Closed CiaranOMara closed 2 years ago
Merging #72 (6ecd4b8) into master (4045711) will not change coverage. The diff coverage is
100.00%
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## master #72 +/- ##
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Coverage 87.95% 87.95%
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Files 16 16
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Hits 986 986
Misses 135 135
Impacted Files | Coverage Δ | |
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src/submat.jl | 98.29% <100.00%> (ø) |
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@CiaranOMara I don't see a reason to bump BioAlignments version to 3.0.0, AFAIK, this is not a breaking change. If someone has BioSequences v2 installed, this change will not be breaking, because the Pkg resolver will simply not install this version. Conversely, bumping the major version can cause a bunch of issues for downstream packages that rely on BioAlignments but not BioSequences.
Otherwise LGTM
The code in this PR doesn't appear to warrant a major version, but since v2 of this package, the method signature for the AlignmentAnchor
changed, which warrants the major version change or some sort of patch (reported in #69).
@CiaranOMara Ah, I see. Maybe it's better to revert the breaking change from 2.0.0, since there seem to not be a release that actually includes the change, now that 2.1.0 has been yanked?
Having had another look to get back up to speed, the breaking change of the adition of the alnpos
field to the AlignmentAnchor
struct was merged in #44. My sense is that adding alnpos
is a useful optimisation, though I've not yet done much in this area. The inclusion of the field is at least important to @alyst.
I'm in favour of moving forward, mainly because #44 was the bulk of the work since v2, but on reflection, it would be worth slowing down to address other breaking changes suggested in https://github.com/BioJulia/BioAlignments.jl/pull/44#issuecomment-697350429 before incrementing a major version number.
If moving forward with alnpos
, I think we'd need a few new outer constructors as well as push!
and append!
methods for Alignment
to help with usability by calculating alnpos
as Operation
and their lengths are added, but these would be features.
I've removed the major version increment and have edited the initial comment of this thread to reflect the changes made.
I think this illustrates very well why most people think that fields of structs should be implementation details, and the API instead should only expose accessor functions - but I digress. You're right - we can have a minor version change for now, then later review what breaking changes we want, if any,
You're right - we can have a minor version change for now, then later review what breaking changes we want, if any,
We'd need to branch and set a new master before #44 to take/accept minor changes.
Any progress on this? I'm excited for a new release of BioAlignments, but everything seems to be stuck here. I think this needs to be treated as a hotfix under OneFlow.
git checkout -b hotfix/2.2.0 118c5ad3
git remote add ciaranomara git@github.com:CiaranOMara/BioAlignments.jl.git
git fetch ciaranomara
git cherry-pick c32e7678
...
hotfix/2.2.0
branch to GitHubhotfix/2.2.0
into master
and delete
git merge hotfix/2.2.0 master
git push origin :hotfix/2.2.0
I have done steps 1-4 on my own machine, so I know that works as expected, but everything else needs to be done by someone with write access to the repo.
@MillironX Can you not do 1-5 on a fork and then PR?
I'm happy to take these steps, but don't want to do so until one of @CiaranOMara or @jakobnissen has weighed in
@MillironX Can you not do 1-5 on a fork and then PR?
I can prepare a PR, but it won't have a target (and it won't show up in GitHub) until someone creates the hotfix
branch on this repo.
Oh, I get it.
@MillironX, that is an excellent suggestion; I have drafted the hotfix branch and will invite people to review it in the next few days.
I'll tidy up this PR so that it can be merged. After merging this PR into master, we can neatly cherry-pick it into the hotfix.
I think this is ready for review again.
This PR: