Using BioMASS without Graphviz

[himoto]

Discussed in #158

^{Originally posted by himoto July 23, 2022}
BioMass requires users to manually install Graphviz for graph visualization but some packages derived from biomass, e.g., pasmpy, do not need it. Currently if we run import biomass without Graphviz, it will raise an ImportError.
I would like to make this optional so that biomass-derived packages can be run without error even if Graphviz is not installed.

Ideas:

• Move pygraphviz and pyvis from requirements.txt to extras_require in setup.py
• Modify graph.py as follows:

def to_graph(self):
    try:
        import pygraphviz as pgv
    except ImportError:
        print("pygraphviz is required to run this function.")
    ...

def dynamic_plot(self, ...):
    try:
        from pyvis.network import Network
    except ImportError:
        print("pyvis is required to run this function.")

@formersbach
I would be grateful if you could give me comments on this. I have a branch working on this and if it's ok, I will send a PR.

[formersbach]

I agree with the changes!
Have you checked whether import pygraphviz raises an ImportError when graphviz is not installed? I suspect it might be able to import pygraphviz, but fail further down the line.

[himoto]

Hi @formersbach, thanks for your reply. I am sorry but I was wrong. When you run import biomass without Graphviz, it will not raise ImportError but show different error message. Please refer to https://github.com/pasmopy/pasmopy/actions/runs/2742861321.

[formersbach]

Hey @himoto, So it already fails during the installation...
I found this code which allows to install a package inside a script:

import subprocess
import sys
def install(package):
    subprocess.check_call([sys.executable, "-m", "pip", "install", package])

We could replace

try:
    import pygraphviz as pgv 

with

try:
    install("pygraphviz") #install being the function defined above
    import pygraphviz

Note that subprocess.check_call will raise a CalledProcessError if installation fails.

[himoto]

@formersbach
Sorry for confusing you but the error message above is raised before updating the code.
It works as I expected after the update.

[formersbach]

Aah I see, I did notice the attached pull request. Changes look good!

P.S.: Why are you working at 3 in the mornign? 😄

[himoto]

Because coding is above sleeping 😆