diff --git a/.github/workflows/Benchmark.yml b/.github/workflows/Benchmark.yml index a3369af8..b4adfd54 100644 --- a/.github/workflows/Benchmark.yml +++ b/.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 BenchmarkCI@0.1"' + - 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 diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml index 693e1637..fe705ada 100644 --- a/.github/workflows/Documentation.yml +++ b/.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)' diff --git a/Project.toml b/Project.toml index 05c87ea9..4166d74b 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "GenomicFeatures" uuid = "899a7d2d-5c61-547b-bef9-6698a8d05446" authors = ["Kenta Sato ", "Sabrina J. Ward ", "Ciarán O’Mara "] -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"] diff --git a/benchmark/Project.toml b/benchmark/Project.toml index cb67d234..c21e1d63 100644 --- a/benchmark/Project.toml +++ b/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" diff --git a/benchmark/runbenchmarks.jl b/benchmark/runbenchmarks.jl index a9fa569b..890e9adc 100644 --- a/benchmark/runbenchmarks.jl +++ b/benchmark/runbenchmarks.jl @@ -1,7 +1,6 @@ using Pkg Pkg.activate(@__DIR__) -Pkg.instantiate() Pkg.status() diff --git a/src/GenomicFeatures.jl b/src/GenomicFeatures.jl index 4184f041..10f63c2a 100644 --- a/src/GenomicFeatures.jl +++ b/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, diff --git a/test/runtests.jl b/test/runtests.jl index a1bd14c2..a617b80e 100644 --- a/test/runtests.jl +++ b/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