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Update user manual #160

Merged
merged 14 commits into from
Jun 20, 2021
Merged

Update user manual #160

merged 14 commits into from
Jun 20, 2021

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TransGirlCodes
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@TransGirlCodes TransGirlCodes commented Apr 30, 2021

This PR is to address issue #140

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).
  • πŸ› Bug fix (A non-breaking change, which fixes an issue).
  • πŸ’₯ Breaking change (fix or feature that would cause existing functionality to change).

πŸ“‹ Additional detail

  • Add documentation section on Interfaces.
  • Document Alphabets interface.
  • Document BioSequence interface.
  • Remove "not implemented" errors.
  • Add iscomplete trait to Alphabets interface (see Add trait "iscomplete" to AlphabetΒ #151).
  • Make minimal examples unit tests, and or doctests.

β˜‘οΈ Checklist

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

@TransGirlCodes TransGirlCodes marked this pull request as draft April 30, 2021 16:59
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codecov bot commented Apr 30, 2021

Codecov Report

Merging #160 (418886f) into v3 (9d40795) will not change coverage.
The diff coverage is 100.00%.

Impacted file tree graph

@@           Coverage Diff           @@
##               v3     #160   +/-   ##
=======================================
  Coverage   82.14%   82.14%           
=======================================
  Files          31       31           
  Lines        2156     2156           
=======================================
  Hits         1771     1771           
  Misses        385      385           
Flag Coverage Ξ”
unittests 82.14% <100.00%> (ΓΈ)

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

Impacted Files Coverage Ξ”
src/alphabet.jl 81.66% <ΓΈ> (ΓΈ)
src/biosequence/biosequence.jl 91.42% <ΓΈ> (ΓΈ)
src/biosequence/predicates.jl 98.03% <ΓΈ> (ΓΈ)
src/longsequences/longsequence.jl 100.00% <ΓΈ> (ΓΈ)
src/longsequences/counting.jl 91.30% <100.00%> (ΓΈ)

Continue to review full report at Codecov.

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@TransGirlCodes TransGirlCodes force-pushed the interfaces branch 2 times, most recently from cf701da to 61d708b Compare June 18, 2021 17:43
@TransGirlCodes TransGirlCodes force-pushed the interfaces branch 2 times, most recently from 2dd286e to 7cb114c Compare June 18, 2021 19:19
@TransGirlCodes TransGirlCodes changed the title Refine, Define, Document, Test Interfaces. Update user manual Jun 18, 2021
@TransGirlCodes TransGirlCodes marked this pull request as ready for review June 20, 2021 19:56
@TransGirlCodes TransGirlCodes merged commit 87f806c into v3 Jun 20, 2021
@TransGirlCodes TransGirlCodes deleted the interfaces branch June 20, 2021 20:21
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