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Update petab v2 tests #80

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83354fd
Update petab v2 tests
dweindl Dec 9, 2024
68c0c6e
experimentId
dweindl Dec 16, 2024
fc17260
..
dweindl Dec 18, 2024
b098ea0
refactor
dweindl Dec 18, 2024
1e5328a
updated experiment ids
dweindl Dec 18, 2024
5e29d3e
pysb0002
dweindl Dec 18, 2024
825bee7
pc
dweindl Dec 18, 2024
573dc63
-v
dweindl Dec 18, 2024
ab57318
pysb 4+5
dweindl Dec 18, 2024
2f3a873
pysb 6+7
dweindl Dec 18, 2024
e9b012d
pysb 8+9
dweindl Dec 18, 2024
f4885e4
pysb 10+11
dweindl Dec 18, 2024
f11d2de
pysb 12+13
dweindl Dec 19, 2024
63ee755
pysb 14+15
dweindl Dec 19, 2024
e684041
..
dweindl Dec 19, 2024
564512f
..
dweindl Dec 19, 2024
e9bd03d
..
dweindl Dec 20, 2024
eef6cfb
valueType -> operationType
dweindl Mar 12, 2025
63f371a
update
dweindl Mar 13, 2025
1babd6c
add reinitialization test
dweindl Mar 17, 2025
697a796
PetabV2TestCase
dweindl Mar 18, 2025
14df610
0023
dweindl Mar 18, 2025
5ef05dc
separate v1 and v2 test cases, update to new conditions table
dweindl Mar 21, 2025
8007289
..
dweindl Mar 21, 2025
e4f55dd
steady state & events
dweindl Mar 26, 2025
e560824
fix estimate
dweindl Mar 27, 2025
7f840af
..
dweindl Mar 27, 2025
a91a055
..
dweindl Mar 28, 2025
7fc6713
evaluate -> v2
dweindl Mar 31, 2025
716750d
Drop parameter scale
dweindl Apr 28, 2025
4ed706b
Fix test case 0002 (https://github.com/PEtab-dev/PEtab/issues/624)
dweindl May 9, 2025
5c3145f
Merge branch 'main' into update_v2
dweindl May 9, 2025
61da4e3
Further v2 updates
dweindl May 12, 2025
1398e5e
fix obs transformation; re-initialization
dweindl May 12, 2025
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4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0001/0001.py
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import pandas as pd
from petab.v1.C import *

from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
from petabtests import DEFAULT_SBML_FILE, PetabV1TestCase, analytical_a

DESCRIPTION = cleandoc("""
## Objective
Expand Down Expand Up @@ -63,7 +63,7 @@
]


case = PetabTestCase(
case = PetabV1TestCase(
id=1,
brief="Simulation. Nothing special.",
description=DESCRIPTION,
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0002/0002.py
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import pandas as pd
from petab.v1.C import *

from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
from petabtests import DEFAULT_SBML_FILE, PetabV1TestCase, analytical_a

DESCRIPTION = cleandoc("""
## Objective
Expand Down Expand Up @@ -71,7 +71,7 @@
*[analytical_a(t, 0.9, 1, 0.8, 0.6) for t in [0, 10]],
]

case = PetabTestCase(
case = PetabV1TestCase(
id=2,
brief="Simulation. Two conditions. Numeric parameter override.",
description=DESCRIPTION,
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0003/0003.py
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import pandas as pd
from petab.v1.C import *

from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
from petabtests import DEFAULT_SBML_FILE, PetabV1TestCase, analytical_a

DESCRIPTION = cleandoc("""
## Objective
Expand Down Expand Up @@ -71,7 +71,7 @@
0.5 * analytical_a(t, 1, 0, 0.8, 0.6) + 2 for t in simulation_df[TIME]
]

case = PetabTestCase(
case = PetabV1TestCase(
id=3,
brief="Simulation. Numeric observable parameter overrides in measurement "
"table.",
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0004/0004.py
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Expand Up @@ -3,7 +3,7 @@
import pandas as pd
from petab.v1.C import *

from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
from petabtests import DEFAULT_SBML_FILE, PetabV1TestCase, analytical_a

DESCRIPTION = cleandoc("""
## Objective
Expand Down Expand Up @@ -68,7 +68,7 @@
0.5 * analytical_a(t, 1, 0, 0.8, 0.6) + 2 for t in simulation_df[TIME]
]

case = PetabTestCase(
case = PetabV1TestCase(
id=4,
brief="Simulation. Observable parameters only defined in parameter table.",
description=DESCRIPTION,
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0005/0005.py
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import pandas as pd
from petab.v1.C import *

from petabtests import PetabTestCase, analytical_a, antimony_to_sbml_str
from petabtests import PetabV1TestCase, analytical_a, antimony_to_sbml_str

DESCRIPTION = cleandoc("""
## Objective
Expand Down Expand Up @@ -88,7 +88,7 @@
*(analytical_a(10, 1, 0, 0.8, 0.6) + offset for offset in [2, 3]),
]

case = PetabTestCase(
case = PetabV1TestCase(
id=5,
brief="Simulation. Condition-specific parameters only defined in "
"parameter table.",
Expand Down
2 changes: 1 addition & 1 deletion petabtests/cases/v1.0.0/sbml/0005/_model.xml
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@@ -1,5 +1,5 @@
<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.14.0 with libSBML version 5.20.2. -->
<!-- Created by libAntimony version v2.15.0 with libSBML version 5.20.2. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model metaid="petab_test_0011" id="petab_test_0011">
<listOfCompartments>
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0006/0006.py
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Expand Up @@ -3,7 +3,7 @@
import pandas as pd
from petab.v1.C import *

from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
from petabtests import DEFAULT_SBML_FILE, PetabV1TestCase, analytical_a

DESCRIPTION = cleandoc("""
## Objective
Expand Down Expand Up @@ -67,7 +67,7 @@
15 * analytical_a(10, 1, 0, 0.8, 0.6),
]

case = PetabTestCase(
case = PetabV1TestCase(
id=6,
brief="Simulation. Time-point specific numeric observable parameter "
"overrides.",
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0007/0007.py
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Expand Up @@ -5,7 +5,7 @@

from petabtests import (
DEFAULT_SBML_FILE,
PetabTestCase,
PetabV1TestCase,
analytical_a,
analytical_b,
)
Expand Down Expand Up @@ -72,7 +72,7 @@
analytical_b(10, 1, 0, 0.8, 0.6),
]

case = PetabTestCase(
case = PetabV1TestCase(
id=7,
brief="Simulation. Observable transformation log10.",
description=DESCRIPTION,
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0008/0008.py
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Expand Up @@ -3,7 +3,7 @@
import pandas as pd
from petab.v1.C import *

from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
from petabtests import DEFAULT_SBML_FILE, PetabV1TestCase, analytical_a

DESCRIPTION = cleandoc("""
## Objective
Expand Down Expand Up @@ -64,7 +64,7 @@
analytical_a(t, 1, 0, 0.8, 0.6) for t in simulation_df[TIME]
]

case = PetabTestCase(
case = PetabV1TestCase(
id=8,
brief="Simulation. Replicate measurements.",
description=DESCRIPTION,
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0009/0009.py
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Expand Up @@ -5,7 +5,7 @@

from petabtests import (
DEFAULT_SBML_FILE,
PetabTestCase,
PetabV1TestCase,
analytical_a,
analytical_b,
)
Expand Down Expand Up @@ -76,7 +76,7 @@
for t in simulation_df[TIME]
]

case = PetabTestCase(
case = PetabV1TestCase(
id=9,
brief="Simulation. Preequilibration.",
description=DESCRIPTION,
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0010/0010.py
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Expand Up @@ -3,7 +3,7 @@
import pandas as pd
from petab.v1.C import *

from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
from petabtests import DEFAULT_SBML_FILE, PetabV1TestCase, analytical_a

DESCRIPTION = cleandoc("""
## Objective
Expand Down Expand Up @@ -72,7 +72,7 @@
analytical_a(t, steady_state_a, 1, 0.8, 0.6) for t in simulation_df[TIME]
]

case = PetabTestCase(
case = PetabV1TestCase(
id=10,
brief="Simulation. Preequilibration. One species reinitialized, one not. "
"InitialAssignment to species overridden.",
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0011/0011.py
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Expand Up @@ -3,7 +3,7 @@
import pandas as pd
from petab.v1.C import *
from pathlib import Path
from petabtests import PetabTestCase, analytical_a, antimony_to_sbml_str
from petabtests import PetabV1TestCase, analytical_a, antimony_to_sbml_str

DESCRIPTION = cleandoc("""
## Objective
Expand Down Expand Up @@ -79,7 +79,7 @@
analytical_a(t, 1, 2, 0.8, 0.6) for t in simulation_df[TIME]
]

case = PetabTestCase(
case = PetabV1TestCase(
id=11,
brief="Simulation. InitialAssignment to species overridden.",
description=DESCRIPTION,
Expand Down
2 changes: 1 addition & 1 deletion petabtests/cases/v1.0.0/sbml/0011/_model.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.14.0 with libSBML version 5.20.2. -->
<!-- Created by libAntimony version v2.15.0 with libSBML version 5.20.2. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model metaid="petab_test_0011" id="petab_test_0011">
<listOfCompartments>
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0012/0012.py
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Expand Up @@ -3,7 +3,7 @@
import pandas as pd
from petab.v1.C import *

from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
from petabtests import DEFAULT_SBML_FILE, PetabV1TestCase, analytical_a

DESCRIPTION = cleandoc("""
## Objective
Expand Down Expand Up @@ -64,7 +64,7 @@
analytical_a(t, 1, 1, 0.8, 0.6) for t in simulation_df[TIME]
]

case = PetabTestCase(
case = PetabV1TestCase(
id=12,
brief="Simulation. Initial compartment size in condition table.",
description=DESCRIPTION,
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0013/0013.py
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Expand Up @@ -3,7 +3,7 @@
import pandas as pd
from petab.v1.C import *

from petabtests import PetabTestCase, analytical_a
from petabtests import PetabV1TestCase, analytical_a

DESCRIPTION = cleandoc("""
## Objective
Expand Down Expand Up @@ -64,7 +64,7 @@
analytical_a(t, 1, 7, 0.8, 0.6) for t in simulation_df[TIME]
]

case = PetabTestCase(
case = PetabV1TestCase(
id=13,
brief="Simulation. Species with InitialAssignment overridden by "
"parameter.",
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0014/0014.py
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Expand Up @@ -3,7 +3,7 @@
import pandas as pd
from petab.v1.C import *

from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
from petabtests import DEFAULT_SBML_FILE, PetabV1TestCase, analytical_a

DESCRIPTION = cleandoc("""
## Objective
Expand Down Expand Up @@ -62,7 +62,7 @@
analytical_a(t, 1, 0, 0.8, 0.6) for t in simulation_df[TIME]
]

case = PetabTestCase(
case = PetabV1TestCase(
id=14,
brief="Simulation. Multiple numeric noise parameter overrides.",
description=DESCRIPTION,
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0015/0015.py
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Expand Up @@ -3,7 +3,7 @@
import pandas as pd
from petab.v1.C import *

from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
from petabtests import DEFAULT_SBML_FILE, PetabV1TestCase, analytical_a

DESCRIPTION = cleandoc("""
## Objective
Expand Down Expand Up @@ -62,7 +62,7 @@
analytical_a(t, 1, 0, 0.8, 0.6) for t in simulation_df[TIME]
]

case = PetabTestCase(
case = PetabV1TestCase(
id=15,
brief="Simulation. Single parametric noise parameter override.",
description=DESCRIPTION,
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0016/0016.py
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Expand Up @@ -5,7 +5,7 @@

from petabtests import (
DEFAULT_SBML_FILE,
PetabTestCase,
PetabV1TestCase,
analytical_a,
analytical_b,
)
Expand Down Expand Up @@ -71,7 +71,7 @@
analytical_b(10, 1, 0, 0.8, 0.6),
]

case = PetabTestCase(
case = PetabV1TestCase(
id=16,
brief="Simulation. Observable transformation log.",
description=DESCRIPTION,
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0017/0017.py
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Expand Up @@ -5,7 +5,7 @@

from petabtests import (
DEFAULT_SBML_FILE,
PetabTestCase,
PetabV1TestCase,
analytical_a,
analytical_b,
)
Expand Down Expand Up @@ -83,7 +83,7 @@
analytical_a(t, 1, steady_state_b, 0.8, 0.6) for t in simulation_df[TIME]
]

case = PetabTestCase(
case = PetabV1TestCase(
id=17,
brief="Simulation. Preequilibration. One species reinitialized, one not "
"(NaN in condition table). InitialAssignment to species overridden.",
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0018/0018.py
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Expand Up @@ -4,7 +4,7 @@
from petab.v1.C import *
from pathlib import Path
from petabtests import (
PetabTestCase,
PetabV1TestCase,
analytical_a,
analytical_b,
antimony_to_sbml_str,
Expand Down Expand Up @@ -106,7 +106,7 @@
][3:]


case = PetabTestCase(
case = PetabV1TestCase(
id=18,
brief="Simulation. Preequilibration and RateRules. One state "
"reinitialized, one not (NaN in condition table). InitialAssignment "
Expand Down
2 changes: 1 addition & 1 deletion petabtests/cases/v1.0.0/sbml/0018/_model.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.14.0 with libSBML version 5.20.2. -->
<!-- Created by libAntimony version v2.15.0 with libSBML version 5.20.2. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model metaid="petab_test_0018" id="petab_test_0018">
<listOfCompartments>
Expand Down
2 changes: 1 addition & 1 deletion petabtests/cases/v1.0.0/sbml/0018/model.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.14.0 with libSBML version 5.20.2. -->
<!-- Created by libAntimony version v2.15.0 with libSBML version 5.20.2. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model metaid="petab_test_0018" id="petab_test_0018">
<listOfCompartments>
Expand Down
4 changes: 2 additions & 2 deletions petabtests/cases/v1.0.0/sbml/0019/0019.py
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Expand Up @@ -3,7 +3,7 @@
import pandas as pd
from petab.v1.C import *

from petabtests import PetabTestCase, analytical_a, antimony_to_sbml_str
from petabtests import PetabV1TestCase, analytical_a, antimony_to_sbml_str
from pathlib import Path

DESCRIPTION = cleandoc("""
Expand Down Expand Up @@ -84,7 +84,7 @@
analytical_a(t, 2, 3, 0.8, 0.6) for t in simulation_df[TIME]
]

case = PetabTestCase(
case = PetabV1TestCase(
id=19,
brief="Simulation. Estimated initial value via conditions table.",
description=DESCRIPTION,
Expand Down
2 changes: 1 addition & 1 deletion petabtests/cases/v1.0.0/sbml/0019/_model.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.14.0 with libSBML version 5.20.2. -->
<!-- Created by libAntimony version v2.15.0 with libSBML version 5.20.2. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model metaid="petab_test_0011" id="petab_test_0011">
<listOfCompartments>
Expand Down
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