alyst commented 2 years ago

Update docs with alignment position

This template is rather extensive. Fill out all that you can, if are a new contributor or you're unsure about any section, leave it unchanged and a reviewer will help you :smile:. This template is simply a tool to help everyone remember the BioJulia guidelines, if you feel anything in this template is not relevant, simply delete it.

Types of changes

This PR implements the following changes: No functional changes, just update the documentation with AlignmentAnchor.alnpos introduced by #44. Also serves as a gentle reminder to tag a new minor version, since this anchor functionality is only available in the master branch ;)

[ ] :sparkles: New feature (A non-breaking change which adds functionality).
[ ] :bug: Bug fix (A non-breaking change, which fixes an issue).
[ ] :boom: Breaking change (fix or feature that would cause existing functionality to change).

:clipboard: Additional detail

If you have implemented new features or behaviour
- Provide a description of the addition in as many details as possible.
- Provide justification of the addition.
- Provide a runnable example of use of your addition. This lets reviewers and others try out the feature before it is merged or makes it's way to release.
If you have changed current behaviour...
- Describe the behaviour prior to you changes
- Describe the behaviour after your changes and justify why you have made the changes, Please describe any breakages you anticipate as a result of these changes.
- Does your change alter APIs or existing exposed methods/types? If so, this may cause dependency issues and breakages, so the maintainer will need to consider this when versioning the next release.
- If you are implementing changes that are intended to increase performance, you should provide the results of a simple performance benchmark exercise demonstrating the improvement. Especially if the changes make code less legible.

:ballot_box_with_check: Checklist

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

codecov[bot] commented 2 years ago

Codecov Report

Merging #61 (f0ab859) into master (5a3354e) will increase coverage by 0.31%. The diff coverage is n/a.

@@            Coverage Diff             @@
##           master      #61      +/-   ##
==========================================
+ Coverage   87.64%   87.95%   +0.31%     
==========================================
  Files          16       16              
  Lines        1052     1121      +69     
==========================================
+ Hits          922      986      +64     
- Misses        130      135       +5

Impacted Files	Coverage Δ
src/pairwise/algorithms/banded_needleman_wunsch.jl	`75.00% <0.00%> (-1.36%)`	:arrow_down:
src/pairwise/algorithms/needleman_wunsch.jl	`83.59% <0.00%> (-0.71%)`	:arrow_down:
src/anchors.jl	`100.00% <0.00%> (ø)`
src/pairwise/algorithms/edit_distance.jl	`100.00% <0.00%> (ø)`
src/pairwise/algorithms/hamming_distance.jl	`100.00% <0.00%> (ø)`
src/pairwise/alignment.jl	`98.26% <0.00%> (+0.04%)`	:arrow_up:
src/submat.jl	`98.29% <0.00%> (+0.21%)`	:arrow_up:
src/pairwise/algorithms/common.jl	`90.62% <0.00%> (+0.30%)`	:arrow_up:
src/models.jl	`85.50% <0.00%> (+0.43%)`	:arrow_up:
src/pairwise/algorithms/smith_waterman.jl	`89.00% <0.00%> (+0.45%)`	:arrow_up:
... and 4 more

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TransGirlCodes commented 2 years ago

Thanks @alyst!

alyst commented 2 years ago

Sorry, I've realized that the alignment anchor SVG figure also have to be updated. I'm working on it at the moment.

BioJulia / BioAlignments.jl