all tests pass

.gitignore

@@ -3,16 +3,6 @@
 /vscode
 *.code-workspace
 
-# Ignore data files
-*.brenda.txt
-
-# Ignore working files
-/notebooks_and_scripts/imgs
-/notebooks_and_scripts/fluxes
-/notebooks_and_scripts/.ipynb_checkpoints
-/notebooks_and_scripts/ipynb_checkpoints
-/notebooks_and_scripts/testpkg.jl
-
 # Build artifacts for creating documentation generated by the Documenter package
 docs/build/
 docs/site/
@@ -23,8 +13,5 @@ docs/site/
 # environment.
 Manifest.toml
 
-# Ignore logo files
-*pptx
-
-# Ignore images
-*.png
\ No newline at end of file
+# Ignore temporary script for testing functions
+temp.jl
\ No newline at end of file

Project.toml

@@ -5,35 +5,34 @@ version = "0.1.0"
 
 [deps]
 Clp = "e2554f3b-3117-50c0-817c-e040a3ddf72d"
+Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 DistributedData = "f6a0035f-c5ac-4ad0-b410-ad102ced35df"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 GLPK = "60bf3e95-4087-53dc-ae20-288a0d20c6a6"
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
 JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
-Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
-SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
-JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"
 OSQP = "ab2f91bb-94b4-55e3-9ba0-7f65df51de79"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 SBML = "e5567a89-2604-4b09-9718-f5f78e97c3bb"
 SBML_jll = "bb12108a-f4ef-5f88-8ef3-0b33ff7017f1"
+SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Tulip = "6dd1b50a-3aae-11e9-10b5-ef983d2400fa"
 
-
 [compat]
-julia = "1"
 DistributedData = "0.1.3"
+julia = "1"

src/COBREXA.jl

@@ -7,7 +7,6 @@ using LinearAlgebra
 using JuMP
 using MAT
 using Distributed
-using SBML
 using DistributedData
 using Requires
 using JSON
@@ -20,6 +19,7 @@ using OSQP # for QPs, but it kinda sucks
 
 import Base: findfirst, getindex, show
 import Pkg
+import SBML # conflict with Reaction struct name
 
 # import src files
 include(joinpath("header", "header.jl"))
@@ -46,8 +46,15 @@ banner = "
 
 print(banner)
 
+# order issue
+include("base/gene.jl")
+include("base/metabolite.jl")
+include("base/reaction.jl")
+include("base/model.jl")
+include("base/solver.jl")
+include("base/utilities.jl")
 
-loadSource(["base", "io", "reconstruction", "analysis"], @__DIR__)
+loadSource(["io", "reconstruction", "analysis", "sampling"], @__DIR__)
 
 # export functions
 ∅ = Metabolite("∅") # for exchange reactions

src/base/model.jl

@@ -37,11 +37,11 @@ function Base.show(io::IO, ::MIME"text/plain", m::CobraModel)
 end
 
 """
-Model()
+CobraModel()
 
 Empty model constructor.
 """
-function Model()
+function CobraModel()
     CobraModel("blank", Array{Reaction,1}(), Array{Metabolite,1}(), Array{Gene,1}())
 end
 

test/analysis/basic_analysis_test.jl

 @testset "Basic analysis" begin
-    model = CobraTools.read_model(joinpath("data", "e_coli_core.json"))
+    model = read_model(download("http://bigg.ucsd.edu/static/models/e_coli_core.json", joinpath("data", "e_coli_core.json")))
     @test length(model.reactions) == 95 # read in correctly
 
     # FBA

test/base/model_test.jl

@@ -31,7 +31,7 @@
     genes = [g1, g2, g3]
     rxns = [r1, r2, r3, r4]
 
-    model = CobraTools.Model()
+    model = CobraModel()
     model.id = "model"
     model.reactions = rxns
     model.metabolites = mets

test/base/reaction_test.jl

@@ -109,6 +109,4 @@
     @test bal
 
     @test isnothing(findfirst(rxns, "nope"))
-
-
 end

test/io/io_tools_test.jl → test/io/io_test.jl

 @testset "IO" begin
 
-    # E. coli models - realistic size model
-    iJO1366_xml = joinpath("data", "iJO1366.xml")
-    sbmlmodel_ecoli = CobraTools.read_model(iJO1366_xml)
+    # E. coli models - realistic size models
+    iJO1366_xml = download("http://bigg.ucsd.edu/static/models/iJO1366.xml", joinpath("data", "iJO1366.xml")) 
+    sbmlmodel_ecoli = read_model(iJO1366_xml)
     @test_broken length(sbmlmodel_ecoli.reactions) == 2583
 
-    iJO1366_mat = joinpath("data", "iJO1366.mat")
-    matlabmodel_ecoli = CobraTools.read_model(iJO1366_mat)
+    iJO1366_mat = download("http://bigg.ucsd.edu/static/models/iJO1366.mat", joinpath("data", "iJO1366.mat"))
+    matlabmodel_ecoli = read_model(iJO1366_mat)
     @test length(matlabmodel_ecoli.reactions) == 2583
 
-    iJO1366_json = joinpath("data", "iJO1366.json")
-    jsonmodel_ecoli = CobraTools.read_model(iJO1366_json)
+    iJO1366_json = download("http://bigg.ucsd.edu/static/models/iJO1366.json", joinpath("data", "iJO1366.json"))
+    jsonmodel_ecoli = read_model(iJO1366_json)
     @test length(jsonmodel_ecoli.reactions) == 2583
 
     @test model_comparison_test(jsonmodel_ecoli, matlabmodel_ecoli)

test/reconstruction/construction_overloading_test.jl

 @testset "Construction overloading" begin
-    model = CobraTools.read_model(joinpath("data", "iJO1366.json"))
+    model = read_model(joinpath("data", "iJO1366.json"))
 
     rxn_original = findfirst(model.reactions, "NADH16pp")
     nadh = findfirst(model.metabolites, "nadh_c")

test/reconstruction/model_manipulations_test.jl

@@ -26,7 +26,7 @@
 
     rxns = [r1, r2]
 
-    model = CobraTools.Model()
+    model = CobraModel()
     model.id = "model"
     model.reactions = rxns
     model.metabolites = mets

test/runtests.jl

@@ -9,7 +9,6 @@ using MAT
 using SHA
 using Distributed
 using JuMP
-
 using Tulip
 using OSQP
 using Statistics
@@ -31,38 +30,15 @@ end
 
 # load the test models
 include(joinpath("data", "testModels.jl"))
+# load some convenience functions for testing
+include("testing_functions.jl") 
 
 # import base files
 @testset "COBREXA test suite" begin
-    for testSet in ["base", "io", "reconstruction", "analysis"]
+    for testSet in ["base", "io", "reconstruction", "analysis", "sampling"]
         @testset "$testSet" begin
             runSuite(testSet)
         end
     end
 end
 
-
-const testdir = dirname(@__FILE__)
-
-include("testing_functions.jl") # load some testing functions
-
-tests = [
-    "base/gene_test.jl",
-    "base/metabolite_test.jl",
-    "base/model_test.jl",
-    "base/reaction_test.jl",
-    "io/io_tools_test.jl",
-    "construction/construction_overloading_test.jl",
-    "construction/model_manipulations_test.jl",
-    "optimization_analysis/basic_analysis_test.jl",
-    "sampling/sampling_tools_test.jl",
-    "external/brenda_tests.jl",
-]
-
-@testset "CobraTools" begin
-    for t in tests
-        tp = joinpath(testdir, t)
-        include(tp)
-    end
-end
-

test/sampling/sampling_tools_test.jl

 @testset "Sampling Tests" begin
-    model = CobraTools.read_model(joinpath("data", "e_coli_core.json"))
+    # these tests are not very good - sampling needs work
+    model = read_model(download("http://bigg.ucsd.edu/static/models/e_coli_core.json", joinpath("data", "e_coli_core.json")))
     @test length(model.reactions) == 95 # read in correctly
 
 

test/testing_functions.jl

@@ -32,8 +32,8 @@ function model_comparison_test(model1, model2)
     grrs_same = true
     for rxn1 in model1.reactions
         rxn2 = findfirst(model2.reactions, rxn1.id)
-        rxn1_grr_string = string(split(CobraTools.unparse_grr(rxn1.grr), "")) # use hash
-        rxn2_grr_string = string(split(CobraTools.unparse_grr(rxn2.grr), ""))
+        rxn1_grr_string = string(split(COBREXA.unparse_grr(rxn1.grr), ""))
+        rxn2_grr_string = string(split(COBREXA.unparse_grr(rxn2.grr), ""))
         rxn1_ints = sum(Int.([x[1] for x in rxn1_grr_string]))
         rxn2_ints = sum(Int.([x[1] for x in rxn2_grr_string]))
         if rxn1_ints != rxn2_ints
@@ -51,18 +51,9 @@ Test if model is the same after it was read in, saved, and then re-read.
 function read_write_read_test(model, format)
     tmpfile = joinpath("data", "temp." * format)
 
-    CobraTools.save_model(model, tmpfile)
-    tmpmodel = CobraTools.read_model(tmpfile)
+    save_model(model, tmpfile)
+    tmpmodel = read_model(tmpfile)
 
     rm(tmpfile)
     model_comparison_test(model, tmpmodel)
-end
-
-
-
-# function atom_test(model)
-#     biomass_rxn = findfirst(model.rxns, "BIOMASS_Ec_iJO1366_WT_53p95M")
-#     pfbasol = CobraTools.pfba(model, biomass_rxn)
-#     ad = CobraTools.atom_exchange(pfbasol)
-#     return ad["C"]/ad["H"] ≈ 0.6362486422376349
-# end
+end
\ No newline at end of file