Merge pull request #34 from BioJulia/release/v2.0.1

release/v2.0.1
BioJulia · May 21, 2020 · a63ab3c · a63ab3c · CiaranOMara · May 22, 2020
2 parents c757dcd + a0c45e3
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diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml
@@ -2,23 +2,15 @@ name: CompatHelper
 
 on:
   schedule:
-    - cron: '00 * * * *'
+    - cron: '00 00 * * *'
 
 jobs:
   CompatHelper:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        julia-version: [1.3.0]
-        julia-arch: [x86]
-        os: [ubuntu-latest]
+    runs-on: ubuntu-latest
     steps:
-      - uses: julia-actions/setup-julia@latest
-        with:
-          version: ${{ matrix.julia-version }}
       - name: Add CompatHelper
         run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main
+      - name: Run CompatHelper
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: julia -e '

diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml
@@ -1,34 +1,28 @@
 name: Documentation
 
 on:
-    push:
-        branches:
-            - 'master'
-            - 'develop'
-            - 'release/.*'
-        tags: '*'
-    pull_request:
+  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]
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1.0.0
+      - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@latest
         with:
-          version: ${{ matrix.julia-version }}
+          version: '1.4'
       - name: Install dependencies
         run: |
-          julia ci_prep.jl
-          julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+          julia ci_prep.jl;
+          julia --color=yes --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
+        run: julia --color=yes --project=docs/ docs/make.jl
diff --git a/.github/workflows/UnitTests.yml b/.github/workflows/UnitTests.yml
@@ -0,0 +1,34 @@
+name: Unit tests
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: ['1.1', '1.2', '1.3', '1.4']
+        julia-arch: [x86]
+        os: [ubuntu-latest, windows-latest, macOS-latest]
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+      - name: Install dependencies
+        run: julia ci_prep.jl
+      - name: Run tests
+        uses: julia-actions/julia-runtest@latest
+      - name: Create CodeCov
+        uses: julia-actions/julia-processcoverage@v1
+      - name: Upload CodeCov
+        uses: codecov/codecov-action@v1
+        with:
+          file: ./lcov.info
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: false
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.travis.yml b/.travis.yml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,11 +5,17 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+
+## [2.0.1] - 2020-05-21
+
+### Changed
+- Documentation.
+- Updated CI.
+
+## [2.0.0] - 2020-02-16
 ### Added
 - BioJulia registry.
 
-## [2.0.0] - 2020-01-
-
 ### Changed
 - Migrated from BioCore to [BioGenerics](https://github.com/BioJulia/BioGenerics.jl/tree/v0.1.0).
 - Updated CI.
@@ -65,8 +71,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Code from Bio.jl.
 - Support for GFF3 and BigWig.
 
-[Unreleased]: https://github.com/BioJulia/GenomicFeatures.jl/compare/v2.0.0...HEAD
-[1.0.4]: https://github.com/BioJulia/GenomicFeatures.jl/compare/v1.0.4...v2.0.0
+[Unreleased]: https://github.com/BioJulia/GenomicFeatures.jl/compare/v2.0.1...HEAD
+[2.0.1]: https://github.com/BioJulia/GenomicFeatures.jl/compare/v2.0.0...v2.0.1
+[2.0.0]: https://github.com/BioJulia/GenomicFeatures.jl/compare/v1.0.4...v2.0.0
 [1.0.4]: https://github.com/BioJulia/GenomicFeatures.jl/compare/v1.0.3...v1.0.4
 [1.0.3]: https://github.com/BioJulia/GenomicFeatures.jl/compare/v1.0.2...v1.0.3
 [1.0.2]: https://github.com/BioJulia/GenomicFeatures.jl/compare/v1.0.1...v1.0.2

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "GenomicFeatures"
 uuid = "899a7d2d-5c61-547b-bef9-6698a8d05446"
 authors = ["Kenta Sato <[email protected]>", "Ben J. Ward <[email protected]>", "Ciarán O’Mara <[email protected]>"]
-version = "2.0.0"
+version = "2.0.1"
 
 [deps]
 BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"

diff --git a/README.md b/README.md
@@ -1,20 +1,19 @@
 # <img src="./sticker.svg" width="30%" align="right" /> GenomicFeatures
 
 [![latest release](https://img.shields.io/github/release/BioJulia/GenomicFeatures.jl.svg)](https://github.com/BioJulia/GenomicFeatures.jl/releases/latest)
-[![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/GenomicFeatures.jl/blob/master/LICENSE) 
+[![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/GenomicFeatures.jl/blob/master/LICENSE)
 [![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/GenomicFeatures.jl/stable)
-[![Latest documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://biojulia.github.io/GenomicFeatures.jl/latest/)
+[![Latest documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/GenomicFeatures.jl/dev/)
 [![lifecycle](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![Chat](https://img.shields.io/gitter/room/BioJulia/GenomicFeatures.svg)](https://gitter.im/BioJulia/GenomicFeatures.jl)
 
 ## Description
-GenomicFeatures provides utilities for working with interval based genomic annotations.
+The GenomicFeatures package provides utilities for working with interval based genomic annotations.
 It builds on [IntervalTrees](https://github.com/biojulia/intervaltrees.jl) to provide a data-structures and algorithms for various formats such as [BED](https://github.com/biojulia/bed.jl), [GFF3](https://github.com/biojulia/gff3.jl), [bigWig](https://github.com/biojulia/bigwig.jl) and [bigBed](https://github.com/biojulia/bigbed.jl).  
 
 ## Installation
 Releases of GenomicFeatures version 2.0.0 and above are registered and 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 GenomicFeatures.
 
 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
@@ -34,8 +33,8 @@ GenomicFeatures is tested against Julia `1.X` on Linux, OS X, and Windows.
 
 **Latest build status:**
 
-[![Build Status](https://travis-ci.org/BioJulia/GenomicFeatures.jl.svg?branch=develop)](https://travis-ci.org/BioJulia/GenomicFeatures.jl)
-[![Build status](https://ci.appveyor.com/api/projects/status/dnup6vbbvai92bl8/branch/master?svg=true)](https://ci.appveyor.com/project/BenJWard/genomicfeatures-jl/branch/master)
+[![Unit tests](https://github.com/BioJulia/GenomicFeatures.jl/workflows/Unit%20tests/badge.svg?branch=master)](https://github.com/BioJulia/GenomicFeatures.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster)
+[![Documentation](https://github.com/BioJulia/GenomicFeatures.jl/workflows/Documentation/badge.svg?branch=master)](https://github.com/BioJulia/GenomicFeatures.jl/actions?query=workflow%3ADocumentation+branch%3Amaster)
 [![codecov](https://codecov.io/gh/BioJulia/GenomicFeatures.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/GenomicFeatures.jl)
 
 

diff --git a/appveyor.yml b/appveyor.yml
diff --git a/coverage/Project.toml b/coverage/Project.toml
diff --git a/coverage/coverage.jl b/coverage/coverage.jl
diff --git a/docs/src/api/api.md b/docs/src/api/api.md
@@ -6,7 +6,7 @@ Modules = [GenomicFeatures]
 Private = false
 ```
 
-## Private
+## Internal
 ```@autodocs
 Modules = [GenomicFeatures]
 Public = false

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,20 +1,19 @@
 # GenomicFeatures
 
 [![latest release](https://img.shields.io/github/release/BioJulia/GenomicFeatures.jl.svg)](https://github.com/BioJulia/GenomicFeatures.jl/releases/latest)
-[![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/GenomicFeatures.jl/blob/master/LICENSE) 
+[![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/GenomicFeatures.jl/blob/master/LICENSE)
 [![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/GenomicFeatures.jl/stable)
-[![Latest documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://biojulia.github.io/GenomicFeatures.jl/latest/)
-[![lifecycle](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wi)
+[![Latest documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/GenomicFeatures.jl/dev/)
+[![lifecycle](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![Chat](https://img.shields.io/gitter/room/BioJulia/GenomicFeatures.svg)](https://gitter.im/BioJulia/GenomicFeatures.jl)
 
 ## Description
-GenomicFeatures provides utilities for working with interval based genomic annotations.
+The GenomicFeatures package provides utilities for working with interval based genomic annotations.
 It builds on [IntervalTrees](https://github.com/biojulia/intervaltrees.jl) to provide a data-structures and algorithms for various formats such as [BED](https://github.com/biojulia/bed.jl), [GFF3](https://github.com/biojulia/gff3.jl), [bigWig](https://github.com/biojulia/bigwig.jl) and [bigBed](https://github.com/biojulia/bigbed.jl).  
 
 ## Installation
 Releases of GenomicFeatures version 2.0.0 and above are registered and 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 GenomicFeatures.
 
 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
@@ -34,8 +33,8 @@ GenomicFeatures is tested against Julia `1.X` on Linux, OS X, and Windows.
 
 **Latest build status:**
 
-[![Build Status](https://travis-ci.org/BioJulia/GenomicFeatures.jl.svg?branch=develop)](https://travis-ci.org/BioJulia/GenomicFeatures.jl)
-[![Build status](https://ci.appveyor.com/api/projects/status/dnup6vbbvai92bl8/branch/master?svg=true)](https://ci.appveyor.com/project/BenJWard/genomicfeatures-jl/branch/master)
+[![Unit tests](https://github.com/BioJulia/GenomicFeatures.jl/workflows/Unit%20tests/badge.svg?branch=master)](https://github.com/BioJulia/GenomicFeatures.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster)
+[![Documentation](https://github.com/BioJulia/GenomicFeatures.jl/workflows/Documentation/badge.svg?branch=master)](https://github.com/BioJulia/GenomicFeatures.jl/actions?query=workflow%3ADocumentation+branch%3Amaster)
 [![codecov](https://codecov.io/gh/BioJulia/GenomicFeatures.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/GenomicFeatures.jl)
 
 

diff --git a/docs/src/man/intervals.md b/docs/src/man/intervals.md
@@ -10,7 +10,7 @@ Similarly when writing data, you should not have to reason about off-by-one erro
 
 The `Interval` type is defined as
 ```julia
-struct Interval{T} <: AbstractInterval{Int64}
+struct Interval{T} <: IntervalTrees.AbstractInterval{Int64}
     seqname::String
     first::Int64
     last::Int64