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Lood/calc weights#319

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thomashopf wants to merge 13 commits intodevelopdebbiemarkslab/EVcouplings:developfrom lood/calc_weightsdebbiemarkslab/EVcouplings:lood/calc_weightsCopy head branch name to clipboard

+423-61

Commits

Commits on Jun 9, 2022

• updating collections.Iterable -> collections.abc.Iterable (since Python 3.3)

  loodvn

  committed
  3693c09

• added parallel numba option, that ignores gaps and doesn't treat them as equal in sequence similarity

  loodvn

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  4f580c1

• updated collections.Mapping -> collections.abc.Mapping too

  loodvn

  committed
  31dfcd6

Commits on Jun 10, 2022

• added choice of weights calc method; renamed legacy method to num_cluster_members_legacy

  loodvn

  committed
  f6ad22c

Commits on Jun 13, 2022

• changed sequence_weight_strategy name to "uniform"

  Show description for 6efc8cf
  loodvn

  committed
  6efc8cf

• added test helper to clean tests up

  loodvn

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  88a2979

• added legacy tests, renamed test_helper as it was getting run as a test itself

  loodvn

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  d13211d

• note to self

  loodvn

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  83e7a3d

Commits on Jun 14, 2022

• changed test threshold to 0.6 to avoid 1-theta confusion

  Show description for d1190fe
  loodvn

  committed
  d1190fe

• added custom weight loading for when we use a file

  loodvn

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  7ca86d3

• moved weights calc out to weights.py, will import from where I end up using it

  loodvn

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  b92d912

Commits on Jun 17, 2022

• moved weights calc out to weights.py, will import from where I end up using it

  Show description for e845714
  loodvn

  committed
  e845714

Commits on Aug 1, 2023

• pinned yaml version

  loodvn

  committed
  5fd1f3a