Merge pull request #168 from matthiaskoenig/sensitivity

Sensitivity refactoring and FAST implementation

Author: matthiaskoenig

pyproject.toml

@@ -50,7 +50,7 @@ dependencies = [
     # dependencies
     "dill>=0.4.0",
     "SAlib>=1.5.2",
-    "petab>=0.7.0",
+    "petab>=0.8.1",
     # "tables>=3.10.2",
     "statsmodels>=0.14.6",
     "typst>=0.14.5",

src/sbmlsim/combine/mathml.py

@@ -3,7 +3,7 @@
 Using sympy to evaluate the expressions.
 """
 from typing import Any, Dict, Set, Tuple
-from sbmlutils import log
+from pymetadata import log
 import libsedml
 from sympy import Symbol, lambdify, sympify
 

src/sbmlsim/combine/sedml/data.py

@@ -9,7 +9,7 @@
 import libsbml
 import libsedml
 import pandas as pd
-from sbmlutils import log
+from pymetadata import log
 
 from .numl import NumlParser
 

src/sbmlsim/combine/sedml/io.py

@@ -9,7 +9,7 @@
 
 import libsedml
 from pymetadata import omex as pyomex
-from sbmlutils import log
+from pymetadata import log
 
 
 logger = log.get_logger(__name__)

src/sbmlsim/combine/sedml/numl.py

@@ -10,7 +10,7 @@
 import libsedml
 import numpy as np
 import pandas as pd
-from sbmlutils import log
+from pymetadata import log
 
 
 logger = log.get_logger(__name__)

src/sbmlsim/combine/sedml/parser.py

@@ -89,7 +89,7 @@
 from pint import Quantity
 
 from pymetadata import omex as pyomex
-from sbmlutils import log
+from pymetadata import log
 
 from sbmlsim.combine.mathml import formula_to_astnode
 from sbmlsim.combine.sedml.data import DataDescriptionParser

src/sbmlsim/combine/sedml/task.py

@@ -1,7 +1,7 @@
 from typing import List
 
 import libsedml
-from sbmlutils import log
+from pymetadata import log
 
 
 logger = log.get_logger(__name__)

src/sbmlsim/data.py

@@ -4,7 +4,7 @@
 from typing import Dict, List, Optional, Union
 
 import pandas as pd
-from sbmlutils import log
+from pymetadata import log
 
 from sbmlsim.combine import mathml
 from sbmlsim.result import XResult

src/sbmlsim/diff.py

@@ -10,8 +10,8 @@
 import pandas as pd
 import seaborn as sns
 from matplotlib import pyplot as plt
-from sbmlutils import log
-from sbmlutils.console import console
+from pymetadata import log
+from pymetadata.console import console
 
 from sbmlsim.utils import timeit
 

src/sbmlsim/experiment/experiment.py

@@ -8,7 +8,7 @@
 from pathlib import Path
 from typing import Dict, Iterable, List, Union
 
-from sbmlutils import log
+from pymetadata import log
 
 from sbmlsim.data import Data, DataSet
 from sbmlsim.fit import FitMapping