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Use legacy numpy versions for ks 4.1.1-4.1.6 tests #4591

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alejoe91 merged 2 commits into from
May 20, 2026
+21 −3
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Use legacy numpy versions for ks 4.1.1-4.1.6 tests #4591

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36980b7
Use appropriate numpy version in kilosor tests
chrishalcrow May 20, 2026
74ca4d3
oups
chrishalcrow May 20, 2026
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16 changes: 13 additions & 3 deletions .github/workflows/test_kilosort4.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,11 @@ name: Testing Kilosort4
on:
workflow_dispatch:
schedule:
- cron: "0 12 * * 0" # Weekly on Sunday at noon UTC
- cron: "0 12 * * 0" # Weekly on Sunday at noon UTC
pull_request:
paths:
- '**/kilosort4.py'
- '**/test_kilosort4_ci.py'
- "**/kilosort4.py"
- "**/test_kilosort4_ci.py"

jobs:
versions:
Expand Down Expand Up @@ -76,6 +76,16 @@ jobs:
if: matrix.ks_version == '4.0.16' || matrix.ks_version == '4.0.17' || matrix.ks_version == '4.0.18'
run: uv pip install --system setuptools==78.0.2

- name: Install legacy numpy for KS4 4.1.1 - 4.1.5
if: |
matrix.ks_version == '4.1.1' ||
matrix.ks_version == '4.1.2' ||
matrix.ks_version == '4.1.3' ||
matrix.ks_version == '4.1.4' ||
matrix.ks_version == '4.1.5' ||
matrix.ks_version == '4.1.6'
run: uv pip install --system "numpy<2.4"

- name: Install Kilosort
run: |
uv pip install --system kilosort==${{ matrix.ks_version }}
Expand Down
8 changes: 8 additions & 0 deletions src/spikeinterface/sorters/external/kilosort4.py
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Expand Up @@ -147,6 +147,7 @@ def _setup_recording(cls, recording, sorter_output_folder, params, verbose):
@classmethod
def _run_from_folder(cls, sorter_output_folder, params, verbose):
from kilosort import __version__ as ks_version
from numpy import __version__ as np_version
from kilosort.run_kilosort import (
set_files,
initialize_ops,
Expand All @@ -161,6 +162,13 @@ def _run_from_folder(cls, sorter_output_folder, params, verbose):
from kilosort.io import load_probe, RecordingExtractorAsArray, BinaryFiltered, save_preprocessing
from kilosort.parameters import DEFAULT_SETTINGS

if (version.parse("4.1.1") <= version.parse(ks_version) <= version.parse("4.1.6")) and version.parse(
np_version
) >= version.parse("2.4.0"):
raise RuntimeError(
"Kilosort versions between 4.1.1 and 4.1.6 are not compatible with numpy versions above 2.4. Either upgrade Kilosort to 4.1.7 or above, or downgrade numpy to 2.3 or below."
)

if version.parse(ks_version) >= version.parse("4.0.33"):
HAS_DIAGNOSTIC_PLOTS = True
import kilosort.plots as kplots
Expand Down
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