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Update Continuous Integration workflows
- Includes doctest in tests.
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parent
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commit
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8 changed files with 52 additions and 29 deletions
25
.github/workflows/CompatHelper.yml
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25
.github/workflows/CompatHelper.yml
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@ -1,17 +1,26 @@
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name: CompatHelper
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on:
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schedule:
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- cron: '0 0 * * *'
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- cron: 0 0 * * *
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workflow_dispatch:
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jobs:
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CompatHelper:
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runs-on: ubuntu-latest
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steps:
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- name: 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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- name: "Install CompatHelper"
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run: |
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import Pkg
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name = "CompatHelper"
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uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
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version = "2"
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Pkg.add(; name, uuid, version)
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shell: julia --color=yes {0}
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- name: "Run CompatHelper"
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run: |
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import CompatHelper
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CompatHelper.main(master_branch = "master")
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shell: julia --color=yes {0}
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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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")'
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COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
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# COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
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19
.github/workflows/Documentation.yml
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19
.github/workflows/Documentation.yml
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@ -1,5 +1,4 @@
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name: Build Documentation
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name: Documentation
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on:
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push:
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branches:
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@ -10,17 +9,13 @@ on:
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pull_request:
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jobs:
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build:
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Documenter:
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name: Documentation
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runs-on: ubuntu-latest
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steps:
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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: '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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- uses: julia-actions/julia-buildpkg@v1
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- uses: julia-actions/julia-docdeploy@v1
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env:
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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 --color=yes --project=docs/ docs/make.jl
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
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11
.github/workflows/TagBot.yml
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11
.github/workflows/TagBot.yml
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@ -1,12 +1,17 @@
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name: TagBot
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on:
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schedule:
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- cron: '0 0 * * *'
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issue_comment:
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types:
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- created
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workflow_dispatch:
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jobs:
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TagBot:
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if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
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runs-on: ubuntu-latest
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steps:
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- uses: JuliaRegistries/TagBot@v1
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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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ssh: ${{ secrets.DOCUMENTER_KEY }}
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6
.github/workflows/UnitTests.yml
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6
.github/workflows/UnitTests.yml
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@ -6,6 +6,7 @@ on:
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jobs:
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test:
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name: Julia ${{ matrix.julia-version }} - ${{ matrix.os }} - ${{ matrix.julia-arch }} - ${{ github.event_name }}
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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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- '1'
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julia-arch: [x64, x86]
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os: [ubuntu-latest, windows-latest, macOS-latest]
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exclude:
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- os: macOS-latest
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julia-arch: x86
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experimental: [false]
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include:
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- julia-version: nightly
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@ -31,7 +35,7 @@ jobs:
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with:
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version: ${{ matrix.julia-version }}
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- name: Run Tests
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uses: julia-actions/julia-runtest@latest
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uses: julia-actions/julia-runtest@v1
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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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@ -26,8 +26,9 @@ TranscodingStreams = "0.6, 0.7, 0.8, 0.9"
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julia = "1"
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[extras]
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Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
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FormatSpecimens = "3372ea36-2a1a-11e9-3eb7-996970b6ffbd"
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Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
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[targets]
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test = ["FormatSpecimens", "Test"]
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test = ["Documenter", "FormatSpecimens", "Test"]
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@ -3,4 +3,4 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
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Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
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[compat]
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Documenter = "0.24"
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Documenter = "0.27"
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@ -2,6 +2,8 @@ using Pkg
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using Documenter, XAM
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makedocs(
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checkdocs = :all,
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linkcheck = true,
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format = Documenter.HTML(
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edit_link = "develop"
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),
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@ -1,4 +1,5 @@
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using Test
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using Documenter
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using BioGenerics
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using FormatSpecimens
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@ -23,6 +24,12 @@ function randrange(range)
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end
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include("test_sam.jl")
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include("test_bam.jl")
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include("test_crosscheck.jl")
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@testset "XAM" begin
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include("test_sam.jl")
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include("test_bam.jl")
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include("test_crosscheck.jl")
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# Include doctests.
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DocMeta.setdocmeta!(XAM, :DocTestSetup, :(using XAM); recursive=true)
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doctest(XAM; manual = false)
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end
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