Documentation

README.md

@@ -1 +1,82 @@
-# Indexes.jl
+# <img src="./docs/src/assets/logo.svg" width="30%" align="right" /> Indexes.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/Indexes.jl.svg)](https://github.com/BioJulia/Indexes.jl/releases/latest)
+[![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/Indexes.jl/blob/master/LICENSE)
+[![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/Indexes.jl/stable)
+[![Latest documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/Indexes.jl/dev/)
+[![Join the chat at https://gitter.im/BioJulia/Indexes.jl](https://badges.gitter.im/BioJulia/Indexes.jl.svg)](https://gitter.im/BioJulia/Indexes.jl)
+
+> This project follows the [semver](http://semver.org) pro forma and uses the [git-flow branching model](https://nvie.com/posts/a-successful-git-branching-model/ "original
+blog post").
+
+## Description
+Handles indexes required to iterate through various IO streams.
+For example:
+- Generic index for tab-delimited files.
+- An index type for BGZFStream.
+
+## Installation
+`Indexes` is bundled into packages like [BED](https://github.com/BioJulia/BED.jl), [GFF3](https://github.com/BioJulia/GFF3.jl), and [XAM](https://github.com/BioJulia/XAM.jl) to assist them with IO streams, so you may not need to install this package explicitly.
+However, if you do, `Indexes` is made available to install through BioJulia's package registry.
+By default, Julia's package manager only uses the "General" package registry.
+Your Julia configuration needs to include the BioJulia registry to be able to install the latest version of `Indexes`.
+
+To add the BioJulia registry 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/), then enter the following command:
+```julia
+registry add https://github.com/BioJulia/BioJuliaRegistry.git
+```
+
+After adding the registry to your configuration, you can install `Indexes` while in [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/) with the following:
+```julia
+add Indexes
+```
+
+If you are interested in the cutting edge of the development, please check out the [develop branch](https://github.com/BioJulia/Indexes.jl/tree/develop) to try new features before release.
+
+
+## Testing
+Indexes is tested against Julia `1.X` on Linux, OS X, and Windows.
+
+**Latest build status:**
+
+[![Unit tests](https://github.com/BioJulia/indexes.jl/workflows/Unit%20tests/badge.svg?branch=master)](https://github.com/BioJulia/indexes.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster)
+[![Documentation](https://github.com/BioJulia/indexes.jl/workflows/Documentation/badge.svg?branch=master)](https://github.com/BioJulia/indexes.jl/actions?query=workflow%3ADocumentation+branch%3Amaster)
+[![codecov](https://codecov.io/gh/BioJulia/Indexes.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/Indexes.jl)
+
+## Contributing
+We appreciate [contributions](https://github.com/BioJulia/Indexes.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) 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 [Gitter](https://gitter.im/BioJulia/General), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).

docs/Project.toml

@@ -0,0 +1,6 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+
+[compat]
+Documenter = "0.24"

docs/make.jl

@@ -0,0 +1,20 @@
+using Pkg
+using Documenter, Indexes
+
+makedocs(
+    format = Documenter.HTML(
+        edit_link = "develop"
+    ),
+    modules = [Indexes],
+    sitename = "Indexes.jl",
+    pages = [
+        "Home" => "index.md",
+        "API Reference" => "man/api.md"
+    ],
+    authors = replace(join(Pkg.TOML.parsefile("Project.toml")["authors"], ", "), r" <.*?>" => "" ) * ", The BioJulia Organisation, and other contributors."
+)
+deploydocs(
+    repo = "github.com/BioJulia/Indexes.jl.git",
+    devbranch = "develop",
+    push_preview = true
+)

docs/src/index.md

@@ -0,0 +1,80 @@
+# Indexes.jl
+
+[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
+[![Latest Release](https://img.shields.io/github/release/BioJulia/Indexes.jl.svg)](https://github.com/BioJulia/Indexes.jl/releases/latest)
+[![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/Indexes.jl/blob/master/LICENSE)
+[![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/Indexes.jl/stable)
+[![Latest documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/Indexes.jl/dev/)
+[![Join the chat at https://gitter.im/BioJulia/Indexes.jl](https://badges.gitter.im/BioJulia/Indexes.jl.svg)](https://gitter.im/BioJulia/Indexes.jl)
+
+> This project follows the [semver](http://semver.org) pro forma and uses the [git-flow branching model](https://nvie.com/posts/a-successful-git-branching-model/).
+
+## Description
+Handles indexes required to iterate through various IO streams.
+For example:
+- Generic index for tab-delimited files.
+- An index type for BGZFStream.
+
+## Installation
+`Indexes` is bundled into packages like [BED](https://github.com/BioJulia/BED.jl), [GFF3](https://github.com/BioJulia/GFF3.jl), and [XAM](https://github.com/BioJulia/XAM.jl) to assist them with IO streams, so you may not need to install this package explicitly.
+However, if you do, `Indexes` is made available to install through BioJulia's package registry.
+By default, Julia's package manager only uses the "General" package registry.
+Your Julia configuration needs to include the BioJulia registry to be able to install the latest version of `Indexes`.
+
+To add the BioJulia registry 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/), then enter the following command:
+```julia
+registry add https://github.com/BioJulia/BioJuliaRegistry.git
+```
+
+After adding the registry to your configuration, you can install `Indexes` while in [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/) with the following:
+```julia
+add Indexes
+```
+
+If you are interested in the cutting edge of the development, please check out the [develop branch](https://github.com/BioJulia/Indexes.jl/tree/develop) to try new features before release.
+
+## Testing
+Indexes is tested against Julia `1.X` on Linux, OS X, and Windows.
+
+**Latest build status:**
+
+[![Unit tests](https://github.com/BioJulia/indexes.jl/workflows/Unit%20tests/badge.svg?branch=master)](https://github.com/BioJulia/indexes.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster)
+[![Documentation](https://github.com/BioJulia/indexes.jl/workflows/Documentation/badge.svg?branch=master)](https://github.com/BioJulia/indexes.jl/actions?query=workflow%3ADocumentation+branch%3Amaster)
+[![codecov](https://codecov.io/gh/BioJulia/Indexes.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/Indexes.jl)
+
+## Contributing
+We appreciate [contributions](https://github.com/BioJulia/Indexes.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) 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 [Gitter](https://gitter.im/BioJulia/General), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).

docs/src/man/api.md

@@ -0,0 +1,14 @@
+# API Reference
+
+## Public
+```@autodocs
+Modules = [Indexes]
+private = false
+```
+
+## Internal
+
+```@autodocs
+Modules = [Indexes]
+public = false
+```