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Implement broadcasting for BioSequences #171

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Types of changes

This PR implements the following changes:
(Please tick any or all of the following that are applicable)

  • ✨ New feature (A non-breaking change which adds functionality).
  • 🐛 Bug fix (A non-breaking change, which fixes an issue).
  • 💥 Breaking change (fix or feature that would cause existing functionality to change).

☑️ Checklist

  • 🎨 The changes implemented is consistent with the julia style guide.
  • 📘 I have updated and added relevant docstrings, in a manner consistent with the documentation styleguide.
  • 📘 I have added or updated relevant user and developer manuals/documentation in docs/src/.
  • 🆗 There are unit tests that cover the code changes I have made.
  • 🆗 The unit tests cover my code changes AND they pass.
  • 📝 I have added an entry to the [UNRELEASED] section of the manually curated CHANGELOG.md file for this repository.
  • 🆗 All changes should be compatible with the latest stable version of Julia.
  • 💭 I have commented liberally for any complex pieces of internal code.

@TransGirlCodes TransGirlCodes changed the base branch from master to v3 July 20, 2021 12:04
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codecov bot commented Jul 20, 2021

Codecov Report

Merging #171 (2865850) into v3 (a8e5b48) will decrease coverage by 0.18%.
The diff coverage is 37.50%.

Impacted file tree graph

@@            Coverage Diff             @@
##               v3     #171      +/-   ##
==========================================
- Coverage   82.16%   81.97%   -0.19%     
==========================================
  Files          31       32       +1     
  Lines        2159     2164       +5     
==========================================
  Hits         1774     1774              
- Misses        385      390       +5     
Flag Coverage Δ
unittests 81.97% <37.50%> (-0.19%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
src/biosequence/seqbroadcast.jl 0.00% <0.00%> (ø)
src/longsequences/indexing.jl 93.54% <ø> (ø)
src/biosequence/biosequence.jl 82.05% <33.33%> (-9.38%) ⬇️
src/biosequence/predicates.jl 98.07% <100.00%> (ø)

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@TransGirlCodes
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@jakobnissen Ok so, because broadcasting is a bit complex, I'm going to properly document every choice I make, and everything I've learned so far about the machinery here, as I make commits.

@TransGirlCodes TransGirlCodes self-assigned this Jul 20, 2021
@TransGirlCodes TransGirlCodes added this to the v3.0.0 milestone Jul 20, 2021
@TransGirlCodes TransGirlCodes linked an issue Jul 20, 2021 that may be closed by this pull request
@jakobnissen
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Looks good! I'll follow from the sidelines :)

@jakobnissen
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If you get to understand how broadcasting works, can you perhaps check this method ambiguity out?

Base.Broadcast.BroadcastStyle(s1::BioSequences.PFMBroadcastStyle, s2::Base.Broadcast.BroadcastStyle) in BioSequences at /home/jakob/code/BioSequences.jl/src/search/pwm.jl:76

vs

Base.Broadcast.BroadcastStyle(::S, ::Base.Broadcast.Unknown) where S<:Base.Broadcast.BroadcastStyle in Base.Broadcast at broadcast.jl:133

Is this a runtime error waiting to happen or is it OK?

@TransGirlCodes TransGirlCodes removed this from the v3.0.0 milestone Oct 12, 2021
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I've cleared this from the v3.0 milestone, we're officially gonna push this back to a version 3.X.

@CiaranOMara CiaranOMara added the v4 Scheduled for v3.X.X to v4. label Dec 31, 2021
@CiaranOMara CiaranOMara added this to the v4.0.0 milestone Dec 31, 2021
@jakobnissen
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Can you rebase this on master? (no rush though)

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Implement broadcasting for biosequences
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