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yaml2sbml-dev / yaml2sbml

Tool to convert an ODE model specified in the YAML format to SBML.
https://yaml2sbml.readthedocs.io/en/latest/
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Feature check sbml success #118

Closed jvanhoefer closed 3 years ago

jvanhoefer commented 3 years ago

Adds additional checks when the SBML is created, if e.g. parameter/species creation was successful (i.e. if the id is a valid SBML identifier) and if the math can be parsed...

codecov-io commented 3 years ago

Codecov Report

Merging #118 (0f3c7cb) into develop (3c45897) will increase coverage by 9.30%. The diff coverage is 84.00%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #118      +/-   ##
===========================================
+ Coverage    77.85%   87.15%   +9.30%     
===========================================
  Files            5        6       +1     
  Lines          429      475      +46     
===========================================
+ Hits           334      414      +80     
+ Misses          95       61      -34
Impacted Files Coverage Δ
yaml2sbml/YamlModel.py 84.00% <77.77%> (-0.49%) :arrow_down:
yaml2sbml/yaml_validation.py 89.65% <77.77%> (+17.65%) :arrow_up:
yaml2sbml/yaml2sbml.py 85.18% <80.64%> (+9.80%) :arrow_up:
yaml2sbml/__init__.py 100.00% <100.00%> (ø)
yaml2sbml/version.py 100.00% <100.00%> (ø)
yaml2sbml/yaml2PEtab.py 94.17% <100.00%> (+23.46%) :arrow_up:

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jvanhoefer commented 3 years ago

@dilpath There is a weird AMICI issue when importing AMICI in the notebook tests, that was not there yesterday (since then only the string of Error messages changed, but not the code in this PR). Do you have any idea, why this could be the case?