update notebooks

[clewis7]

align notebooks with fastplotlib changes

#213

[kushalkolar]

@clewis7 can you confirm that these work with latest fpl from pip? There are users searching the docs for the old line slider numerous times so we really need to merge this.

[kushalkolar]

not sure why build failed, might have been an issue in something upstream last month, probably caiman. Did a minor commit to trigger CI.

[kushalkolar]

we are getting the weirdest build failures.

The conda installs don't work becaues mamba is being weird.

linux: https:/nel-lab/mesmerize-core/actions/runs/5988262161/job/16243264758?pr=218

mamba env update -n base --file environment.yml
  caimanmanager.py install
  pip install .
  shell: /usr/bin/bash -e {0}
  env:
    pythonLocation: /opt/hostedtoolcache/Python/[3](https:/nel-lab/mesmerize-core/actions/runs/5988262161/job/16243264758?pr=218#step:6:3).10.12/x6[4](https:/nel-lab/mesmerize-core/actions/runs/5988262161/job/16243264758?pr=218#step:6:4)
    LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.10.12/x64/lib


Looking for: ["caiman[version='>=1.9.10']", "pandas[version='>=1.[5](https:/nel-lab/mesmerize-core/actions/runs/5988262161/job/16243264758?pr=218#step:6:5).0']", 'requests', 'click', 'jupyterlab', 'tqdm', 'psutil']


warning  libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
Could not solve for environment specs
The following packages are incompatible
└─ caiman >=1.9.10  is installable with the potential options
   ├─ caiman [1.9.10|1.9.11|...|1.9.15] would require
   │  └─ python >=3.10,<3.11.0a0 , which can be installed;
   ├─ caiman [1.9.10|1.9.11|...|1.9.15] would require
   │  └─ python >=3.[8](https:/nel-lab/mesmerize-core/actions/runs/5988262161/job/16243264758?pr=218#step:6:8),<3.[9](https:/nel-lab/mesmerize-core/actions/runs/5988262161/job/16243264758?pr=218#step:6:10).0a0 , which can be installed;
   └─ caiman [1.9.[10](https:/nel-lab/mesmerize-core/actions/runs/5988262161/job/16243264758?pr=218#step:6:11)|1.9.[11](https:/nel-lab/mesmerize-core/actions/runs/5988262161/job/16243264758?pr=218#step:6:12)|...|1.9.[15](https:/nel-lab/mesmerize-core/actions/runs/5988262161/job/16243264758?pr=218#step:6:16)] would require
      └─ python >=3.9,<3.10.0a0 , which can be installed.

MacOS: https:/nel-lab/mesmerize-core/actions/runs/5988262158/job/16243264691?pr=218

Run mamba env update -n base --file environment.yml
  mamba env update -n base --file environment.yml
  caimanmanager.py install
  pip install .
  shell: /bin/bash -e {0}
  env:
    pythonLocation: /Users/runner/hostedtoolcache/Python/3.10.1[2](https:/nel-lab/mesmerize-core/actions/runs/5988262158/job/16243264691?pr=218#step:6:2)/x64
Traceback (most recent call last):
  File "/usr/local/miniconda/bin/mamba", line 7, in <module>
    from mamba.mamba import main
  File "/usr/local/miniconda/lib/python[3](https:/nel-lab/mesmerize-core/actions/runs/5988262158/job/16243264691?pr=218#step:6:3).11/site-packages/mamba/mamba.py", line [4](https:/nel-lab/mesmerize-core/actions/runs/5988262158/job/16243264691?pr=218#step:6:4)9, in <module>
    import libmambapy as api
  File "/usr/local/miniconda/lib/python3.11/site-packages/libmambapy/__init__.py", line [7](https:/nel-lab/mesmerize-core/actions/runs/5988262158/job/16243264691?pr=218#step:6:7), in <module>
    raise e
  File "/usr/local/miniconda/lib/python3.[11](https:/nel-lab/mesmerize-core/actions/runs/5988262158/job/16243264691?pr=218#step:6:12)/site-packages/libmambapy/__init__.py", line 4, in <module>
    from libmambapy.bindings import *  # noqa: F401,F403
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ImportError: dlopen(/usr/local/miniconda/lib/python3.11/site-packages/libmambapy/bindings.cpython-311-darwin.so, 0x0002): Library not loaded: '@rpath/libarchive.[13](https:/nel-lab/mesmerize-core/actions/runs/5988262158/job/16243264691?pr=218#step:6:14).dylib'
  Referenced from: '/usr/local/miniconda/lib/libmamba.2.0.0.dylib'
  Reason: tried: '/usr/local/miniconda/lib/libarchive.13.dylib' (no such file), '/usr/local/miniconda/lib/python3.11/site-packages/libmambapy/../../../libarchive.13.dylib' (no such file), '/usr/local/miniconda/lib/python3.11/site-packages/libmambapy/../../../libarchive.13.dylib' (no such file), '/usr/local/miniconda/bin/../lib/libarchive.13.dylib' (no such file), '/usr/local/miniconda/bin/../lib/libarchive.13.dylib' (no such file), '/usr/local/lib/libarchive.13.dylib' (no such file), '/usr/lib/libarchive.13.dylib' (no such file)

The pip install runs, but weird issue with running CNMFE:

https:/nel-lab/mesmerize-core/actions/runs/5988262157/job/16243264692?pr=218#step:7:1541

E           Traceback (most recent call last):
E             File "/home/runner/work/mesmerize-core/mesmerize-core/mesmerize_core/algorithms/cnmfe.py", line 89, in run_algo
E               cnm = cnm.fit(images)
E             File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/caiman/source_extraction/cnmf/cnmf.py", line 594, in fit
E               self.estimates.sn, self.estimates.optional_outputs = run_CNMF_patches(
E             File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/caiman/source_extraction/cnmf/map_reduce.py", line 476, in run_CNMF_patches
E               B_tot = np.array(B_tot, dtype=np.float32)
E           TypeError: float() argument must be a string or a number, not 'coo_matrix'

[clewis7]

I don't know why the build is failing, but the notebooks worked on my end in a fresh environment with latest pip install of fpl, caiman, and mescore

[kushalkolar]

I'm merging this for now, the only changes are nbs so we can fix the build issues later, will track in a new issue.