Merge pull request #7 from LCSB-BioCore/add-travis

add travis CI

.travis.yml

+language: julia
+
+branches:
+  only:
+    - master
+
+os:
+    - linux
+
+julia:
+    - 1.5
+
+notifications:
+    email: false

Manifest.toml

+# This file is machine-generated - editing it directly is not advised
+
+[[Artifacts]]
+deps = ["Pkg"]
+git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744"
+uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
+version = "1.3.0"
+
+[[Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[Distributed]]
+deps = ["Random", "Serialization", "Sockets"]
+uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+
+[[InteractiveUtils]]
+deps = ["Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+
+[[JLLWrappers]]
+git-tree-sha1 = "a431f5f2ca3f4feef3bd7a5e94b8b8d4f2f647a0"
+uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
+version = "1.2.0"
+
+[[LibGit2]]
+deps = ["Printf"]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+
+[[Libdl]]
+uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
+
+[[Libiconv_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "8e924324b2e9275a51407a4e06deb3455b1e359f"
+uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531"
+version = "1.16.0+7"
+
+[[Logging]]
+uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
+
+[[Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[[Pkg]]
+deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+
+[[Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+
+[[REPL]]
+deps = ["InteractiveUtils", "Markdown", "Sockets"]
+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+
+[[Random]]
+deps = ["Serialization"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[[SBML_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XML2_jll", "Zlib_jll"]
+git-tree-sha1 = "4787b76c8914002ab3a9d2b1ae002fe82376bfba"
+uuid = "bb12108a-f4ef-5f88-8ef3-0b33ff7017f1"
+version = "5.19.0+1"
+
+[[SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+
+[[Serialization]]
+uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+
+[[Sockets]]
+uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
+
+[[Test]]
+deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[[UUIDs]]
+deps = ["Random", "SHA"]
+uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
+
+[[Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
+
+[[XML2_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"]
+git-tree-sha1 = "be0db24f70aae7e2b89f2f3092e93b8606d659a6"
+uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
+version = "2.9.10+3"
+
+[[Zlib_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "320228915c8debb12cb434c59057290f0834dbf6"
+uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
+version = "1.2.11+18"

README.md

@@ -25,5 +25,5 @@ m.compartments
 There are several helper functions, for example you can get a nice list of reactions, metabolites and the stoichiometric matrix as follows:
 
 ```julia
-mets, rxns, S = getS(model)
+mets, rxns, S = getS(m)
 ```

test/loadEColi.jl

@@ -2,7 +2,7 @@
 sbmlfile = "EColi.xml"
 
 if !isfile(sbmlfile)
-    download("https://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
 
 if bytes2hex(sha256(sbmlfile)) != "e3d18499660a0f7fc15a5a44f33f001c7881ac99a2e8a6a461edf1cf3d69a537"
@@ -13,11 +13,11 @@ end
     mdl = readSBML(sbmlfile)
 
     @test typeof(mdl) == Model
-    
+
     @test_throws SystemError readSBML(sbmlfile * ".does.not.really.exist")
 
     @test length(mdl.compartments) == 2
-    
+
     mets, rxns, S = getS(mdl)
 
     @test length(mets) == 77