Fixes Apptainer bug plus small fixes #2053

mhhennig · 2023-09-29T11:15:04Z

Main change: change to pip install --user for sorters run in containers so python packages are installed in writable location. This otherwise breaks apptainer.

There are a few small changes, sorry they all end up in the same pull request. There were some type issues in the mda and numpy extractors.

…main Conflicts: src/spikeinterface/core/base.py src/spikeinterface/core/numpyextractors.py

…main

Apptainer fails to pip install into the system directory (not writable by default, no space when writable), and the --user flag ensures packages are installed in a writable location. Note not tested with docker.

for more information, see https://pre-commit.ci

alejoe91 · 2023-09-29T11:33:48Z

Thanks @mhhennig !!

Yeah no worries about the small changes this time! They are smalle enough :)

src/spikeinterface/extractors/mdaextractors.py

samuelgarcia · 2023-09-29T12:00:14Z

Hi Matthias.
What are the issue with numpy extractors ?

alejoe91 · 2023-09-29T12:01:57Z

Hi Matthias. What are the issue with numpy extractors ?

Seems only MdaSorting

mhhennig · 2023-09-29T13:02:35Z

Hi Matthias. What are the issue with numpy extractors ?

Seems only MdaSorting

NumpyExtractor: assert times.dtype.kind == 'i', 'numpy array of spike times must be integer'
We must check for any integer type (failed for me for a sorting I had), so needs to be:
assert (times.dtype.kind == 'i') or (times.dtype.kind == 'u'), 'numpy array of spike times must be integer'

src/spikeinterface/extractors/mdaextractors.py

alejoe91 · 2023-10-02T11:32:05Z

@mhhennig to keep the repo clean, we all make PRs from forks, and not internal branches. Could you also do it next time? ;)

src/spikeinterface/extractors/mdaextractors.py

alejoe91 · 2023-10-02T11:40:35Z

@mhhennig to keep the repo clean, we all make PRs from forks, and not internal branches. Could you also do it next time? ;)

This is what I mean:

alejoe91 · 2023-10-02T13:27:04Z

Hi Matthias. What are the issue with numpy extractors ?

Seems only MdaSorting

NumpyExtractor: assert times.dtype.kind == 'i', 'numpy array of spike times must be integer' We must check for any integer type (failed for me for a sorting I had), so needs to be: assert (times.dtype.kind == 'i') or (times.dtype.kind == 'u'), 'numpy array of spike times must be integer'

I don't see that assertion, can you share the link?

mhhennig and others added 9 commits June 29, 2023 12:44

Allow any integer type.

5fd2627

Fix problem with non-numeric unit IDs.

077a7fe

Allow any integer type.

6c861a4

Fixed docstring

9b86b48

Merge branch 'main' of github.com:SpikeInterface/spikeinterface into …

47ff64e

…main Conflicts: src/spikeinterface/core/base.py src/spikeinterface/core/numpyextractors.py

Merge branch 'main' of github.com:SpikeInterface/spikeinterface into …

ac8d061

…main

Pip install into working directory for containers

8c633ac

Apptainer fails to pip install into the system directory (not writable by default, no space when writable), and the --user flag ensures packages are installed in a writable location. Note not tested with docker.

Merge branch 'main' of github.com:SpikeInterface/spikeinterface

5a72604

[pre-commit.ci] auto fixes from pre-commit.com hooks

4f2a50d

for more information, see https://pre-commit.ci

alejoe91 added the container Issues related to container (docker/singularity) versions of sorters label Sep 29, 2023

samuelgarcia reviewed Sep 29, 2023

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