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Update CI and documentation for the general registry
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‎.github/workflows/CompatHelper.yml

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@@ -8,26 +8,10 @@ jobs:
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CompatHelper:
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runs-on: ubuntu-latest
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steps:
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- uses: julia-actions/setup-julia@latest
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with:
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version: 1.3
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- name: Add CompatHelper
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run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
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run: julia --color=yes -e 'using Pkg; Pkg.add("CompatHelper")'
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- name: Run CompatHelper
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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run: julia -e '
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using CompatHelper, Pkg;
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my_registries = [
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Pkg.RegistrySpec(
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name = "BioJuliaRegistry",
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uuid = "ccbd2cc2-2954-11e9-1ccf-f3e7900901ca",
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url = "https://github.com/BioJulia/BioJuliaRegistry.git"
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),
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Pkg.RegistrySpec(
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name = "General",
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uuid = "23338594-aafe-5451-b93e-139f81909106",
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url = "https://github.com/JuliaRegistries/General.git"
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)
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];
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CompatHelper.main(; registries = my_registries, master_branch = "master");'
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COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
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run: julia --color=yes -e 'using CompatHelper; CompatHelper.main(master_branch = "master")'

‎.github/workflows/Documentation.yml

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name: Documentation
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name: Build Documentation
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on:
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push:
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branches:
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- 'master'
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- 'develop'
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- 'release/.*'
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tags: '*'
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pull_request:
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push:
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branches:
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- master
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- develop
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- release/*
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tags: '*'
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pull_request:
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jobs:
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build:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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julia-version: [1.3.0]
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julia-arch: [x86]
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os: [ubuntu-latest]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v1.0.0
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- uses: julia-actions/setup-julia@latest
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- uses: actions/checkout@v2
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- uses: julia-actions/setup-julia@v1
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with:
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version: ${{ matrix.julia-version }}
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- name: Install dependencies
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run: |
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julia ci_prep.jl;
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julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
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- name: Build and deploy
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version: '1'
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- name: Install Dependencies
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run: julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
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- name: Build and Deploy
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env:
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# https://github.com/JuliaDocs/Documenter.jl/issues/1177
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# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
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DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
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run: julia --project=docs/ --color=yes docs/make.jl
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run: julia --color=yes --project=docs/ docs/make.jl

‎.github/workflows/TagBot.yml

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

‎.github/workflows/UnitTests.yml

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name: Unit tests
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name: Unit Tests
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on: [push, pull_request]
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on:
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- push
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- pull_request
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jobs:
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test:
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runs-on: ${{ matrix.os }}
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continue-on-error: ${{ matrix.experimental }}
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strategy:
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fail-fast: false
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matrix:
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julia-version: ['1.1', '1.2', '1.3']
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julia-arch: [x64]
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julia-version:
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- '1.0' # LTS
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- '1'
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julia-arch: [x86]
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os: [ubuntu-latest, windows-latest, macOS-latest]
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experimental: [false]
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include:
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- julia-version: nightly
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julia-arch: x86
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os: ubuntu-latest
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experimental: true
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steps:
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- uses: actions/checkout@v1.0.0
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- uses: julia-actions/setup-julia@v1
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- name: Checkout Repository
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uses: actions/checkout@v2
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- name: Setup Julia
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uses: julia-actions/setup-julia@v1
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with:
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version: ${{ matrix.julia-version }}
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arch: ${{ matrix.julia-arch }}
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- name: Install dependencies
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run: julia ci_prep.jl
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- uses: julia-actions/julia-runtest@master
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- name: Run Tests
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uses: julia-actions/julia-runtest@latest
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- name: Create CodeCov
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uses: julia-actions/julia-processcoverage@v1
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- name: Upload CodeCov
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uses: codecov/codecov-action@v1
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with:
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file: ./lcov.info
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flags: unittests
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name: codecov-umbrella
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fail_ci_if_error: false
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token: ${{ secrets.CODECOV_TOKEN }}

‎Project.toml

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@@ -14,7 +14,7 @@ BGZFStreams = "0.3"
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BioCore = "2"
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BufferedStreams = "1"
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GenomicFeatures = "2"
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julia = "1.1"
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julia = "1"
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[extras]
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Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

‎README.md

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- An index type for BGZFStream.
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## Installation
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`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.
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However, if you do, `Indexes` is made available to install through BioJulia's package registry.
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By default, Julia's package manager only uses the "General" package registry.
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Your Julia configuration needs to include the BioJulia registry to be able to install the latest version of `Indexes`.
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The Indexes package 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.
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However, if you do, Indexes is made available to install through the [https://github.com/juliaregistries/General](General package registry).
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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:
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```julia
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registry add https://github.com/BioJulia/BioJuliaRegistry.git
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```
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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:
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You can install Indexes from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/).
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Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
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```julia
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add Indexes
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```

‎ci_prep.jl

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This file was deleted.

‎coverage/Project.toml

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‎coverage/coverage.jl

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‎docs/src/index.md

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- An index type for BGZFStream.
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## Installation
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`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.
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However, if you do, `Indexes` is made available to install through BioJulia's package registry.
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By default, Julia's package manager only uses the "General" package registry.
22-
Your Julia configuration needs to include the BioJulia registry to be able to install the latest version of `Indexes`.
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The Indexes package 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.
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However, if you do, Indexes is made available to install through the [https://github.com/juliaregistries/General](General package registry).
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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:
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```julia
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registry add https://github.com/BioJulia/BioJuliaRegistry.git
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```
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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:
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You can install Indexes from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/).
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Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
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```julia
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add Indexes
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```

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