Update Continuous Integration workflows

- Includes doctest in tests.

.github/workflows/CompatHelper.yml

@@ -1,17 +1,26 @@
 name: CompatHelper
-
 on:
   schedule:
-    - cron: '0 0 * * *'
-
+    - cron: 0 0 * * *
+  workflow_dispatch:
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - name: Add CompatHelper
-        run: julia --color=yes -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: Run CompatHelper
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "2"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main(master_branch = "master")
+        shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
-        run: julia --color=yes -e 'using CompatHelper; CompatHelper.main(master_branch = "master")'
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/Documentation.yml

@@ -1,5 +1,4 @@
-name: Build Documentation
-
+name: Documentation
 on:
   push:
     branches:
@@ -10,17 +9,13 @@ on:
   pull_request:
 
 jobs:
-  build:
+  Documenter:
+    name: Documentation
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: '1'
-      - name: Install Dependencies
-        run: julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and Deploy
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
         env:
-          # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
-        run: julia --color=yes --project=docs/ docs/make.jl
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/TagBot.yml

@@ -1,12 +1,17 @@
 name: TagBot
+
 on:
-  schedule:
-    - cron: '0 0 * * *'
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+
 jobs:
   TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
     runs-on: ubuntu-latest
     steps:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.TAGBOT_KEY }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/UnitTests.yml

@@ -6,6 +6,7 @@ on:
 
 jobs:
   test:
+    name: Julia ${{ matrix.julia-version }} - ${{ matrix.os }} - ${{ matrix.julia-arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
     continue-on-error: ${{ matrix.experimental }}
     strategy:
@@ -16,6 +17,9 @@ jobs:
           - '1'
         julia-arch: [x64, x86]
         os: [ubuntu-latest, windows-latest, macOS-latest]
+        exclude:
+          - os: macOS-latest
+            julia-arch: x86
         experimental: [false]
         include:
           - julia-version: nightly
@@ -31,7 +35,7 @@ jobs:
         with:
           version: ${{ matrix.julia-version }}
       - name: Run Tests
-        uses: julia-actions/julia-runtest@latest
+        uses: julia-actions/julia-runtest@v1
       - name: Create CodeCov
         uses: julia-actions/julia-processcoverage@v1
       - name: Upload CodeCov

Project.toml

@@ -26,8 +26,9 @@ TranscodingStreams = "0.6, 0.7, 0.8, 0.9"
 julia = "1"
 
 [extras]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 FormatSpecimens = "3372ea36-2a1a-11e9-3eb7-996970b6ffbd"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["FormatSpecimens", "Test"]
+test = ["Documenter", "FormatSpecimens", "Test"]

docs/Project.toml

@@ -3,4 +3,4 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [compat]
-Documenter = "0.24"
+Documenter = "0.27"

docs/make.jl

@@ -2,6 +2,8 @@ using Pkg
 using Documenter, XAM
 
 makedocs(
+    checkdocs = :all,
+    linkcheck = true,
     format = Documenter.HTML(
         edit_link = "develop"
     ),

test/runtests.jl

@@ -1,4 +1,5 @@
 using Test
+using Documenter
 
 using BioGenerics
 using FormatSpecimens
@@ -23,6 +24,12 @@ function randrange(range)
 end
 
 
-include("test_sam.jl")
-include("test_bam.jl")
-include("test_crosscheck.jl")
+@testset "XAM" begin
+    include("test_sam.jl")
+    include("test_bam.jl")
+    include("test_crosscheck.jl")
+
+    # Include doctests.
+    DocMeta.setdocmeta!(XAM, :DocTestSetup, :(using XAM); recursive=true)
+    doctest(XAM; manual = false)
+end