Setup the environment for lumicks-pylake and C_Trap-Multimer-photontrack.ipynb

https://lumicks-pylake.readthedocs.io/en/v0.8.2/install.html#updating

https://github.com/JamesLiWan/MultimerizationCode/blob/main/C_Trap-Multimer-photontrack.ipynb

1. Fix which pylake we should use for the legacy-code.

   Yep – you’re absolutely right, the channel parameter was added in pylake v0.9.0. If you look at the changelog:
   
   v0.9.0 (Jul 29 2021) introduces unit support and other updates, which also aligns with introducing the channel argument in track_greedy()
   
   Versions before v0.9.0, like v0.8.2 (Apr 30 2021), use the old signature:
   
   track_greedy(kymograph, line_width, pixel_threshold, …)
   with no channel argument.
   
   Since your code uses track_greedy(data, …) without specifying channel, you should install: pylake v0.8.2
   

2. Create mamba environment for pylake v0.8.2

   mamba env remove -n pylake_082_clean
   mamba env create -f pylake_082_env.yml
   
       name: pylake_082_clean
       channels:
       - conda-forge
       - defaults
       dependencies:
       - python=3.8
       - pip
       - jupyterlab
       - ipywidgets
       - numpy
       - matplotlib
       - h5py
       - pandas
       - scipy
   
   mamba activate pylake_082_clean
   
   #IMPORTANT:
   mamba install -c conda-forge lumicks.pylake=0.8.2
   mamba install -c conda-forge  numpy matplotlib ipywidgets scipy scikit-image pandas
   
   python -c "import lumicks.pylake; print(lumicks.pylake.__version__)"
   
   mamba install notebook=6
   
   #+ ipython_genutils    0.2.0  pyhd8ed1ab_1  conda-forge     Cached
   #+ nbclassic           1.1.0  pyhd8ed1ab_0  conda-forge     Cached
   #+ notebook            6.5.7  pyha770c72_0  conda-forge     Cached
   
   #Downgrade:
   #─────────────────────────────────────────────────────────────────────
   
   #- jupyter_client      8.6.3  pyhd8ed1ab_0  conda-forge     Cached
   #+ jupyter_client      7.4.9  pyhd8ed1ab_0  conda-forge     Cached
   
   jupyter notebook --version
   #pip show notebook
   
   (pylake_082_clean) jhuang@WS-2290C:/mnt/md1/DATA/Data_Vero_Kymographs$ mamba list jupyter
   # packages in environment at /home/jhuang/mambaforge/envs/pylake_082_clean:
   #
   # Name                    Version                   Build  Channel
   jupyter-lsp               2.2.5              pyhd8ed1ab_0    conda-forge
   jupyter_client            7.4.9              pyhd8ed1ab_0    conda-forge
   jupyter_core              5.8.1              pyh31011fe_0    conda-forge
   jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
   jupyter_server            2.14.2             pyhd8ed1ab_0    conda-forge
   jupyter_server_terminals  0.5.3              pyhd8ed1ab_0    conda-forge
   jupyterlab                4.3.0              pyhd8ed1ab_0    conda-forge
   jupyterlab_pygments       0.3.0              pyhd8ed1ab_1    conda-forge
   jupyterlab_server         2.27.3             pyhd8ed1ab_0    conda-forge
   jupyterlab_widgets        3.0.13             pyhd8ed1ab_0    conda-forge
   (pylake_082_clean) jhuang@WS-2290C:/mnt/md1/DATA/Data_Vero_Kymographs$ mamba list notebook
   # packages in environment at /home/jhuang/mambaforge/envs/pylake_082_clean:
   #
   # Name                    Version                   Build  Channel
   notebook                  6.5.7              pyha770c72_0    conda-forge
   notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
   
   #Note that Notebook v6.x and Notebook v7 is different, we have to notebook v6 More Detailed Breakdown:
   #Version    Backend Used    Notes
   #Notebook v6.x and below    notebook (classic Tornado-based server) No jupyter_server dependency
   #Notebook v7+   Uses jupyter_server under the hood  Required dependency
   

3. Install extension for the recognization of %%javascript, %matplotlib inline, and %matplotlib notebook

   mamba install widgetsnbextension -c conda-forge
   jupyter nbextension enable --py widgetsnbextension --sys-prefix
   #ModuleNotFoundError: No module named 'ipympl', but we don't need it!    jupyter nbextension enable --py ipympl --sys-prefix
   jupyter nbextension list
   

4. BUG_1: ModuleNotFoundError: No module named 'matplotlib_venn'

   mamba install -c conda-forge matplotlib-venn
   

5. BUG_2: TypeError: init() got an unexpected keyword argument 'drawtype'

   #indicates that your version of Matplotlib is too new, and it no longer supports the drawtype argument in matplotlib.widgets.RectangleSelector. Only <= 3.4.3 supprts drawtype!
   
   mamba list matplotlib
   # packages in environment at /home/jhuang/mambaforge/envs/pylake_082_clean:
   #
   # Name                    Version                   Build  Channel
   #matplotlib                3.7.3            py38h578d9bd_0    conda-forge
   #matplotlib-base           3.7.3            py38h58ed7fa_0    conda-forge
   #matplotlib-inline         0.1.7              pyhd8ed1ab_0    conda-forge
   #matplotlib-venn           1.1.1              pyhd8ed1ab_0    conda-forge
   
   #DEBUG:         # MODIFIED: Delete "drawtype='box'," in kymowidget.py
   self.area_selector = RectangleSelector(self._axes, self.track_kymo,
                                           useblit=True,
                                       button=[3],
                                       minspanx=5, minspany=5,
                                       spancoords='pixels',
                                       interactive=False)
   

6. OPTIONAL_BUG (NOT_DONE): [W 13:13:49.115 NotebookApp] Error loading server extension jupyterlab

   #Traceback (most recent call last):
   #  File "/home/jhuang/mambaforge/envs/pylake_082/lib/python3.8/site-packages/notebook/notebookapp.py", line 2050, in init_server_extensions
   #    func(self)
   #  File "/home/jhuang/mambaforge/envs/pylake_082/lib/python3.8/site-packages/jupyterlab/serverextension.py", line 71, in load_jupyter_server_extension
   #    extension.initialize()
   #  File "/home/jhuang/mambaforge/envs/pylake_082/lib/python3.8/site-packages/jupyterlab/labapp.py", line 921, in initialize
   #    super().initialize()
   #  File "/home/jhuang/mambaforge/envs/pylake_082/lib/python3.8/site-packages/jupyter_server/extension/application.py", line 437, in initialize
   #    self._prepare_handlers()
   #  File "/home/jhuang/mambaforge/envs/pylake_082/lib/python3.8/site-packages/jupyter_server/extension/application.py", line 327, in _prepare_handlers
   #    self.initialize_handlers()
   #  File "/home/jhuang/mambaforge/envs/pylake_082/lib/python3.8/site-packages/jupyterlab/labapp.py", line 735, in initialize_handlers
   #    page_config["token"] = self.serverapp.identity_provider.token
   #AttributeError: 'NotebookApp' object has no attribute 'identity_provider'
   
   jupyter serverextension disable jupyterlab
   mamba remove jupyterlab (or pip uninstall jupyterlab)
   

7. Run notebook on (pylake_082_clean) jhuang@WS-2290C:/mnt/md1/DATA/Data_Vero_Kymographs/MultimerizationCode-main_v082

   (pylake_082_clean) jhuang@WS-2290C:/mnt/md1/DATA/Data_Vero_Kymographs/MultimerizationCode-main_v082$ jupyter notebook
   
   #jupyter notebook --no-browser --port=8888
   

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