modelbase 1.49.2__tar.gz → 1.49.3__tar.gz

{modelbase-1.49.2 → modelbase-1.49.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: modelbase
-Version: 1.49.2
+Version: 1.49.3
 Summary: A package to build metabolic models
 Home-page: https://gitlab.com/qtb-hhu/modelbase-software
 License: GPL-3.0-or-later
@@ -54,6 +54,7 @@ Description-Content-Type: text/markdown
 [![PyPi](https://img.shields.io/pypi/v/modelbase)](https://pypi.org/project/modelbase/)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Checked with mypy](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
+[![security: bandit](https://img.shields.io/badge/security-bandit-yellow.svg)](https://github.com/PyCQA/bandit)
 [![Downloads](https://pepy.tech/badge/modelbase)](https://pepy.tech/project/modelbase)
 
 

{modelbase-1.49.2 → modelbase-1.49.3}/README.md

@@ -7,6 +7,7 @@
 [![PyPi](https://img.shields.io/pypi/v/modelbase)](https://pypi.org/project/modelbase/)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![Checked with mypy](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
+[![security: bandit](https://img.shields.io/badge/security-bandit-yellow.svg)](https://github.com/PyCQA/bandit)
 [![Downloads](https://pepy.tech/badge/modelbase)](https://pepy.tech/project/modelbase)
 
 

{modelbase-1.49.2 → modelbase-1.49.3}/pyproject.toml

@@ -8,6 +8,10 @@ requires = ["poetry-core>=1.0.0"]
 line-length = 90
 target-version = ['py310']
 
+
+[tool.bandit]
+skips = ["B101", "B301", "B403", "B404", "B603", "B607"]
+
 [tool.isort]
 honor_noqa = true
 import_heading_firstparty = ""
@@ -55,7 +59,7 @@ maintainers = ["Marvin van Aalst <marvin.vanaalst@gmail.com>"]
 name = "modelbase"
 readme = "README.md"
 repository = "https://gitlab.com/qtb-hhu/modelbase-software"
-version = "1.49.2"
+version = "1.49.3"
 
 [tool.poetry.dependencies]
 black = "^22.12.0"

modelbase-1.49.3/setup.py

@@ -0,0 +1,52 @@
+# -*- coding: utf-8 -*-
+from setuptools import setup
+
+package_dir = \
+{'': 'src'}
+
+packages = \
+['modelbase',
+ 'modelbase.core',
+ 'modelbase.ode',
+ 'modelbase.ode.integrators',
+ 'modelbase.ode.models',
+ 'modelbase.ode.simulators',
+ 'modelbase.ode.utils',
+ 'modelbase.sbml',
+ 'modelbase.utils']
+
+package_data = \
+{'': ['*']}
+
+install_requires = \
+['black>=22.12.0,<23.0.0',
+ 'gitchangelog>=3.0.4,<4.0.0',
+ 'ipywidgets>=8.0.6,<9.0.0',
+ 'matplotlib>=3.7.1,<4.0.0',
+ 'numpy>=1.25.0,<2.0.0',
+ 'pandas>=2.0.2,<3.0.0',
+ 'python-libsbml>=5.20.1,<6.0.0',
+ 'scipy>=1.11.0,<2.0.0',
+ 'sympy>=1.9,<2.0',
+ 'tqdm>=4.65.0,<5.0.0',
+ 'typing-extensions>=4.6.3,<5.0.0']
+
+setup_kwargs = {
+    'name': 'modelbase',
+    'version': '1.49.3',
+    'description': 'A package to build metabolic models',
+    'long_description': '# modelbase\n\n[![DOI](https://img.shields.io/badge/DOI-10.1186%2Fs12859--021--04122--7-blue)](https://doi.org/10.1186/s12859-021-04122-7)\n[![pipeline status](https://gitlab.com/qtb-hhu/modelbase-software/badges/main/pipeline.svg)](https://gitlab.com/qtb-hhu/modelbase-software/-/commits/main)\n[![coverage report](https://gitlab.com/qtb-hhu/modelbase-software/badges/main/coverage.svg)](https://gitlab.com/qtb-hhu/modelbase-software/-/commits/main)\n[![Documentation](https://img.shields.io/badge/Documentation-Gitlab-success)](https://qtb-hhu.gitlab.io/modelbase-software/)\n[![PyPi](https://img.shields.io/pypi/v/modelbase)](https://pypi.org/project/modelbase/)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n[![Checked with mypy](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)\n[![security: bandit](https://img.shields.io/badge/security-bandit-yellow.svg)](https://github.com/PyCQA/bandit)\n[![Downloads](https://pepy.tech/badge/modelbase)](https://pepy.tech/project/modelbase)\n\n\nmodelbase is a python package to help you build and analyze dynamic mathematical models of biological systems. It has originally been designed for the simulation of metabolic systems, but can be used for virtually any processes, in which some substances get converted into others.\n\nmodelbase incorporates an easy construction method to define \'reactions\'. A rate law and the stoichiometry need to be specified, and the system of differential equations is assembled automatically.\n\nmodelbase allows \'algebraic modules\', which are useful to implement rapid equilibrium or quasi steady-state approximations. In the simplest instance, they allow easy incorporation of conserved quantities.\n\nmodelbase also allows a simple construction of isotope-specific models. This class contains a constructor method that automatically construct all isotope specific versions of a particular reaction. Very cool - check it out!\n\n## Release notes\n\nVersions 1.0 and 0.4.0 introduced changes not compatible with the previous official\nrelease 0.2.5. API changes are summarised in [this notebook](docs/source/api-changes.ipynb)\n\n[Version 0.4.5](https://gitlab.com/qtb-hhu/modelbase-software/-/tags/0.4.5) was the prior stable version\n\n[Version 0.2.5](https://gitlab.com/qtb-hhu/modelbase-software/-/tags/initial-release)\nis the official release for the submission of the\nmansucript "Building mathematical models of biological systems\nwith modelbase, a Python package for semi-automatic ODE assembly\nand construction of isotope-specific models" to the Journal of Open\nResearch Software.\n\nSee changelog.md for details on changes of earlier versions.\n\n## Installation\n\nIf you quickly want to test out modelbase, or do not require assimulo support, install modelbase via\n\n```bash\npip install modelbase\n```\n\nTo enable assimulo support, the easiest way is to install modelbase via conda. We also recommend using the conda-forge channels.\n\n```bash\n# recommended to avoid package clashes\nconda config --add channels conda-forge\n\n# Create a new environment (not necessary, but recommended)\nconda create -n mb39 python=3.9\nconda install -c conda-forge modelbase\n```\n\n## License\n\n[GPL 3](https://gitlab.com/qtb-hhu/modelbase-software/blob/main/LICENSE)\n\n## Documentation\n\nThe official documentation is hosted [here on gitlab](https://qtb-hhu.gitlab.io/modelbase-software/).\n\n## Issues and support\n\nIf you experience issues using the software please contact us through our [issues](https://gitlab.com/qtb-hhu/modelbase-software/issues) page.\n\n## Contributing to modelbase\n\nAll contributions, bug reports, bug fixes, documentation improvements, enhancements and ideas are welcome. See our [contribution guide](https://gitlab.com/qtb-hhu/modelbase-software/blob/main/CONTRIBUTING.md) for more information.\n\n## How to cite\n\nIf you use this software in your scientific work, please cite [this article](https://rdcu.be/ckOSa):\n\nvan Aalst, M., Ebenhöh, O. & Matuszyńska, A. Constructing and analysing dynamic models with modelbase v1.2.3: a software update. BMC Bioinformatics 22, 203 (2021)\n\n- [doi](https://doi.org/10.1186/s12859-021-04122-7)\n- [bibtex file](https://gitlab.com/qtb-hhu/modelbase-software/blob/main/citation.bibtex)\n',
+    'author': 'Marvin van Aalst',
+    'author_email': 'marvin.vanaalst@gmail.com',
+    'maintainer': 'Marvin van Aalst',
+    'maintainer_email': 'marvin.vanaalst@gmail.com',
+    'url': 'https://gitlab.com/qtb-hhu/modelbase-software',
+    'package_dir': package_dir,
+    'packages': packages,
+    'package_data': package_data,
+    'install_requires': install_requires,
+    'python_requires': '>=3.9,<3.13',
+}
+
+
+setup(**setup_kwargs)

{modelbase-1.49.2 → modelbase-1.49.3}/src/modelbase/core/__init__.py

@@ -7,9 +7,10 @@ __all__ = [
     "ParameterMixin",
     "RateMixin",
     "StoichiometricMixin",
+    "Readout",
 ]
 
-from .algebraicmixin import AlgebraicMixin
+from .algebraicmixin import AlgebraicMixin, Readout
 from .basemodel import BaseModel
 from .compoundmixin import CompoundMixin
 from .parametermixin import ParameterMixin

{modelbase-1.49.2 → modelbase-1.49.3}/src/modelbase/core/parametermixin.py

@@ -148,8 +148,17 @@ class ParameterMixin(BaseModel):
         self._parameters[parameter_name] = parameter_value
         return self
 
-    def scale_parameter(self, parameter_name: str, factor: float) -> Self:
+    def scale_parameter(
+        self,
+        parameter_name: str,
+        factor: float,
+        verbose: bool = False,
+    ) -> Self:
         self.update_parameter(parameter_name, self._parameters[parameter_name] * factor)
+        if verbose:
+            print(
+                f"Updating parameter {parameter_name} to {self.parameters[parameter_name]:.2e}"
+            )
         return self
 
     def update_parameters(
@@ -300,6 +309,7 @@ class ParameterMixin(BaseModel):
         )
         for parameter in parameters:
             self._derived_from_parameters.add(parameter)
+        self._check_and_insert_ids([parameter_name], context="add_derived_parameter")
 
         # Initial calculation
         # self.add_parameter(
@@ -339,6 +349,7 @@ class ParameterMixin(BaseModel):
             if all(i not in j["parameters"] for j in self.derived_parameters.values()):
                 self._derived_from_parameters.remove(i)
         self._sort_derived_parameters()
+        self._remove_ids([parameter_name])
         return self
 
     def store_parameters_to_file(

{modelbase-1.49.2 → modelbase-1.49.3}/src/modelbase/ode/models/model.py

@@ -25,6 +25,7 @@ from ...core import (
     CompoundMixin,
     ParameterMixin,
     RateMixin,
+    Readout,
     StoichiometricMixin,
 )
 from ...core.utils import convert_id_to_sbml
@@ -204,6 +205,7 @@ class Model(_AbstractRateModel, BaseModel):
         rates: Dict[str, dict] | None = None,
         stoichiometries: Dict[str, dict] | None = None,
         functions: Dict[str, Callable] | None = None,
+        readouts: Dict[str, Readout] | None = None,
     ) -> Self:
         if compounds is not None:
             self.add_compounds(compounds)
@@ -217,6 +219,9 @@ class Model(_AbstractRateModel, BaseModel):
             self.add_stoichiometries(stoichiometries)
         if functions is not None:
             self.add_functions(functions)
+        if readouts is not None:
+            for name, readout in readouts.items():
+                self.add_readout(name, readout.function, readout.args)
         return self
 
     def update(
@@ -226,6 +231,7 @@ class Model(_AbstractRateModel, BaseModel):
         rates: Dict[str, dict] | None = None,
         stoichiometries: Dict[str, dict] | None = None,
         functions: Dict[str, Callable] | None = None,
+        readouts: Dict[str, Readout] | None = None,
     ) -> Self:
         if parameters is not None:
             self.update_parameters(parameters)
@@ -237,6 +243,9 @@ class Model(_AbstractRateModel, BaseModel):
             self.update_stoichiometries(stoichiometries)
         if functions is not None:
             self.update_functions(functions)
+        if readouts is not None:
+            for name, readout in readouts.items():
+                self.add_readout(name, readout.function, readout.args)
         return self
 
     def remove(

{modelbase-1.49.2 → modelbase-1.49.3}/src/modelbase/ode/simulators/abstract_simulator.py

@@ -574,11 +574,13 @@ class _BaseRateSimulator(Generic[RATE_MODEL_TYPE], _BaseSimulator[RATE_MODEL_TYP
         self,
         parameter_name: str,
         factor: float,
+        verbose: bool = False,
     ) -> Self:
         """Scale a model parameter."""
         self.model.scale_parameter(
             parameter_name=parameter_name,
             factor=factor,
+            verbose=verbose,
         )
         return self
 

{modelbase-1.49.2 → modelbase-1.49.3}/src/modelbase/ode/simulators/simulator.py

@@ -179,6 +179,7 @@ class _Simulate(_BaseRateSimulator[Model]):
         consuming_names: list[str] = []
         time = self.get_time()
         fluxes = self.get_fluxes_df()
+        title = compound if title is None else title
         if fluxes is None or time is None:
             return None, None
         for rate_name, factor in self.model.stoichiometries_by_compounds[
@@ -192,7 +193,10 @@ class _Simulate(_BaseRateSimulator[Model]):
                 consuming_names.append(rate_name)
 
         return plot_grid(
-            plot_groups=[(time, np.array(producing).T), (time, np.array(consuming).T)],
+            plot_groups=[
+                (time, np.array(producing).T),
+                (time, np.array(consuming).T),
+            ],
             legend_groups=[producing_names, consuming_names],
             xlabels=xlabel,
             ylabels=ylabel,

{modelbase-1.49.2 → modelbase-1.49.3}/src/modelbase/sbml/parser.py

@@ -903,7 +903,7 @@ class Parser:
             ]
         )
         try:
-            exec(func_str, globals(), None)
+            exec(func_str, globals(), None)  # nosec
         except SyntaxError as e:
             raise SyntaxError(f"Invalid function definition: {func_str}") from e
         python_func = globals()[func.sbml_id]

modelbase-1.49.2/setup.py

@@ -1,52 +0,0 @@
-# -*- coding: utf-8 -*-
-from setuptools import setup
-
-package_dir = \
-{'': 'src'}
-
-packages = \
-['modelbase',
- 'modelbase.core',
- 'modelbase.ode',
- 'modelbase.ode.integrators',
- 'modelbase.ode.models',
- 'modelbase.ode.simulators',
- 'modelbase.ode.utils',
- 'modelbase.sbml',
- 'modelbase.utils']
-
-package_data = \
-{'': ['*']}
-
-install_requires = \
-['black>=22.12.0,<23.0.0',
- 'gitchangelog>=3.0.4,<4.0.0',
- 'ipywidgets>=8.0.6,<9.0.0',
- 'matplotlib>=3.7.1,<4.0.0',
- 'numpy>=1.25.0,<2.0.0',
- 'pandas>=2.0.2,<3.0.0',
- 'python-libsbml>=5.20.1,<6.0.0',
- 'scipy>=1.11.0,<2.0.0',
- 'sympy>=1.9,<2.0',
- 'tqdm>=4.65.0,<5.0.0',
- 'typing-extensions>=4.6.3,<5.0.0']
-
-setup_kwargs = {
-    'name': 'modelbase',
-    'version': '1.49.2',
-    'description': 'A package to build metabolic models',
-    'long_description': '# modelbase\n\n[![DOI](https://img.shields.io/badge/DOI-10.1186%2Fs12859--021--04122--7-blue)](https://doi.org/10.1186/s12859-021-04122-7)\n[![pipeline status](https://gitlab.com/qtb-hhu/modelbase-software/badges/main/pipeline.svg)](https://gitlab.com/qtb-hhu/modelbase-software/-/commits/main)\n[![coverage report](https://gitlab.com/qtb-hhu/modelbase-software/badges/main/coverage.svg)](https://gitlab.com/qtb-hhu/modelbase-software/-/commits/main)\n[![Documentation](https://img.shields.io/badge/Documentation-Gitlab-success)](https://qtb-hhu.gitlab.io/modelbase-software/)\n[![PyPi](https://img.shields.io/pypi/v/modelbase)](https://pypi.org/project/modelbase/)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n[![Checked with mypy](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)\n[![Downloads](https://pepy.tech/badge/modelbase)](https://pepy.tech/project/modelbase)\n\n\nmodelbase is a python package to help you build and analyze dynamic mathematical models of biological systems. It has originally been designed for the simulation of metabolic systems, but can be used for virtually any processes, in which some substances get converted into others.\n\nmodelbase incorporates an easy construction method to define \'reactions\'. A rate law and the stoichiometry need to be specified, and the system of differential equations is assembled automatically.\n\nmodelbase allows \'algebraic modules\', which are useful to implement rapid equilibrium or quasi steady-state approximations. In the simplest instance, they allow easy incorporation of conserved quantities.\n\nmodelbase also allows a simple construction of isotope-specific models. This class contains a constructor method that automatically construct all isotope specific versions of a particular reaction. Very cool - check it out!\n\n## Release notes\n\nVersions 1.0 and 0.4.0 introduced changes not compatible with the previous official\nrelease 0.2.5. API changes are summarised in [this notebook](docs/source/api-changes.ipynb)\n\n[Version 0.4.5](https://gitlab.com/qtb-hhu/modelbase-software/-/tags/0.4.5) was the prior stable version\n\n[Version 0.2.5](https://gitlab.com/qtb-hhu/modelbase-software/-/tags/initial-release)\nis the official release for the submission of the\nmansucript "Building mathematical models of biological systems\nwith modelbase, a Python package for semi-automatic ODE assembly\nand construction of isotope-specific models" to the Journal of Open\nResearch Software.\n\nSee changelog.md for details on changes of earlier versions.\n\n## Installation\n\nIf you quickly want to test out modelbase, or do not require assimulo support, install modelbase via\n\n```bash\npip install modelbase\n```\n\nTo enable assimulo support, the easiest way is to install modelbase via conda. We also recommend using the conda-forge channels.\n\n```bash\n# recommended to avoid package clashes\nconda config --add channels conda-forge\n\n# Create a new environment (not necessary, but recommended)\nconda create -n mb39 python=3.9\nconda install -c conda-forge modelbase\n```\n\n## License\n\n[GPL 3](https://gitlab.com/qtb-hhu/modelbase-software/blob/main/LICENSE)\n\n## Documentation\n\nThe official documentation is hosted [here on gitlab](https://qtb-hhu.gitlab.io/modelbase-software/).\n\n## Issues and support\n\nIf you experience issues using the software please contact us through our [issues](https://gitlab.com/qtb-hhu/modelbase-software/issues) page.\n\n## Contributing to modelbase\n\nAll contributions, bug reports, bug fixes, documentation improvements, enhancements and ideas are welcome. See our [contribution guide](https://gitlab.com/qtb-hhu/modelbase-software/blob/main/CONTRIBUTING.md) for more information.\n\n## How to cite\n\nIf you use this software in your scientific work, please cite [this article](https://rdcu.be/ckOSa):\n\nvan Aalst, M., Ebenhöh, O. & Matuszyńska, A. Constructing and analysing dynamic models with modelbase v1.2.3: a software update. BMC Bioinformatics 22, 203 (2021)\n\n- [doi](https://doi.org/10.1186/s12859-021-04122-7)\n- [bibtex file](https://gitlab.com/qtb-hhu/modelbase-software/blob/main/citation.bibtex)\n',
-    'author': 'Marvin van Aalst',
-    'author_email': 'marvin.vanaalst@gmail.com',
-    'maintainer': 'Marvin van Aalst',
-    'maintainer_email': 'marvin.vanaalst@gmail.com',
-    'url': 'https://gitlab.com/qtb-hhu/modelbase-software',
-    'package_dir': package_dir,
-    'packages': packages,
-    'package_data': package_data,
-    'install_requires': install_requires,
-    'python_requires': '>=3.9,<3.13',
-}
-
-
-setup(**setup_kwargs)