New align + news descriptors + some cleaning

[hadim]

Checklist:

• [x] 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.
• [x] Added a news entry.
  • copy news/TEMPLATE.rst to news/my-feature-or-branch.rst) and edit it.

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I still need to add the new align code.

[codecov[bot]]

Codecov Report

Merging #93 (88fd48d) into main (85e36ba) will increase coverage by 1.21%. The diff coverage is 98.46%.

@@            Coverage Diff             @@
##             main      #93      +/-   ##
==========================================
+ Coverage   82.49%   83.71%   +1.21%     
==========================================
  Files          46       48       +2     
  Lines        3176     3420     +244     
==========================================
+ Hits         2620     2863     +243     
- Misses        556      557       +1     

Flag	Coverage Δ
unittests	83.71% <98.46%> (+1.21%)	:arrow_up:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
datamol/fp.py	84.50% <ø> (ø)
datamol/utils/jobs.py	100.00% <ø> (ø)
datamol/viz/utils.py	80.00% <ø> (-6.67%)	:arrow_down:
datamol/io.py	88.88% <75.00%> (+0.13%)	:arrow_up:
datamol/data.py	92.59% <90.90%> (-7.41%)	:arrow_down:
datamol/descriptors/descriptors.py	96.77% <91.30%> (-3.23%)	:arrow_down:
datamol/convert.py	92.65% <94.11%> (+0.08%)	:arrow_up:
datamol/__init__.py	100.00% <100.00%> (ø)
datamol/_version.py	100.00% <100.00%> (ø)
datamol/align.py	100.00% <100.00%> (ø)
... and 6 more

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[hadim]

It seems like a long PR but most of it is about adding Optional[] and types cleaning. New things are essentially the descriptors and the new align module + tests.

[hadim]

@MichelML putting you in review FYI. This PR contains code for aligning molecules. The API is essentially the same as Manu's gist. Feel free to use it kernel side.

[hadim]

In short you can simply do:

import datamol as dm

# get a list molecules
mols = dm.cdk2(as_df=False)

# align them if needed
if dm.align.should_align(mols):
    aligned_mols = dm.align.auto_align_many(mols)

[MichelML]

Very nice, once this is release I'll replace my copy-paste of Manu's code too, currently working on alignment on upload

(I like the API)

[hadim]

Thanks!