Update Python version requirements and installation instructions - #1398
Update Python version requirements and installation instructions#1398Sachuriga wants to merge 3 commits into
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Thanks for working through the legacy Kwik dependencies! I think it would be simplest if Since reclustering requires The main phy dependencies could then remain on Also, could we move the new Thanks again! |
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Thanks for the update and for working through these tricky legacy dependencies! Could we keep Could we also move the new reclustering plugin and related changes into a separate PR? It would help keep this PR focused. One small detail: the changes reference Thanks again! |
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HI,
Yes! will work on that.
Best,
Sachuriga
Cyrille Rossant ***@***.***> 于2026年7月23日周四 16:37写道：
… *rossant* left a comment (cortex-lab/phy#1398)
<#1398 (comment)>
Thanks for the update and for working through these tricky legacy
dependencies!
Could we keep phy[kwik] for the legacy Kwik GUI, with numpy>=1.23,<1.24,
and document that it requires Python 3.10 or 3.11?
Could we also move the new reclustering plugin and related changes into a
separate PR? It would help keep this PR focused.
One small detail: the changes reference phy[recluster], but only phy[kwik]
is defined.
Thanks again!
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--
Sachuriga
Postdoctoral fellowship , Ph.D.
https://quattrocololab.com
<https://l.jumpto.es/l/0fb29be00ba1d1ffd01eb9c775fcee1719aef6e6?u=12414310>
Kavli Institute for Systems Neuroscience
Olav Kyrres gate 9
7030 Trondheim
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Hi, yes will work on that. |
phy's own code uses no numpy API removed in 2.0, so the main dependency set
moves to numpy>=1.23 with no upper bound and requires-python stays >=3.10.
Regular users get numpy 2.x and Python 3.13.
Everything the legacy Kwik GUI needs is confined to the kwik extra, which
provides one self-contained, fully working setup -- opening .kwik files,
curating them, and the recluster action (shift+ctrl+K, re-running KlustaKwik2):
numpy>=1.23,<1.24 the last numpy the legacy klusta/klustakwik2 stack was
written against; keeps the whole Kwik surface on tested
ground. Caps the Kwik GUI at Python 3.10-3.11 (numpy 1.23
ships no cp312 wheels).
setuptools<81 klusta/__init__.py imports pkg_resources, dropped in 81
six klusta declares no dependencies of its own
The numpy pin is deliberately conservative rather than strictly required:
reclustering runs on newer numpy (verified via klusta.launch.cluster(), the
function the GUI action calls, on numpy 1.26.4), and even numpy 2 works once
ndarray.tostring() -> .tobytes() in klusta/kwik/h5.py and
klustakwik2/precomputations.py is fixed upstream. Pinning to <1.24 trades those
newer versions for a single tested baseline; the cap can be relaxed later.
Verified: phy[kwik] resolves on Python 3.11 (numpy 1.23.5, scipy 1.15.3) and the
full KwikCreator -> KwikModel -> launch.cluster() round-trip passes.
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Thanks! I updated the PR branch on top of current master and adapted the changes to our uv-first workflow. Could you review the edits and let us know what you think? |
2 participants
Update Python version requirements and installation instructions in README and pyproject.toml