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Hotfix/2.2.0 #76

Merged
merged 15 commits into from
Aug 3, 2022
Merged

Hotfix/2.2.0 #76

merged 15 commits into from
Aug 3, 2022

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CiaranOMara
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@CiaranOMara CiaranOMara marked this pull request as draft June 7, 2022 01:17
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codecov bot commented Jun 7, 2022 •
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Codecov Report

Merging #76 (a5bebe8) into master (118c5ad) will decrease coverage by 0.74%.
The diff coverage is 82.08%.

❗ Current head a5bebe8 differs from pull request most recent head 6d96e79. Consider uploading reports for the commit 6d96e79 to get more accurate results

@@            Coverage Diff             @@
##           master      #76      +/-   ##
==========================================
- Coverage   88.82%   88.08%   -0.75%     
==========================================
  Files          17       16       -1     
  Lines        1056     1133      +77     
==========================================
+ Hits          938      998      +60     
- Misses        118      135      +17
Impacted Files Coverage Δ
src/pairwise/result.jl 45.83% <0.00%> (-6.80%) ⬇️
src/alignment.jl 80.46% <77.77%> (-3.32%) ⬇️
src/pairwise/alignment.jl 98.26% <93.75%> (-0.85%) ⬇️
src/alignedseq.jl 97.40% <100.00%> (+0.79%) ⬆️
src/anchors.jl 100.00% <100.00%> (+25.00%) ⬆️
src/operations.jl 87.50% <100.00%> (-2.83%) ⬇️
src/pairwise/algorithms/common.jl 90.62% <100.00%> (+3.66%) ⬆️
src/pairwise/algorithms/hamming_distance.jl 100.00% <100.00%> (ø)
src/submat.jl 98.44% <100.00%> (+0.39%) ⬆️
src/pairwise/algorithms/banded_needleman_wunsch.jl 75.00% <0.00%> (-4.32%) ⬇️
... and 14 more

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@CiaranOMara CiaranOMara mentioned this pull request Jun 7, 2022
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Merge pull request #77 from CiaranOMara/housekeeping
af441d3 
- Backfill CHANGELOG entries.
- Updates CI.
@CiaranOMara
Merge pull request #78 from CiaranOMara/doctests
a5bba8e 
- Include doctests as part of the unit tests.
- Doctest corrections.
@CiaranOMara
Merge pull request #72 from CiaranOMara/develop
25602e1 
- Increments BioSequences compatibility to v3.
- Increments BioSymbols compatibility to v5.
- Updates doctests.
- Drops support for julia less than v1.6.
@CiaranOMara CiaranOMara marked this pull request as ready for review June 8, 2022 15:48
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CiaranOMara commented Jun 8, 2022 •
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I think this is ready for review.

Has anything been missed?

CC: @MillironX, @jakobnissen, @kescobo, @SabrinaJaye

MillironX
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@CiaranOMara CiaranOMara marked this pull request as draft June 8, 2022 22:29
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CiaranOMara commented Jun 8, 2022 •
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I've converted this PR to a draft to get feedback on merging #60 and including it here. I think #60 is potentially the last outstanding non-breaking feature request.

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jakobnissen
jakobnissen approved these changes Jun 15, 2022
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Thank you for this work. I only have minor comments.

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Project.toml
IntervalTrees = "1"
julia = "1"
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Don't we require Julia 1.6? I seem to recall we do for some of our dependencies.

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BioJulia/BioSequences.jl@3c8f501

timholy and others added 5 commits July 2, 2022 09:05
@timholy @CiaranOMara
Add more SubstitutionMatrix operations (#60)
c023a3c 
SubstitutionMatrix is not a subtype of AbstractArray.
This may or may not be intentional, but currently, the number of supported operations is fairly minimal.
This provides a few more conveniences for users who might want to manipulate them beyond mere lookup tables.
@CiaranOMara
Increment version
2f38c3a
@CiaranOMara
CHANGELOG entries
d86d69d
@CiaranOMara @MillironX
Apply suggestions from code review
7414bb4 
Update `CHANGELOG.md` to better reflect the state of the project.

Co-authored-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
@CiaranOMara @jakobnissen
Apply suggestions from code review
6d96e79 
Change type from `Int8` to `UInt8` for efficiency.

Co-authored-by: Jakob Nybo Nissen <jakobnybonissen@gmail.com>
@CiaranOMara CiaranOMara force-pushed the hotfix/2.2.0 branch 2 times, most recently from a5bebe8 to 6d96e79 Compare July 1, 2022 23:55
@CiaranOMara CiaranOMara marked this pull request as ready for review July 1, 2022 23:55
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PR #60 was merged into master and cherry-picked into this branch.

I think this branch is ready for registration, then merging into master. I'll proceed if no comments to the contrary get raised before 9 am on the 7th of July AEST. Alternatively, if I get an "ok" from all involved, I may be able to proceed earlier.

CC: @MillironX, @jakobnissen, @kescobo, @SabrinaJaye

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kescobo commented Jul 2, 2022

I trust your judgement on this. Go forth!

@CiaranOMara CiaranOMara merged commit 782063c into master Aug 3, 2022
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@jakobnissen jakobnissen jakobnissen approved these changes

@MillironX MillironX MillironX approved these changes

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@CiaranOMara @kescobo @jakobnissen @MillironX @JuliaRegistrator @timholy