Running the TheisInference notebook on fresh installation results in error

[Martin Modrák]

• Installed MUQ via conda into a fresh python3 environment.

When running the cell with

graph.Visualize('PosteriorGraph_Step1.png')
Image('PosteriorGraph_Step1.png')

I get:

‌

sh: 1: dot: not found

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
~/miniconda3/envs/muq/lib/python3.9/site-packages/IPython/core/display.py in _data_and_metadata(self, always_both)
   1299         try:
-> 1300             b64_data = b2a_base64(self.data).decode('ascii')
   1301         except TypeError:

TypeError: a bytes-like object is required, not 'str'

During handling of the above exception, another exception occurred:

FileNotFoundError                         Traceback (most recent call last)
~/miniconda3/envs/muq/lib/python3.9/site-packages/IPython/core/formatters.py in __call__(self, obj, include, exclude)
    968 
    969             if method is not None:
--> 970                 return method(include=include, exclude=exclude)
    971             return None
    972         else:

~/miniconda3/envs/muq/lib/python3.9/site-packages/IPython/core/display.py in _repr_mimebundle_(self, include, exclude)
   1288         if self.embed:
   1289             mimetype = self._mimetype
-> 1290             data, metadata = self._data_and_metadata(always_both=True)
   1291             if metadata:
   1292                 metadata = {mimetype: metadata}

~/miniconda3/envs/muq/lib/python3.9/site-packages/IPython/core/display.py in _data_and_metadata(self, always_both)
   1300             b64_data = b2a_base64(self.data).decode('ascii')
   1301         except TypeError:
-> 1302             raise FileNotFoundError(
   1303                 "No such file or directory: '%s'" % (self.data))
   1304         md = {}

FileNotFoundError: No such file or directory: 'PosteriorGraph_Step1.png'

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
~/miniconda3/envs/muq/lib/python3.9/site-packages/IPython/core/display.py in _data_and_metadata(self, always_both)
   1299         try:
-> 1300             b64_data = b2a_base64(self.data).decode('ascii')
   1301         except TypeError:

TypeError: a bytes-like object is required, not 'str'

During handling of the above exception, another exception occurred:

FileNotFoundError                         Traceback (most recent call last)
~/miniconda3/envs/muq/lib/python3.9/site-packages/IPython/core/formatters.py in __call__(self, obj)
    343             method = get_real_method(obj, self.print_method)
    344             if method is not None:
--> 345                 return method()
    346             return None
    347         else:

~/miniconda3/envs/muq/lib/python3.9/site-packages/IPython/core/display.py in _repr_png_(self)
   1318     def _repr_png_(self):
   1319         if self.embed and self.format == self._FMT_PNG:
-> 1320             return self._data_and_metadata()
   1321 
   1322     def _repr_jpeg_(self):

~/miniconda3/envs/muq/lib/python3.9/site-packages/IPython/core/display.py in _data_and_metadata(self, always_both)
   1300             b64_data = b2a_base64(self.data).decode('ascii')
   1301         except TypeError:
-> 1302             raise FileNotFoundError(
   1303                 "No such file or directory: '%s'" % (self.data))
   1304         md = {}

FileNotFoundError: No such file or directory: 'PosteriorGraph_Step1.png'

The error does not seem to affect computation (which runs without problems), just the visualisation.

[Matthew Parno]

This is an issue that arises when graphviz is not installed. It doesn’t impact any computations, it just won’t create the PosteriorGraph_Step.png file. However, I think we should make sure that graphviz is installed with the MUQ conda package. I will work on updating our conda recipe to make sure graphviz is installed.

This is related to Issue 17.