Merge branch 'release/v2.3.0'

Author: CiaranOMara

.github/workflows/CompatHelper.yml

@@ -3,24 +3,43 @@ 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 = "2"
+          version = "3"
           Pkg.add(; name, uuid, version)
         shell: julia --color=yes {0}
       - name: "Run CompatHelper"
         run: |
           import CompatHelper
-          CompatHelper.main(master_branch = "master")
+          CompatHelper.main()
         shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/TagBot.yml

@@ -1,11 +1,25 @@
 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'
@@ -14,4 +28,6 @@ jobs:
       - 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 }}

.github/workflows/UnitTests.yml

@@ -4,6 +4,11 @@ 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 }}
@@ -13,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         julia-version:
-          - '1.0' # LTS
+          - '1.6' # LTS
           - '1'
         julia-arch: [x64, x86]
         os: [ubuntu-latest, windows-latest, macOS-latest]
@@ -29,17 +34,23 @@ jobs:
 
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v2
+        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@v1
+        uses: codecov/codecov-action@v4
         with:
-          file: ${{ steps.coverage-processing.outputs.lcov-file }}
-          fail_ci_if_error: false
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false

Project.toml

@@ -1,7 +1,7 @@
 name = "Bedgraph"
 uuid = "0bcc2ff6-69eb-520d-bede-0374fc5bd2fd"
 authors = ["Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
-version = "2.2.0"
+version = "2.3.0"
 
 [compat]
 julia = "0.7, 1"

src/record.jl

@@ -33,8 +33,14 @@ end
 
 Base.convert(::Type{NamedTuple}, record::Record) = convert(NamedTuple{(:chrom, :first, :last, :value)}, record)
 
-function Base.convert(::Type{Record}, nt::NamedTuple{(:chrom, :first, :last, :value)})
-    return Record(nt.chrom, nt.first, nt.last, nt.value)
+function Base.convert(::Type{T}, nt::NamedTuple{(:chrom, :first, :last, :value),Tuple{String, Int, Int, R}}) where {R <: Real, T<: Bedgraph.Record}
+    @debug "Convert - strictly named tuples."
+    return T(nt.chrom, nt.first, nt.last, nt.value)
+end
+
+function Base.convert(::Type{T}, nt::NamedTuple{names,Tuple{String, Int, Int, R}}) where {R <: Real, names, T<: Bedgraph.Record}
+    @debug "Convert - loosely named tuples."
+    return T(nt[1], nt[2], nt[3], nt[4])
 end
 
 function Base.convert(::Type{Record}, str::AbstractString)

test/runtests.jl

@@ -84,8 +84,9 @@ end
 
 	# Seek test.
 	open(Bag.file, "r") do io
+		@info "" readline(io, keep = true)
 	    seek(io, Record)
-	    # @test position(io) == 536 #TOOD: determine why the returned position on windows machines is 545.
+	    @test position(io) == 536 || position(io) == 545 #TODO: determine why the returned position on windows machines is 545.
 	    @test readline(io) == Bag.line1
 	end
 
@@ -286,26 +287,32 @@ end #testset Internal Helpers
 
 @testset "NamedTuple" begin
 
-	record = Record(Bag.line1)
+	# Check strictly named fields.
 
-	nt = (
-		chrom = Bag.chroms[1],
-		first = Bag.firsts[1],
-		last = Bag.lasts[1],
-		value = Bag.values[1],
+	nt_strict_names = (
+		chrom = Bag.record1.chrom, 
+		first=Bag.record1.first, 
+		last=Bag.record1.last, 
+		value=Bag.record1.value
 	)
 
-	@test record == Record(nt)
+	@test convert(NamedTuple{(:chrom, :first, :last, :value)}, Bag.record1) == convert(NamedTuple, Bag.record1) == nt_strict_names
+	@test Bag.record1 == convert(Record, nt_strict_names)
+	@test Bag.record1 == Record(nt_strict_names)
 
-	@test convert(NamedTuple{(:chrom, :first, :last, :value)}, record) == convert(NamedTuple, record) == nt
+	# Check loosely named fields.
 
-	# Check renaming of fields.
-	@test convert(NamedTuple{(:chrom, :left, :right, :value)}, record) == (
-		chrom = Bag.chroms[1],
-		left = Bag.firsts[1],
-		right = Bag.lasts[1],
-		value = Bag.values[1],
+	nt_loose_names = (
+		chrom = Bag.record1.chrom, 
+		left=Bag.record1.first, 
+		right=Bag.record1.last, 
+		value=Bag.record1.value
 	)
+
+	@test convert(NamedTuple{(:chrom, :left, :right, :value)}, Bag.record1) == nt_loose_names
+	@test Bag.record1 == convert(Record, nt_loose_names)
+	@test Bag.record1 == Record(nt_loose_names)
+
 end
 
 end # total testset