed
bdf2b9f

Commits on May 24, 2024

Commits on May 28, 2024

fix: minor bug in spikes ingestion
ttngu207
committed
76dfc94
update: bump version
ttngu207
committed
9094754
feat: add `memoized_result` on spike sorting
ttngu207
committed
51e2ced
Merge pull request #190 from ttngu207/dev_spikeinterface_v101
MilagrosMarin
authored
2a4b166
chore: minor code cleanup
ttngu207
committed
0afb452
fix: merge fix & formatting
ttngu207
committed
e8f445c
fix: calling `_run_sorter()`
ttngu207
committed
6155f13

Commits on May 29, 2024

Commits on Jun 3, 2024

feat: replace `output_folder` with `folder` when calling `run_sorter`, use default value for `peak_sign`
ttngu207
committed
1a1b18f

Commits on Jun 4, 2024

Merge pull request #193 from ttngu207/dev_spikeinterface_v101
kushalbakshi
authored
212a54f

Commits on Jun 5, 2024

Commits on Jul 5, 2024

Commits on Jul 6, 2024

Commits on Jul 30, 2024

fix: bugfix spikeinterface extractor name
ttngu207
committed
097d9bb

Commits on Aug 15, 2024

Merge remote-tracking branch 'upstream/datajoint-spikeinterface' into datajoint-spikeinterface
ttngu207
committed
6aca235
update: element-interface `main` branch
ttngu207
committed
b6f131b
Merge branch 'main' into datajoint-spikeinterface
ttngu207
committed
84c38d1
Merge branch 'main' into datajoint-spikeinterface
ttngu207
committed
6b14486
Merge branch 'main' into datajoint-spikeinterface
ttngu207
committed
c2f2a79
Merge branch 'main' into datajoint-spikeinterface
ttngu207
committed
726a2bb

Commits on Aug 16, 2024

Merge branch 'main' into datajoint-spikeinterface
ttngu207
committed
5dc5953

Commits on Aug 19, 2024

Merge pull request #200 from ttngu207/datajoint-spikeinterface
kushalbakshi
authored
b510cb8

Commits on Sep 10, 2024

rearrange(all): major refactor of modules
ttngu207
committed
ccd23fc
rearrange: remove the `ecephys_spike_sorting` flow
ttngu207
committed
0eef1cb
chore: clean up diagrams
ttngu207
committed
c2bd5ad

Commits on Sep 19, 2024

Commits on Sep 20, 2024

Commits on Sep 26, 2024

Commits on Oct 1, 2024

0.3.6
semantic-release
committed
6bad001

Commits on Oct 8, 2024

Commits on Oct 9, 2024

fix(spike_sorting): create empty `sorting_analyzer` folder when no units found
ttngu207
committed
b1104ce

Commits on Oct 10, 2024

Merge branch 'datajoint-spikeinterface' into dev_new_main
ttngu207
committed
bb27fd0

Commits on Oct 25, 2024

Merge pull request #13 from kushalbakshi/dev_new-main-docs
ttngu207
authored
40dc3c0

Commits on Nov 1, 2024

Commits on Nov 4, 2024

Merge pull request #210 from kushalbakshi/main
ttngu207
authored
626327c

Commits on Jan 13, 2025

Merge remote-tracking branch 'upstream/main' into dev_new_main
ttngu207
committed
7128acc
update: fix docs, new version is `0.4.0`
ttngu207
committed
0508c94

Commits on Jan 14, 2025

update: make this the `1.0.0` release
ttngu207
committed
284106a

Commits on Jan 16, 2025

chore: revert semantic release and changelog
MilagrosMarin
committed
7c3f0ef
chore: typo
MilagrosMarin
committed
0fcb8c0
fix: update changelog and semantic release
MilagrosMarin
committed
77d001d

Commits on Jan 24, 2025

Merge pull request #211 from MilagrosMarin/chore/update-gha
ttngu207
authored
02476bb
Merge remote-tracking branch 'upstream/main' into dev_new_main
ttngu207
committed
0f51791
update: version 0.4.0
ttngu207
committed
e4d959d

Commits on Jan 28, 2025

fix: fix release titles in Changelog
MilagrosMarin
committed
d4e08ee
Merge pull request #212 from MilagrosMarin/chore/update-gha
ttngu207
authored
89e4d68
Merge branch 'main' into dev_new_main
ttngu207
authored
20770f1
update: version 0.4.0
ttngu207
committed
7dee019
style: black format
ttngu207
committed
ba25812
update(GHA): remove old python versions
ttngu207
committed
0ee86d2
Merge pull request #201 from ttngu207/dev_new_main
kushalbakshi
authored
d2492ee

Commits on Feb 13, 2025

fix(ephys): skip_duplicates in Probe.insert - allow probe reuse
ttngu207
authored
682ed17
update: version + changelog
ttngu207
committed
4c0bfc9

Commits on Feb 14, 2025

Commits on Mar 4, 2025

update: install neo from source until 0.14.1 release
ttngu207
authored
a0df46b

Commits on Mar 25, 2025

fix: add key_source to `ProbeLevelReport` to filter for 'good' quality units

MilagrosMarin
authored and
ttngu207
committed
2454b96
bump version and update changelog

MilagrosMarin
authored and
ttngu207
committed
a1bc2cf
fix: add key_source to `ProbeLevelReport` to filter for 'good' quality units

MilagrosMarin
authored and
ttngu207
committed
4c01ac7
update: bump version
ttngu207
committed
80926c8

Commits on Apr 21, 2025

Merge pull request #217 from ttngu207/main
ttngu207
authored
b1775af

Commits on May 9, 2025

chore: minor code optimization
ttngu207
committed
58cdfaa

Commits on May 13, 2025

Merge pull request #218 from ttngu207/main
kushalbakshi
authored
1d4f888

Commits on May 19, 2025

fix(docs): update home URL from `datajoint.com/docs` to `docs.datajoint.com`
MilagrosMarin
committed
234f38e
style: apply formatting
MilagrosMarin
committed
efb91b8

Commits on May 20, 2025

Merge remote-tracking branch 'upstream/main' into update-docs
MilagrosMarin
committed
fbf83de
style: black formatting
MilagrosMarin
committed
3bdf7e7
Merge pull request #220 from MilagrosMarin/update-docs
ttngu207
authored
0464fe2

Commits on Jun 4, 2025

Commits on Jun 6, 2025

update: update params in test/tutorials
ttngu207
committed
3b187cb
chore: update changelog
ttngu207
committed
fd837ec
chore: set up jupyter kernel in devcontainer
ttngu207
committed
9391f97
chore: update dockerfile
ttngu207
committed
9d03efb
fix: fix devcontainer
ttngu207
committed
6fbf5d4

Commits on Jun 9, 2025

Update setup.py - supports python3.11
ttngu207
authored
f61416b
fix: jupyter kernel
ttngu207
committed
1cd35a9
fix: jupyter kernel
ttngu207
committed
e2c03ba
chore: update si params in notebook
ttngu207
committed
bac296b
chore: minor bugfix
ttngu207
committed
d5eb76f

Commits on Jun 11, 2025

Merge pull request #223 from ttngu207/main
dimitri-yatsenko
authored
44548d3

Commits on Jul 8, 2025

update notebook with spectrogram plot
MilagrosMarin
committed
c5a2285
remove `skip_duplicates`
MilagrosMarin
committed
15874d0
Merge pull request #224 from MilagrosMarin/main
ttngu207
authored
776aa93

Commits on Sep 16, 2025

black formatting
MilagrosMarin
committed
c395bd0
fix: rename `env.yml` to `conda_env.yml` for consistency with other projects
MilagrosMarin
committed
f0939d1
bump version and update CHANGELOG
MilagrosMarin
committed
db99d0d

Commits on Sep 17, 2025

Merge pull request #225 from MilagrosMarin/main
ttngu207
authored
7dc76e8

Commits on Dec 10, 2025