v1.13.0

This is a major release, replacing machine-learning parts of Caiman that were written in Tensorflow with Keras/Pytorch implementations. In validating these major changes we've gone through most of the notebooks and made some other improvements along the way. With the packaging changes, the conda releases for Windows should (ideally) resume for the first time in a year, as pytorch is an easier dependency.

Changelog

Workflow:

• A lot of path fixes for the notebooks for temporary/working files
• evaluate_components_CNN() builds path for model_name at runtime rather than parse-time

API Changes:

• The default for add_to_movie is now a small float, fixing a bug (thanks to @ethanbb)
• Reworked tensorflow models into keras/pytorch equivalent, thanks to a lot of hard work from @manuelpaeza ; this does slightly change numeric results from some calls
• Add a reliable marker and method to hdf5 files (from OnACID or CNMF serialisation) so it's easy to tell which code-path a given file came from
• Fix OnACID time-statistics recording so that code that depends on these statistics doesn't need to parse pessimistically (probably only used for time-stats for demo_Ring_CNN)
• Fix another call that depended on the useless return call from cnmf.fit() thanks to @rob-the-bot
• For register_ROIs(), cast Cn to an np.array to avoid np.matrix math semantics

Code Quality:

• Remove some legacy dynamic imports
• More type-compliance for float arguments (some of which default to int values)
• Remove and/or update some ipython magic using an older now-removed syntax

Docs and messages:

• README: Added a reference to Pluvianus, an external Qt6-based result visualiser
• With CNMF class, dont document deprecated constructor arguments
• Fix various typos and better strings
• Adjusted calls to ML code to avoid large amounts of verbose output

Demos:

• Modify most demos to allow for better control over whether videos play and ensure that choosing not to have them play does not skip other parts of the pipeline that are important
• More demos save an hdf5 file so users won't miss the utility of this
• Fixed some windows-specific path-building that crept into some notebooks some time back