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MouseLand / suite2p

cell detection in calcium imaging recordings
http://www.suite2p.org
GNU General Public License v3.0
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Update installation instructions for Macs, min version of rastermap #1009

Closed rly closed 1 year ago

rly commented 1 year ago

  1. By setting the env var CONDA_SUBDIR=osx-64, I think that using iTerm with Rosetta is no longer needed. Without it, I was able to pip install "suite2p[all]" on my Mac M1 and run it with images in an h5 file (an nwb file) just fine. So I simplified the instructions for Mac M1 machines.

  2. I reverted the note about scanimage-tiff-reader mac incompatibility. The latest release 1.4.1.4 adds support for Mac M1. See https://gitlab.com/vidriotech/scanimagetiffreader-python/-/commit/9f4de14aa3186b0643608c5d203890f2ca1a8172 . I don't know if there was a separate issue with non-M1 macs, but I could install suite2p on both a Mac with Apple Silicon and one with an Intel processor. Fix #981.

  3. I updated the minimum version of rastermap to one that supports from rastermap.rastermap import Rastermap

  4. My editor removes trailing spaces at the end of lines automatically...

codecov[bot] commented 1 year ago

Codecov Report

Merging #1009 (3c7e11d) into main (9ab4ca1) will not change coverage. The diff coverage is n/a.

@@           Coverage Diff           @@
##             main    #1009   +/-   ##
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  Coverage   58.52%   58.52%           
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  Files          40       40           
  Lines        4567     4567           
=======================================
  Hits         2673     2673           
  Misses       1894     1894
rly commented 1 year ago

Just to add - pyqt6 has released wheels for all mac os machines. I believe the reason why CONDA_SUBDIR=osx-64 has to be added to the instructions for Mac arm64 machines is that without it, pyqt5 would need to be built for arm64 from source, which is not straightforward. If suite2p were updated to use pyqt6, then I think having separate instructions for Mac x86 and Mac arm64 will no longer be necessary.

carsen-stringer commented 1 year ago

thanks! we've upgraded now to qtpy with pyqt6 support. I don't have a mac M1/M2 to test but hopefully it works more easily now

rly commented 1 year ago

Yep, I can install the latest on my mac M1 with the updated instructions now. Thanks!