Use petab.v1 (#74)

Be compatible with, and require petab>=0.4.0
PEtab-dev · Jul 1, 2024 · 4a1b1b0 · 4a1b1b0
1 parent 0f34f23
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Showing 65 changed files with 88 additions and 66 deletions.
diff --git a/petabtests/C.py b/petabtests/C.py
@@ -1,6 +1,7 @@
 """Constants."""
 
 from pathlib import Path
+import sys
 
 # paths
 BASE_DIR = Path(__file__).parent
@@ -20,3 +21,9 @@
 TOL_SIMULATIONS = "tol_simulations"
 TOL_CHI2 = "tol_chi2"
 TOL_LLH = "tol_llh"
+
+__all__ = [
+    x
+    for x in dir(sys.modules[__name__])
+    if not x.startswith("_") and x not in {"sys", "Path"}
+]
diff --git a/petabtests/cases/v1.0.0/sbml/0001/0001.py b/petabtests/cases/v1.0.0/sbml/0001/0001.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v1.0.0/sbml/0002/0002.py b/petabtests/cases/v1.0.0/sbml/0002/0002.py
@@ -2,7 +2,7 @@
 from math import nan
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v1.0.0/sbml/0003/0003.py b/petabtests/cases/v1.0.0/sbml/0003/0003.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v1.0.0/sbml/0004/0004.py b/petabtests/cases/v1.0.0/sbml/0004/0004.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v1.0.0/sbml/0005/0005.py b/petabtests/cases/v1.0.0/sbml/0005/0005.py
@@ -2,7 +2,7 @@
 from pathlib import Path
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v1.0.0/sbml/0006/0006.py b/petabtests/cases/v1.0.0/sbml/0006/0006.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v1.0.0/sbml/0007/0007.py b/petabtests/cases/v1.0.0/sbml/0007/0007.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import (
     DEFAULT_SBML_FILE,

diff --git a/petabtests/cases/v1.0.0/sbml/0008/0008.py b/petabtests/cases/v1.0.0/sbml/0008/0008.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v1.0.0/sbml/0009/0009.py b/petabtests/cases/v1.0.0/sbml/0009/0009.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import (
     DEFAULT_SBML_FILE,

diff --git a/petabtests/cases/v1.0.0/sbml/0010/0010.py b/petabtests/cases/v1.0.0/sbml/0010/0010.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v1.0.0/sbml/0011/0011.py b/petabtests/cases/v1.0.0/sbml/0011/0011.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v1.0.0/sbml/0012/0012.py b/petabtests/cases/v1.0.0/sbml/0012/0012.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v1.0.0/sbml/0013/0013.py b/petabtests/cases/v1.0.0/sbml/0013/0013.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v1.0.0/sbml/0014/0014.py b/petabtests/cases/v1.0.0/sbml/0014/0014.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v1.0.0/sbml/0015/0015.py b/petabtests/cases/v1.0.0/sbml/0015/0015.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v1.0.0/sbml/0016/0016.py b/petabtests/cases/v1.0.0/sbml/0016/0016.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import (
     DEFAULT_SBML_FILE,

diff --git a/petabtests/cases/v1.0.0/sbml/0017/0017.py b/petabtests/cases/v1.0.0/sbml/0017/0017.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import (
     DEFAULT_SBML_FILE,

diff --git a/petabtests/cases/v1.0.0/sbml/0018/0018.py b/petabtests/cases/v1.0.0/sbml/0018/0018.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 from pathlib import Path
 from petabtests import PetabTestCase, analytical_a, analytical_b
 

diff --git a/petabtests/cases/v1.0.0/sbml/0019/0019.py b/petabtests/cases/v1.0.0/sbml/0019/0019.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/pysb/0001/0001.py b/petabtests/cases/v2.0.0/pysb/0001/0001.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/pysb/0002/0002.py b/petabtests/cases/v2.0.0/pysb/0002/0002.py
@@ -2,7 +2,7 @@
 from math import nan
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/pysb/0003/0003.py b/petabtests/cases/v2.0.0/pysb/0003/0003.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/pysb/0004/0004.py b/petabtests/cases/v2.0.0/pysb/0004/0004.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/pysb/0005/0005.py b/petabtests/cases/v2.0.0/pysb/0005/0005.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/pysb/0006/0006.py b/petabtests/cases/v2.0.0/pysb/0006/0006.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/pysb/0007/0007.py b/petabtests/cases/v2.0.0/pysb/0007/0007.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import (
     DEFAULT_PYSB_FILE,

diff --git a/petabtests/cases/v2.0.0/pysb/0008/0008.py b/petabtests/cases/v2.0.0/pysb/0008/0008.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/pysb/0009/0009.py b/petabtests/cases/v2.0.0/pysb/0009/0009.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import (
     DEFAULT_PYSB_FILE,

diff --git a/petabtests/cases/v2.0.0/pysb/0010/0010.py b/petabtests/cases/v2.0.0/pysb/0010/0010.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/pysb/0011/0011.py b/petabtests/cases/v2.0.0/pysb/0011/0011.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/pysb/0012/0012.py b/petabtests/cases/v2.0.0/pysb/0012/0012.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/pysb/0013/0013.py b/petabtests/cases/v2.0.0/pysb/0013/0013.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/pysb/0014/0014.py b/petabtests/cases/v2.0.0/pysb/0014/0014.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/pysb/0015/0015.py b/petabtests/cases/v2.0.0/pysb/0015/0015.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/pysb/0016/0016.py b/petabtests/cases/v2.0.0/pysb/0016/0016.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import (
     DEFAULT_PYSB_FILE,

diff --git a/petabtests/cases/v2.0.0/pysb/0017/0017.py b/petabtests/cases/v2.0.0/pysb/0017/0017.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import (
     DEFAULT_PYSB_FILE,

diff --git a/petabtests/cases/v2.0.0/pysb/0018/0018.py b/petabtests/cases/v2.0.0/pysb/0018/0018.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_PYSB_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/sbml/0001/0001.py b/petabtests/cases/v2.0.0/sbml/0001/0001.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/sbml/0002/0002.py b/petabtests/cases/v2.0.0/sbml/0002/0002.py
@@ -2,7 +2,7 @@
 from math import nan
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
 
 DESCRIPTION = cleandoc("""

diff --git a/petabtests/cases/v2.0.0/sbml/0003/0003.py b/petabtests/cases/v2.0.0/sbml/0003/0003.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/sbml/0004/0004.py b/petabtests/cases/v2.0.0/sbml/0004/0004.py
@@ -1,7 +1,7 @@
 from inspect import cleandoc
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import DEFAULT_SBML_FILE, PetabTestCase, analytical_a
 

diff --git a/petabtests/cases/v2.0.0/sbml/0005/0005.py b/petabtests/cases/v2.0.0/sbml/0005/0005.py
@@ -2,7 +2,7 @@
 from pathlib import Path
 
 import pandas as pd
-from petab.C import *
+from petab.v1.C import *
 
 from petabtests import PetabTestCase, analytical_a