[joss] More clarity on (optional) dependencies

[szhorvat]

I followed the installation instructions in https://hypernetx.readthedocs.io/en/latest/install.html and installed into a new virtual environment from PyPI using pip install hypernetx. When I load the package, the following message is shown:

>>> import hypernetx
 No module named 'igraph'. If you need to use hypernetx.algorithms.hypergraph_modularity, please install additional packages by running the following command: pip install .['all']

This is not an ideal user experience, and is likely confusing to some new users. They may be wondering: "Did I install correctly? Will some essential functionality not be working?"

I suggest:

• Include more information in the documentation about what dependencies are requires for significant submodules
• Since most people install from PyPI, include instructions on how install all optional dependencies with a single command
• The warning message on package load gives instructions which only work when installing from sources. This is not user friendly. Most people would install from PyPI
• Would it make sense to issue this warning only when people actually try to use hypernetx.algorithms.hypergraph_modularity instead of on package load? This is a more common practice.

Ref: https://github.com/openjournals/joss-reviews/issues/6016

[bonicim]

Resolved in release 2.14

[szhorvat]

Is pip install hypenetx['all'] something that should be suggested?

[bonicim]

pip install hypenetx['all'] installs Jupyter, allowing the user to open one of the tutorials in the repo; it also installs the dependencies needed for the contagion and modularity sub-modules. The documentation recommends this.

[szhorvat]

Could you please clarify where the documentation mentions this command? I can only see pip install -e .['all'] in the section about installing from source.

My impression was that the target audience of this library is not just developers, but mainly researchers. I expect most of them won't want to install from source and won't necessarily notice that pip install hypenetx['all'] is also a valid command.

[bonicim]

I see your point about the target audience being researchers. I will update the installing from PyPi instructions to include a snippet about pip install hypernetx['all']

[bonicim]

Have just updated installation steps on the docs: https://hypernetx.readthedocs.io/en/latest/install.html#id1