Add Project.toml #31

rasmushenningsson · 2020-08-18T16:26:49Z

Add Project.toml

Types of changes

This PR implements the following changes:

✨ 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).

📋 Additional detail

Updated from old REQUIRE to new Project.toml specification.
Fixed some deprecation warnings.
Updated travis and appveyor to run tests on Julia 1.5.

☑️ 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.

Also fixed deprecation warnings.

codecov · 2020-08-18T16:49:12Z

Codecov Report

Merging #31 into master will increase coverage by 28.48%.
The diff coverage is 33.33%.

@@             Coverage Diff             @@
##           master      #31       +/-   ##
===========================================
+ Coverage   56.33%   84.82%   +28.48%     
===========================================
  Files          14       17        +3     
  Lines        1026     1120       +94     
===========================================
+ Hits          578      950      +372     
+ Misses        448      170      -278

Impacted Files	Coverage Δ
src/GeneticVariation.jl	`100.00% <ø> (ø)`
src/site_counting.jl	`60.86% <33.33%> (+35.86%)`	⬆️
src/distances/proportion.jl	`0.00% <0.00%> (ø)`
src/vcf/vcf.jl	`100.00% <0.00%> (ø)`
src/bcf/bcf.jl	`100.00% <0.00%> (ø)`
src/allele_freq.jl	`94.73% <0.00%> (+1.40%)`	⬆️
src/vcf/header.jl	`96.55% <0.00%> (+8.55%)`	⬆️
src/vcf/writer.jl	`100.00% <0.00%> (+12.50%)`	⬆️
src/vcf/record.jl	`84.78% <0.00%> (+21.40%)`	⬆️
... and 9 more

Continue to review full report at Codecov.

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kescobo

Any idea why there's such a massive coverage hit? Might be something about how coverage is calculated, I think I remember reading about that. In any case, there's nothing here that should affect it, so I don't think that should hold it up.

Just one minor change (add testing for julia 1.0) from me, and, if you have the energy, taking a look at compat bounds (though I'm fine with leaving those as-is until / unless someone complains).

I don't actually have merge rights on this repo, but looks good AFAICT

kescobo · 2020-09-09T20:15:13Z

Project.toml

+IntervalTrees = "524e6230-43b7-53ae-be76-1e9e4d08d11b"
+Twiddle = "7200193e-83a8-5a55-b20d-5d36d44a0795"
+
+[compat]


How sure about these compat bounds are you? I suppose we can just set the bounds to current versions, and then test and relax things if anyone complains.

I've checked and relaxed the compat bounds.
The biggest issue is incompatibility with BioSequences v2. But that requires larger changes and I think that's better to solve in another release. (And a better approach might be to split out a VCF.jl from this package that will simplify the compatibility situation.)

Yeah, fixing that seems outside the scope of this PR.

kescobo · 2020-09-09T20:16:19Z

appveyor.yml

@@ -1,6 +1,6 @@
 environment:
  matrix:
-  - julia_version: 1


If we're going to say it's compatible with 1.0, I think we should test on 1.0.

kescobo · 2020-09-09T20:16:43Z

src/GeneticVariation.jl

@@ -73,11 +73,9 @@ import IntervalTrees: Interval, IntervalValue
 import Twiddle:
    enumerate_nibbles,
    nibble_mask,
-    count_zero_nibbles,
+    count_0000_nibbles,


kescobo · 2020-09-09T20:20:15Z

Project.toml

+[compat]
+Automa = "0.8"
+BGZFStreams = "0.3"
+BioCore = "2.0.5"


What's going on here? According to SemVer, this should be the same as 2.0, shouldn't it?

No, BioCore has some changes (bug fixes?) that we need. The tests won't pass unless we require at least v2.0.5.

kescobo · 2020-09-09T20:23:26Z

Any idea why there's such a massive coverage hit?

Ignore this - I see that's just the patch 👍

kescobo · 2020-09-11T16:04:52Z

This LGTM - @benjward ?

biona001 · 2021-02-08T21:02:44Z

Not to rush anyone, but will this PR be merged? I'm hoping this will solve a lot of the package compatibility issues I'm having with GeneticVariation.

kescobo · 2021-02-11T17:04:25Z

I would, but don't have permission. @benjward bump?

jonathanBieler · 2021-02-12T14:04:16Z

Would be great to have this merged yes, I just installed GeneticVariation and saw all my bio packages downgraded a major version or two :/

rasmushenningsson · 2021-02-14T09:41:13Z

I know it has been discussed before, so I decided to move the VCF/BCF functionality to a separate package - VCF.jl. It's currently in the process of being registered.

CiaranOMara · 2023-04-16T10:49:38Z

Trusting the review, I'll merge and release this so that things may progress.

Add Project.toml

7b7fa34

Also fixed deprecation warnings.

rasmushenningsson mentioned this pull request Aug 18, 2020

Add Project.toml #29

Closed

kescobo reviewed Sep 9, 2020

View reviewed changes

Compat fixes

06cf100

CiaranOMara merged commit b4789a1 into BioJulia:master Apr 16, 2023

This was referenced Apr 16, 2023

Cannot install the package for Julia 1.0.1 #22

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Cannot install this package #32

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Add Project.toml #31

Add Project.toml #31

rasmushenningsson commented Aug 18, 2020 •

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kescobo commented Sep 9, 2020

kescobo commented Sep 11, 2020

biona001 commented Feb 8, 2021

kescobo commented Feb 11, 2021

jonathanBieler commented Feb 12, 2021

rasmushenningsson commented Feb 14, 2021

CiaranOMara commented Apr 16, 2023

Add Project.toml #31

Add Project.toml #31

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rasmushenningsson commented Aug 18, 2020 • edited Loading

Add Project.toml

Types of changes

📋 Additional detail

☑️ Checklist

codecov bot commented Aug 18, 2020 • edited Loading

Codecov Report

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kescobo commented Sep 9, 2020

kescobo commented Sep 11, 2020

biona001 commented Feb 8, 2021

kescobo commented Feb 11, 2021

jonathanBieler commented Feb 12, 2021

rasmushenningsson commented Feb 14, 2021

CiaranOMara commented Apr 16, 2023

rasmushenningsson commented Aug 18, 2020 •

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