Merge branch 'master' into develop

.github/workflows/Benchmark.yml

@@ -15,6 +15,8 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - name: Install Dependencies
         run: julia -e 'using Pkg; pkg"add PkgBenchmark [email protected]"'
+      - name: Instantiate
+        run: julia --project=benchmark/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Run Benchmarks
         run: julia -e "using BenchmarkCI; BenchmarkCI.judge()"
       - name: Post Results

.github/workflows/Documentation.yml

@@ -10,14 +10,23 @@ on:
 
 jobs:
   Documenter:
+    runs-on: ubuntu-latest
     permissions:
       contents: write
-    name: Documentation
-    runs-on: ubuntu-latest
+      statuses: write
     steps:
       - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-docdeploy@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+      - run: |
+          julia --project=docs -e '
+            using Documenter: DocMeta, doctest
+            using GenomicFeatures
+            DocMeta.setdocmeta!(GenomicFeatures, :DocTestSetup, :(using GenomicFeatures); recursive=true)
+            doctest(GenomicFeatures)'

Project.toml

@@ -1,7 +1,7 @@
 name = "GenomicFeatures"
 uuid = "899a7d2d-5c61-547b-bef9-6698a8d05446"
 authors = ["Kenta Sato <[email protected]>", "Sabrina J. Ward <[email protected]>", "Ciarán O’Mara <[email protected]>"]
-version = "2.1.0"
+version = "3.0.0"
 
 [deps]
 BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
@@ -21,4 +21,4 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Distributions", "Documenter", "Random", "Test"]
+test = ["Distributions", "Random", "Test"]

benchmark/Project.toml

@@ -4,6 +4,3 @@ Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
 PkgBenchmark = "32113eaa-f34f-5b0d-bd6c-c81e245fc73d"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-
-[compat]
-GenomicFeatures = "2"

benchmark/runbenchmarks.jl

@@ -1,7 +1,6 @@
 using Pkg
 
 Pkg.activate(@__DIR__)
-Pkg.instantiate()
 
 Pkg.status()
 

src/GenomicFeatures.jl

@@ -10,7 +10,7 @@ export
     STRAND_BOTH,
 
     GenomicInterval,
-	groupname,
+    groupname,
     seqname,
     leftposition,
     rightposition,
@@ -23,7 +23,7 @@ export
     GenomicIntervalCollection,
     eachoverlap,
     coverage,
-	hasintersection,
+    hasintersection,
 
     isfilled,
     hasseqname,

test/runtests.jl

@@ -1,6 +1,5 @@
 using GenomicFeatures
 using Test
-using Documenter
 
 import Random
 
@@ -561,8 +560,4 @@ end
 
 end #testset "Custom Concrete Types"
 
-# Include doctests.
-DocMeta.setdocmeta!(GenomicFeatures, :DocTestSetup, :(using GenomicFeatures); recursive=true)
-doctest(GenomicFeatures; manual = false)
-
 end #testset GenomicFeatures