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merge DataLinks to MetcalfScoring class #249

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CunliangGeng merged 9 commits into from
Jun 10, 2024
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merge DataLinks to MetcalfScoring class #249

CunliangGeng merged 9 commits into from
Jun 10, 2024

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@CunliangGeng CunliangGeng commented May 31, 2024 •
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The role of class DataLinks is to calculate the presence and co-presence for given e.g. GCFs, spectra and strains. The presence matrix are required to compute the Metcalf scores.

This PR merge the role DataLinks to MetCalfScoring and utils to improve the clarity of codebase and to simplify the scoring process.

DataLinks also has a get_common_strains method that will be merged to ObjectLink class in next PR.

Major changes:

  • move functions of calculating presence to utils
  • merge function of calculating co-presence and raw score to MetcalfScoring
  • remove whole linking folder
  • remove deprecated and unused code

This was referenced May 31, 2024
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CunliangGeng commented May 31, 2024 •
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@CunliangGeng CunliangGeng mentioned this pull request May 31, 2024
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@CunliangGeng CunliangGeng self-assigned this May 31, 2024
@CunliangGeng CunliangGeng requested a review from gcroci2 May 31, 2024 08:58
@CunliangGeng CunliangGeng marked this pull request as ready for review May 31, 2024 08:58
This was referenced May 31, 2024
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@CunliangGeng CunliangGeng force-pushed the merge_LinkFinder_to_MetcalfScoring branch from 3a92298 to 89aa35e Compare June 6, 2024 07:16
@CunliangGeng CunliangGeng force-pushed the merge_DataLinks_to_MetcalfScoring branch from 52960e6 to 7ef55a9 Compare June 6, 2024 07:16
@CunliangGeng CunliangGeng force-pushed the merge_LinkFinder_to_MetcalfScoring branch from 89aa35e to 145bd22 Compare June 6, 2024 07:20
@CunliangGeng CunliangGeng force-pushed the merge_DataLinks_to_MetcalfScoring branch 2 times, most recently from be49128 to abdc779 Compare June 6, 2024 07:24
@CunliangGeng CunliangGeng force-pushed the merge_LinkFinder_to_MetcalfScoring branch from 3974c23 to d13d883 Compare June 6, 2024 07:27
Base automatically changed from merge_LinkFinder_to_MetcalfScoring to dev June 6, 2024 07:29
@CunliangGeng CunliangGeng force-pushed the merge_DataLinks_to_MetcalfScoring branch from abdc779 to 1857d31 Compare June 6, 2024 13:49
@CunliangGeng CunliangGeng mentioned this pull request Jun 7, 2024
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@CunliangGeng CunliangGeng mentioned this pull request Jun 7, 2024
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CunliangGeng commented Jun 10, 2024 •
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@CunliangGeng CunliangGeng merged commit 5ba9e31 into dev Jun 10, 2024
@CunliangGeng CunliangGeng deleted the merge_DataLinks_to_MetcalfScoring branch June 10, 2024 07:25
This was referenced Jun 10, 2024
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@CunliangGeng CunliangGeng mentioned this pull request Jun 18, 2024
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