Add PyPi publishing to kegg-pathways-completeness

[chrisAta]

I have added everything needed to make this tool publishable on PyPi. I added aliases for four scripts, including the two important ones give_pathways.py and plot_completeness_graphs.py, but also the scripts needed for generating an hmmtable since those would probably get used in future pipelines.

I haven't published the package to PyPi yet, but I built it locally and installed it from the wheel and it works fine as is. Let me know if anything else should be added (more aliases?) or vice versa if some of these wouldn't get used and can be removed. Once this PR is merged I'll publish it for the first time.

[mberacochea]

I did a quick review, the code looks sensible to me. We need to format the code with black before the release.

[mberacochea]

If we want to support python < 3.10 we need to change the networkx version:

 ERROR: Could not find a version that satisfies the requirement networkx==3.3 (from kegg-pathways-completeness) (from versions: 0.34, 0.35, 0.35.1, 0.36, 0.37, 0.99, 1.0rc1, 1.0, 1.0.1, 1.1, 1.2rc1, 1.2, 1.3rc1, 1.3, 1.4rc1, 1.4, 1.5rc1, 1.5, 1.6rc1, 1.6, 1.7rc1, 1.7, 1.8rc1, 1.8, 1.8.1, 1.9rc1, 1.9, 1.9.1, 1.10rc2, 1.10, 1.11rc1, 1.11rc2, 1.11, 2.0, 2.1, 2.2rc1, 2.2, 2.3rc3, 2.3rc4, 2.3, 2.4rc1, 2.4rc2, 2.4, 2.5rc1, 2.5, 2.5.1, 2.6rc1, 2.6rc2, 2.6.2, 2.6.3, 2.7rc1, 2.7, 2.7.1, 2.8rc1, 2.8, 2.8.1rc1, 2.8.1, 2.8.2, 2.8.3, 2.8.4, 2.8.5, 2.8.6, 2.8.7, 2.8.8, 3.0b1, 3.0rc1, 3.0, 3.1rc0, 3.1, 3.2rc0, 3.2, 3.2.1)

[chrisAta]

If we want to support python < 3.10 we need to change the networkx version:

 ERROR: Could not find a version that satisfies the requirement networkx==3.3 (from kegg-pathways-completeness) (from versions: 0.34, 0.35, 0.35.1, 0.36, 0.37, 0.99, 1.0rc1, 1.0, 1.0.1, 1.1, 1.2rc1, 1.2, 1.3rc1, 1.3, 1.4rc1, 1.4, 1.5rc1, 1.5, 1.6rc1, 1.6, 1.7rc1, 1.7, 1.8rc1, 1.8, 1.8.1, 1.9rc1, 1.9, 1.9.1, 1.10rc2, 1.10, 1.11rc1, 1.11rc2, 1.11, 2.0, 2.1, 2.2rc1, 2.2, 2.3rc3, 2.3rc4, 2.3, 2.4rc1, 2.4rc2, 2.4, 2.5rc1, 2.5, 2.5.1, 2.6rc1, 2.6rc2, 2.6.2, 2.6.3, 2.7rc1, 2.7, 2.7.1, 2.8rc1, 2.8, 2.8.1rc1, 2.8.1, 2.8.2, 2.8.3, 2.8.4, 2.8.5, 2.8.6, 2.8.7, 2.8.8, 3.0b1, 3.0rc1, 3.0, 3.1rc0, 3.1, 3.2rc0, 3.2, 3.2.1)

End of life for python 3.9 is september 2025, so a little over a year, worth it?