Modernize package

[jiahao]

• Update CI
• Update requirements files
• Pulls upstream PRs WIP: Get test passing madeleineudell/LowRankModels.jl#96 Remove Float64 restriction madeleineudell/LowRankModels.jl#99 Fix NonNegOneReg madeleineudell/LowRankModels.jl#100

[codecov-io]

Codecov Report

❗ No coverage uploaded for pull request base (master@2daff36). Click here to learn what that means.
The diff coverage is n/a.

@@            Coverage Diff            @@
##             master       #2   +/-   ##
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  Coverage          ?   60.51%           
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  Files             ?       26           
  Lines             ?     1674           
  Branches          ?        0           
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  Hits              ?     1013           
  Misses            ?      661           
  Partials          ?        0           

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[jiahao]

Notes on package modernization

Recommend tool chain (and badges)

• CI: travis-ci.com (macOS, Linux) and appveyor.com (Windows)
• Code coverage: Codecov.io
• Documentation: Documenter (2 badges for stable and dev)

General things

• Travis now has allowed_failures
• Travis and CodeCov and the like no longer use GitHub services which are now deprecated.
  • Instead, you should log on to each service and authorize them as GitHub OAuth apps.
  • Make sure to delete old webhooks from your repo under Repo > Settings > Webhooks otherwise tools like Travis will send conflicting messages from both the app webhook and the old github service-migrated webhook
• Travis is in the midst of migrating from travis-ci.org to travis-ci.com.
  • To trigger the migration manually, go to Travis-ci.org > profile > settings > repositories > migrate
  • Don't forget to update your CI badges to travis-ci.com!
• Manifest.toml
  • For a package, you don't need to commit Manifest.toml unless you have a specific need to pin down a very specific working environment.
  • Remember to .gitignore Manifest.toml and git rm Manifest.toml if you don't want it checked in
  • If your repo contains Julia code for a paper or experiments then you will probably want to commit Manifest.toml for reproducibility
• If you need to create a Project.toml file (eg your repo only has the obsolete REQUIRES file)
  • julia -e 'using Pkg; Pkg.instantiate()' to create the template
  • julia --project=. points Pkg to the current working directory. ] add Foo will add the package Foo as a dependency.
    No need to manually look up the UUID of a package!
  • Remember to git rm REQUIRES when you're done
  • If there's a pinned dependency, try freeing the version requirement and see if it works with the latest version.

TODO

• Codecov.io now comments on PRs and the like to generate code coverage reports.
  However, if you have multiple build environments in Travis then Codecov will blindly update the comment over and over again as the build for each environment completes.
  This is a problem when different build environments result in different code coverage numbers,
  which introduces indeterminacy in the code coverage PR hook for checking that code coverage must not decrease.
  Need to solve this race condition! Probably by getting only one build to report code coverage numbers.
• How to register new versions?
• How to migrate from Attobot to JuliaRegistrator?
• How to enable package benchmarking? Is Nanosoldier.jl still around and available?
• How to tag Zenodo DOIs? Is it still manual?