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Obsolete dependency python-spams #1339

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pgunn opened this issue Apr 30, 2024 · 3 comments
Closed

Obsolete dependency python-spams #1339

pgunn opened this issue Apr 30, 2024 · 3 comments

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@pgunn
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pgunn commented Apr 30, 2024

The spams package, used in:

  • caiman/base/movies.extract_components() if the dict_learn method_factorization setting is used instead of nmf
  • caiman.behavior.behavior.online_NMF()

Is no longer maintained or packaged for modern versions of Python.

The latter function appears to be dead code. The former function is used (with this option) by the CLI demo demo_behaviour.py.

This is one of the remaining conditional imports in the codebase.

It is probably best to remove the dead fuction and the option of using dict_learn with caiman.base.movies.extract_components()

@pgunn
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pgunn commented Apr 30, 2024

In the cli_demos_refactor branch, I adjusted the CLI demo to use the nmf factorisation method instead of dict_learn; I may mix the fix for this into that branch as it'll be landing soon and I'm doing related work (really testing the CLI demos is what's finding these issues).

@pgunn
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pgunn commented May 1, 2024

Will be fixed when #1211 lands (fixed in that branch, where I noticed the issue while testing CLI demos)

@pgunn
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pgunn commented May 1, 2024

1211 landed; this is now fixed in dev.

@pgunn pgunn closed this as completed May 1, 2024
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