Big refresh, slightly breaking

[gdalle]

Hey there @michel2323!

This PR fixes #9 by modernizing and cleaning up the package, in the hope of getting it the appreciation it deserves. I tried to apply the current best practices in terms of package structure, as described in my blog https://modernjuliaworkflows.github.io/. I also added a lot of documentation, and a few breaking changes which I feel make sense (see below). However, the basic functionalities were not altered.

These changes affect ADNLPModels.jl (ping @amontoison) but the fixes are easy to apply so I'll take care of them if you accept.

Source code

• BREAKING: Remove AbstractColoring, AbstractOrdering and the lists COLORINGS and ORDERINGS
• BRERAKING: Replace them by single structs ColoringMethod and ColoringOrder with one string attribute (instead of an abstract type)
• BREAKING: Implement d1_coloring and friends as shortcuts to these structs (instead of identical but separate structs). They no longer accept a string argument, since it was redundant.
• BREAKING: Change the ColPackColoring to use references instead of length-1 vectors
• Replace ccall with the macro @ccall
• Structure into subfiles

Strictly speaking, since nothing was documented, these changes could be considered non-breaking, because in Julia the docs is the API ;)

Documentation

• Set up a Documenter.jl pipeline for a proper docs website
• Add tutorial page
• Add API reference page
• Write docstrings for everything (please double check that I understood the code correctly)
• Clean up README

Tests

• Fix the source of randomness for the sparse matrix with StableRNGs.jl (otherwise it depends on the value of Julia)
• Adjust the number of colors we expect with each coloring
• Add formal test with Aqua.jl and JET.jl
• Add doctests with Documenter.jl
• Structure into subfiles
• Run Julia 1.6 in CI

Example

• Remove example file (see #10)

Esthetics

• Add .JuliaFormatter.toml file for uniform style enforcement, apply formatting with JuliaFormatter.jl

Compat

• Bump version to v0.4.0
• Add compat bounds on Julia stdlibs
• Only test with Aqua.jl and JET.jl on Julia v1.10 and above

CI

• Add dependabot.yml to track outdated dependencies
• Modernize Test.yml and TagBot.yml
• Add Documentation.yml to build a docs website and deploy it

[michel2323]

LGTM (besides the missing new line in the yml files). As per the discussion with @amontoison I'd move the package to the Exanauts org if you don't mind. I added you to this repository so you can push the branch and the CI runs.

[gdalle]

Cool, thanks! I'll finish the PR tomorrow. I'm also writing a pure Julia version so we'll be able to compare speed 😊

[amontoison]

@gdalle Can you update the Julia wrappers to use the macro @ccall?

[codecov-commenter]

Welcome to Codecov :tada:

Once you merge this PR into your default branch, you're all set! Codecov will compare coverage reports and display results in all future pull requests.

Thanks for integrating Codecov - We've got you covered :open_umbrella:

[gdalle]

LGTM (besides the missing new line in the yml files).

To have passing tests I had to fix the source of randomness generating the sparse matrix (otherwise the results you get depend on the version of Julia). I also had to modify the number of colors accordingly for some coloring algorithms. @michel2323 can you check that it still looks okay? Then I think we're good to merge.

@gdalle Can you update the Julia wrappers to use the macro @ccall?

@amontoison it's done but I've never written a line of C so please double-check

[gdalle]

@michel2323 should we merge?