Version 0.3.0: Use ViennaRNA.jl v0.11.0, ViennaRNA_jll v2.6.2, add Aqua tests (#9)

* Add Aqua.test_all to tests

* Do not run some tests from Aqua.test_all that fail on julia-1.6

* Update to ViennaRNA.jl 0.11

* v0.3.0

Author: marcom

Project.toml

@@ -1,7 +1,7 @@
 name = "PlotRNA"
 uuid = "eab79ae3-43af-4078-b4a3-b180fd2797a7"
 authors = ["Marco Matthies <[email protected]>"]
-version = "0.2.2"
+version = "0.3.0"
 
 [deps]
 BioStockholm = "eeb925a3-6f9d-43e6-829e-e0ea03b76ecf"
@@ -14,7 +14,16 @@ Scratch = "6c6a2e73-6563-6170-7368-637461726353"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 ViennaRNA = "05a721ad-238d-4945-8c85-8b5c1fff3465"
 
+[weakdeps]
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
+
+[extensions]
+CairoMakieExt = "CairoMakie"
+UnicodePlotsExt = "UnicodePlots"
+
 [compat]
+Aqua = "0.6"
 BioStockholm = "0.1"
 CairoMakie = "0.10"
 ColorSchemes = "3.18"
@@ -24,23 +33,16 @@ R2R_jll = "=1.0.6"
 Requires = "1.3"
 Scratch = "1.1"
 UnicodePlots = "3"
-ViennaRNA = "0.9,0.10"
+ViennaRNA = "0.11"
 julia = "1.6"
 
-[extensions]
-CairoMakieExt = "CairoMakie"
-UnicodePlotsExt = "UnicodePlots"
-
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 BioStockholm = "eeb925a3-6f9d-43e6-829e-e0ea03b76ecf"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
 ViennaRNA = "05a721ad-238d-4945-8c85-8b5c1fff3465"
 
 [targets]
-test = ["BioStockholm", "CairoMakie", "Test", "UnicodePlots", "ViennaRNA"]
-
-[weakdeps]
-CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
-UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
+test = ["Aqua", "BioStockholm", "CairoMakie", "Test", "UnicodePlots", "ViennaRNA"]

README.md

@@ -1,6 +1,7 @@
 # PlotRNA.jl
 
 [![Build Status](https://github.com/marcom/PlotRNA.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/marcom/PlotRNA.jl/actions/workflows/CI.yml?query=branch%3Amain)
+[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 
 Plot nucleic acid secondary structures with Julia.
 

test/aqua.jl

@@ -0,0 +1,15 @@
+import Aqua
+using PlotRNA
+
+@testset "Aqua.test_all" begin
+    showtestset()
+    if VERSION >= v"1.7"
+        Aqua.test_all(PlotRNA)
+    else
+        # Aqua-0.6.4 on julia-1.6 complains about method ambiguities
+        # and Project.toml formatting, julia-1.9 does not
+        # Ref for Project.toml formatting: https://github.com/JuliaTesting/Aqua.jl/issues/105
+        # Method ambiguities might be due to the compiler in julia-1.6 being a lot older
+        Aqua.test_all(PlotRNA; ambiguities=false, project_toml_formatting=false)
+    end
+end

test/runtests.jl

@@ -6,6 +6,7 @@ showtestset() = println(" "^(2 * Test.get_testset_depth()), "testing ",
 
 @testset verbose=true "PlotRNA" begin
     showtestset()
+    include("aqua.jl")
     include("plot_structure.jl")
     if isnothing(Sys.which("java"))
         @warn "Can't find java executable, skipping VARNA tests"