Merge pull request #38 from LCSB-BioCore/mk-reformat

apply juliaformatter

docs/make.jl

 using Documenter, SBML
 
-makedocs(modules = [SBML],
+makedocs(
+    modules = [SBML],
     clean = false,
     format = Documenter.HTML(
         prettyurls = !("local" in ARGS),
-        canonical = "https://lcsb-biocore.github.io/DistributedData.jl/stable/"),
+        canonical = "https://lcsb-biocore.github.io/DistributedData.jl/stable/",
+    ),
     sitename = "SBML.jl",
     authors = "The developers of SBML.jl",
     linkcheck = !("skiplinks" in ARGS),
-    pages = [
-        "Documentation" => "index.md",
-    ],
+    pages = ["Documentation" => "index.md"],
 )
 
 deploydocs(
     repo = "github.com/LCSB-BioCore/SBML.jl.git",
     target = "build",
     branch = "gh-pages",
-    push_preview = true
+    push_preview = true,
 )

test/ecoli_flux.jl

@@ -2,7 +2,10 @@
 sbmlfile = "Ec_core_flux1.xml"
 
 if !isfile(sbmlfile)
-    download("http://systemsbiology.ucsd.edu/sites/systemsbiology.ucsd.edu/files/Attachments/Images/InSilicoOrganisms/Ecoli/Ecoli_SBML/Ec_core_flux1.xml", sbmlfile)
+    download(
+        "http://systemsbiology.ucsd.edu/sites/systemsbiology.ucsd.edu/files/Attachments/Images/InSilicoOrganisms/Ecoli/Ecoli_SBML/Ec_core_flux1.xml",
+        sbmlfile,
+    )
 end
 
 cksum = bytes2hex(sha256(open(sbmlfile)))
@@ -23,12 +26,12 @@ end
     mets, rxns, S = getS(mdl)
 
     @test typeof(S) <: AbstractMatrix{Float64}
-    @test typeof(getS(mdl; zeros=spzeros)[3]) <: SparseMatrixCSC{Float64}
-    @test typeof(getS(mdl; zeros=zeros)[3]) == Matrix{Float64}
+    @test typeof(getS(mdl; zeros = spzeros)[3]) <: SparseMatrixCSC{Float64}
+    @test typeof(getS(mdl; zeros = zeros)[3]) == Matrix{Float64}
 
     @test length(mets) == 77
     @test length(rxns) == 77
-    @test size(S) == (length(mets),length(rxns))
+    @test size(S) == (length(mets), length(rxns))
 
     # totally arbitrary value tests
     @test isapprox(sum(S), 42.1479)
@@ -47,10 +50,10 @@ end
     @test length(getLBs(mdl)) == length(rxns)
     @test length(getUBs(mdl)) == length(rxns)
 
-    getunit = (val,unit)::Tuple -> unit
+    getunit = (val, unit)::Tuple -> unit
     @test all([broadcast(getunit, lbs) broadcast(getunit, ubs)] .== "mmol_per_gDW_per_hr")
 
-    getval = (val,unit)::Tuple -> val
+    getval = (val, unit)::Tuple -> val
     lvals = broadcast(getval, lbs)
     uvals = broadcast(getval, ubs)
     @test isapprox(lvals[27], uvals[27])

test/loadmodels.jl

 
 sbmlfiles = [
     # a test model from BIGG
-    ("e_coli_core.xml",
+    (
+        "e_coli_core.xml",
         "http://bigg.ucsd.edu/static/models/e_coli_core.xml",
         "b4db506aeed0e434c1f5f1fdd35feda0dfe5d82badcfda0e9d1342335ab31116",
         72,
-     95),
+        95,
+    ),
     # a relatively new non-curated model from biomodels
-    ("T1M1133.xml",
+    (
+        "T1M1133.xml",
         "https://www.ebi.ac.uk/biomodels/model/download/MODEL1909260004.4?filename=T1M1133.xml",
         "2b1e615558b6190c649d71052ac9e0dc1635e3ad281e541bc7d4fdf2892a5967",
         2517,
-     3956),
+        3956,
+    ),
     # a curated model from biomodels
-    ("Dasgupta2020.xml",
+    (
+        "Dasgupta2020.xml",
         "https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000973.3?filename=Dasgupta2020.xml",
         "958b131d4df2f215dae68255433542f228601db0326d26a54efd08ddcf823489",
-     2, 6),
+        2,
+        6,
+    ),
 ]
 
 @testset "Loading of models from various sources" begin

test/version.jl

 
 @testset "CCall to SBML works and SBML returns a version" begin
-    @test typeof(SBMLVersion())==Pkg.VersionNumber
+    @test typeof(SBMLVersion()) == Pkg.VersionNumber
 end