Feature/improve speed and limit memory (#11)

[sambenfredj]

Improve speed and limit memory consumption

• stream input files for inference
• add feature: skip deduplication
• add feature: ensemble model
• add feature: rescale input before inference with pre-trained models

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 89.75469% with 71 lines in your changes missing coverage. Please review.

Project coverage is 83.21%. Comparing base (da2d545) to head (6726dea). Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
mokapot/confidence.py	88.10%	22 Missing :warning:
mokapot/dataset.py	87.15%	14 Missing :warning:
mokapot/mokapot.py	71.87%	9 Missing :warning:
mokapot/model.py	70.37%	8 Missing :warning:
mokapot/parsers/pin.py	90.69%	8 Missing :warning:
mokapot/aggregatePsmsToPeptides.py	89.28%	6 Missing :warning:
mokapot/brew.py	97.32%	3 Missing :warning:
mokapot/utils.py	98.63%	1 Missing :warning:

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #100      +/-   ##
==========================================
- Coverage   85.36%   83.21%   -2.15%     
==========================================
  Files          19       21       +2     
  Lines        1640     2032     +392     
==========================================
+ Hits         1400     1691     +291     
- Misses        240      341     +101     

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[gessulat]

Thanks @sambenfredj for taking care of the tests! Samia replaced some function working on data in-memory with streaming-based counterparts. Some of the "old" functions are still in the code base, but not used and the tests were removed, while the new functions should be covered. This still leads to the regressions reported by codecov.

We didn't want to remove the "old" functions just yet, before you have a look and are happy with the changes @wfondrie 😄

[jspaezp]

https://github.com/wfondrie/mokapot/pull/119 <- changes added here