Merge pull request #108 from ArnoStrouwen/qa

typos and Aqua CI

.github/dependabot.yml

@@ -5,3 +5,6 @@ updates:
     directory: "/" # Location of package manifests
     schedule:
       interval: "weekly"
+    ignore:
+      - dependency-name: "crate-ci/typos"
+        update-types: ["version-update:semver-patch"]

.github/workflows/SpellCheck.yml

@@ -0,0 +1,13 @@
+name: Spell Check
+
+on: [pull_request]
+
+jobs:
+  typos-check:
+    name: Spell Check with Typos
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Actions Repository
+        uses: actions/checkout@v3
+      - name: Check spelling
+        uses: crate-ci/[email protected] 

.typos.toml

@@ -0,0 +1 @@
+[default.extend-words]

Project.toml

@@ -11,13 +11,25 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 
 [compat]
+Aqua = "0.8"
+CSVFiles = "1"
 Catalyst = "13"
+DataFrames = "1"
 DataStructures = "0.18"
+DiffEqBase = "6"
+LinearAlgebra = "1"
 ModelingToolkit = "8.47"
+OrdinaryDiffEq = "6"
+Plots = "1"
+SparseArrays = "1"
+Sundials = "4"
 Symbolics = "5.0.3"
+TimerOutputs = "0.5"
+Test = "1"
 julia = "1.6"
 
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 CSVFiles = "5d742f6a-9f54-50ce-8119-2520741973ca"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
@@ -29,4 +41,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 
 [targets]
-test = ["CSVFiles", "DataFrames", "DiffEqBase", "LinearAlgebra", "OrdinaryDiffEq", "Plots", "Sundials", "Test", "TimerOutputs"]
+test = ["Aqua", "CSVFiles", "DataFrames", "DiffEqBase", "LinearAlgebra", "OrdinaryDiffEq", "Plots", "Sundials", "Test", "TimerOutputs"]

src/parsing_routines_matrixnetworks.jl

@@ -187,7 +187,7 @@ function loadrxnetwork(cmn::ComplexMatrixNetwork{S, T, U, V, W, X};
 
     rxs = Vector{Reaction}(undef, numrxs)
     sc_ind = argmin(cmn.incidencemat, dims = 1)  # cartesian indices of substrate complexes
-    pc_ind = argmax(cmn.incidencemat, dims = 1)  # cartesian indicies of products complexes
+    pc_ind = argmax(cmn.incidencemat, dims = 1)  # cartesian indices of products complexes
     for i in 1:numrxs
 
         # substrate index for i'th reaction in species(rn)
@@ -232,7 +232,7 @@ function loadrxnetwork(cmn::ComplexMatrixNetwork{S, T, U, V, W, X};
 
     rxs = Vector{Reaction}(undef, numrxs)
     sc_ind = argmin(cmn.incidencemat, dims = 1)  # cartesian indices of substrate complexes
-    pc_ind = argmax(cmn.incidencemat, dims = 1)  # cartesian indicies of products complexes
+    pc_ind = argmax(cmn.incidencemat, dims = 1)  # cartesian indices of products complexes
     rows = rowvals(cmn.stoichmat)
     vals = nonzeros(cmn.stoichmat)
     for i in 1:numrxs

test/qa.jl

@@ -0,0 +1,11 @@
+using ReactionNetworkImporters, Aqua
+@testset "Aqua" begin
+    Aqua.find_persistent_tasks_deps(ReactionNetworkImporters)
+    Aqua.test_ambiguities(ReactionNetworkImporters, recursive = false)
+    Aqua.test_deps_compat(ReactionNetworkImporters)
+    Aqua.test_piracies(ReactionNetworkImporters)
+    Aqua.test_project_extras(ReactionNetworkImporters)
+    Aqua.test_stale_deps(ReactionNetworkImporters)
+    Aqua.test_unbound_args(ReactionNetworkImporters)
+    Aqua.test_undefined_exports(ReactionNetworkImporters)
+end

test/runtests.jl

@@ -1,6 +1,7 @@
 using ReactionNetworkImporters, Test
 
 @time begin
+    @time @testset "Quality Assurance" begin include("qa.jl") end
     @time @testset "BNG Birth-Death Test" begin include("test_nullrxs_odes.jl") end
     @time @testset "BNG Repressilator Test" begin include("test_repressilator_odes.jl") end
     @time @testset "BNG Higher Order Test" begin include("test_higherorder_odes.jl") end