Merge pull request #159 from SciML/pl/citation_cff

Add citation.cff

Project.toml

@@ -13,15 +13,15 @@ Aqua = "0.8"
 CSV = "0.10.5"
 Catalyst = "13"
 DataFrames = "1"
+Downloads = "1"
 ModelingToolkit = "8.51"
 OrdinaryDiffEq = "6.42"
 Plots = "1.11"
 SBML = "1.4.4"
 SBMLToolkitTestSuite = "0.0.3"
 SafeTestsets = "0.1"
 Sundials = "4.14"
-SymbolicUtils = "1"
-Downloads = "1"
+SymbolicUtils = "1, 2"
 Test = "1"
 julia = "1.10"
 

README.md

@@ -55,10 +55,20 @@ odesys = readSBML("my_model.xml", ODESystemImporter())
 
 The package is released under the [MIT license](https://github.com/SciML/SBMLToolkit.jl/blob/main/LICENSE).
 
-## Development team
+## Questions and comments
 
-This package was developed by [Paul F. Lang](https://www.linkedin.com/in/paul-lang-7b54a81a3/) at the University of Oxford, UK and [Anand Jain](https://github.com/anandijain) at the University of Chicago, USA.
+Please use GitHub issues and the #sciml-sysbio channel in the [Julia Slack workspace](https://julialang.org/slack/) with any questions or comments.
 
-## Questions and comments
+# Citation
+
+If you use SBMLToolkit.jl in your research, please cite [this paper](https://www.degruyter.com/document/doi/10.1515/jib-2024-0003/html):
 
-Please use GitHub issues, the #sciml-sysbio channel in the [Julia Slack workspace](https://julialang.org/slack/) or email [Paul F. Lang](mailto:[email protected]) with any questions or comments.
+```
+@article{lang_sbmltoolkitjl_2024,
+	title = {{SBMLToolkit}.jl: a {Julia} package for importing {SBML} into the {SciML} ecosystem},
+	doi = {10.1515/jib-2024-0003},
+	journal = {Journal of Integrative Bioinformatics},
+	author = {Lang, Paul F. and Jain, Anand and Rackauckas, Christopher},
+	year = {2024},
+}
+```

test/systems.jl

@@ -74,8 +74,8 @@ rs = ReactionSystem(MODEL2)  # Contains reversible reaction
 @test isequal(Catalyst.get_states(rs), [s1])
 @test isequal(Catalyst.get_ps(rs), [k1, c1])
 
-@test_nowarn convert(ModelingToolkit.ODESystem, rs)
-@test_nowarn structural_simplify(convert(ModelingToolkit.ODESystem, rs))
+@test convert(ModelingToolkit.ODESystem, rs) isa ODESystem
+@test structural_simplify(convert(ModelingToolkit.ODESystem, rs)) isa ODESystem
 
 # Test ODESystem constructor
 odesys = ODESystem(MODEL1)
@@ -89,7 +89,7 @@ par = [k1 => 1.0, c1 => 2.0]
 @test isequal(ModelingToolkit.defaults(odesys), ModelingToolkit._merge(u0, par))  # PL: @Anand: for some reason this does not work with `Catalyst.get_default()`
 @named odesys = ODESystem(MODEL1)
 isequal(nameof(odesys), :odesys)
-@test_nowarn structural_simplify(odesys)
+@test structural_simplify(odesys) isa ODESystem
 
 odesys = ODESystem(readSBML(sbmlfile))
 m = readSBML(sbmlfile)
@@ -106,7 +106,7 @@ par = [k1 => 1.0, c1 => 2.0]
 @named odesys = ODESystem(MODEL1)
 isequal(nameof(odesys), :odesys)
 
-@test_nowarn ODEProblem(odesys, [], [0.0, 1.0], [])
+@test ODEProblem(odesys, [], [0.0, 1.0], []) isa ODEProblem
 
 # # Test ODEProblem
 # oprob = ODEProblem(ODESystem(MODEL1), [], [0.0, 1.0], [])