Merge branch 'release/v2.0.3'

.github/workflows/Benchmark.yml

@@ -0,0 +1,27 @@
+name: Run Benchmarks
+
+on:
+  - push
+  - pull_request
+
+jobs:
+  Benchmark:
+    runs-on: ubuntu-latest
+    env:
+      JULIA_DEBUG: BenchmarkCI
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: 1
+      - name: Install Dependencies
+        run: julia -e 'using Pkg; pkg"add PkgBenchmark [email protected]"'
+      - name: Run Benchmarks
+        run: julia -e "using BenchmarkCI; BenchmarkCI.judge()"
+      - name: Post Results
+        if: ${{ github.event_name == 'pull_request'}}
+        run: julia -e "using BenchmarkCI; BenchmarkCI.postjudge()"
+      - name: Print Judgement
+        run: julia -e 'using BenchmarkCI; BenchmarkCI.displayjudgement()'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/CompatHelper.yml

@@ -9,22 +9,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Add CompatHelper
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+        run: julia --color=yes -e 'using Pkg; Pkg.add("CompatHelper")'
       - name: Run CompatHelper
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: julia -e '
-                using CompatHelper, Pkg;
-                my_registries = [
-                    Pkg.RegistrySpec(
-                        name = "BioJuliaRegistry",
-                        uuid = "ccbd2cc2-2954-11e9-1ccf-f3e7900901ca",
-                        url = "https://github.com/BioJulia/BioJuliaRegistry.git"
-                    ),
-                    Pkg.RegistrySpec(
-                        name = "General",
-                        uuid = "23338594-aafe-5451-b93e-139f81909106",
-                        url = "https://github.com/JuliaRegistries/General.git"
-                    )
-                ];
-                CompatHelper.main(; registries = my_registries, master_branch = "master");'
+          COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
+        run: julia --color=yes -e 'using CompatHelper; CompatHelper.main(master_branch = "master")'

.github/workflows/Documentation.yml

@@ -1,4 +1,4 @@
-name: Documentation
+name: Build Documentation
 
 on:
   push:
@@ -14,14 +14,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - uses: julia-actions/setup-julia@v1
         with:
-          version: '1.4'
-      - name: Install dependencies
-        run: |
-          julia ci_prep.jl;
-          julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and deploy
+          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
         env:
           # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key

.github/workflows/TagBot.yml

@@ -1,7 +1,7 @@
 name: TagBot
 on:
   schedule:
-    - cron: '0 * * * *'
+    - cron: 0 0 * * *
 jobs:
   TagBot:
     runs-on: ubuntu-latest
@@ -10,4 +10,3 @@ jobs:
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           ssh: ${{ secrets.TAGBOT_KEY }}
-          registry: BioJulia/BioJuliaRegistry

.github/workflows/UnitTests.yml

@@ -1,4 +1,4 @@
-name: Unit tests
+name: Unit Tests
 
 on:
   - push
@@ -7,20 +7,30 @@ on:
 jobs:
   test:
     runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.experimental }}
     strategy:
+      fail-fast: false
       matrix:
-        julia-version: ['1.1', '1.2', '1.3', '1.4']
+        julia-version:
+          - '1.0' # LTS
+          - '1'
         julia-arch: [x86]
         os: [ubuntu-latest, windows-latest, macOS-latest]
+        experimental: [false]
+        include:
+          - julia-version: nightly
+            julia-arch: x86
+            os: ubuntu-latest
+            experimental: true
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.julia-version }}
-      - name: Install dependencies
-        run: julia ci_prep.jl
-      - name: Run tests
+      - name: Run Tests
         uses: julia-actions/julia-runtest@latest
       - name: Create CodeCov
         uses: julia-actions/julia-processcoverage@v1

.gitignore

@@ -24,3 +24,7 @@ docs/site/
 Manifest.toml
 
 .DS_Store
+
+.benchmarkci
+benchmark/*.json
+benchmark/results

CHANGELOG.md

@@ -6,6 +6,16 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## [Unreleased]
 
+## [2.0.3] - 2020-06-13
+
+### Added
+- Julia LTS Support
+- Benchmarks
+
+### Changed
+- Documentation.
+- Updated CI for General Repository.
+
 ## [2.0.2] - 2020-05-21
 
 ### Fixed

Project.toml

@@ -1,7 +1,7 @@
 name = "GenomicFeatures"
 uuid = "899a7d2d-5c61-547b-bef9-6698a8d05446"
 authors = ["Kenta Sato <[email protected]>", "Ben J. Ward <[email protected]>", "Ciarán O’Mara <[email protected]>"]
-version = "2.0.2"
+version = "2.0.3"
 
 [deps]
 BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
@@ -12,7 +12,7 @@ IntervalTrees = "524e6230-43b7-53ae-be76-1e9e4d08d11b"
 BioGenerics = "0.1"
 DataStructures = "0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17"
 IntervalTrees = "1.0"
-julia = "1.1"
+julia = "1"
 
 [extras]
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"

README.md

@@ -12,15 +12,8 @@ The GenomicFeatures package provides utilities for working with interval based g
 It builds on [IntervalTrees](https://github.com/biojulia/intervaltrees.jl) to provide a data-structures and algorithms for various formats such as [BED](https://github.com/biojulia/bed.jl), [GFF3](https://github.com/biojulia/gff3.jl), [bigWig](https://github.com/biojulia/bigwig.jl) and [bigBed](https://github.com/biojulia/bigbed.jl).  
 
 ## Installation
-Releases of GenomicFeatures version 2.0.0 and above are registered and made available to install through BioJulia's package registry.
-By default, Julia's package manager only uses the "General" package registry.
-
-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:
-```julia
-registry add https://github.com/BioJulia/BioJuliaRegistry.git
-```
-
-After adding the registry to your configuration, you can install GenomicFeatures while in [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/) with the following:
+You can install the GenomicFeatures package 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:
 ```julia
 add GenomicFeatures
 ```

benchmark/Project.toml

@@ -0,0 +1,9 @@
+[deps]
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+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/benchmarks.jl

@@ -0,0 +1,55 @@
+using BenchmarkTools
+# using BenchmarkTools: @benchmarkable, BenchmarkGroup
+
+using GenomicFeatures
+
+include(joinpath(@__DIR__, "..", "test", "Utilities.jl"))
+
+import ..Utilities: random_intervals
+
+N = 1000
+SEED = 1234
+SEQNAMES = "chr" .* string.(1:3)
+
+intervals = random_intervals(SEQNAMES, 1000, N, SEED)
+intervals_sorted = sort(intervals)
+
+SUITE = BenchmarkGroup()
+
+let suite = SUITE["accessors"] = BenchmarkGroup()
+    s0 = suite["$(typeof(intervals))"] = BenchmarkGroup()
+    s0["seqname"] = @benchmarkable(seqname.($intervals))
+    s0["leftposition"] = @benchmarkable(leftposition.($intervals))
+    s0["rightposition"] = @benchmarkable(rightposition.($intervals))
+    s0["strand"] = @benchmarkable(strand.($intervals))
+    s0["metadata"] = @benchmarkable(metadata.($intervals))
+end
+
+let suite = SUITE["sort"] = BenchmarkGroup()
+    suite["$(typeof(intervals))"] = @benchmarkable(sort(i), setup=(i = copy($intervals)))
+end
+
+let suite = SUITE["insert"] = BenchmarkGroup()
+    suite["shorthand"] = @benchmarkable(IntervalCollection($intervals_sorted))
+    suite["type"] = @benchmarkable(IntervalCollection{Int}($intervals_sorted))
+end
+
+let suite = SUITE["push"] = BenchmarkGroup()
+    suite["$(typeof(intervals))"] = @benchmarkable([push!(col, i) for i in $intervals], setup=(col=IntervalCollection{Int}()))
+end
+
+let suite = SUITE["eachoverlap"] = BenchmarkGroup()
+    intervals_a = intervals_sorted
+    intervals_b = sort(random_intervals(SEQNAMES, 1000, N, SEED+1))
+
+    col_a = IntervalCollection(intervals_a)
+    col_b = IntervalCollection(intervals_b)
+
+    As = [intervals_a, col_a]
+    Bs = [intervals_b, col_b]
+
+    for (A, B) in Iterators.product(As,Bs)
+        str = "$(typeof(A)), $(typeof(B))"
+        suite[str] = @benchmarkable(collect(eachoverlap($A,$B)))
+    end
+end

benchmark/runbenchmarks.jl

@@ -0,0 +1,24 @@
+using Pkg
+
+Pkg.activate(@__DIR__)
+Pkg.instantiate()
+
+Pkg.status()
+
+using PkgBenchmark
+
+results = benchmarkpkg(
+    dirname(@__DIR__),
+    BenchmarkConfig(
+        env = Dict(
+            "JULIA_NUM_THREADS" => "1",
+            "OMP_NUM_THREADS" => "1",
+        ),
+    )
+)
+
+dir_results = joinpath(@__DIR__, "results")
+mkpath(dir_results)
+
+writeresults(joinpath(dir_results, "$(results.date).json"), results)
+export_markdown(joinpath(dir_results, "$(results.date).md"), results)

docs/make.jl

@@ -5,6 +5,8 @@ Pkg.instantiate()
 
 using Documenter, GenomicFeatures
 
+DocMeta.setdocmeta!(GenomicFeatures, :DocTestSetup, :(using GenomicFeatures); recursive=true)
+
 makedocs(
     format = Documenter.HTML(
         edit_link = :commit

docs/src/index.md

@@ -12,15 +12,8 @@ The GenomicFeatures package provides utilities for working with interval based g
 It builds on [IntervalTrees](https://github.com/biojulia/intervaltrees.jl) to provide a data-structures and algorithms for various formats such as [BED](https://github.com/biojulia/bed.jl), [GFF3](https://github.com/biojulia/gff3.jl), [bigWig](https://github.com/biojulia/bigwig.jl) and [bigBed](https://github.com/biojulia/bigbed.jl).  
 
 ## Installation
-Releases of GenomicFeatures version 2.0.0 and above are registered and made available to install through BioJulia's package registry.
-By default, Julia's package manager only uses the "General" package registry.
-
-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:
-```julia
-registry add https://github.com/BioJulia/BioJuliaRegistry.git
-```
-
-After adding the registry to your configuration, you can install GenomicFeatures while in [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/) with the following:
+You can install the GenomicFeatures package 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:
 ```julia
 add GenomicFeatures
 ```