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flatironinstitute / CaImAn

Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
https://caiman.readthedocs.io
GNU General Public License v2.0
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caiman manager install fails #1369

Closed smbaca closed 4 months ago

smbaca commented 4 months ago
  1. Operating System (Linux, MacOS, Windows): Mac OS Sonoma 14.5
  2. Hardware type (x86, ARM..) and RAM: ARM M3
  3. Python Version (e.g. 3.9): 3.11
  4. Caiman version (e.g. 1.9.12): Latest
  5. How you installed Caiman (pure conda, conda + compile, colab, ..): conda
    1. Details: trying to install caimanmanager fails and with either x86 or arm version of conda. I get the following error:

ImportError: cannot import name 'simps' from 'scipy.integrate' (/opt/anaconda3/envs/mescore/lib/python3.11/site-packages/scipy/integrate/init.py)

smbaca commented 4 months ago

https://docs.scipy.org/doc/scipy/release/1.14.0-notes.html#backwards-incompatible-changes

Looks like they got rid of simps in the latest version...

pgunn commented 4 months ago

I'll file an issue with peakutils; in the meantime we may need to pin scipy in the next release.

pgunn commented 4 months ago

Actually, looks like there's already an issue filed - https://bitbucket.org/lucashnegri/peakutils/issues/117/not-compatible-with-scipy-114

Looks like peakutils 1.3.5 has the fix (cut 3 days ago) but they haven't yet finished the whole release. If this isn't fixed early next week I'll cut a minor release to add max-version pins (although maybe min-version-pins are the right thing to do after the peakutils maintainers finish).

pgunn commented 4 months ago

peakutils 1.3.5 is out; new installs should not run into this issue. I'll add a minimum version pin and then close the issue.

pgunn commented 4 months ago

This is now loosely fixed (still possible someone gets an old peakutils depending on their solver, but most users should get 1.3.5 with new environment builds), and I made the changes both in-repo and on the feedstock to have a hard min-version-pin; the latter will go out with the next release.

Closing.