Closed dweindl closed 3 years ago
Merging #60 (72a65e6) into develop (d481eda) will increase coverage by
0.05%
. The diff coverage is100.00%
.
@@ Coverage Diff @@
## develop #60 +/- ##
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+ Coverage 78.79% 78.85% +0.05%
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Files 24 24
Lines 2334 2331 -3
Branches 552 552
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- Hits 1839 1838 -1
+ Misses 361 359 -2
Partials 134 134
Impacted Files | Coverage Δ | |
---|---|---|
petab/parameter_mapping.py | 69.00% <100.00%> (+0.61%) |
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I think it would actually be nice to have an error message when mapping is not possible.
I think it would actually be nice to have an error message when mapping is not possible.
Such a case would be invalid PEtab and should be reported by petablint
. In the parameter mapping we widely assume we have valid PEtab files. If you have an example where this is not correctly detected, please share.
I think it would actually be nice to have an error message when mapping is not possible.
Such a case would be invalid PEtab and should be reported by
petablint
. In the parameter mapping we widely assume we have valid PEtab files. If you have an example where this is not correctly detected, please share.
This is not detected for pysb-petab. Used observableParameters_$obs_id$
(extra s) or misspelled obs_id and both definitely did not yield the results I wanted.
This is not detected for pysb-petab. Used
observableParameters_$obs_id$
(extra s) or misspelled obs_id and both definitely did not yield the results I wanted.
Hm.... changing petab test case 0003:
diff --git a/petabtests/cases/pysb/0003/_observables.tsv b/petabtests/cases/pysb/0003/_observables.tsv
index dc2a127..43e4a45 100644
--- a/petabtests/cases/pysb/0003/_observables.tsv
+++ b/petabtests/cases/pysb/0003/_observables.tsv
@@ -1,2 +1,2 @@
observableId observableFormula noiseFormula
-obs_a observableParameter1_obs_a * A + observableParameter2_obs_a 0.5
+obs_a observableParameter1_obs_a * A + observableParameters2_obs_a 0.5
gives me
petablint -y 0003/_0003.yaml
SBML model not available. Skipping.
Mismatch of observable parameter overrides for obs_a (observableParameter1_obs_a * A + observableParameters2_obs_a)in:
observableId obs_a
simulationConditionId c0
time 0
measurement 0.7
observableParameters 0.5;2
Name: 0, dtype: object
Expected 0 or 1 but got 2
Not OK
What am I doing differently?
…for_observable (fixes #59)
Revert "More informative error messages in case of wrongly set observable and noise parameters (Closes PEtab-dev/PEtab#118) (PEtab-dev/PEtab#155)"
This reverts commit 8fab85e2b581ff501ee0a5595faa4d28543c0257.