Closed dilpath closed 3 years ago
Merging #135 (8a312bc) into develop (3c45897) will increase coverage by
9.74%
. The diff coverage is86.27%
.
@@ Coverage Diff @@
## develop #135 +/- ##
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+ Coverage 77.85% 87.60% +9.74%
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Files 5 6 +1
Lines 429 476 +47
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+ Hits 334 417 +83
+ Misses 95 59 -36
Impacted Files | Coverage Δ | |
---|---|---|
yaml2sbml/YamlModel.py | 84.00% <77.77%> (-0.49%) |
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yaml2sbml/yaml_validation.py | 89.65% <77.77%> (+17.65%) |
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yaml2sbml/yaml2sbml.py | 86.50% <84.37%> (+11.11%) |
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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%) |
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Hey @dilpath & @yannikschaelte, Thank you for pointing this out! I would suggest instead of removing the SBML checks, to not assign Units in the SBML in the first place, as the SBML checks can be useful. For example to check, if every parameter appearing in the right hand side of the ODEs is defined in the parameter section etc. ...
Hey @dilpath & @yannikschaelte, Thank you for pointing this out! I would suggest instead of removing the SBML checks, to not assign Units in the SBML in the first place, as the SBML checks can be useful. For example to check, if every parameter appearing in the right hand side of the ODEs is defined in the parameter section etc. ...
This PR only disables unit checks, but other SBML checks should still be enabled.
And one more problem with this approach: If you remove the SBML validity checks, your .yaml
model will still result in an invalid SBML (and your simulator should complain about that later on...). Hence I would go for outputting a valid SBML instead :)
@dilpath thank you for pointing me, that I overlooked, that the other tests are still in place. Hence I am fine with merging :) Sorry for the confusion :)
Units are always dimensionless in the generated SBML models https://github.com/yaml2sbml-dev/yaml2sbml/blob/6f42ee593796765605f2735066e157c7b1352861/yaml2sbml/yaml2sbml.py#L288 https://github.com/yaml2sbml-dev/yaml2sbml/blob/6f42ee593796765605f2735066e157c7b1352861/yaml2sbml/yaml2sbml.py#L328 https://github.com/yaml2sbml-dev/yaml2sbml/blob/6f42ee593796765605f2735066e157c7b1352861/yaml2sbml/yaml2sbml.py#L446
This can lead to inconsistent units. With the following YAML, the SBML
checkConsistency
results in a segmentation fault (python-libsbml == 5.19.0
).Units have no effect in SBML so these false inconsistencies can be ignored.