BioJulia / Kmers.jl

In development: Kmer types and methods for julia
MIT License
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Fix iterator constructor and other failing tests #32

Closed cjprybol closed 1 year ago

cjprybol commented 1 year ago

Fixes https://github.com/BioJulia/Kmers.jl/issues/33 but depends on https://github.com/BioJulia/BioSequences.jl/pull/271 in order to pass all tests

$ julia runtests.jl 
Test Summary:          | Pass  Total
BioSequences Interface |    8      8
Test Summary:                | Pass  Total
Construction and Conversions |  260    260
Test Summary: | Pass  Total
Comparisons   |   86     86
Test Summary: | Pass  Total
Length        |   15     15
Test Summary:         | Pass  Total
Access and Iterations |   57     57
Test Summary: |  Pass  Total
Random        | 12448  12448
Test Summary: | Pass  Total
Find          |   33     33
Test Summary: | Pass  Total
Print         |    5      5
Test Summary: | Pass  Total
Show          |    5      5
Test Summary:   | Pass  Total
Transformations | 3848   3848
Test Summary: | Pass  Total
Mismatches    | 3200   3200
Test Summary: | Pass  Total
Matches       | 3200   3200
Test Summary:       | Pass  Total
De Bruijn Neighbors |    4      4
Test Summary: | Pass  Total
EveryKmer     |   14     14
Test Summary: | Pass  Total
SpacedKmers   |   14     14
Test Summary:      | Pass  Total
EveryCanonicalKmer |   18     18
Test Summary:        | Pass  Total
SpacedCanonicalKmers |   26     26
Test Summary: | Pass  Total
Translation   |   39     39
Test Summary: | Pass  Total
CodonSet      |  241    241
Test Summary:       | Pass  Total
Reverse translation |  148    148
cjprybol commented 1 year ago

Rad, thanks for all the help with this package.!

Glad to help, thanks for the assistance with the PRs!

To be clear - it looks like the dependency you referenced at the beginning has been merged - is there a release of BioSequences that includes it yet? Once it is, this PR should include an update to the [compat] section of Project.toml.

I don't see a new release yet but happy to update the compat once one is available

kescobo commented 1 year ago

@jakobnissen is there something holding back a release of BioSequences with https://github.com/BioJulia/BioSequences.jl/pull/271 ? I'm happy to do it, but wanted to double check.

jakobnissen commented 1 year ago

Nope, please do cut a release. Also nice to get the other changes since last release. They're all bugfixes, so it can be a patch release, 3.1.3.

kescobo commented 1 year ago

https://github.com/JuliaRegistries/General/pull/79281

@cjprybol Once that gets merged, I think bump the compat entry, which should also re-run the tests, and then I think it will be good to go

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 100.00% and project coverage change: +0.23 :tada:

Comparison is base (f7a1328) 87.43% compared to head (7febcd0) 87.67%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #32 +/- ## ========================================== + Coverage 87.43% 87.67% +0.23% ========================================== Files 13 13 Lines 581 584 +3 ========================================== + Hits 508 512 +4 + Misses 73 72 -1 ``` | Flag | Coverage Δ | | |---|---|---| | unittests | `87.67% <100.00%> (+0.23%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://codecov.io/gh/BioJulia/Kmers.jl/pull/32?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia) | Coverage Δ | | |---|---|---| | [src/revtrans.jl](https://codecov.io/gh/BioJulia/Kmers.jl/pull/32?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL3JldnRyYW5zLmps) | `100.00% <ø> (+1.92%)` | :arrow_up: | | [src/kmer.jl](https://codecov.io/gh/BioJulia/Kmers.jl/pull/32?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL2ttZXIuamw=) | `79.88% <100.00%> (+0.23%)` | :arrow_up: | ... and [5 files with indirect coverage changes](https://codecov.io/gh/BioJulia/Kmers.jl/pull/32/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia) Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia)

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cjprybol commented 1 year ago

Thanks for finishing this off @SabrinaJaye, and thanks for the helpful reviews @kescobo!