Accelerate yacht train

[chunyuma]

This PR is created to integrate Mahmudur's new algorithm and post-processing method written with cpp script to accelerate yacht train

We need to do the following tasks:

• add the cpp scripts into the branch (under ./yacht/cpp_scripts) @mahmudhera.
• modify related scripts for integrating these cpp scripts in YACHT @chunyuma
• create a makefile and other related scripts for pre-processing @mahmudhera @chunyuma
• modify some tests @chunyuma
• integrate into the main branch

[mahmudhera]

Hi @chunyuma, as this is now implemented in KoslickiLab/fast_yacht_train#3, do I still need to add the cpp code in the repository? Also, it looks like some code duplication has blocked this PR. What are your plans on this? Do you want me to take some things off your plate?

[chunyuma]

No worries @mahmudhera. I can handle the rest. I have added your cpp scripts to YACHT and they looks good. I just need a few more tests.

[mahmudhera]

Excellent, LMK if I can help.

[codecov]

Codecov Report

Attention: Patch coverage is 62.26415% with 20 lines in your changes missing coverage. Please review.

Project coverage is 83.44%. Comparing base (be99fe4) to head (4f09e53).
Report is 27 commits behind head on main.

Files with missing lines	Patch %	Lines
src/yacht/utils.py	59.18%	20 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #125      +/-   ##
==========================================
- Coverage   85.18%   83.44%   -1.75%     
==========================================
  Files          11       11              
  Lines        1080     1081       +1     
==========================================
- Hits          920      902      -18     
- Misses        160      179      +19     

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[mahmudhera]

Hello @chunyuma I see some tests blocking the merge. Do you want me to work on any of these?

[chunyuma]

Thank @mahmudhera, it is not a block but the merging needs at least 1 approving review. The code has passed all tests now. But there are some problems about conda install I need to figure out before merging. I will let you know when it is done.

[mahmudhera]

LGTM, but cautiously waiting for @dkoslicki to approve.

[dkoslicki]

From what I can see, this looks good to me. @chunyuma LMK when the conda issue is resolved and you or I can merge this in

[sonarqubecloud]

Quality Gate passed

Issues
12 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud