Change the default atom mapping in the CLI to Kartograf

[jthorton]

Fixes #1493 by changing the default atom mapper used in the CLI to Kartograf.

Note:

• I added the flag to map hydrogens to hydrogens only, as these are later removed in the protocol anyway, it should make the mapping visualisation clearer as well, and this is planned to be the new default setting in kartograf in the future.

Checklist

• Added a news entry

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.20%. Comparing base (2d3af6a) to head (aeb26c8).
⚠️ Report is 11 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1530      +/-   ##
==========================================
- Coverage   95.25%   93.20%   -2.05%     
==========================================
  Files         172      172              
  Lines       14482    14487       +5     
==========================================
- Hits        13795    13503     -292     
- Misses        687      984     +297     

Flag	Coverage Δ
fast-tests	93.20% <100.00%> (?)
slow-tests	?

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[IAlibay]

lgtm on my end, although I'm concerned that no tests failed when you did that 🤔 is there a long test that checks the network generation maybe?

[IAlibay]

Please let @atravitz be the approver here

[jthorton]

We do have a planning test for the CLI, but in this case we are lucky and got the same edges (tyk2 has good alignment and we made the edge order reproducible!), so no test failed. I have added a check for the default settings used in the CLI by matching some info in the output stream. This could be improved in future when we have provenance on the LigandNetwork and AlchemicalNetwork objects.

[mikemhenry]

wow called out

did we decide that this isn't a 2.0 breaking change since we don't promise that the CLI defaults don't change?

[IAlibay]

did we decide that this isn't a 2.0 breaking change since we don't promise that the CLI defaults don't change?

Yeah - board approved it too. We're selling it as "this is what was used in the industry benchmarks".

[atravitz]

LGTM, and I agree with @jthorton about adding more tests once we store this info.

[github-actions]

No API break detected ✅