remove doc tests

test/doctests.jl

@@ -4,8 +4,6 @@ ex = quote
     using COBREXA, Tulip
     include(joinpath(dirname(pathof(COBREXA)), "..", "test", "data_static.jl"))
     model = test_LP()
-    include(joinpath(dirname(pathof(COBREXA)), "..", "test", "test_functions.jl")) # expose functions for downloading
-    include(joinpath(dirname(pathof(COBREXA)), "..", "test", "doctest_models.jl"))
 end
 
 # set module-level metadata

test/docttest_models.jl

-core_path = download_data_file(
-    "http://bigg.ucsd.edu/static/models/e_coli_core.json",
-    joinpath("data", "e_coli_core.json"),
-    "7bedec10576cfe935b19218dc881f3fb14f890a1871448fc19a9b4ee15b448d8",
-)

test/reconstruction/CoreModel.jl

@@ -194,13 +194,7 @@ end
 end
 
 @testset "Remove metabolites" begin
-    core_json = download_data_file(
-        "http://bigg.ucsd.edu/static/models/e_coli_core.json",
-        joinpath("data", "e_coli_core.json"),
-        "7bedec10576cfe935b19218dc881f3fb14f890a1871448fc19a9b4ee15b448d8",
-    )
-
-    model = load_model(CoreModel, core_json)
+    model = load_model(CoreModel, model_paths["e_coli_core.json"])
 
     m1 = remove_metabolites(model, ["glc__D_e", "for_c"])
     m2 = remove_metabolites(model, "glc__D_e")

test/reconstruction/community.jl

 @testset "Small model join" begin
-    model_path = download_data_file(
-        "http://bigg.ucsd.edu/static/models/e_coli_core.json",
-        joinpath("data", "e_coli_core.json"),
-        "7bedec10576cfe935b19218dc881f3fb14f890a1871448fc19a9b4ee15b448d8",
-    )
-
-    m1 = load_model(model_path)
-    m2 = load_model(CoreModel, model_path)
+    m1 = load_model(model_paths["e_coli_core.json"])
+    m2 = load_model(CoreModel, model_paths["e_coli_core.json"])
 
     boundary_rxn_ids, boundary_met_ids = boundary_reactions_metabolites(m2)
     exchange_rxn_ids = filter(startswith("EX_"), boundary_rxn_ids)
@@ -43,20 +37,9 @@
 end
 
 @testset "Heterogenous model join" begin
-    iJO1366_mat = download_data_file(
-        "http://bigg.ucsd.edu/static/models/iJO1366.mat",
-        joinpath("data", "iJO1366.mat"),
-        "b5cfe21b6369a00e45d600b783f89521f5cc953e25ee52c5f1d0a3f83743be30",
-    )
-    core_json = download_data_file(
-        "http://bigg.ucsd.edu/static/models/e_coli_core.json",
-        joinpath("data", "e_coli_core.json"),
-        "7bedec10576cfe935b19218dc881f3fb14f890a1871448fc19a9b4ee15b448d8",
-    )
-
-    m1 = load_model(CoreModel, core_json)
-    m2 = load_model(CoreModel, iJO1366_mat)
-
+    m1 = load_model(CoreModel, model_paths["e_coli_core.json"])
+    m2 = load_model(CoreModel, model_paths["iJO1366.mat"])
+    
     boundary_rxn_ids, boundary_met_ids = boundary_reactions_metabolites(m2)
     exchange_rxn_ids = filter(startswith("EX_"), boundary_rxn_ids)
     exchange_met_ids = filter(endswith("_e"), boundary_met_ids)
@@ -107,13 +90,8 @@ end
 end
 
 @testset "Community model modifications" begin
-    model_path = download_data_file(
-        "http://bigg.ucsd.edu/static/models/e_coli_core.json",
-        joinpath("data", "e_coli_core.json"),
-        "7bedec10576cfe935b19218dc881f3fb14f890a1871448fc19a9b4ee15b448d8",
-    )
+    m1 = load_model(CoreModel, model_paths["e_coli_core.json"])
 
-    m1 = load_model(CoreModel, model_path)
     boundary_rxn_ids, boundary_met_ids = boundary_reactions_metabolites(m1)
     exchange_rxn_ids = filter(startswith("EX_"), boundary_rxn_ids)
     exchange_met_ids = filter(endswith("_e"), boundary_met_ids)
@@ -132,7 +110,7 @@ end
     community.xl[env_ex_inds] .= m1.xl[m1_ex_inds]
     community.xu[env_ex_inds] .= m1.xu[m1_ex_inds]
 
-    m2 = load_model(CoreModel, model_path)
+    m2 = load_model(CoreModel, model_paths["e_coli_core.json"])
 
     community = add_model(
         community,

test/test_functions.jl

-function run_test_file(path...)
-    fn = joinpath(path...)
-    t = @elapsed include(fn)
-    @info "$(fn) done in $(round(t; digits = 2))s"
-end
-
-function run_test_dir(dir, comment = "Directory $dir/")
-    @testset "$comment" begin
-        run_test_file.(joinpath.(dir, filter(fn -> endswith(fn, ".jl"), readdir(dir))))
-    end
-end
-
-function check_data_file_hash(path, expected_checksum)
-    actual_checksum = bytes2hex(sha256(open(path)))
-    if actual_checksum != expected_checksum
-        @error "The downloaded data file `$path' seems to be different from the expected one. Tests will likely fail." actual_checksum expected_checksum
-    end
-end
-
-function download_data_file(url, path, hash)
-    if isfile(path)
-        check_data_file_hash(path, hash)
-        @info "using cached `$path'"
-        return path
-    end
-
-    Downloads.download(url, path)
-    check_data_file_hash(path, hash)
-    return path
-end