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[MRG] manylinux1 wheels and travis build improvements #507

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merged 6 commits into from
Jun 27, 2018
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@luizirber luizirber commented Jun 25, 2018

This PR configures Travis to build wheels for manylinux1 (the catch-all version for compatible binary Python wheels). Wheel building is executed only on tags, and for now it is deploying to GitHub Releases (we want to deploy it to PyPI too)

I'm using an OAuth token linked to my account to upload the wheels to GitHub, so we might want to figure out another approach (maybe make a diblab-release account, and add it to PyPI/bio.tools and other services too?)

Bonus: since I generated the khmer wheels for this, I also uploaded them to PyPI and now the Travis jobs run way faster (because we don't need to recompile khmer every time...)

Not covered here:

  • We are currently not builiding on macOS, so next step is to turn it on again on Travis
  • Windows (via appveyor) seems achievable, but need to fix khmer first...
  • Build stages would also be a welcome improvement, but it requires more thinking/rewriting on the travis configuration file

checklist

  • Is it mergeable?
  • make test Did it pass the tests?
  • make coverage Is the new code covered?
  • Did it change the command-line interface? Only additions are allowed
    without a major version increment. Changing file formats also requires a
    major version number increment.
  • Was a spellchecker run on the source code and documentation after
    changes were made?

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codecov-io commented Jun 25, 2018

Codecov Report

Merging #507 into master will increase coverage by 0.08%.
The diff coverage is n/a.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #507      +/-   ##
==========================================
+ Coverage   90.69%   90.78%   +0.08%     
==========================================
  Files          33       33              
  Lines        4999     5003       +4     
  Branches       36       36              
==========================================
+ Hits         4534     4542       +8     
+ Misses        464      461       -3     
+ Partials        1        0       -1
Impacted Files Coverage Δ
third-party/smhasher/MurmurHash3.cc 35.37% <0%> (-0.58%) ⬇️
sourmash/kmer_min_hash.hh 100% <0%> (+0.64%) ⬆️

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deploy:
provider: releases
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are you sure you want this checked in?

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@luizirber
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(for those curious: this is how many tries it took to figure out this PR
https://travis-ci.com/luizirber/sourmash-1/builds
https://github.com/luizirber/sourmash-1/releases
)

@luizirber luizirber changed the title [WIP] manylinux1 wheels and travis build improvements [MRG] manylinux1 wheels and travis build improvements Jun 25, 2018
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Ready for review and merge @ctb

@luizirber luizirber requested a review from ctb June 27, 2018 14:50
@ctb ctb merged commit eb75f96 into master Jun 27, 2018
@luizirber luizirber deleted the build/manylinux branch June 27, 2018 15:03
luizirber added a commit that referenced this pull request Jul 23, 2018
- avoid calling node.data (#516)
  This makes `sourmash gather` ~40% faster...
- make sourmash compatible with khmer 3 (#508)
  Even tho khmer 3 it's not released, there is an alpha version on bioconda
- manylinux1 wheels and travis build improvements (#507)
- PyPI fixes (#504)
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3 participants