Merge branch 'release/v0.1.0'

.codecov.yml

@@ -0,0 +1 @@
+comment: false

.github/FUNDING.yml

@@ -0,0 +1 @@
+open_collective: biojulia

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,40 @@
+<!--- Provide a general summary of the issue in the Title above -->
+
+> _This template is rather extensive. Fill out all that you can, if are a new contributor or you're unsure about any section, leave it unchanged and a reviewer will help you_ :smile:. _This template is simply a tool to help everyone remember the BioJulia guidelines, if you feel anything in this template is not relevant, simply delete it._
+
+## Expected Behavior
+<!--- If you're describing a bug, tell us what you expect to happen -->
+<!--- If you're suggesting a change/improvement, tell us how it should work -->
+
+## Current Behavior
+<!--- If describing a bug, tell us what happens instead of the expected behavior -->
+<!--- If suggesting a change/improvement, explain the difference from current behavior -->
+
+## Possible Solution / Implementation
+<!--- If describing a bug, suggest a fix/reason for the bug (optional) -->
+<!--- If you're suggesting a change/improvement, suggest ideas how to implement the addition or change -->
+
+## Steps to Reproduce (for bugs)
+<!--- You may include copy/pasteable snippets or a list of steps to reproduce the bug -->
+1.
+2.
+3.
+4.
+
+<!--- Optionally, provide a link to a live example -->
+<!--- You can use [this tool](https://www.cockos.com/licecap/) -->
+<!--- ...Or [this tool](https://github.com/colinkeenan/silentcast) -->
+<!--- ...Or [this tool](https://github.com/GNOME/byzanz) on Linux -->
+
+## Context
+<!--- How has this issue affected you? What are you trying to accomplish? -->
+<!--- Providing context helps us come up with a solution that is most useful in the real world -->
+
+## Your Environment
+<!--- Include as many relevant details about the environment you experienced the bug in -->
+- Package Version used:
+- Julia Version used:
+- Operating System and version (desktop or mobile):
+- Link to your project:
+
+<!-- Can you list installed packages here? -->

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,47 @@
+# A clear and descriptive title (No issue numbers please)
+
+> _This template is rather extensive. Fill out all that you can, if are a new contributor or you're unsure about any section, leave it unchanged and a reviewer will help you_ :smile:. _This template is simply a tool to help everyone remember the BioJulia guidelines, if you feel anything in this template is not relevant, simply delete it._
+
+## Types of changes
+
+This PR implements the following changes:
+_(Please tick any or all of the following that are applicable)_
+
+* [ ] :sparkles: New feature (A non-breaking change which adds functionality).
+* [ ] :bug: Bug fix (A non-breaking change, which fixes an issue).
+* [ ] :boom: Breaking change (fix or feature that would cause existing functionality to change).
+
+## :clipboard: Additional detail
+
+- If you have implemented new features or behaviour
+  - **Provide a description of the addition** in as many details as possible.
+
+  - **Provide justification of the addition**.
+
+  - **Provide a runnable example of use of your addition**. This lets reviewers
+    and others try out the feature before it is merged or makes it's way to release.
+
+- If you have changed current behaviour...
+  - **Describe the behaviour prior to you changes**
+
+  - **Describe the behaviour after your changes** and justify why you have made the changes,
+    Please describe any breakages you anticipate as a result of these changes.
+
+  - **Does your change alter APIs or existing exposed methods/types?**
+    If so, this may cause dependency issues and breakages, so the maintainer
+    will need to consider this when versioning the next release.
+
+  - If you are implementing changes that are intended to increase performance, you
+    should provide the results of a simple performance benchmark exercise
+    demonstrating the improvement. Especially if the changes make code less legible.
+
+## :ballot_box_with_check: Checklist
+
+- [ ] :art: The changes implemented is consistent with the [julia style guide](https://docs.julialang.org/en/stable/manual/style-guide/).
+- [ ] :blue_book: I have updated and added relevant docstrings, in a manner consistent with the [documentation styleguide](https://docs.julialang.org/en/stable/manual/documentation/).
+- [ ] :blue_book: I have added or updated relevant user and developer manuals/documentation in `docs/src/`.
+- [ ] :ok: There are unit tests that cover the code changes I have made.
+- [ ] :ok: The unit tests cover my code changes AND they pass.
+- [ ] :pencil: I have added an entry to the `[UNRELEASED]` section of the manually curated `CHANGELOG.md` file for this repository.
+- [ ] :ok: All changes should be compatible with the latest stable version of Julia.
+- [ ] :thought_balloon: I have commented liberally for any complex pieces of internal code.

.github/workflows/CompatHelper.yml

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+name: CompatHelper
+
+on:
+  schedule:
+    - cron: '00 00 * * *'
+
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: 1.3
+      - name: Add CompatHelper
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: Run CompatHelper
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: julia -e '
+                using CompatHelper, Pkg;
+                my_registries = [
+                    Pkg.RegistrySpec(
+                        name = "BioJuliaRegistry",
+                        uuid = "ccbd2cc2-2954-11e9-1ccf-f3e7900901ca",
+                        url = "https://github.com/BioJulia/BioJuliaRegistry.git"
+                    ),
+                    Pkg.RegistrySpec(
+                        name = "General",
+                        uuid = "23338594-aafe-5451-b93e-139f81909106",
+                        url = "https://github.com/JuliaRegistries/General.git"
+                    )
+                ];
+                CompatHelper.main(; registries = my_registries, master_branch = "master");'

.github/workflows/Documentation.yml

@@ -0,0 +1,34 @@
+name: Documentation
+
+on:
+    push:
+        branches:
+            - 'master'
+            - 'develop'
+            - 'release/.*'
+        tags: '*'
+    pull_request:
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1.3.0]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: actions/checkout@v1.0.0
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+      - name: Install dependencies
+        run: |
+          julia ci_prep.jl;
+          julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          # https://github.com/JuliaDocs/Documenter.jl/issues/1177
+          # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+        run: julia --project=docs/ --color=yes docs/make.jl

.github/workflows/TagBot.yml

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+name: TagBot
+on:
+  schedule:
+    - cron: '0 * * * *'
+jobs:
+  TagBot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.TAGBOT_KEY }}
+          registry: BioJulia/BioJuliaRegistry

.github/workflows/UnitTests.yml

@@ -0,0 +1,22 @@
+name: Unit tests
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: ['1.1', '1.2', '1.3']
+        julia-arch: [x64]
+        os: [ubuntu-latest, windows-latest, macOS-latest]
+
+    steps:
+      - uses: actions/checkout@v1.0.0
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+          arch: ${{ matrix.julia-arch }}
+      - name: Install dependencies
+        run: julia ci_prep.jl
+      - uses: julia-actions/julia-runtest@master

Project.toml

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+name = "Indexes"
+uuid = "4ffb77ac-cb80-11e8-1b35-4b78cc642f6d"
+authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <benjward@protonmail.com>", "Ciarán O’Mara <CiaranOMara@utas.edu.au>"]
+version = "0.1.0"
+
+[deps]
+BGZFStreams = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"
+BioCore = "37cfa864-2cd6-5c12-ad9e-b6597d696c81"
+BufferedStreams = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"
+GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
+
+[compat]
+BGZFStreams = "0.3"
+BioCore = "2"
+BufferedStreams = "1"
+GenomicFeatures = "2"
+julia = "1.1"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]

README.md

@@ -1 +1,82 @@
-# Indexes.jl
+# <img src="./docs/src/assets/logo.svg" width="30%" align="right" /> 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/ "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).

ci_prep.jl

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+using Pkg.Registry
+Registry.add(Registry.RegistrySpec(url = "https://github.com/BioJulia/BioJuliaRegistry.git"))
+Registry.add(Registry.RegistrySpec(url = "https://github.com/JuliaRegistries/General.git"))

coverage/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037"

coverage/coverage.jl

@@ -0,0 +1,11 @@
+get(ENV, "TRAVIS_OS_NAME", "") == "linux" || exit()
+get(ENV, "TRAVIS_JULIA_VERSION", "") == "1.3" || exit()
+
+using Pkg
+Pkg.instantiate()
+
+using Coverage
+
+cd(joinpath(@__DIR__, "..")) do
+   Codecov.submit(Codecov.process_folder())
+end

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
+)