fixing tests, fixing flake8, fixing mypy

release-notes/0.9.0.md

@@ -6,9 +6,11 @@ following changes:
 
 # Features
 - bump `pymetadata>=0.4.0` to switch to OLS4
-- python 3.12 support
-- dropping python 3.9
+- python 3.12 support (dropping python 3.9)
 - pydantic fixes
 - bugfixes
+- updated sbml4humans
+- libsbml-4.20.4
+- improved ODE generation
 
 Your sbmlutils team

src/sbmlutils/__init__.py

@@ -1,4 +1,5 @@
 """sbmlutils - Python utilities for SBML."""
+
 from pathlib import Path
 
 __author__ = "Matthias König"

src/sbmlutils/biomodels.py

@@ -1,4 +1,5 @@
 """Utilities for downloading biomodel models."""
+
 import shutil
 import tempfile
 from pathlib import Path

src/sbmlutils/comp/__init__.py

@@ -1,4 +1,5 @@
 """Package for SBML comp."""
+
 from .comp import (
     # Port,
     create_ExternalModelDefinition,

src/sbmlutils/comp/flatten.py

@@ -1,4 +1,5 @@
 """Helpers for model flattening."""
+
 import os
 import time
 from pathlib import Path

src/sbmlutils/console.py

@@ -1,4 +1,5 @@
 """Rich console for logging."""
+
 from rich import pretty
 from rich.console import Console
 from rich.theme import Theme

src/sbmlutils/converters/copasi.py

@@ -1,4 +1,5 @@
 """Helpers to work with COPASI files."""
+
 from pathlib import Path
 
 import libsbml

src/sbmlutils/converters/mathml.py

@@ -6,6 +6,7 @@
     *, /, +, -
     and, or, not
 """
+
 from math import *
 from typing import Any, Dict, Optional, Tuple
 

src/sbmlutils/converters/odefac_example/odefac_example.py

@@ -1,4 +1,5 @@
 """Example of creating markdown and python code."""
+
 from pathlib import Path
 
 from sbmlutils.console import console

src/sbmlutils/converters/xpp_examples.py

@@ -5,6 +5,7 @@
 pip install libroadrunner
 ```
 """
+
 from pathlib import Path
 
 import roadrunner

src/sbmlutils/cytoscape.py

@@ -1,17 +1,20 @@
 """Module for visualiation in Cytoscape."""
+
 import os
 import tempfile
+
+
 os.environ["PY4CYTOSCAPE_DETAIL_LOGGER_DIR"] = str(tempfile.gettempdir())
 
-from pathlib import Path
-from typing import Any, Union
+from pathlib import Path  # noqa: E402
+from typing import Any, Union  # noqa: E402
 
-import py4cytoscape as p4c
-from requests.exceptions import RequestException
+import py4cytoscape as p4c  # type: ignore  # noqa: E402
+from requests.exceptions import RequestException  # noqa: E402
 
-from sbmlutils import log
-from sbmlutils.console import console
-from sbmlutils.parser import antimony_to_sbml
+from sbmlutils import log  # noqa: E402
+from sbmlutils.console import console  # noqa: E402
+from sbmlutils.parser import antimony_to_sbml  # noqa: E402
 
 
 logger = log.get_logger(__name__)

src/sbmlutils/data/interpolation.py

@@ -8,6 +8,7 @@
 The functionality is very useful, but only if this can be applied to existing
 models in a simple manner.
 """
+
 from __future__ import annotations
 
 from pathlib import Path

src/sbmlutils/data/interpolation_example.py

@@ -1,4 +1,5 @@
 """Example demonstrating the interpolation of data."""
+
 import tempfile
 from pathlib import Path
 

src/sbmlutils/data/interpolation_pancreas.py

@@ -1,4 +1,5 @@
 """Example demonstrating the interpolation of data."""
+
 import tempfile
 from pathlib import Path
 from typing import Optional

src/sbmlutils/distrib/distrib_examples.py

@@ -1,4 +1,5 @@
 """Code for working with the libsbml distrib package."""
+
 import tempfile
 
 import libsbml

src/sbmlutils/distrib/distrib_packages.py

@@ -1,4 +1,5 @@
 """Example testing uncertainty with libsbml packages."""
+
 import tempfile
 from pathlib import Path
 

src/sbmlutils/examples/__init__.py

@@ -1,4 +1,5 @@
 """Examples for model creation."""
+
 from pathlib import Path
 from sbmlutils.examples.dallaman import dallaman
 from sbmlutils.examples.demo import demo

src/sbmlutils/examples/algebraic_rule.py

@@ -1,4 +1,5 @@
 """AlgebraicRule example."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.resources import EXAMPLES_DIR

src/sbmlutils/examples/annotation.py

@@ -3,6 +3,7 @@
 Model demonstrates how to annotate model objects with SBOTerms and Terms from
 other ontologies. Annotations use the functionality from `pymetadata`.
 """
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata import *

src/sbmlutils/examples/assignment.py

@@ -1,4 +1,5 @@
 """AssignmentRule and InitialAssignment example."""
+
 from sbmlutils.console import console
 from sbmlutils.converters import odefac
 from sbmlutils.examples import templates

src/sbmlutils/examples/combine_archive/omex_models.py

@@ -2,6 +2,7 @@
 
 This demonstrates just the very core SBML functionality.
 """
+
 from pathlib import Path
 from typing import Optional
 
@@ -69,7 +70,7 @@
 for k in range(n_cells - 1):
     _m.reactions.append(  # type: ignore
         Reaction(
-            sid=f"J{k}", equation=f"S{k} <-> S{k+1}", formula=f"D * (S{k}-S{k+1})"
+            sid=f"J{k}", equation=f"S{k} <-> S{k + 1}", formula=f"D * (S{k} - S{k + 1})"
         ),
     )
 

src/sbmlutils/examples/compartment_species_reaction.py

@@ -1,4 +1,5 @@
 """Compartment, Species, Reaction example."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata.sbo import *

src/sbmlutils/examples/dallaman/__init__.py

@@ -0,0 +1 @@
+"""Module for DallaMan Meal model."""

src/sbmlutils/examples/demo/demo.py

@@ -1,4 +1,5 @@
 """Demo kinetic network."""
+
 from pathlib import Path
 
 from sbmlutils.examples import templates

src/sbmlutils/examples/distrib/distrib_comp.py

@@ -1,4 +1,5 @@
 """Distrib and comp example to check flattening."""
+
 import shutil
 from pathlib import Path
 

src/sbmlutils/examples/distrib/distrib_distributions.py

@@ -1,4 +1,5 @@
 """Distrib example demonstrating distributions."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.validation import ValidationOptions

src/sbmlutils/examples/distrib/distrib_uncertainties.py

@@ -1,4 +1,5 @@
 """Uncertainty example."""
+
 import libsbml
 
 from sbmlutils.examples import templates

src/sbmlutils/examples/fbc/fbc_key_value_pair.py

@@ -1,4 +1,5 @@
 """FBC example for KeyValuePairs."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata.sbo import *

src/sbmlutils/examples/fbc/fbc_mass_charge.py

@@ -1,4 +1,5 @@
 """FBC mass and charge example."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata import *

src/sbmlutils/examples/fbc/fbc_userdefinedconstraints.py

@@ -1,4 +1,5 @@
 """FBA example with UserDefinedConstraints."""
+
 import numpy as np
 
 from sbmlutils.examples import templates

src/sbmlutils/examples/fbc/fbc_v2.py

@@ -1,4 +1,5 @@
 """FBA example with exchange reactions."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata import *

src/sbmlutils/examples/fbc/fbc_v3.py

@@ -1,4 +1,5 @@
 """FBA example with exchange reactions."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata.sbo import *

src/sbmlutils/examples/fbc/fbc_version3.py

@@ -3,6 +3,7 @@
 For latest SBML fbc v3 specification see
 https://github.com/bgoli/sbml-fbc-spec/blob/main/sf_svn/spec/main.pdf
 """
+
 from logging import getLogger
 from pathlib import Path
 

src/sbmlutils/examples/icg/__init__.py

@@ -1,4 +1,5 @@
 """ICG examples."""
+
 from pathlib import Path
 
 ICG_PATH = Path(__file__).parent

src/sbmlutils/examples/icg/factory.py

@@ -1,4 +1,5 @@
 """ICG model factory."""
+
 from pathlib import Path
 from typing import Any, Dict
 

src/sbmlutils/examples/icg/model_body.py

@@ -1,4 +1,5 @@
 """PKPD model for whole-body icg metabolism."""
+
 import os
 
 import numpy as np

src/sbmlutils/examples/icg/model_liver.py

@@ -1,4 +1,5 @@
 """ICG liver model."""
+
 from pathlib import Path
 
 from sbmlutils.cytoscape import visualize_sbml

src/sbmlutils/examples/model.py

@@ -2,6 +2,7 @@
 
 This demonstrates just the very core SBML functionality.
 """
+
 from pathlib import Path
 
 import libsbml

src/sbmlutils/examples/model_definitions.py

@@ -1,4 +1,5 @@
 """Multiple model definitions."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 

src/sbmlutils/examples/multiple_substance_units.py

@@ -1,4 +1,5 @@
 """Example for substance units."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata.sbo import *

src/sbmlutils/examples/notes.py

@@ -1,4 +1,5 @@
 """Example model with notes."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 

src/sbmlutils/examples/parameter.py

@@ -1,4 +1,5 @@
 """Parameter example."""
+
 from sbmlutils.examples import templates
 from sbmlutils.factory import *
 from sbmlutils.metadata import *

src/sbmlutils/examples/reaction.py

@@ -1,4 +1,5 @@
 """Create reaction example."""
+
 import numpy as np
 
 from sbmlutils.examples import templates

src/sbmlutils/examples/templates.py

@@ -1,4 +1,5 @@
 """Template information for the model creation."""
+
 from datetime import datetime
 
 from sbmlutils.factory import Creator

src/sbmlutils/examples/tiny/simulation.py

@@ -10,6 +10,7 @@
 ```
 
 """
+
 from pathlib import Path
 
 import pandas as pd

src/sbmlutils/examples/tiny/tiny.py

@@ -1,4 +1,5 @@
 """Tiny model example."""
+
 from math import inf
 from pathlib import Path
 

src/sbmlutils/examples/tutorial/linear_chain.py

@@ -4,6 +4,7 @@
 `sbmlutils` allows to generate patterns of objects by combining loops in combination
 with string patterns. In this example we create a kinetic model of a linear chain.
 """
+
 from sbmlutils.converters import odefac
 from sbmlutils.cytoscape import visualize_sbml
 from sbmlutils.examples import templates
@@ -34,15 +35,17 @@
             sid=f"S{k + 2}",
             initialConcentration=0.0,
             compartment="cell",
-            name=f"Species {k +2}",
+            name=f"Species {k + 2}",
         ),
     )
     model.parameters.append(
-        Parameter(sid=f"k{k+1}", value=0.1, name=f"rate constant {k+1}"),
+        Parameter(sid=f"k{k + 1}", value=0.1, name=f"rate constant {k + 1}"),
     )
     model.reactions.append(
         Reaction(
-            sid=f"J{k+1}", equation=f"S{k+1} -> S{k+2}", formula=f"k{k+1} * S{k+1}"
+            sid=f"J{k + 1}",
+            equation=f"S{k + 1} -> S{k + 2}",
+            formula=f"k{k + 1} * S{k + 1}",
         ),
     )
 

src/sbmlutils/examples/tutorial/minimal_model.py

@@ -2,6 +2,7 @@
 
 This demonstrates just the very core SBML functionality.
 """
+
 from sbmlutils.cytoscape import visualize_sbml
 from sbmlutils.factory import *
 from sbmlutils.metadata import *

src/sbmlutils/examples/tutorial/minimal_model_annotations.py

@@ -1,4 +1,5 @@
 """Annotate an existing model."""
+
 from pathlib import Path
 
 from sbmlutils.cytoscape import visualize_sbml

src/sbmlutils/examples/tutorial/minimal_model_comp.py

@@ -1,4 +1,5 @@
 """Example creating composite model."""
+
 from pathlib import Path
 
 from sbmlutils.comp import flatten_sbml
@@ -40,7 +41,7 @@
 for k in range(n_cells - 1):
     model.reactions.append(
         Reaction(
-            sid=f"J{k}", equation=f"S{k} <-> S{k+1}", formula=f"D * (S{k}-S{k+1})"
+            sid=f"J{k}", equation=f"S{k} <-> S{k + 1}", formula=f"D * (S{k} - S{k + 1})"
         ),
     )
 

src/sbmlutils/examples/tutorial/model_composition.py

@@ -1,4 +1,5 @@
 """Example for model composition via multiple models."""
+
 from pathlib import Path
 
 from sbmlutils.cytoscape import visualize_sbml