Merge branch 'release/v2.4.0'

CiaranOMara · May 5, 2024 · 0302c76 · 0302c76 · CiaranOMara · May 5, 2024
2 parents 8e89af3 + b1a1c47
commit 0302c76
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diff --git a/.github/CompatHelper.yml b/.github/CompatHelper.yml
@@ -0,0 +1,45 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
diff --git a/.github/TagBot.yml b/.github/TagBot.yml
@@ -0,0 +1,33 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+    inputs:
+      lookback:
+        default: "3"
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
+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 }}
+          # Edit the following line to reflect the actual name of the GitHub Secret containing your private key
+          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          # ssh: ${{ secrets.NAME_OF_MY_SSH_PRIVATE_KEY_SECRET }}
diff --git a/.github/UnitTests.yml b/.github/UnitTests.yml
@@ -0,0 +1,56 @@
+name: Unit Tests
+
+on:
+  - push
+  - pull_request
+
+# needed to allow julia-actions/cache to delete old caches that it has created
+permissions:
+  actions: write
+  contents: read
+
+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:
+      fail-fast: false
+      matrix:
+        julia-version:
+          - '1.6' # LTS
+          - '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
+            julia-arch: x64
+            os: ubuntu-latest
+            experimental: true
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+          arch: ${{ matrix.julia-arch }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - name: Run Tests
+        uses: julia-actions/julia-runtest@v1
+        with:
+          annotate: true
+      - name: Create CodeCov
+        uses: julia-actions/julia-processcoverage@v1
+      - name: Upload CodeCov
+        uses: codecov/codecov-action@v4
+        with:
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "BedgraphFiles"
 uuid = "85eb9095-274b-55ce-be28-9e90f41ac741"
 authors = ["Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
-version = "2.3.1"
+version = "2.4.0"
 
 [deps]
 Bedgraph = "0bcc2ff6-69eb-520d-bede-0374fc5bd2fd"
@@ -14,7 +14,7 @@ TableTraits = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
 TableTraitsUtils = "382cd787-c1b6-5bf2-a167-d5b971a19bda"
 
 [compat]
-Bedgraph = "1.2"
+Bedgraph = "2.3"
 DataValues = "0.4"
 FileIO = "1.0.1"
 IterableTables = "0.9, 0.10, 0.11, 1"

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # BedgraphFiles.jl
 
 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
-![Unit Tests](https://github.com/CiaranOMara/BedgraphFiles.jl/workflows/Unit%20Tests/badge.svg?branch=master)
+[![Unit Tests](https://github.com/CiaranOMara/BedgraphFiles.jl/actions/workflows/UnitTests.yml/badge.svg?branch=master)](https://github.com/CiaranOMara/BedgraphFiles.jl/actions/workflows/UnitTests.yml)
 [![codecov](https://codecov.io/gh/CiaranOMara/BedgraphFiles.jl/branch/master/graph/badge.svg?branch=master)](https://codecov.io/gh/CiaranOMara/BedgraphFiles.jl?branch=master)
 
 > This project follows the [semver](http://semver.org) pro forma and uses the [git-flow branching model](http://nvie.com/git-model "original
@@ -65,7 +65,7 @@ using FileIO, BedgraphFiles, DataTables, IndexedTables, Gadfly
 dt = DataTable(load("data.bedgraph"))
 
 # Load into an IndexedTable
-it = IndexedTable(load("data.bedgraph"))
+it = table(load("data.bedgraph"))
 
 # Plot directly with Gadfly
 plot(load("data.bedgraph"), xmin=:leftposition, xmax=:rightposition, y=:value, Geom.bar)

diff --git a/src/BedgraphFiles.jl b/src/BedgraphFiles.jl
@@ -71,16 +71,6 @@ function Base.collect(T::Type, x::BedgraphFile)
     return collect(T, getiterator(x))
 end
 
-function Base.convert(::Type{T}, nt::NamedTuple{(:chrom, :first, :last, :value),Tuple{String,Int64,Int64,R}}) where {R <: Real, T<: Bedgraph.Record}
-    @debug "Convert - strict."
-    return T(nt.chrom, nt.first, nt.last, nt.value)
-end
-
-function Base.convert(::Type{T}, nt::NamedTuple{names,Tuple{String,Int64,Int64,R}}) where {R <: Real, names, T<: Bedgraph.Record}
-    @debug "Convert - names."
-    return T(nt[1], nt[2], nt[3], nt[4])
-end
-
 function Vector{T}(x) where {T <: Bedgraph.Record}
     return collect(T, getiterator(x))
 end
@@ -96,7 +86,7 @@ function save(file::BedgraphFileFormat, records::Vector{<:Bedgraph.Record}; bump
 
     sort!(records)
 
-    header = Bedgraph.generateBasicHeader(records, bump_forward = bump_forward) #TODO: consolidate header generation and determine whether there is a need for bump_forward.
+    header = Bedgraph.generate_basic_header(records, bump_forward = bump_forward) #TODO: consolidate header generation and determine whether there is a need for bump_forward.
 
     return save(file, header, records)
 end

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -76,10 +76,6 @@ using .Bag
     # Check return of data from save method.
     @test Bag.records == Bag.records |> save(Bag.tmp_output_path)
 
-    # Check convert
-    @test Bag.record == convert(Bedgraph.Record, (chrom = "chr1", first=1, last=1, value=0))
-    @test Bag.record == convert(Bedgraph.Record, (chrom = "chr1", left=1, right=1, value=0))
-
     @testset "Integrations" begin
         include("integrations/test-Tables.jl")
         include("integrations/test-QueryOperators.jl")