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Update v2 tests #88

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6b20661
Update v2 tests
dweindl Aug 21, 2025
f00ea09
libpetab changes
dweindl Aug 26, 2025
96e49e5
fixup22
dweindl Sep 30, 2025
ac03504
fixup2
dweindl Oct 1, 2025
d6eedf2
fixup16
dweindl Oct 1, 2025
dc4204d
more practicable event check 0023
dweindl Oct 1, 2025
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4 changes: 2 additions & 2 deletions petabtests/cases/v2.0.0/pysb/0001/0001.py
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Expand Up @@ -22,8 +22,8 @@

problem.add_observable("obs_a", "A", noise_formula=0.5)

problem.add_measurement("obs_a", "", time=0, measurement=0.7)
problem.add_measurement("obs_a", "", time=10, measurement=0.1)
problem.add_measurement("obs_a", time=0, measurement=0.7)
problem.add_measurement("obs_a", time=10, measurement=0.1)

problem.add_parameter("a0", lb=0, ub=10, nominal_value=1)
problem.add_parameter("b0", lb=0, ub=10, nominal_value=0)
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6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0001/_measurements.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time measurement observableParameters noiseParameters
obs_a 0.0 0.7
obs_a 10.0 0.1
modelId observableId experimentId time measurement observableParameters noiseParameters
obs_a 0.0 0.7
obs_a 10.0 0.1
6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0001/_simulations.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time simulation observableParameters noiseParameters
obs_a 0.0 1.0
obs_a 10.0 0.42857190373069665
modelId observableId experimentId time simulation observableParameters noiseParameters
obs_a 0.0 1.0
obs_a 10.0 0.42857190373069665
8 changes: 4 additions & 4 deletions petabtests/cases/v2.0.0/pysb/0002/0002.py
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Expand Up @@ -33,10 +33,10 @@

problem.add_observable("obs_a", "A", noise_formula=1)

problem.add_measurement("obs_a", "e0", time=0, measurement=0.7)
problem.add_measurement("obs_a", "e0", time=10, measurement=0.1)
problem.add_measurement("obs_a", "e1", time=0, measurement=0.8)
problem.add_measurement("obs_a", "e1", time=10, measurement=0.2)
problem.add_measurement("obs_a", experiment_id="e0", time=0, measurement=0.7)
problem.add_measurement("obs_a", experiment_id="e0", time=10, measurement=0.1)
problem.add_measurement("obs_a", experiment_id="e1", time=0, measurement=0.8)
problem.add_measurement("obs_a", experiment_id="e1", time=10, measurement=0.2)

problem.add_parameter("k1", lb=0, ub=10, nominal_value=0.8, estimate=True)
problem.add_parameter("k2", lb=0, ub=10, nominal_value=0.6, estimate=True)
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10 changes: 5 additions & 5 deletions petabtests/cases/v2.0.0/pysb/0002/_measurements.tsv
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@@ -1,5 +1,5 @@
observableId experimentId time measurement observableParameters noiseParameters
obs_a e0 0.0 0.7
obs_a e0 10.0 0.1
obs_a e1 0.0 0.8
obs_a e1 10.0 0.2
modelId observableId experimentId time measurement observableParameters noiseParameters
obs_a e0 0.0 0.7
obs_a e0 10.0 0.1
obs_a e1 0.0 0.8
obs_a e1 10.0 0.2
10 changes: 5 additions & 5 deletions petabtests/cases/v2.0.0/pysb/0002/_simulations.tsv
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@@ -1,5 +1,5 @@
observableId experimentId time simulation observableParameters noiseParameters
obs_a e0 0.0 0.8
obs_a e0 10.0 0.771428595186535
obs_a e1 0.0 0.9
obs_a e1 10.0 0.8142857855596045
modelId observableId experimentId time simulation observableParameters noiseParameters
obs_a e0 0.0 0.8
obs_a e0 10.0 0.771428595186535
obs_a e1 0.0 0.9
obs_a e1 10.0 0.8142857855596045
4 changes: 2 additions & 2 deletions petabtests/cases/v2.0.0/pysb/0003/0003.py
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Expand Up @@ -34,10 +34,10 @@
)

problem.add_measurement(
"obs_a", "", time=0, measurement=0.7, observable_parameters=(0.5, 2)
"obs_a", time=0, measurement=0.7, observable_parameters=(0.5, 2)
)
problem.add_measurement(
"obs_a", "", time=10, measurement=0.1, observable_parameters=(0.5, 2)
"obs_a", time=10, measurement=0.1, observable_parameters=(0.5, 2)
)

problem.add_parameter("a0", lb=0, ub=10, nominal_value=1)
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6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0003/_measurements.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time measurement observableParameters noiseParameters
obs_a 0.0 0.7 0.500000000000000;2
obs_a 10.0 0.1 0.500000000000000;2
modelId observableId experimentId time measurement observableParameters noiseParameters
obs_a 0.0 0.7 0.500000000000000;2
obs_a 10.0 0.1 0.500000000000000;2
6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0003/_simulations.tsv
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observableId experimentId time simulation observableParameters noiseParameters
obs_a 0.0 2.5 0.500000000000000;2
obs_a 10.0 2.214285951865348 0.500000000000000;2
modelId observableId experimentId time simulation observableParameters noiseParameters
obs_a 0.0 2.5 0.500000000000000;2
obs_a 10.0 2.214285951865348 0.500000000000000;2
2 changes: 0 additions & 2 deletions petabtests/cases/v2.0.0/pysb/0004/0004.py
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Expand Up @@ -34,13 +34,11 @@

problem.add_measurement(
"obs_a",
"",
time=0,
measurement=0.7,
)
problem.add_measurement(
"obs_a",
"",
time=10,
measurement=0.1,
)
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6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0004/_measurements.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time measurement observableParameters noiseParameters
obs_a 0.0 0.7
obs_a 10.0 0.1
modelId observableId experimentId time measurement observableParameters noiseParameters
obs_a 0.0 0.7
obs_a 10.0 0.1
6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0004/_simulations.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time simulation observableParameters noiseParameters
obs_a 0.0 2.5
obs_a 10.0 2.214285951865348
modelId observableId experimentId time simulation observableParameters noiseParameters
obs_a 0.0 2.5
obs_a 10.0 2.214285951865348
4 changes: 2 additions & 2 deletions petabtests/cases/v2.0.0/pysb/0005/0005.py
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Expand Up @@ -39,13 +39,13 @@

problem.add_measurement(
"obs_a",
"e0",
experiment_id="e0",
time=10,
measurement=2.1,
)
problem.add_measurement(
"obs_a",
"e1",
experiment_id="e1",
time=10,
measurement=3.2,
)
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6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0005/_measurements.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time measurement observableParameters noiseParameters
obs_a e0 10.0 2.1
obs_a e1 10.0 3.2
modelId observableId experimentId time measurement observableParameters noiseParameters
obs_a e0 10.0 2.1
obs_a e1 10.0 3.2
6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0005/_simulations.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time simulation observableParameters noiseParameters
obs_a e0 10.0 2.4285719037306968
obs_a e1 10.0 3.4285719037306968
modelId observableId experimentId time simulation observableParameters noiseParameters
obs_a e0 10.0 2.4285719037306968
obs_a e1 10.0 3.4285719037306968
4 changes: 2 additions & 2 deletions petabtests/cases/v2.0.0/pysb/0006/0006.py
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Expand Up @@ -30,10 +30,10 @@
)

problem.add_measurement(
"obs_a", "", time=0, measurement=0.7, observable_parameters=(10,)
"obs_a", time=0, measurement=0.7, observable_parameters=(10,)
)
problem.add_measurement(
"obs_a", "", time=10, measurement=0.1, observable_parameters=(15,)
"obs_a", time=10, measurement=0.1, observable_parameters=(15,)
)

problem.add_parameter("a0", lb=0, ub=10, nominal_value=1, estimate=True)
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6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0006/_measurements.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time measurement observableParameters noiseParameters
obs_a 0.0 0.7 10
obs_a 10.0 0.1 15
modelId observableId experimentId time measurement observableParameters noiseParameters
obs_a 0.0 0.7 10
obs_a 10.0 0.1 15
6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0006/_simulations.tsv
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observableId experimentId time simulation observableParameters noiseParameters
obs_a 0.0 10.0 10
obs_a 10.0 6.42857855596045 15
modelId observableId experimentId time simulation observableParameters noiseParameters
obs_a 0.0 10.0 10
obs_a 10.0 6.42857855596045 15
4 changes: 2 additions & 2 deletions petabtests/cases/v2.0.0/pysb/0007/0007.py
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Expand Up @@ -36,8 +36,8 @@
"obs_b", "B", noise_formula=0.6, noise_distribution=LOG_NORMAL
)

problem.add_measurement("obs_a", "", time=10, measurement=0.2)
problem.add_measurement("obs_b", "", time=10, measurement=0.8)
problem.add_measurement("obs_a", time=10, measurement=0.2)
problem.add_measurement("obs_b", time=10, measurement=0.8)

problem.add_parameter("a0", lb=0, ub=10, nominal_value=1, estimate=True)
problem.add_parameter("b0", lb=0, ub=10, nominal_value=0, estimate=True)
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6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0007/_measurements.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time measurement observableParameters noiseParameters
obs_a 10.0 0.2
obs_b 10.0 0.8
modelId observableId experimentId time measurement observableParameters noiseParameters
obs_a 10.0 0.2
obs_b 10.0 0.8
6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0007/_simulations.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time simulation observableParameters noiseParameters
obs_a 10.0 0.42857190373069665
obs_b 10.0 0.5714280962693035
modelId observableId experimentId time simulation observableParameters noiseParameters
obs_a 10.0 0.42857190373069665
obs_b 10.0 0.5714280962693035
6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0008/0008.py
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Expand Up @@ -24,9 +24,9 @@

problem.add_observable("obs_a", "A", noise_formula=0.5)

problem.add_measurement("obs_a", "", time=0, measurement=0.7)
problem.add_measurement("obs_a", "", time=10, measurement=0.1)
problem.add_measurement("obs_a", "", time=10, measurement=0.2)
problem.add_measurement("obs_a", time=0, measurement=0.7)
problem.add_measurement("obs_a", time=10, measurement=0.1)
problem.add_measurement("obs_a", time=10, measurement=0.2)

problem.add_parameter("a0", lb=0, ub=10, nominal_value=1, estimate=True)
problem.add_parameter("b0", lb=0, ub=10, nominal_value=0, estimate=True)
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8 changes: 4 additions & 4 deletions petabtests/cases/v2.0.0/pysb/0008/_measurements.tsv
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@@ -1,4 +1,4 @@
observableId experimentId time measurement observableParameters noiseParameters
obs_a 0.0 0.7
obs_a 10.0 0.1
obs_a 10.0 0.2
modelId observableId experimentId time measurement observableParameters noiseParameters
obs_a 0.0 0.7
obs_a 10.0 0.1
obs_a 10.0 0.2
8 changes: 4 additions & 4 deletions petabtests/cases/v2.0.0/pysb/0008/_simulations.tsv
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@@ -1,4 +1,4 @@
observableId experimentId time simulation observableParameters noiseParameters
obs_a 0.0 1.0
obs_a 10.0 0.42857190373069665
obs_a 10.0 0.42857190373069665
modelId observableId experimentId time simulation observableParameters noiseParameters
obs_a 0.0 1.0
obs_a 10.0 0.42857190373069665
obs_a 10.0 0.42857190373069665
4 changes: 2 additions & 2 deletions petabtests/cases/v2.0.0/pysb/0009/0009.py
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Expand Up @@ -34,8 +34,8 @@

problem.add_observable("obs_a", "A", noise_formula=0.5)

problem.add_measurement("obs_a", "e0", time=1, measurement=0.7)
problem.add_measurement("obs_a", "e0", time=10, measurement=0.1)
problem.add_measurement("obs_a", experiment_id="e0", time=1, measurement=0.7)
problem.add_measurement("obs_a", experiment_id="e0", time=10, measurement=0.1)

problem.add_parameter("a0", lb=0, ub=10, nominal_value=1, estimate=True)
problem.add_parameter("b0", lb=0, ub=10, nominal_value=0, estimate=True)
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6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0009/_measurements.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time measurement observableParameters noiseParameters
obs_a e0 1.0 0.7
obs_a e0 10.0 0.1
modelId observableId experimentId time measurement observableParameters noiseParameters
obs_a e0 1.0 0.7
obs_a e0 10.0 0.1
6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0009/_simulations.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time simulation observableParameters noiseParameters
obs_a e0 1.0 0.48728499141466824
obs_a e0 10.0 0.42857162655445696
modelId observableId experimentId time simulation observableParameters noiseParameters
obs_a e0 1.0 0.48728499141466824
obs_a e0 10.0 0.42857162655445696
4 changes: 2 additions & 2 deletions petabtests/cases/v2.0.0/pysb/0010/0010.py
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Expand Up @@ -31,8 +31,8 @@

problem.add_observable("obs_a", "A", noise_formula=0.5)

problem.add_measurement("obs_a", "e0", time=1, measurement=0.7)
problem.add_measurement("obs_a", "e0", time=10, measurement=0.1)
problem.add_measurement("obs_a", experiment_id="e0", time=1, measurement=0.7)
problem.add_measurement("obs_a", experiment_id="e0", time=10, measurement=0.1)

problem.add_parameter("k2", lb=0, ub=10, nominal_value=0.6, estimate=True)
problem.add_mapping("A", "A_() ** compartment")
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6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0010/_measurements.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time measurement observableParameters noiseParameters
obs_a e0 1.0 0.7
obs_a e0 10.0 0.1
modelId observableId experimentId time measurement observableParameters noiseParameters
obs_a e0 1.0 0.7
obs_a e0 10.0 0.1
6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0010/_simulations.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time simulation observableParameters noiseParameters
obs_a e0 1.0 0.7025430017170664
obs_a e0 10.0 0.7142856746891086
modelId observableId experimentId time simulation observableParameters noiseParameters
obs_a e0 1.0 0.7025430017170664
obs_a e0 10.0 0.7142856746891086
4 changes: 2 additions & 2 deletions petabtests/cases/v2.0.0/pysb/0011/0011.py
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Expand Up @@ -27,8 +27,8 @@

problem.add_observable("obs_a", "A", noise_formula=0.5)

problem.add_measurement("obs_a", "e0", time=0, measurement=0.7)
problem.add_measurement("obs_a", "e0", time=10, measurement=0.1)
problem.add_measurement("obs_a", experiment_id="e0", time=0, measurement=0.7)
problem.add_measurement("obs_a", experiment_id="e0", time=10, measurement=0.1)

problem.add_parameter("k1", lb=0, ub=10, nominal_value=0.8, estimate=True)
problem.add_parameter("k2", lb=0, ub=10, nominal_value=0.6, estimate=True)
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6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0011/_measurements.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time measurement observableParameters noiseParameters
obs_a e0 0.0 0.7
obs_a e0 10.0 0.1
modelId observableId experimentId time measurement observableParameters noiseParameters
obs_a e0 0.0 0.7
obs_a e0 10.0 0.1
6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0011/_simulations.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time simulation observableParameters noiseParameters
obs_a e0 0.0 1.0
obs_a e0 10.0 1.2857140481346516
modelId observableId experimentId time simulation observableParameters noiseParameters
obs_a e0 0.0 1.0
obs_a e0 10.0 1.2857140481346516
4 changes: 2 additions & 2 deletions petabtests/cases/v2.0.0/pysb/0012/0012.py
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Expand Up @@ -23,8 +23,8 @@
problem.add_experiment("e0", 0, "c0")
problem.add_observable("obs_a", "A", noise_formula=0.5)

problem.add_measurement("obs_a", "e0", time=0, measurement=0.7)
problem.add_measurement("obs_a", "e0", time=10, measurement=0.1)
problem.add_measurement("obs_a", experiment_id="e0", time=0, measurement=0.7)
problem.add_measurement("obs_a", experiment_id="e0", time=10, measurement=0.1)
problem.add_parameter("k1", lb=0, ub=10, nominal_value=0.8, estimate=True)
problem.add_parameter("k2", lb=0, ub=10, nominal_value=0.6, estimate=True)

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6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0012/_measurements.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time measurement observableParameters noiseParameters
obs_a e0 0.0 0.7
obs_a e0 10.0 0.1
modelId observableId experimentId time measurement observableParameters noiseParameters
obs_a e0 0.0 0.7
obs_a e0 10.0 0.1
6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0012/_simulations.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time simulation observableParameters noiseParameters
obs_a e0 0.0 1.0
obs_a e0 10.0 0.8571429759326742
modelId observableId experimentId time simulation observableParameters noiseParameters
obs_a e0 0.0 1.0
obs_a e0 10.0 0.8571429759326742
4 changes: 2 additions & 2 deletions petabtests/cases/v2.0.0/pysb/0013/0013.py
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Expand Up @@ -23,8 +23,8 @@
problem.add_experiment("e0", 0, "c0")
problem.add_observable("obs_a", "A", noise_formula=0.5)

problem.add_measurement("obs_a", "e0", time=0, measurement=0.7)
problem.add_measurement("obs_a", "e0", time=10, measurement=0.1)
problem.add_measurement("obs_a", experiment_id="e0", time=0, measurement=0.7)
problem.add_measurement("obs_a", experiment_id="e0", time=10, measurement=0.1)

problem.add_parameter("k1", lb=0, ub=10, nominal_value=0.8, estimate=True)
problem.add_parameter("k2", lb=0, ub=10, nominal_value=0.6, estimate=True)
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6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0013/_measurements.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time measurement observableParameters noiseParameters
obs_a e0 0.0 0.7
obs_a e0 10.0 0.1
modelId observableId experimentId time measurement observableParameters noiseParameters
obs_a e0 0.0 0.7
obs_a e0 10.0 0.1
6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0013/_simulations.tsv
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@@ -1,3 +1,3 @@
observableId experimentId time simulation observableParameters noiseParameters
obs_a e0 0.0 1.0
obs_a e0 10.0 3.4285694091445396
modelId observableId experimentId time simulation observableParameters noiseParameters
obs_a e0 0.0 1.0
obs_a e0 10.0 3.4285694091445396
12 changes: 10 additions & 2 deletions petabtests/cases/v2.0.0/pysb/0014/0014.py
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Expand Up @@ -25,10 +25,18 @@
noise_placeholders=["noise_placeholder1", "noise_placeholder2"],
)
problem.add_measurement(
"obs_a", "", time=0, measurement=0.7, noise_parameters=(0.5, 2)
"obs_a",
experiment_id="",
time=0,
measurement=0.7,
noise_parameters=(0.5, 2),
)
problem.add_measurement(
"obs_a", "", time=10, measurement=0.1, noise_parameters=(0.5, 2)
"obs_a",
experiment_id="",
time=10,
measurement=0.1,
noise_parameters=(0.5, 2),
)
problem.add_parameter("a0", lb=0, ub=10, nominal_value=1, estimate=True)
problem.add_parameter("b0", lb=0, ub=10, nominal_value=0, estimate=True)
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6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0014/_measurements.tsv
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observableId experimentId time measurement observableParameters noiseParameters
obs_a 0.0 0.7 0.500000000000000;2
obs_a 10.0 0.1 0.500000000000000;2
modelId observableId experimentId time measurement observableParameters noiseParameters
obs_a 0.0 0.7 0.500000000000000;2
obs_a 10.0 0.1 0.500000000000000;2
6 changes: 3 additions & 3 deletions petabtests/cases/v2.0.0/pysb/0014/_simulations.tsv
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Original file line number Diff line number Diff line change
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observableId experimentId time simulation observableParameters noiseParameters
obs_a 0.0 1.0 0.500000000000000;2
obs_a 10.0 0.42857190373069665 0.500000000000000;2
modelId observableId experimentId time simulation observableParameters noiseParameters
obs_a 0.0 1.0 0.500000000000000;2
obs_a 10.0 0.42857190373069665 0.500000000000000;2
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