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@pgunn pgunn released this 15 Jan 02:09
· 1 commit to main since this release
v1.11.4
02cbba6
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This release has three major install changes:

  • Because of license changes with the main/defaults channel on conda, we now suggest users use the miniforge conda distro, which defaults to conda-forge rather than defaults/main
  • On Windows, because tensorflow is not nicely packaged for that platform on conda-forge, we document an alternative install path
  • We are ready to begin supporting pip installs of caiman again after a many-years hiatus; pip-based installs are still more difficult than the prebuilt packages, being easiest on Linux, slightly more difficult on OSX, and fairly difficult on Windows. It may take us some time to get fully up to speed on pip again, and we still (for now) recommend users use conda if possible

Other changes:

  • Caiman Central is deprecated (too much effort to maintain it) and is no longer mentioned in the readme
  • Fixed some bad formatting in the contributors document and ensured intended people got credit
  • We now recommend "jupyter lab" rather than "jupyter notebook" for our notebooks; this provides a slightly newer interface
  • Fixes to online CNMF (some codepaths had unbound variable errors, correlation images also no longer fail validation if they contain NaNs), thanks to @ethanbb
  • Better handling of sparce matrices, thanks to @ethanbb
  • Better memory handling in motion correction, thanks to @deMalmazet
  • Better handling of sparce matrices and related code with certain option flag permutations, thanks to @proektlab
  • Some docs fixes
  • Moved pip-based dependencies into pyproject.toml to better support alternative packaging tools
  • Removed skcuda and some dead code from the motion correction pipeline
  • load_memmap and related functions now support .npy files as well, thanks to @fdeguire03
  • Numerous fixes to tile_and_correct and shifts code, thanks to @ethanbb
  • Threaded an ability to adjust the l1_ratio used by sparse nmf (previously hardcoded but something we adjusted in a past release) in CNMF params
  • Changed default loglevel for most notebooks to be at least logging.WARNING rather than logging.info, and also downgraded some particularly noisy and low-value messages from logging.INFO to logging.DEBUG; together these changes should make the notebooks less likely to fill with non-useful messages

Contributors

ethanbb, deMalmazet, and 2 other contributors
Assets 2
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