Notebook Testing Issues

[bnmajor]

We will need to add testing for the example notebooks, but there are a few issues that need to be resolved in order to do so:

• [ ] When running a test (for example: pytest --nbmake examples/NumPyArrayPointSet.ipynb) we get the following error (full error below):

  ========================================= short test summary info =========================================
  FAILED examples/NumPyArrayPointSet.ipynb:: - AttributeError: 'NoneType' object has no attribute 'group'
  
  

• [ ] Due to the asynchronous nature of loading the viewer, sequential cells that rely on the viewer are called before the viewer has completely loaded, which will cause them to fail.

[bnmajor]

Full error output:

================================================================================================= FAILURES ==================================================================================================
________________________________________________________________ /home/local/KHQ/brianna.major/itkwidgets/examples/NumPyArrayPointSet.ipynb _________________________________________________________________
---------------------------------------------------------------------------
import numpy as np
from itkwidgets import view
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Input In [2], in <cell line: 2>()
      1 import numpy as np
----> 2 from itkwidgets import view

File ~/itkwidgets/itkwidgets/__init__.py:6, in <module>
      3 __version__ = "1.0a6"
      5 from imjoy_rpc import register_default_codecs
----> 6 register_default_codecs()
      8 from .imjoy import register_itkwasm_imjoy_codecs
      9 register_itkwasm_imjoy_codecs()

File ~/.virtualenvs/test-itkwidgets/lib/python3.8/site-packages/imjoy_rpc/utils.py:347, in register_default_codecs(options)
    344 if options is None or "zarr-array" in options:
    345     import zarr
--> 347     api.registerCodec(
    348         {"name": "zarr-array", "type": zarr.Array, "encoder": encode_zarr_store}
    349     )
    351 if options is None or "zarr-group" in options:
    352     import zarr

File ~/.virtualenvs/test-itkwidgets/lib/python3.8/site-packages/imjoy_rpc/werkzeug/local.py:349, in LocalProxy.__getattr__(self, name)
    347 if name == "__members__":
    348     return dir(self._get_current_object())
--> 349 return getattr(self._get_current_object(), name)

File ~/.virtualenvs/test-itkwidgets/lib/python3.8/site-packages/imjoy_rpc/__init__.py:46, in ApiWrapper.__getattr__(self, attr)
     44 if not self.__initialized:
     45     connection_type = os.environ.get("IMJOY_RPC_CONNECTION") or type_of_script()
---> 46     setup_connection(_rpc_context, connection_type, logger)
     47     self.__initialized = True
     48 return _rpc_context.api[attr]

File ~/.virtualenvs/test-itkwidgets/lib/python3.8/site-packages/imjoy_rpc/utils.py:501, in setup_connection(_rpc_context, connection_type, logger, on_ready_callback, on_error_callback)
    498     logger.info("Using jupyter connection for imjoy-rpc")
    499 from .connection.jupyter_connection import JupyterCommManager
--> 501 manager = JupyterCommManager(_rpc_context)
    502 _rpc_context.api = dotdict(
    503     init=manager.init,
    504     export=manager.set_interface,
    505     registerCodec=manager.register_codec,
    506     register_codec=manager.register_codec,
    507 )
    508 manager.start(
    509     on_ready_callback=on_ready_callback, on_error_callback=on_error_callback
    510 )

File ~/.virtualenvs/test-itkwidgets/lib/python3.8/site-packages/imjoy_rpc/connection/jupyter_connection.py:32, in JupyterCommManager.__init__(self, rpc_context)
     30 self.rpc_context = rpc_context
     31 self._codecs = {}
---> 32 self.kernel_id = re.search(
     33     "kernel-(.*).json", ipykernel.connect.get_connection_file()
     34 ).group(1)
     35 # for loading plugin from source code,
     36 # we can benifit from the syntax highlighting for HTML()
     37 self.register_codec({"name": "HTML", "type": HTML, "encoder": lambda x: x.data})

AttributeError: 'NoneType' object has no attribute 'group'

It seems that the kernel is not being found, although it's not clear to me at this point why that would be.