diff --git a/docs/Project.toml b/docs/Project.toml index dfa65cd..b284c6f 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -1,2 +1,6 @@ [deps] Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" +Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" + +[compat] +Documenter = "0.27" diff --git a/docs/make.jl b/docs/make.jl index d20f2b3..e723972 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -1,15 +1,22 @@ +using Pkg using Documenter using SequenceVariation -makedocs( - sitename = "SequenceVariation", +makedocs(; + checkdocs = :exports, + linkcheck = true, + sitename = "SequenceVariation.jl", format = Documenter.HTML(), - modules = [SequenceVariation] + modules = [SequenceVariation], + pages = [ + "Home" => "index.md", + "API Reference" => "api.md", + ], + authors = replace(join(Pkg.TOML.parsefile("Project.toml")["authors"], ", "), r" <.*?>" => "" ) * ", The BioJulia Organisation, and other contributors." ) -# Documenter can also automatically deploy documentation to gh-pages. -# See "Hosting Documentation" and deploydocs() in the Documenter manual -# for more information. -#=deploydocs( - repo = "" -)=# +deploydocs( + repo = "github.com/BioJulia/SequenceVariation.jl.git", + devbranch = "master", + push_preview = true, +) diff --git a/docs/src/api.md b/docs/src/api.md new file mode 100644 index 0000000..548c73f --- /dev/null +++ b/docs/src/api.md @@ -0,0 +1,12 @@ +```@meta +CurrentModule = SequenceVariation +DocTestSetup = quote + using SequenceVariation +end +``` + +# API Reference + +```@autodocs +Modules = SequenceVariation +``` diff --git a/docs/src/index.md b/docs/src/index.md index 9a90589..c454b95 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -1,3 +1,73 @@ # SequenceVariation.jl -Documentation for SequenceVariation.jl +[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip) +[![Latest Release](https://img.shields.io/github/release/BioJulia/SequenceVariation.jl.svg)](https://github.com/BioJulia/SequenceVariation.jl/releases/latest) +[![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/SequenceVariation.jl/blob/master/LICENSE) +[![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/SequenceVariation.jl/stable) +[![Latest documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/SequenceVariation.jl/dev/) + +> This project follows the [semver](https://semver.org) _pro forma_ and uses the [OneFlow branching model](https://www.endoflineblog.com/oneflow-a-git-branching-model-and-workflow). + +## Description + +SequenceVariation provides a Julia vocabulary for comparing genetic mutations within biological sequences. + +## Installation + +You can install SequenceVariation from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/). +Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), and enter the following: + +```julia +add https://github.com/SequenceVariation.jl +``` + +## Testing + +SequenceVariation is tested against Julia `1.X` on Linux, OS X, and Windows. + +**Latest build status:** + +[![Unit tests](https://github.com/BioJulia/SequenceVariation.jl/workflows/Unit%20tests/badge.svg?branch=master)](https://github.com/BioJulia/SequenceVariation.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster) +[![Documentation](https://github.com/BioJulia/SequenceVariation.jl/workflows/Documentation/badge.svg?branch=master)](https://github.com/BioJulia/SequenceVariation.jl/actions?query=workflow%3ADocumentation+branch%3Amaster) +[![codecov](https://codecov.io/gh/BioJulia/SequenceVariation.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/SequenceVariation.jl) + +## Contributing + +We appreciate [contributions](https://github.com/BioJulia/SequenceVariation.jl/graphs/contributors) from users including reporting bugs, fixing issues, improving performance and adding new features. + +Take a look at the [contributing files](https://github.com/BioJulia/Contributing) for detailed contributor and maintainer guidelines, and code of conduct. + +### Financial contributions + +We also welcome financial contributions in full transparency on our [open collective](https://opencollective.com/biojulia). +Anyone can file an expense. +If the expense makes sense for the development the core contributors and the person who filed the expense will be reimbursed. + + +## Backers & Sponsors + +Thank you to all our backers and sponsors! + +Love our work and community? [Become a backer](https://opencollective.com/biojulia#backer). + +[![backers](https://opencollective.com/biojulia/backers.svg?width=890)](https://opencollective.com/biojulia#backers) + +Does your company use BioJulia? +Help keep BioJulia feature rich and healthy by [sponsoring the project](https://opencollective.com/biojulia#sponsor). +Your logo will show up here with a link to your website. + +[![](https://opencollective.com/biojulia/sponsor/0/avatar.svg)](https://opencollective.com/biojulia/sponsor/0/website) +[![](https://opencollective.com/biojulia/sponsor/1/avatar.svg)](https://opencollective.com/biojulia/sponsor/1/website) +[![](https://opencollective.com/biojulia/sponsor/2/avatar.svg)](https://opencollective.com/biojulia/sponsor/2/website) +[![](https://opencollective.com/biojulia/sponsor/3/avatar.svg)](https://opencollective.com/biojulia/sponsor/3/website) +[![](https://opencollective.com/biojulia/sponsor/4/avatar.svg)](https://opencollective.com/biojulia/sponsor/4/website) +[![](https://opencollective.com/biojulia/sponsor/5/avatar.svg)](https://opencollective.com/biojulia/sponsor/5/website) +[![](https://opencollective.com/biojulia/sponsor/6/avatar.svg)](https://opencollective.com/biojulia/sponsor/6/website) +[![](https://opencollective.com/biojulia/sponsor/7/avatar.svg)](https://opencollective.com/biojulia/sponsor/7/website) +[![](https://opencollective.com/biojulia/sponsor/8/avatar.svg)](https://opencollective.com/biojulia/sponsor/8/website) +[![](https://opencollective.com/biojulia/sponsor/9/avatar.svg)](https://opencollective.com/biojulia/sponsor/9/website) + + +## Questions? + +If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.org/slack/), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).