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Add citation.cff #159

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merged 5 commits into from
Jun 27, 2024
Merged

Add citation.cff #159

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94c3cc8
link citation in readme
paulflang Jun 5, 2024
bb5c078
update istree to iscall
paulflang Jun 26, 2024
7a269ef
update SymbolicUtils
paulflang Jun 26, 2024
2d0c1f8
fix istree deprecation warning
paulflang Jun 26, 2024
df0b5f6
pass tests despite warnings
paulflang Jun 26, 2024
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4 changes: 2 additions & 2 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
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why would we add back 1?

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I thought the less restrictive we are with our compats, the less likely developers who may depend on SBMLtk have compatibility issues. Also because of a compatibility requirement with the latest Catalyst release. Looks like the next release will no longer have a SymbolicUtils requirement, tho.

Test = "1"
julia = "1.10"

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18 changes: 14 additions & 4 deletions README.md
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Expand Up @@ -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:plang@biosim.ai) 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},
}
```
8 changes: 4 additions & 4 deletions test/systems.jl
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Expand Up @@ -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)
Expand All @@ -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)
Expand All @@ -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], [])
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