Merge pull request #115 from ArnoStrouwen/qa

typos + 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 +1,5 @@
+[default.extend-words]
+ba = "ba"
+caf = "caf"
+ths = "ths"
+allo = "allo"

Project.toml

@@ -14,18 +14,23 @@ SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
+Aqua = "0.8"
 EzXML = "1.1"
 MathML = "0.1.9"
 Memoize = "0.4"
 ModelingToolkit = "7, 8"
+Random = "1"
 Setfield = "0.8, 1"
 SymbolicUtils = "0.16, 0.18, 0.19, 1"
+OrdinaryDiffEq = "6"
+Test = "1"
 julia = "1.6"
 
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test", "ModelingToolkit", "OrdinaryDiffEq"]
+test = ["Aqua", "Test", "ModelingToolkit", "OrdinaryDiffEq"]

README.md

@@ -43,7 +43,7 @@ Pkg.add("CellMLToolkit")
   ml = CellModel("models/lorenz.cellml.xml")
   prob = ODEProblem(ml, (0,100.0))
   sol = solve(prob)
-  plot(sol, idxs=(1,3))       # idxs keyword has superceded vars keyword
+  plot(sol, idxs=(1,3))       # idxs keyword has superseded vars keyword
 ```
 
 Note that `model` is a directory of the CellMLToolkit package. You can find its path as
@@ -84,7 +84,7 @@ In addition to the model equations, the initial conditions and parameters are al
   using DifferentialEquations, Plots
 
   sol = solve(prob)
-  plot(sol, idxs=(1,3))       # idxs keyword has superceded vars keyword
+  plot(sol, idxs=(1,3))       # idxs keyword has superseded vars keyword
 ```
 
 As expected,
@@ -156,7 +156,7 @@ The rest is the same as before.
   plot(sol, idxs=7)   # 7 is the index of membrane₊V
 ```
 
-For the next example, we chose a complex model to stress the ODE solvers: [the O'Hara-Rudy left ventricular model](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002061). This model has 49 state variables, is very stiff, and is prone to oscillation. In the previous versions of this document, we used `CVODE_BDF` from the Sundial suite (`using Sundials`) to solve this problem. Fortunatelly, DifferentialEquations.jl has advanced signigficantly such that an efficient and pure Julia solution to the O'Hara-Rudy model is possible.
+For the next example, we chose a complex model to stress the ODE solvers: [the O'Hara-Rudy left ventricular model](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002061). This model has 49 state variables, is very stiff, and is prone to oscillation. In the previous versions of this document, we used `CVODE_BDF` from the Sundial suite (`using Sundials`) to solve this problem. Fortunately, DifferentialEquations.jl has advanced signigficantly such that an efficient and pure Julia solution to the O'Hara-Rudy model is possible.
 
 ```Julia
   ml = CellModel("models/ohara_rudy_cipa_v1_2017.cellml.xml")

models/beeler_reuter_1977.cellml.xml

@@ -1347,7 +1347,7 @@ The breakdown of the model into components and the definition of encapsulation a
   </rdf:Description>
   <rdf:Description rdf:about="rdf:#77f98dda-c979-49f1-9bcf-da4944906f91">
     <dcterms:modified rdf:resource="rdf:#e7527bce-f615-4263-afc0-c075d70b6e23"/>
-    <rdf:value>Added an intial value for X1 to enable the model to run.</rdf:value>
+    <rdf:value>Added an initial value for X1 to enable the model to run.</rdf:value>
     <cmeta:modifier rdf:resource="rdf:#baef8605-6d17-47bc-b214-261f23273934"/>
   </rdf:Description>
   <rdf:Description rdf:about="rdf:#9c5e9628-92e3-4989-a4b1-21fce295ab89">

src/CellMLToolkit.jl

@@ -21,9 +21,9 @@ end
 ##############################################################################
 
 export CellModel, ODEProblem
-export read_cellml, parse_cellml
+export read_cellml
 export list_params, list_states
-export readxml, getxml, getsys
+export readxml, getsys
 export update_list!
 
 getsys(ml::CellModel) = ml.sys

src/components.jl

@@ -102,7 +102,7 @@ list_all_lhs(doc::Document) = ∪([list_component_lhs(c) for c in components(doc
 
 """
     find_equivalence_groups categorizes all the variables in the doc document
-    based on the connections into equivalnce groups
+    based on the connections into equivalence groups
     it returns a Dictionary of Var to groups (Set of Vars)
 """
 @memoize function find_equivalence_groups(doc::Document)
@@ -197,7 +197,7 @@ end
     post_substitution generates the substitution rules to be applied to
     the merged system after structural_simplify is applied
 
-    if changes the names of the indepedent variable (iv) in each system
+    if changes the names of the independent variable (iv) in each system
     to the global iv name
 
     TODO: this function assumes the basic iv name is the same among all systems

src/import.jl

@@ -62,7 +62,7 @@ find_component(doc::Document, name) = find_component(doc.comps, name)
 implicit_name(sym) = Symbol("$(string(sym))")
 
 """
-    resolve_imports recursivelly resolves the imported components of doc.
+    resolve_imports recursively resolves the imported components of doc.
 """
 function resolve_imports!(doc::Document)
     for ϵ in list_imports(doc)  # εισαγωγή == import
@@ -113,7 +113,7 @@ function resolve_imports!(doc::Document)
 end
 
 """
-    find_closure finds the transitive closure of a list of componenets (l) minus
+    find_closure finds the transitive closure of a list of components (l) minus
     the list itself, i.e., it returns the list of components in doc which are
     reachable through a chain of connections starting from any component in l.
 """

test/qa.jl

@@ -0,0 +1,12 @@
+using CellMLToolkit, Aqua
+@testset "Aqua" begin
+    Aqua.find_persistent_tasks_deps(CellMLToolkit)
+    Aqua.test_ambiguities(CellMLToolkit, recursive = false)
+    Aqua.test_deps_compat(CellMLToolkit)
+    Aqua.test_piracies(CellMLToolkit,
+        treat_as_own = [])
+    Aqua.test_project_extras(CellMLToolkit)
+    Aqua.test_stale_deps(CellMLToolkit)
+    Aqua.test_unbound_args(CellMLToolkit)
+    Aqua.test_undefined_exports(CellMLToolkit)
+end

test/runtests.jl

@@ -4,6 +4,7 @@ using OrdinaryDiffEq
 using ModelingToolkit
 
 @testset "CellMLToolkit.jl" begin
+    @testset "Quality Assurance" begin include("qa.jl") end
     @testset "beeler.jl" begin include("beeler.jl") end
     @testset "noble_1962.jl" begin include("noble_1962.jl") end
 end