Missing dependency: pygraphviz?

[artemiy-dmitriev]

Looks like pygraphviz is required but is not pulled via dependencies during installation (this is on Mac OS):

(finesse3) Artemiis-MacBook-Pro:~ admitriev$ python3
Python 3.8.2 (default, Mar 26 2020, 10:43:30)
[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from simba import transfer_function_to_graph, tf2rss, adiabatically_eliminate
>>> from sympy import symbols
>>> s = symbols('s')
>>> gamma_f, lmbda = symbols('gamma_f lambda', real=True, positive=True)
>>> tf = (s**2 + s * gamma_f - lmbda) / (s**2 - s * gamma_f - lmbda)
>>> transfer_function_to_graph(tf, 'active_coupled_cavity.png', layout='dot')
0
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/admitriev/miniconda3/envs/finesse3/lib/python3.8/site-packages/simba/graph.py", line 266, in transfer_function_to_graph
    g = nodes_from_dofs(*split_system(ss.to_slh())).as_graphviz_agraph()
  File "/Users/admitriev/miniconda3/envs/finesse3/lib/python3.8/site-packages/simba/graph.py", line 113, in as_graphviz_agraph
    import pygraphviz as pgv
ModuleNotFoundError: No module named 'pygraphviz'

Note that on Mac OS installing pygraphviz via pip requires graphviz to be already installed on the system, which can be done via brew or via conda if the latter is being used. I managed to get a working pygraphviz installation via

conda install graphviz
pip install pygraphviz

After doing that, the example code above worked without errors.

[joebentley]

Whoops, I missed this!

requirements.txt and environment.yml both have pygraphviz listed so I'm not sure why it isn't being installed. I'll leave this open