Commit c5421284 authored by Miroslav Kratochvil's avatar Miroslav Kratochvil
Browse files

reformat code before release

parent 4164057d
......@@ -73,10 +73,10 @@ readSBML("example.xml", libsbml_convert("stripPackage", package="layout"))
```
"""
libsbml_convert(converter::String, report_severities = ["Fatal", "Error"]; kwargs...) =
libsbml_convert([
converter => Dict{String,String}(string(k) => string(v) for (k, v) in kwargs),
],
report_severities)
libsbml_convert(
[converter => Dict{String,String}(string(k) => string(v) for (k, v) in kwargs)],
report_severities,
)
"""
convert_simplify_math
......
......@@ -149,7 +149,8 @@ readSBMLFromString(
str::AbstractString,
sbml_conversion = document -> nothing;
report_severities = ["Fatal", "Error"],
)::SBML.Model = _readSBML(:readSBMLFromString, String(str), sbml_conversion, report_severities)
)::SBML.Model =
_readSBML(:readSBMLFromString, String(str), sbml_conversion, report_severities)
get_notes(x::VPtr)::Maybe{String} = get_optional_string(x, :SBase_getNotesString)
get_annotation(x::VPtr)::Maybe{String} = get_optional_string(x, :SBase_getAnnotationString)
......
......@@ -32,8 +32,7 @@ are accompanied with the unit of the corresponding value (this behavior is based
specification).
"""
flux_bounds(m::SBML.Model)::NTuple{2,Vector{Tuple{Float64,String}}} =
(broadcast(x -> x.lb, values(m.reactions)),
broadcast(x -> x.ub, values(m.reactions)))
(broadcast(x -> x.lb, values(m.reactions)), broadcast(x -> x.ub, values(m.reactions)))
"""
flux_objective(m::SBML.Model)::Vector{Float64}
......@@ -244,13 +243,14 @@ get_unit(u::VPtr) =
sbml(:UnitKind_toString),
Cstring,
(Cint,),
ccall(sbml(:Unit_getKind), Cint, (VPtr,), u)
))] ^
ccall(sbml(:Unit_getExponent), Cint, (VPtr,), u) *
ccall(sbml(:Unit_getKind), Cint, (VPtr,), u),
),
)]^ccall(sbml(:Unit_getExponent), Cint, (VPtr,), u) *
exp10(ccall(sbml(:Unit_getScale), Cint, (VPtr,), u)) *
ccall(sbml(:Unit_getMultiplier), Cdouble, (VPtr,), u)
# Get `Unitful` quantity out of a `UnitDefinition_t`.
get_units(ud::VPtr) =
prod(get_unit(ccall(sbml(:UnitDefinition_getUnit), VPtr, (VPtr, Cuint), ud, j - 1))
for j = 1:ccall(sbml(:UnitDefinition_getNumUnits), Cuint, (VPtr,), ud))
get_units(ud::VPtr) = prod(
get_unit(ccall(sbml(:UnitDefinition_getUnit), VPtr, (VPtr, Cuint), ud, j - 1)) for
j = 1:ccall(sbml(:UnitDefinition_getNumUnits), Cuint, (VPtr,), ud)
)
......@@ -74,7 +74,10 @@ sbmlfiles = [
),
]
@testset "Loading of models from various sources - $(reader)" for reader in (readSBML, readSBMLFromString)
@testset "Loading of models from various sources - $(reader)" for reader in (
readSBML,
readSBMLFromString,
)
for (sbmlfile, url, hash, expected_mets, expected_rxns) in sbmlfiles
if !isfile(sbmlfile)
Downloads.download(url, sbmlfile)
......@@ -103,7 +106,9 @@ sbmlfiles = [
end
@testset "readSBMLFromString" begin
@test_logs (:error, r"^SBML reported error") @test_throws AssertionError readSBMLFromString("")
@test_logs (:error, r"^SBML reported error") @test_throws AssertionError readSBMLFromString(
"",
)
end
@testset "Time variables in math" begin
......@@ -187,9 +192,11 @@ end
@test test_math.args[2].fn == "sin"
@test test_math.args[2].args[1].val == 2.1
@test_logs (:warn,) (:warn,) (:warn,) (:warn,) readSBML(joinpath(@__DIR__, "data", "01234-sbml-l3v2.xml"),
doc -> libsbml_convert("expandInitialAssignments", ["Fatal", "Error", "Warning"])(doc)
)
@test_logs (:warn,) (:warn,) (:warn,) (:warn,) readSBML(
joinpath(@__DIR__, "data", "01234-sbml-l3v2.xml"),
doc ->
libsbml_convert("expandInitialAssignments", ["Fatal", "Error", "Warning"])(doc),
)
end
@testset "relational operators are decoded correctly" begin
......
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