Update documentation

docs/Project.toml

@@ -1,2 +1,6 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+
+[compat]
+Documenter = "0.27"

docs/make.jl

@@ -1,15 +1,22 @@
+using Pkg
 using Documenter
 using SequenceVariation
 
-makedocs(
+makedocs(;
-    sitename = "SequenceVariation",
+    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.
+deploydocs(
-# See "Hosting Documentation" and deploydocs() in the Documenter manual
+    repo = "github.com/BioJulia/SequenceVariation.jl.git",
-# for more information.
+    devbranch = "master",
-#=deploydocs(
+    push_preview = true,
-    repo = "<repository url>"
+)
-)=#

docs/src/api.md

@@ -0,0 +1,12 @@
+```@meta
+CurrentModule = SequenceVariation
+DocTestSetup = quote
+    using SequenceVariation
+end
+```
+
+# API Reference
+
+```@autodocs
+Modules = SequenceVariation
+```

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).