cleanup code

Author: matthiaskoenig

oven/multiprocessing/ray_init.py

@@ -2,14 +2,15 @@
 ray start --head --port=6379
 """
 
-
+import ray
 import time
+
 tstart = time.time()
-import ray
 
-ray.init(address='auto')
+
+ray.init(address="auto")
 # ray.init()
 
 
 tend = time.time()
-print(f"ray start time:", tend-tstart)
+print("ray start time:", tend - tstart)

src/sbmlsim/combine/datagenerator.py

@@ -1,7 +1,5 @@
 """DataGenerator."""
 
-from typing import Dict
-
 from sbmlsim.data import DataSet
 from sbmlsim.result import XResult
 
@@ -10,8 +8,8 @@ class DataGeneratorFunction:
     """DataGeneratorFunction."""
 
     def __call__(
-        self, xresults: Dict[str, XResult], dsets: Dict[str, DataSet] = None
-    ) -> Dict[str, XResult]:
+        self, xresults: dict[str, XResult], dsets: dict[str, DataSet] = None
+    ) -> dict[str, XResult]:
         """Call the function."""
         raise NotImplementedError
 
@@ -24,7 +22,7 @@ def __init__(self, index: int, dimension: str = "_time"):
         self.index = index
         self.dimension = dimension
 
-    def __call__(self, xresults: Dict[str, XResult], dsets=None) -> Dict[str, XResult]:
+    def __call__(self, xresults: dict[str, XResult], dsets=None) -> dict[str, XResult]:
         """Reduce based on '_time' dimension with given index."""
         results = {}
         for key, xres in xresults.items():
@@ -50,8 +48,8 @@ class DataGenerator:
     def __init__(
         self,
         f: DataGeneratorFunction,
-        xresults: Dict[str, XResult],
-        dsets: Dict[str, DataSet] = None,
+        xresults: dict[str, XResult],
+        dsets: dict[str, DataSet] = None,
     ):
         """Initialize DataGenerator."""
         self.xresults = xresults

src/sbmlsim/combine/mathml.py

@@ -3,7 +3,7 @@
 Using sympy to evaluate the expressions.
 """
 
-from typing import Any, Dict, Set
+from typing import Any
 from pymetadata import log
 import libsedml
 from sympy import lambdify, sympify
@@ -92,17 +92,17 @@ def expr_from_formula(formula: str):
     return expr
 
 
-def evaluate(astnode: libsedml.ASTNode, variables: Dict):
+def evaluate(astnode: libsedml.ASTNode, variables: dict):
     """Evaluate the astnode with values."""
     expr = parse_astnode(astnode)
     f = lambdify(args=list(expr.free_symbols), expr=expr)
     res = f(**variables)
     return res
 
 
-def _get_variables(astnode: libsedml.ASTNode, variables=None) -> Set[str]:
+def _get_variables(astnode: libsedml.ASTNode, variables=None) -> set[str]:
     """Add variable names to the variables."""
-    variables: Set
+    variables: set
     if variables is None:
         variables = set()
 

src/sbmlsim/combine/sedml/data.py

@@ -1,10 +1,11 @@
 """Reading NUML, CSV and TSV data from DataDescriptions."""
+
 import http.client as httplib
 import importlib
 import os
 import tempfile
 from pathlib import Path
-from typing import Dict, Optional
+from typing import Optional
 
 import libsbml
 import libsedml
@@ -30,7 +31,7 @@ class DataDescriptionParser:
     @classmethod
     def parse(
         cls, dd: libsedml.SedDataDescription, working_dir: Path = None
-    ) -> Dict[str, pd.Series]:
+    ) -> dict[str, pd.Series]:
         """Parse single DataDescription.
 
         Returns dictionary of data sources {DataSource.id, slice_data}
@@ -129,7 +130,6 @@ def parse(
         # -------------------------------
         data_sources = {}
         for ds in dd.getListOfDataSources():
-
             dsid = ds.getId()
 
             # log DataSource

src/sbmlsim/combine/sedml/io.py

@@ -1,10 +1,11 @@
 """Template functions to run the example cases."""
+
 import importlib
 import os
 import zipfile
 from enum import Enum
 from pathlib import Path
-from typing import Dict, Optional, Tuple, Union
+from typing import Optional, Tuple, Union
 from xml.etree import ElementTree
 
 import libsedml
@@ -147,7 +148,6 @@ def read_sedml(self) -> Tuple[libsedml.SedDocument, SEDMLInputType]:
                 omex = pyomex.Omex.from_omex(omex_path=file_path)
                 sedml_entries = omex.entries_by_format(format_key="sed-ml")
                 for entry in sedml_entries:
-
                     logger.info("SED-ML location: ", entry.location)
                     if entry.master:
                         sedml_path = omex.get_path(entry.location)