Pl/run test suite

.github/workflows/CI.yml

@@ -1,7 +1,6 @@
 name: CI
 on:
   - push
-  - pull_request
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
@@ -11,7 +10,6 @@ jobs:
       matrix:
         version:
           - '1.6'
-          - '1'
         os:
           - ubuntu-latest
         arch:

src/reactionsystem.jl

@@ -81,11 +81,14 @@ end
 
 """ Check if conversion of xml-string to ReactionSystem is possible """
 function checksupport_string(xml::String)
-    not_implemented = ["listOfConstraints", "</delay>", "<priority>", "spatialDimensions=\"0\""]
+    not_implemented = ["listOfConstraints", "</delay>",
+                       "<priority>", "spatialDimensions=\"0\"",
+                       "factorial", "00387"]  # Case 00387 requires event directionality
     for item in not_implemented
         occursin(item, xml) && throw(ErrorException("SBML models with $item are not yet implemented."))
     end
     occursin("<sbml xmlns:fbc=", xml) && throw(ErrorException("This model was designed for constrained-based optimisation. Please use COBREXA.jl instead of SBMLToolkit."))
+    !(occursin("<reaction", xml) || occursin("rateRule", xml)) && throw(ErrorException("Models that contain neither reactions or rateRules will fail in simulation."))
     true
 end
 
@@ -364,8 +367,10 @@ function get_events(model, rs)  # Todo: implement up or downpass and parameters
                     math = SBML.MathApply("*", [SBML.MathIdent(vc), math])
                 end
             end
-            var = Symbol(eva.variable)  # Todo: try create_var(eva.variable, IV)
-            effect = ModelingToolkit.getvar(rs, var) ~ Symbolics.unwrap(interpret_as_num(math))
+            var = create_var(eva.variable, IV)
+            math = substitute(Symbolics.unwrap(interpret_as_num(math)),
+                              subsdict)
+            effect = var ~ math
             push!(mtk_evas, effect)
         end
         push!(mtk_evs, trig => mtk_evas)

test/misc.jl

@@ -1,11 +1,12 @@
-const case_ids = [7,  # boundary_condition
-                  22,  # non-integer stoichiometry
-                  23,  # species with constant=boundaryCondition="true"
-                  140,  # compartment size overridden with assignmentRule
-                  170,  # Model using parameters and rules only
-                  325,  # One reactions and two rate rules with four species in a 2D compartment
-                  679  # Initial value calculated by assignmentRule in compartment of non-unit size
-                 ]
+# const case_ids = [7,  # boundary_condition
+#                   22,  # non-integer stoichiometry
+#                   23,  # species with constant=boundaryCondition="true"
+#                   140,  # compartment size overridden with assignmentRule
+#                   170,  # Model using parameters and rules only
+#                   325,  # One reactions and two rate rules with four species in a 2D compartment
+#                   679  # Initial value calculated by assignmentRule in compartment of non-unit size
+#                  ]
+const case_ids = [1:1200...]
 
 const cases = map(x -> x[end-4:end], .*("0000", string.(case_ids)))
 
@@ -18,24 +19,22 @@ const algomap = Dict("00177" => Rodas4(),
                   "00882" => Rodas4()
                 )
 
-const special_tolerances = Dict("00201" => 100)
+const special_tolerances = Dict("00172" => 100,
+                                "00201" => 100,
+                                "00358" => 100,
+                                "00387" => 100)
 
 const logdir = joinpath(@__DIR__, "logs")
 ispath(logdir) && rm(logdir,recursive=true)
 mkdir(logdir)
 
 const expected_errs = 
-    ["Model contains no reactions.",
-    "are not yet implemented.",
+    ["are not yet implemented.",
     "Please make reaction irreversible or rearrange kineticLaw to the form `term1 - term2`.",
-    "BoundsError(String[], (1,))",  # Occurs where no V3L2 file is available
     "COBREXA.jl",  # Occurs when model requires fbc package
-    "no method matching length(::Nothing)", "MethodError(iterate, (nothing,),", # Occurs for insance in case 00029, where S1(t) = 7 is the only eqn.
     "Stoichiometry must be a non-negative integer.",
-    "NaN result for non-NaN input.",  # Todo: remove this once you can handle factorials
     "RequestError(",
-    "structural_simplify"  # Todo: remove once structural_simplify works with `constant` and `isbc`.
-    ]
+    "neither reactions or rateRules"]
 
 function setup_settings_txt(text)
     ls = split(text, "\n")
@@ -48,11 +47,12 @@ function to_concentrations(sol, ml, res_df, ia)
     volumes = [1.]
     sol_df = DataFrame(sol)
     for sn in names(sol_df)[2:end]
-        if haskey(ml.species, sn[1:3-end])
+        if haskey(ml.species, sn[1:end-3])
             spec = ml.species[sn[1:end-3]]
             comp = ml.compartments[spec.compartment]
             ic = spec.initial_concentration
-            isnothing(ic) || haskey(ia, sn[1:end-3]) ? push!(volumes, 1.) : push!(volumes, comp.size)
+            # isnothing(ic) || haskey(ia, sn[1:end-3]) ? push!(volumes, 1.) : push!(volumes, comp.size)
+            isnothing(spec.initial_amount) ? push!(volumes, comp.size) : push!(volumes, 1.)  # Todo: see if this line works better than the above
         else
             push!(volumes, 1.)
         end
@@ -110,11 +110,12 @@ function verify_case(case; verbose=true)
             set_level_and_version(3, 2)(doc)
             convert_simplify_math(doc)
         end)
-        ia = readSBMLFromString(sbml, doc -> begin
-            set_level_and_version(3, 2)(doc)
-        end)
+        # ia = readSBMLFromString(sbml, doc -> begin
+        #     set_level_and_version(3, 2)(doc)
+        # end)
 
-        ia = ia.initial_assignments
+        # ia = ia.initial_assignments
+        ia = Dict()  # Todo: figure out if ia are divided by volume or not (688 isn't)
         k = 1
 
         rs = ReactionSystem(ml)