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BioJulia / Bio.jl

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
http://biojulia.dev
MIT License
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CI failure #476

Closed bicycle1885 closed 7 years ago

bicycle1885 commented 7 years ago

See https://github.com/BioJulia/Bio.jl/pull/468. I think we should make it work soon.

TransGirlCodes commented 7 years ago

There are two options here, A). Fix the tests and fiddle with Bio.Align, or B). Go ahead and remove Bio.Align and replace with BioAlignments, which presumably will also make the CI failure go away.

bicycle1885 commented 7 years ago

I'm not sure why Bio.Align is related to the problem.

TransGirlCodes commented 7 years ago 
Test Summary:               | Pass  Error  Total
  PairwiseAlignment         |  206      1    207
  SubstitutionMatrix        |   22            22
  AffineGapScoreModel       |   21            21
  CostModel                 |    9             9
  Alignment                 |    5             5
  count_<ops>               |    5             5
  Interfaces                |    8             8
  GlobalAlignment           |   55            55
  SemiGlobalAlignment       |   12            12
  OverlapAlignment          |   15            15
  LocalAlignment            |   18      1     19
  zero matching score       |   11            11
  positive matching score   |    7      1      8
   complete match           |    3             3
   partial match            |    3      1      4
   no match                 |    1             1
  EditDistance              |   22            22
  LevenshteinDistance       |    2             2
  HammingDistance           |   12            12

Because the tests that are erroring are currently in Bio.Align. So we can either fix them, or go ahead with replacing Bio.Align with BioAlignments as planned, which makes the CI failure moot.

bicycle1885 commented 7 years ago

Is that due to https://github.com/BioJulia/Bio.jl/pull/468#issuecomment-310861132? If so, the easiest fix is just restoring whitespaces in tests.

bicycle1885 commented 7 years ago

Now restored by #482.