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Updates to kilosort 4: version >= 4.0.16, bad_channels, clear_cache, use_binary_file #3339

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Sep 6, 2024
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0ee0c43
Add bad channels and do version check
chrishalcrow Aug 26, 2024
bc290ff
remove comment about preprocesed spelling
chrishalcrow Aug 27, 2024
0df7141
Add use_binary_file argument and logic to KS4
alejoe91 Aug 27, 2024
a51a5b4
Merge branch 'main' into only-allow-above-ks-4-16
alejoe91 Aug 27, 2024
7638935
Merge branch 'main' of github.com:SpikeInterface/spikeinterface into …
alejoe91 Aug 29, 2024
227b0e7
Update KS4 versions
alejoe91 Aug 31, 2024
2b70788
Merge branch 'only-allow-above-ks-4-16' of github.com:chrishalcrow/sp…
alejoe91 Aug 31, 2024
c23d530
Update actions and always use binary if recording is binary
alejoe91 Sep 2, 2024
f9dfa04
Add highpass_cutoff and fix KS tests
alejoe91 Sep 3, 2024
1964f86
test ks4 on ks4 changes
alejoe91 Sep 3, 2024
8e9995d
Move testing scripts into scripts folder
alejoe91 Sep 3, 2024
219bee4
change trigger
alejoe91 Sep 3, 2024
e26e143
Remove last conditions on prior ks versions
alejoe91 Sep 3, 2024
9c338dd
Fix KS parameters in tests
alejoe91 Sep 3, 2024
87fbe55
More cleanup of KS4 tests
alejoe91 Sep 3, 2024
10b7e1a
Remove last change_nothing
alejoe91 Sep 3, 2024
007b64d
Allow use_binary_file=None (default) and add delete_recording_dat param
alejoe91 Sep 3, 2024
f399f6e
Update .github/scripts/test_kilosort4_ci.py
alejoe91 Sep 4, 2024
464c6e3
Update src/spikeinterface/sorters/external/kilosort4.py
alejoe91 Sep 4, 2024
0ed4876
Extend check on clus
alejoe91 Sep 4, 2024
8fbf100
Expose clear_Cache argument in KS4
alejoe91 Sep 5, 2024
fd61bb6
Explicitly add (spikeinterface parameter) to KS4 param description
alejoe91 Sep 5, 2024
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2 changes: 1 addition & 1 deletion .github/run_tests.sh
Original file line number Diff line number Diff line change
Expand Up @@ -10,5 +10,5 @@ fi

pytest -m "$MARKER" -vv -ra --durations=0 --durations-min=0.001 | tee report.txt; test ${PIPESTATUS[0]} -eq 0 || exit 1
echo "# Timing profile of ${MARKER}" >> $GITHUB_STEP_SUMMARY
python $GITHUB_WORKSPACE/.github/build_job_summary.py report.txt >> $GITHUB_STEP_SUMMARY
python $GITHUB_WORKSPACE/.github/scripts/build_job_summary.py report.txt >> $GITHUB_STEP_SUMMARY
rm report.txt
File renamed without changes.
9 changes: 2 additions & 7 deletions .github/scripts/check_kilosort4_releases.py
Original file line number Diff line number Diff line change
Expand Up @@ -16,13 +16,8 @@ def get_pypi_versions(package_name):
response.raise_for_status()
data = response.json()
versions = list(sorted(data["releases"].keys()))

assert parse(spikeinterface.__version__) < parse("0.101.1"), (
"Kilosort 4.0.5-12 are supported in SpikeInterface < 0.101.1."
"At version 0.101.1, this should be updated to support newer"
"kilosort verrsions."
)
versions = [ver for ver in versions if parse("4.0.12") >= parse(ver) >= parse("4.0.5")]
# Filter out versions that are less than 4.0.16
versions = [ver for ver in versions if parse(ver) >= parse("4.0.16")]
return versions


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