diff --git a/Project.toml b/Project.toml index 74fc9cbed99fbfbf41cb614eb8a043bb544fa051..439c56358e79e7c2eae3e246bf80341d27808efc 100644 --- a/Project.toml +++ b/Project.toml @@ -4,43 +4,47 @@ authors = ["The developers of COBREXA.jl"] version = "1.0.0" [deps] -Clp = "e2554f3b-3117-50c0-817c-e040a3ddf72d" Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" -DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab" Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b" DistributedData = "f6a0035f-c5ac-4ad0-b410-ad102ced35df" -Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6" -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" MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" -OSQP = "ab2f91bb-94b4-55e3-9ba0-7f65df51de79" OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" 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" [compat] -DistributedData = ">=0.1.3" -SBML = ">=0.4" +Clp = "0.8" +DistributedData = "0.1.3" +Documenter = "0.26" +GLPK = "0.14" +JSON = "0.21" +JuMP = "0.21" +Literate = "2.8" +MAT = "0.10" +MacroTools = "0.5.6" +OSQP = "0.6" +OrderedCollections = "1.4" +SBML = "0.4" +Tulip = "0.7" julia = "1" [extras] +Clp = "e2554f3b-3117-50c0-817c-e040a3ddf72d" +Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" +Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6" +GLPK = "60bf3e95-4087-53dc-ae20-288a0d20c6a6" +Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" +OSQP = "ab2f91bb-94b4-55e3-9ba0-7f65df51de79" +SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Tulip = "6dd1b50a-3aae-11e9-10b5-ef983d2400fa" [targets] -test = ["Test", "Tulip"] +test = ["Clp", "Downloads", "GLPK", "OSQP", "SHA", "Test", "Tulip"] diff --git a/src/COBREXA.jl b/src/COBREXA.jl index 05ef0946a865749a7ca35feb3e518c7970c9e070..e32108f69bce7eab9f93bcc4111c21a25656bde9 100644 --- a/src/COBREXA.jl +++ b/src/COBREXA.jl @@ -1,23 +1,17 @@ module COBREXA -using Logging -using SparseArrays -using DelimitedFiles -using LinearAlgebra -using JuMP -using MAT +using Dates using Distributed using DistributedData -using Downloads -using Requires using JSON +using JuMP +using LinearAlgebra +using MAT using MacroTools -using Measurements -using Statistics -using Random -using MacroTools # for DSL :) using OrderedCollections -using Dates +using Random +using SparseArrays +using Statistics import Base: findfirst, getindex, show import Pkg diff --git a/test/runtests.jl b/test/runtests.jl index f4cf775c12b9fc87cad7dcf86e19c1efd26717e4..945a8a5a814b526abc335dc7778144cc4d03d988 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,21 +1,19 @@ -using Test -using Logging -using SparseArrays -using JuMP -using GLPK +using COBREXA, Test + using Clp -using COBREXA -using MAT -using SHA using Distributed +using Downloads +using GLPK +using JSON using JuMP -using Tulip +using LinearAlgebra +using MAT +using OrderedCollections using OSQP +using SHA +using SparseArrays using Statistics -using JSON -using Measurements -using OrderedCollections -using LinearAlgebra +using Tulip # tolerance for comparing analysis results (should be a bit bigger than the # error tolerance in computations) @@ -47,7 +45,7 @@ function download_data_file(url, path, hash) return path end - COBREXA.Downloads.download(url, path) + Downloads.download(url, path) check_data_file_hash(path, hash) return path end