Reaction

[zhu0619]

This PR brings back the reactions module. The reactions/_reactions.py simplified apply_reactions and compute_reaction_product. The reactions/_attachments.py is for attachment point manipulation.

Checklist:

• [ ] Add tests to cover the fixed bug(s) or the new introduced feature(s) (if appropriate).
• [ ] Update the API documentation is a new function is added or an existing one is deleted.
• [ ] Added a news entry.
  • copy news/TEMPLATE.rst to news/my-feature-or-branch.rst) and edit it.
• [ ] Add tutorial.

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Codecov Report

Merging #129 (a5fb1c0) into main (b1bd153) will increase coverage by 6.98%. The diff coverage is 96.20%.

@@            Coverage Diff             @@
##             main     #129      +/-   ##
==========================================
+ Coverage   84.19%   91.17%   +6.98%     
==========================================
  Files          48       46       -2     
  Lines        3569     3208     -361     
==========================================
- Hits         3005     2925      -80     
+ Misses        564      283     -281     

Flag	Coverage Δ
unittests	91.17% <96.20%> (+6.98%)	:arrow_up:

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Impacted Files	Coverage Δ
datamol/graph.py	97.41% <ø> (ø)
datamol/utils/jobs.py	97.39% <ø> (ø)
datamol/viz/_circle_grid.py	78.30% <66.66%> (+0.41%)	:arrow_up:
datamol/_version.py	76.92% <76.92%> (-23.08%)	:arrow_down:
datamol/fragment/_assemble.py	72.40% <77.77%> (+0.19%)	:arrow_up:
datamol/scaffold/_fuzzy.py	88.35% <90.90%> (+0.76%)	:arrow_up:
datamol/reactions/_attachments.py	97.82% <97.82%> (ø)
datamol/align.py	100.00% <100.00%> (ø)
datamol/cluster.py	89.36% <100.00%> (+0.11%)	:arrow_up:
datamol/conformers/_conformers.py	93.16% <100.00%> (ø)
... and 20 more

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[hadim]

Thanks Lu. I'll review it today.

Please be careful next time about starting from an up-to-date main branch to prevent committing many old and unrelated files.

[hadim]

@zhu0619 and @maclandrol: I am done here if you want to review it again.

@zhu0619 : I have made some API modifications. Can you check whether your code still work with this PR? If not then we can discuss whether it's best to change back the API or modify your code.