SimpleSEDML 0.3.0__tar.gz → 0.3.2__tar.gz

{simplesedml-0.3.0/src/SimpleSEDML.egg-info → simplesedml-0.3.2}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: SimpleSEDML
-Version: 0.3.0
-Summary: Python Subnet Discovery for Systems Biology
+Version: 0.3.2
+Summary: Simplified API for creating SED-ML simulation experiment descriptions
 Author-email: Joseph Hellerstein <joseph.hellerstein@gmail.com>, Herbert S Sauro <hsauro@uw.edu>
 License: MIT License
         
@@ -26,11 +26,14 @@ License: MIT License
         SOFTWARE.
         
 Project-URL: Homepage, https://github.com/sys-bio/SimpleSEDML
-Requires-Python: >=3.6
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: brotli
 Requires-Dist: biomodels_qc
 Requires-Dist: biosimulators_utils
+Requires-Dist: setuptools==75.8.2
+Requires-Dist: gmpy2
 Requires-Dist: numpy
 Requires-Dist: build
 Requires-Dist: coverage
@@ -41,14 +44,21 @@ Requires-Dist: pandas
 Requires-Dist: phrasedml
 Requires-Dist: pip
 Requires-Dist: python-libsbml
-Requires-Dist: requests
 Requires-Dist: tabulate
+Requires-Dist: sbmlxdf
 Requires-Dist: tellurium
-Requires-Dist: twine
 Requires-Dist: urllib3
+Provides-Extra: dev
+Requires-Dist: build; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: jupyterlab; extra == "dev"
+Requires-Dist: nose2; extra == "dev"
+Requires-Dist: pip; extra == "dev"
+Requires-Dist: toml; extra == "dev"
+Requires-Dist: twine; extra == "dev"
 Dynamic: license-file
 
-# SimpleSEDML
+# SimpleSEDML 
 
 SimpleSEDML is a simple API for creating directives in the [Simulation Experiment Description Markup Language (SED-ML)](https://sed-ml.org/) community standard for describing simulation experiments.
 
@@ -65,6 +75,8 @@ and (d) output for data reports and plots.
 
 ## Installation
 
+``SimpleSEDML`` has been tested on python 3.10, 3.11.
+
     pip install SimpleSEDML
 
 ## Public API
@@ -90,11 +102,85 @@ All `make*` functions return objects with `getSEDML()`, `getPhraSEDML()`, `execu
 | `end` | float | `5.0` | Simulation end time |
 | `num_point` | int | `11` | Number of output time points |
 | `num_step` | int | `None` | Number of integration steps (alternative to `num_point`) |
-| `display_variables` | list[str] | all species | Variables to plot and include in the report |
-| `simulation_type` | str | `"uniform"` | Simulation algorithm type — `"uniform"` (CVODE), `"uniform_stochastic"` (Gillespie), `"steadystate"`, `"onestep"` |
+| `display_variables` | list[str] | all floating species | Variables to plot and include in the report |
+| `simulation_type` | str | `"uniform"` | Simulation algorithm — `"uniform"` (CVODE), `"uniform_stochastic"` (Gillespie), `"steadystate"`, `"onestep"` |
 | `model_parameter_dct` | dict | `None` | Override model parameter values, e.g. `{"k1": 0.5}` |
+| `algorithm` | str | `None` | KISAO algorithm ID (overrides `simulation_type` algorithm selection) |
 | `title` | str | `""` | Plot title |
 | `is_plot` | bool | `True` | Whether to display a plot when `execute()` is called |
+| `project_dir` | str | `"project/"` | Directory where model SBML files are written |
+
+### Key arguments for `makeMultipleModelTimeCourse`
+
+| Argument | Type | Default | Description |
+| --- | --- | --- | --- |
+| `model_refs` | list[str] | `None` | List of model sources — Antimony/SBML strings, file paths, or URLs |
+| `start` | float | `0.0` | Simulation start time |
+| `end` | float | `5.0` | Simulation end time |
+| `num_point` | int | `11` | Number of output time points |
+| `num_step` | int | `None` | Number of integration steps (alternative to `num_point`) |
+| `display_variables` | list[str] | all floating species | Variables to compare across models |
+| `simulation_type` | str | `"uniform"` | Simulation algorithm — `"uniform"`, `"uniform_stochastic"`, `"steadystate"`, `"onestep"` |
+| `model_parameter_dct` | dict | `None` | Override parameter values applied to all models, e.g. `{"k1": 0.5}` |
+| `algorithm` | str | `None` | KISAO algorithm ID |
+| `is_plot` | bool | `True` | Whether to display plots when `execute()` is called |
+| `project_dir` | str | `"project/"` | Directory where model SBML files are written |
+
+### Key arguments for `makeSingleModelParameterScan`
+
+| Argument | Type | Default | Description |
+| --- | --- | --- | --- |
+| `model_ref` | str | *(required)* | Model source — Antimony/SBML string, file path, or URL |
+| `scan_parameter_dct` | dict | *(required)* | Parameters to scan; each key is a parameter name and the value is a list of values, e.g. `{"k1": [0.1, 0.5, 1.0]}` |
+| `ref_type` | str | auto-detected | Model reference type (see [Model reference types](#model-reference-types)) |
+| `simulation_type` | str | `"steadystate"` | Simulation type for each scan point — `"steadystate"` or `"onestep"` |
+| `time_interval` | float | `0.5` | Integration interval used when `simulation_type="onestep"` |
+| `display_variables` | list[str] | all floating species | Variables to plot on the y-axis |
+| `model_parameter_dct` | dict | `None` | Baseline parameter overrides applied before the scan |
+| `algorithm` | str | `None` | KISAO algorithm ID |
+| `title` | str | `None` | Plot title |
+| `is_plot` | bool | `True` | Whether to display a plot when `execute()` is called |
+| `project_dir` | str | `"project/"` | Directory where model SBML files are written |
+
+### Key arguments for `makeMultipleModelParameterScan`
+
+| Argument | Type | Default | Description |
+| --- | --- | --- | --- |
+| `scan_parameter_df` | pd.DataFrame | *(required)* | DataFrame of parameter values to scan; each column is a parameter name and each row is one scan point |
+| `model_refs` | list[str] | `None` | List of model sources — Antimony/SBML strings, file paths, or URLs |
+| `simulation_type` | str | `"onestep"` | Simulation type for each scan point — `"onestep"` or `"steadystate"` |
+| `time_interval` | float | `100` | Integration interval used when `simulation_type="onestep"` |
+| `display_variables` | list[str] | all floating species | Variables to compare across models |
+| `model_parameter_dct` | dict | `None` | Baseline parameter overrides applied before the scan |
+| `algorithm` | str | `None` | KISAO algorithm ID |
+| `title` | str | `None` | Plot title |
+| `is_plot` | bool | `True` | Whether to display plots when `execute()` is called |
+| `project_dir` | str | `"project/"` | Directory where model SBML files are written |
+
+### Key arguments for `makeExecutor`
+
+`makeExecutor` wraps an existing `SimpleSEDML` object and runs simulations directly via roadrunner, bypassing SED-ML/phraSED-ML generation.
+
+| Argument | Type | Default | Description |
+| --- | --- | --- | --- |
+| `simple` | SimpleSEDML | *(required)* | A constructed `SimpleSEDML` (or subclass) instance |
+
+Once created, the executor exposes three methods:
+
+| Method | Description |
+| --- | --- |
+| `executeTask(task_id=None, scan_parameter_dct=None)` | Run a single task; returns a `pd.DataFrame`. `scan_parameter_dct` overrides parameter values for this run. |
+| `executeRepeatedTask(repeated_task_id=None)` | Run a repeated task (parameter sweep); returns a `pd.DataFrame`. |
+| `executePlot2d(plot_id=None, ax=None, kind='line', is_plot=True)` | Execute the simulation(s) required for a 2D plot and render it; returns a `PlotResult(ax, plot_ids)`. |
+
+### Key arguments for `getModelInformation`
+
+| Argument | Type | Default | Description |
+| --- | --- | --- | --- |
+| `model_ref` | str | *(required)* | Model source — Antimony/SBML string, file path, or URL |
+| `ref_type` | str | auto-detected | Model reference type (see [Model reference types](#model-reference-types)) |
+
+Returns a `ModelInformation` object with attributes: `model_name`, `floating_species_dct`, `boundary_species_dct`, `parameter_dct`, `num_reaction`, `num_species`.
 
 ### Model reference types
 
@@ -225,6 +311,13 @@ which generates the following plot:
 
 ## Versions
 
+* 0.3.2 4/12/2026
+  * Fix bug related to import of pkg_resources is kisao by using setuptools 75.8.2
+
+* 0.3.1 4/12/2026
+  * Update README
+  * Fix package bugs
+
 * 0.3.0 4/10/2026
   * Fixed problem with OMEX files
   * Updated README.md

{simplesedml-0.3.0 → simplesedml-0.3.2}/README.md

@@ -1,4 +1,4 @@
-# SimpleSEDML
+# SimpleSEDML 
 
 SimpleSEDML is a simple API for creating directives in the [Simulation Experiment Description Markup Language (SED-ML)](https://sed-ml.org/) community standard for describing simulation experiments.
 
@@ -15,6 +15,8 @@ and (d) output for data reports and plots.
 
 ## Installation
 
+``SimpleSEDML`` has been tested on python 3.10, 3.11.
+
     pip install SimpleSEDML
 
 ## Public API
@@ -40,11 +42,85 @@ All `make*` functions return objects with `getSEDML()`, `getPhraSEDML()`, `execu
 | `end` | float | `5.0` | Simulation end time |
 | `num_point` | int | `11` | Number of output time points |
 | `num_step` | int | `None` | Number of integration steps (alternative to `num_point`) |
-| `display_variables` | list[str] | all species | Variables to plot and include in the report |
-| `simulation_type` | str | `"uniform"` | Simulation algorithm type — `"uniform"` (CVODE), `"uniform_stochastic"` (Gillespie), `"steadystate"`, `"onestep"` |
+| `display_variables` | list[str] | all floating species | Variables to plot and include in the report |
+| `simulation_type` | str | `"uniform"` | Simulation algorithm — `"uniform"` (CVODE), `"uniform_stochastic"` (Gillespie), `"steadystate"`, `"onestep"` |
 | `model_parameter_dct` | dict | `None` | Override model parameter values, e.g. `{"k1": 0.5}` |
+| `algorithm` | str | `None` | KISAO algorithm ID (overrides `simulation_type` algorithm selection) |
 | `title` | str | `""` | Plot title |
 | `is_plot` | bool | `True` | Whether to display a plot when `execute()` is called |
+| `project_dir` | str | `"project/"` | Directory where model SBML files are written |
+
+### Key arguments for `makeMultipleModelTimeCourse`
+
+| Argument | Type | Default | Description |
+| --- | --- | --- | --- |
+| `model_refs` | list[str] | `None` | List of model sources — Antimony/SBML strings, file paths, or URLs |
+| `start` | float | `0.0` | Simulation start time |
+| `end` | float | `5.0` | Simulation end time |
+| `num_point` | int | `11` | Number of output time points |
+| `num_step` | int | `None` | Number of integration steps (alternative to `num_point`) |
+| `display_variables` | list[str] | all floating species | Variables to compare across models |
+| `simulation_type` | str | `"uniform"` | Simulation algorithm — `"uniform"`, `"uniform_stochastic"`, `"steadystate"`, `"onestep"` |
+| `model_parameter_dct` | dict | `None` | Override parameter values applied to all models, e.g. `{"k1": 0.5}` |
+| `algorithm` | str | `None` | KISAO algorithm ID |
+| `is_plot` | bool | `True` | Whether to display plots when `execute()` is called |
+| `project_dir` | str | `"project/"` | Directory where model SBML files are written |
+
+### Key arguments for `makeSingleModelParameterScan`
+
+| Argument | Type | Default | Description |
+| --- | --- | --- | --- |
+| `model_ref` | str | *(required)* | Model source — Antimony/SBML string, file path, or URL |
+| `scan_parameter_dct` | dict | *(required)* | Parameters to scan; each key is a parameter name and the value is a list of values, e.g. `{"k1": [0.1, 0.5, 1.0]}` |
+| `ref_type` | str | auto-detected | Model reference type (see [Model reference types](#model-reference-types)) |
+| `simulation_type` | str | `"steadystate"` | Simulation type for each scan point — `"steadystate"` or `"onestep"` |
+| `time_interval` | float | `0.5` | Integration interval used when `simulation_type="onestep"` |
+| `display_variables` | list[str] | all floating species | Variables to plot on the y-axis |
+| `model_parameter_dct` | dict | `None` | Baseline parameter overrides applied before the scan |
+| `algorithm` | str | `None` | KISAO algorithm ID |
+| `title` | str | `None` | Plot title |
+| `is_plot` | bool | `True` | Whether to display a plot when `execute()` is called |
+| `project_dir` | str | `"project/"` | Directory where model SBML files are written |
+
+### Key arguments for `makeMultipleModelParameterScan`
+
+| Argument | Type | Default | Description |
+| --- | --- | --- | --- |
+| `scan_parameter_df` | pd.DataFrame | *(required)* | DataFrame of parameter values to scan; each column is a parameter name and each row is one scan point |
+| `model_refs` | list[str] | `None` | List of model sources — Antimony/SBML strings, file paths, or URLs |
+| `simulation_type` | str | `"onestep"` | Simulation type for each scan point — `"onestep"` or `"steadystate"` |
+| `time_interval` | float | `100` | Integration interval used when `simulation_type="onestep"` |
+| `display_variables` | list[str] | all floating species | Variables to compare across models |
+| `model_parameter_dct` | dict | `None` | Baseline parameter overrides applied before the scan |
+| `algorithm` | str | `None` | KISAO algorithm ID |
+| `title` | str | `None` | Plot title |
+| `is_plot` | bool | `True` | Whether to display plots when `execute()` is called |
+| `project_dir` | str | `"project/"` | Directory where model SBML files are written |
+
+### Key arguments for `makeExecutor`
+
+`makeExecutor` wraps an existing `SimpleSEDML` object and runs simulations directly via roadrunner, bypassing SED-ML/phraSED-ML generation.
+
+| Argument | Type | Default | Description |
+| --- | --- | --- | --- |
+| `simple` | SimpleSEDML | *(required)* | A constructed `SimpleSEDML` (or subclass) instance |
+
+Once created, the executor exposes three methods:
+
+| Method | Description |
+| --- | --- |
+| `executeTask(task_id=None, scan_parameter_dct=None)` | Run a single task; returns a `pd.DataFrame`. `scan_parameter_dct` overrides parameter values for this run. |
+| `executeRepeatedTask(repeated_task_id=None)` | Run a repeated task (parameter sweep); returns a `pd.DataFrame`. |
+| `executePlot2d(plot_id=None, ax=None, kind='line', is_plot=True)` | Execute the simulation(s) required for a 2D plot and render it; returns a `PlotResult(ax, plot_ids)`. |
+
+### Key arguments for `getModelInformation`
+
+| Argument | Type | Default | Description |
+| --- | --- | --- | --- |
+| `model_ref` | str | *(required)* | Model source — Antimony/SBML string, file path, or URL |
+| `ref_type` | str | auto-detected | Model reference type (see [Model reference types](#model-reference-types)) |
+
+Returns a `ModelInformation` object with attributes: `model_name`, `floating_species_dct`, `boundary_species_dct`, `parameter_dct`, `num_reaction`, `num_species`.
 
 ### Model reference types
 
@@ -175,6 +251,13 @@ which generates the following plot:
 
 ## Versions
 
+* 0.3.2 4/12/2026
+  * Fix bug related to import of pkg_resources is kisao by using setuptools 75.8.2
+
+* 0.3.1 4/12/2026
+  * Update README
+  * Fix package bugs
+
 * 0.3.0 4/10/2026
   * Fixed problem with OMEX files
   * Updated README.md

{simplesedml-0.3.0 → simplesedml-0.3.2}/pyproject.toml

@@ -1,15 +1,18 @@
 [project]
 name = "SimpleSEDML"
-version = "0.3.0"
-description = "Python Subnet Discovery for Systems Biology"
+version = "0.3.2"
+description = "Simplified API for creating SED-ML simulation experiment descriptions"
 authors = [{ name = "Joseph Hellerstein", email = "joseph.hellerstein@gmail.com" }, {name = "Herbert S Sauro", email = "hsauro@uw.edu"}]
 license = { file = "LICENSE" }
 readme = "README.md"
-requires-python = ">=3.6"
+requires-python = ">=3.9"
 
 dependencies = [
+"brotli",
 "biomodels_qc",
 "biosimulators_utils",
+"setuptools==75.8.2",
+"gmpy2",
 "numpy",
 "build",
 "coverage",
@@ -20,19 +23,26 @@ dependencies = [
 "phrasedml",
 "pip",
 "python-libsbml",
-"requests",
 "tabulate",
+"sbmlxdf",
 "tellurium",
-"twine",
 "urllib3",
 ]
 
+[project.optional-dependencies]
+dev = [
+    "build",
+    "coverage",
+    "jupyterlab",
+    "nose2",
+    "pip",
+    "toml",
+    "twine",
+]
+
 [project.urls]
 Homepage = 'https://github.com/sys-bio/SimpleSEDML'
 
-[options.package_data]
-data = "*.txt, *.csv, *.ant, *.xml"
-
 [build-system]
 requires = ["setuptools>=61.0.0", "wheel"]
 build-backend = "setuptools.build_meta"

{simplesedml-0.3.0 → simplesedml-0.3.2}/src/SimpleSEDML/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.3.0"
+__version__ = "0.3.2"
 from SimpleSEDML.simple_sedml import SimpleSEDML # type:ignore
 from SimpleSEDML.single_model_time_course import SingleModelTimeCourse # type:ignore
 from SimpleSEDML.multiple_model_time_course import MultipleModelTimeCourse # type:ignore

{simplesedml-0.3.0 → simplesedml-0.3.2/src/SimpleSEDML.egg-info}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: SimpleSEDML
-Version: 0.3.0
-Summary: Python Subnet Discovery for Systems Biology
+Version: 0.3.2
+Summary: Simplified API for creating SED-ML simulation experiment descriptions
 Author-email: Joseph Hellerstein <joseph.hellerstein@gmail.com>, Herbert S Sauro <hsauro@uw.edu>
 License: MIT License
         
@@ -26,11 +26,14 @@ License: MIT License
         SOFTWARE.
         
 Project-URL: Homepage, https://github.com/sys-bio/SimpleSEDML
-Requires-Python: >=3.6
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: brotli
 Requires-Dist: biomodels_qc
 Requires-Dist: biosimulators_utils
+Requires-Dist: setuptools==75.8.2
+Requires-Dist: gmpy2
 Requires-Dist: numpy
 Requires-Dist: build
 Requires-Dist: coverage
@@ -41,14 +44,21 @@ Requires-Dist: pandas
 Requires-Dist: phrasedml
 Requires-Dist: pip
 Requires-Dist: python-libsbml
-Requires-Dist: requests
 Requires-Dist: tabulate
+Requires-Dist: sbmlxdf
 Requires-Dist: tellurium
-Requires-Dist: twine
 Requires-Dist: urllib3
+Provides-Extra: dev
+Requires-Dist: build; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: jupyterlab; extra == "dev"
+Requires-Dist: nose2; extra == "dev"
+Requires-Dist: pip; extra == "dev"
+Requires-Dist: toml; extra == "dev"
+Requires-Dist: twine; extra == "dev"
 Dynamic: license-file
 
-# SimpleSEDML
+# SimpleSEDML 
 
 SimpleSEDML is a simple API for creating directives in the [Simulation Experiment Description Markup Language (SED-ML)](https://sed-ml.org/) community standard for describing simulation experiments.
 
@@ -65,6 +75,8 @@ and (d) output for data reports and plots.
 
 ## Installation
 
+``SimpleSEDML`` has been tested on python 3.10, 3.11.
+
     pip install SimpleSEDML
 
 ## Public API
@@ -90,11 +102,85 @@ All `make*` functions return objects with `getSEDML()`, `getPhraSEDML()`, `execu
 | `end` | float | `5.0` | Simulation end time |
 | `num_point` | int | `11` | Number of output time points |
 | `num_step` | int | `None` | Number of integration steps (alternative to `num_point`) |
-| `display_variables` | list[str] | all species | Variables to plot and include in the report |
-| `simulation_type` | str | `"uniform"` | Simulation algorithm type — `"uniform"` (CVODE), `"uniform_stochastic"` (Gillespie), `"steadystate"`, `"onestep"` |
+| `display_variables` | list[str] | all floating species | Variables to plot and include in the report |
+| `simulation_type` | str | `"uniform"` | Simulation algorithm — `"uniform"` (CVODE), `"uniform_stochastic"` (Gillespie), `"steadystate"`, `"onestep"` |
 | `model_parameter_dct` | dict | `None` | Override model parameter values, e.g. `{"k1": 0.5}` |
+| `algorithm` | str | `None` | KISAO algorithm ID (overrides `simulation_type` algorithm selection) |
 | `title` | str | `""` | Plot title |
 | `is_plot` | bool | `True` | Whether to display a plot when `execute()` is called |
+| `project_dir` | str | `"project/"` | Directory where model SBML files are written |
+
+### Key arguments for `makeMultipleModelTimeCourse`
+
+| Argument | Type | Default | Description |
+| --- | --- | --- | --- |
+| `model_refs` | list[str] | `None` | List of model sources — Antimony/SBML strings, file paths, or URLs |
+| `start` | float | `0.0` | Simulation start time |
+| `end` | float | `5.0` | Simulation end time |
+| `num_point` | int | `11` | Number of output time points |
+| `num_step` | int | `None` | Number of integration steps (alternative to `num_point`) |
+| `display_variables` | list[str] | all floating species | Variables to compare across models |
+| `simulation_type` | str | `"uniform"` | Simulation algorithm — `"uniform"`, `"uniform_stochastic"`, `"steadystate"`, `"onestep"` |
+| `model_parameter_dct` | dict | `None` | Override parameter values applied to all models, e.g. `{"k1": 0.5}` |
+| `algorithm` | str | `None` | KISAO algorithm ID |
+| `is_plot` | bool | `True` | Whether to display plots when `execute()` is called |
+| `project_dir` | str | `"project/"` | Directory where model SBML files are written |
+
+### Key arguments for `makeSingleModelParameterScan`
+
+| Argument | Type | Default | Description |
+| --- | --- | --- | --- |
+| `model_ref` | str | *(required)* | Model source — Antimony/SBML string, file path, or URL |
+| `scan_parameter_dct` | dict | *(required)* | Parameters to scan; each key is a parameter name and the value is a list of values, e.g. `{"k1": [0.1, 0.5, 1.0]}` |
+| `ref_type` | str | auto-detected | Model reference type (see [Model reference types](#model-reference-types)) |
+| `simulation_type` | str | `"steadystate"` | Simulation type for each scan point — `"steadystate"` or `"onestep"` |
+| `time_interval` | float | `0.5` | Integration interval used when `simulation_type="onestep"` |
+| `display_variables` | list[str] | all floating species | Variables to plot on the y-axis |
+| `model_parameter_dct` | dict | `None` | Baseline parameter overrides applied before the scan |
+| `algorithm` | str | `None` | KISAO algorithm ID |
+| `title` | str | `None` | Plot title |
+| `is_plot` | bool | `True` | Whether to display a plot when `execute()` is called |
+| `project_dir` | str | `"project/"` | Directory where model SBML files are written |
+
+### Key arguments for `makeMultipleModelParameterScan`
+
+| Argument | Type | Default | Description |
+| --- | --- | --- | --- |
+| `scan_parameter_df` | pd.DataFrame | *(required)* | DataFrame of parameter values to scan; each column is a parameter name and each row is one scan point |
+| `model_refs` | list[str] | `None` | List of model sources — Antimony/SBML strings, file paths, or URLs |
+| `simulation_type` | str | `"onestep"` | Simulation type for each scan point — `"onestep"` or `"steadystate"` |
+| `time_interval` | float | `100` | Integration interval used when `simulation_type="onestep"` |
+| `display_variables` | list[str] | all floating species | Variables to compare across models |
+| `model_parameter_dct` | dict | `None` | Baseline parameter overrides applied before the scan |
+| `algorithm` | str | `None` | KISAO algorithm ID |
+| `title` | str | `None` | Plot title |
+| `is_plot` | bool | `True` | Whether to display plots when `execute()` is called |
+| `project_dir` | str | `"project/"` | Directory where model SBML files are written |
+
+### Key arguments for `makeExecutor`
+
+`makeExecutor` wraps an existing `SimpleSEDML` object and runs simulations directly via roadrunner, bypassing SED-ML/phraSED-ML generation.
+
+| Argument | Type | Default | Description |
+| --- | --- | --- | --- |
+| `simple` | SimpleSEDML | *(required)* | A constructed `SimpleSEDML` (or subclass) instance |
+
+Once created, the executor exposes three methods:
+
+| Method | Description |
+| --- | --- |
+| `executeTask(task_id=None, scan_parameter_dct=None)` | Run a single task; returns a `pd.DataFrame`. `scan_parameter_dct` overrides parameter values for this run. |
+| `executeRepeatedTask(repeated_task_id=None)` | Run a repeated task (parameter sweep); returns a `pd.DataFrame`. |
+| `executePlot2d(plot_id=None, ax=None, kind='line', is_plot=True)` | Execute the simulation(s) required for a 2D plot and render it; returns a `PlotResult(ax, plot_ids)`. |
+
+### Key arguments for `getModelInformation`
+
+| Argument | Type | Default | Description |
+| --- | --- | --- | --- |
+| `model_ref` | str | *(required)* | Model source — Antimony/SBML string, file path, or URL |
+| `ref_type` | str | auto-detected | Model reference type (see [Model reference types](#model-reference-types)) |
+
+Returns a `ModelInformation` object with attributes: `model_name`, `floating_species_dct`, `boundary_species_dct`, `parameter_dct`, `num_reaction`, `num_species`.
 
 ### Model reference types
 
@@ -225,6 +311,13 @@ which generates the following plot:
 
 ## Versions
 
+* 0.3.2 4/12/2026
+  * Fix bug related to import of pkg_resources is kisao by using setuptools 75.8.2
+
+* 0.3.1 4/12/2026
+  * Update README
+  * Fix package bugs
+
 * 0.3.0 4/10/2026
   * Fixed problem with OMEX files
   * Updated README.md

{simplesedml-0.3.0 → simplesedml-0.3.2}/src/SimpleSEDML.egg-info/requires.txt

@@ -1,5 +1,8 @@
+brotli
 biomodels_qc
 biosimulators_utils
+setuptools==75.8.2
+gmpy2
 numpy
 build
 coverage
@@ -10,8 +13,16 @@ pandas
 phrasedml
 pip
 python-libsbml
-requests
 tabulate
+sbmlxdf
 tellurium
-twine
 urllib3
+
+[dev]
+build
+coverage
+jupyterlab
+nose2
+pip
+toml
+twine