Drop pre-LTS Julia support (#311)

This allows us to simplify CI, since we can run the oldest supported Julia
version on aarch64 macos, and also allows us to mark const field const.

Also, remove various downstream tests:
    - BioStructures.jl does not depend on BioSequences.jl directly, but has it
      as a weakdep. And the current downstream tests cannot tests weakdeps.
    - GenomicAnnotation.jl contains a Base piracy which breaks the package on
      Julia 1.10
    - PhyloNetworks, since it makes CI take 1h+
    - The remaining two are not compatible with Julia 1.10 or Julia 1.11.

.github/workflows/Downstream.yml

@@ -19,21 +19,16 @@ jobs:
         package:
           - {user: bioinfologics, repo: Pseudoseq.jl, group: BioSequences}
           - {user: BioJulia, repo: BioAlignments.jl, group: BioSequences}
-          - {user: BioJulia, repo: BioStructures.jl, group: BioSequences}
           - {user: BioJulia, repo: FASTX.jl, group: BioSequences}
           - {user: BioJulia, repo: GenomeGraphs.jl, group: BioSequences}
-          - {user: BioJulia, repo: GenomicAnnotations.jl, group: BioSequences}
           - {user: BioJulia, repo: GFF3.jl, group: BioSequences}
           - {user: BioJulia, repo: KmerAnalysis.jl, group: BioSequences}
           - {user: BioJulia, repo: ReadDatastores.jl, group: BioSequences}
           - {user: BioJulia, repo: TwoBit.jl, group: BioSequences}
           - {user: BioJulia, repo: XAM.jl, group: BioSequences}
-          - {user: crsl4, repo: PhyloNetworks.jl, group: BioSequences}
           - {user: JuliaHealth, repo: CAOS.jl, group: BioSequences}
           - {user: nguyetdang, repo: BioGraph.jl, group: BioSequences}
           - {user: vanOosterhoutLab, repo: SpeedDate.jl, group: BioSequences}
-          - {user: varnerlab, repo: JUGRNModelGenerator.jl, group: BioSequences}
-          - {user: varnerlab, repo: VLConstraintBasedModelGenerationUtilities.jl, group: BioSequences}
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1

.github/workflows/UnitTests.yml

@@ -11,8 +11,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        julia-version:
-          - '1'
+        julia-version: ['1', '1.10']
         os: [ubuntu-latest, macOS-latest, windows-latest]
         experimental: [false]
         include:
@@ -22,19 +21,6 @@ jobs:
             os: ubuntu-latest
             experimental: true
             fail_ci_if_error: false
-          # Windows is extremely slow on 1.6, so we skip this combination,
-          # since it increases CI time by 5x
-          - julia-version: '1.7'
-            os: windows-latest
-            experimental: false
-          # Oldest supported version
-          - julia-version: '1.5'
-            os: ubuntu-latest
-            experimental: false
-          # MacOS Aarch64 reached Tier1 support of Julia in version 1.9
-          - julia-version: '1.9'
-            os: macOS-latest
-            experimental: false
 
     steps:
       - name: Checkout Repository

Project.toml

@@ -15,7 +15,7 @@ PrecompileTools = "1"
 Random = "1.5"
 StableRNGs = "0.1, 1.0"
 Twiddle = "1.1.1"
-julia = "1.5"
+julia = "1.10"
 
 [extras]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"