sbmlsim 0.3.0__py3-none-any.whl

sbmlsim/__init__.py

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+"""sbmlsim package."""
+
+from pathlib import Path
+
+__author__ = "Matthias Koenig"
+__version__ = "0.3.0"
+
+
+BASE_PATH = Path(__file__).parent
+RESOURCES_DIR = BASE_PATH / "resources"

sbmlsim/combine/TODO_SEDML.md

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+
+- [ ] RepeatedTasks with new features
+- [ ] 3D plotting
+- [ ] parameter fitting
+
+
+-----------------------------
+
+sbmlsim.Experiment
+- globally unique identifiers (validate on object creation)
+- identifiers must be SIDs! (so that experiements can be )
+
+- [ ] applied dimensions;
+
+
+# Documentation
+- [ ] create documentation of SED-ML features
+
+- [ ] parse KISAO ontology
+
+# Test cases
+- [ ] execute/update all examples for the specification
+
+# Run COMBINE archive
+- [x] execute COMBINE archives (refactoring required; also store results)
+
+# Serialization (SimulationExperiment -> SED-ML)
+- [ ] datasets !
+  - [ ] slices
+  - [ ] dataRange
+- [x] model
+    - [x] resolve model from URN
+    - [S] AddXML, ChangeXML, RemoveXML
+    - [S] ComputeChange
+    - [~S] support amount, concentration and native species targets
+- [x] simulation
+    - [x] UniformTimecourse
+    - [S] OneStep
+    - [S] SteadyState
+- [~] tasks
+    - [x] Task
+    - [ ] RepeatedTask
+- [x] data generators
+- [x] figures
+  - [x] plot2d
+  - [ ] plot3d 
+  - [x] styles
+- [ ] reports
+- [ ] concentrations/amounts xpath (parse symbols and use for evaluation)
+  - [ ] data generators
+  - [ ] model changes; changesets  
+
+# Parsing (SED-ML -> SimulationExperiment)
+- [ ] datasets !
+
+- [ ] parameters in computation
+
+## Plot2D
+- [x] fix reverse axis
+- [x] support height and width;
+      plots have height & width; these can be directly set in single plot figures;
+      for multi-plot figures the combined height and width must be calculated
+- [x] use curve.name as label in legend
+- [x] support style on axis
+- [x] support setting label (name of axis)
+- [x] plot width and height  
+- [x] curve type (points, bar, ...)
+- [~] error bars; assymetrical error bars; see https://github.com/SED-ML/sed-ml/issues/137
+- [x] styling of bar plots; 
+- [x] yAxis right
+- [x] order of abstract curve
+- [x] shaded areas & fills
+- [x] resolve and apply basestyle
+- [x] update bar styling (see https://github.com/SED-ML/sed-ml/issues/140)
+- [ ] support figure caption via notes (<notes><p xmlns="xhtml">Figure 1 - Example for figure with text legend and sub-plots.</p></notes>)
+
+
+# Reports
+- [ ] reports
+# Repeated Tasks
+- [ ] repeated task
+# Simulation
+- [ ] steady state & one-step
+# Kisao terms
+
+## Plot3D
+- [ ] Plot3D examples (surfaces)
+- [ ] use surface.name as label in legend
+
+# Parameter fitting
+
+# Altair serialization

sbmlsim/combine/__init__.py

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+"""Package for working with COMBINE standards.
+
+COMBINE archive and SED-ML support.
+"""

sbmlsim/combine/datagenerator.py

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+"""DataGenerator."""
+
+from sbmlsim.data import DataSet
+from sbmlsim.result import XResult
+
+
+class DataGeneratorFunction:
+    """DataGeneratorFunction."""
+
+    def __call__(
+        self, xresults: dict[str, XResult], dsets: dict[str, DataSet] = None
+    ) -> dict[str, XResult]:
+        """Call the function."""
+        raise NotImplementedError
+
+
+class DataGeneratorIndexingFunction(DataGeneratorFunction):
+    """DataGeneratorIndexingFunction."""
+
+    def __init__(self, index: int, dimension: str = "_time"):
+        """Initialize DataGeneratorIndexingFunction."""
+        self.index = index
+        self.dimension = dimension
+
+    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():
+            xds_new = xres.xds.isel({self.dimension: self.index})
+            xres_new = XResult(xdataset=xds_new, uinfo=xres.uinfo)
+            results[key] = xres_new
+
+        return results
+
+
+class DataGenerator:
+    """DataGenerator.
+
+    DataGenerators allow to postprocess existing data. This can be a variety of
+    operations.
+
+    - Slicing: reduce the dimension of a given XResult, by slicing a subset on a
+      given dimension
+    - Cumulative processing: mean, sd, ...
+    - Complex processing, such as pharmacokinetics calculation.
+    """
+
+    def __init__(
+        self,
+        f: DataGeneratorFunction,
+        xresults: dict[str, XResult],
+        dsets: dict[str, DataSet] = None,
+    ):
+        """Initialize DataGenerator."""
+        self.xresults = xresults
+        self.dsets = dsets
+        self.f = f
+
+    def process(self) -> XResult:
+        """Process the data generator."""
+        return self.f(xresults=self.xresults, dsets=self.dsets)

sbmlsim/combine/examples/execute_omex.py

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+"""
+Execute a COMBINE archive.
+"""
+from pathlib import Path
+
+from sbmlsim.combine.examples import execute_sedml
+from tests import DATA_DIR
+
+
+def run_repressilator():
+    repressilator_omex = DATA_DIR / "omex" / "tellurium" / "repressilator.omex"
+    working_dir = Path(__file__).parent / "results" / "repressilator_omex"
+    working_dir.mkdir(exist_ok=True)
+    execute_sedml(path=repressilator_omex, working_dir=working_dir)
+
+
+def run_omex(omex_path: Path):
+    # print(omex_path)
+    working_dir = Path(__file__).parent / "results" / omex_path.name
+    # print(working_dir)
+    working_dir.mkdir(parents=True, exist_ok=True)
+    execute_sedml(path=omex_path, working_dir=working_dir, output_path=working_dir)
+
+
+if __name__ == "__main__":
+
+    biomodels_omex_base_path = DATA_DIR / "combine" / "omex" / "biomodels" / "omex"
+    biomodels_omex_paths = []
+    for path in Path(biomodels_omex_base_path).rglob("*.omex"):
+        biomodels_omex_paths.append(path)
+    biomodels_omex_paths = sorted(biomodels_omex_paths)
+
+    for omex_path in [biomodels_omex_base_path / "BIOMD0000000111_fi4_sedml.omex"]:
+        run_omex(omex_path)
+
+    # for omex_path in sorted(biomodels_omex_paths):
+    #     run_biomodel_omex(omex_path)
+
+    "/home/mkoenig/git/sbmlsim/src/sbmlsim/tests/data/combine/omex/jws/omex/fraser2002_fig1a_1b_2a_2b.sedx"
+    "/home/mkoenig/git/sbmlsim/src/sbmlsim/tests/data/combine/omex/jws/omex/levering2012_fig2-user.sedx",
+    "/home/mkoenig/git/sbmlsim/src/sbmlsim/tests/data/combine/omex/jws/omex/levering2012_fig5-user.sedx",
+    "/home/mkoenig/git/sbmlsim/src/sbmlsim/tests/data/combine/omex/jws/omex/martins2016_fig4b.sedx"

sbmlsim/combine/examples/execute_sedml.py

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+"""Execute SED-ML."""
+from pathlib import Path
+
+from sbmlsim.combine.sedml.runner import execute_sedml
+
+
+examples_dir = Path(__file__).parent / "l1v4"
+# examples_dir = Path(__file__).parent / "l1v4_l1v3"
+
+l1v4_l1v3_files = ["repeated-stochastic-runs/repeated-stochastic-runs.sedml"]
+
+l1v4_files = [
+    # plotting
+    "algorithm_parameters.sedml",
+    # "axis.sedml",
+    # "axis_grids.sedml",
+    # "axis_minmax.sedml",
+    # "axis_minmax_smaller.sedml",
+    # "axis_minormax.sedml",
+    # "concentration_amount.sedml",  # FIXME
+    # "concentration_amount_b.sedml"  # FIXME
+    # "curve_types.sedml",
+    # "curve_types_errors.sedml",
+    # "heat_map_ls.sedml",
+    # "markertype.sedml",
+    # "linetype.sedml",
+    # "right_yaxis.sedml",
+    # "line_overlap_order.sedml",
+    # "repressilator_figure.xml",
+    # "repressilator.xml",
+    # "repressilator_urn.xml",
+    # "test_file_1.sedml",
+    # "test_line_fill.sedml",
+    # "stacked_bar.sedml",
+    # "test_3hbarstacked.sedml",
+    # "test_bar.sedml",
+    # "test_bar3stacked.sedml",
+    # "test_file.sedml",
+    # "test_hbar_stacked.sedml",
+    # "test_shaded_area.sedml",
+    # "test_shaded_area_overlap_order.sedml",
+    # "test_base_styles.sedml",
+]
+
+if __name__ == "__main__":
+    # ----------------------
+    # L1V4 Plotting
+    # ----------------------
+    working_dir = examples_dir
+    for sedml_file in l1v4_files:
+        # for sedml_file in l1v4_l1v3_files:
+        execute_sedml(
+            path=examples_dir / sedml_file,
+            working_dir=examples_dir / "sbmlsim",
+            output_path=examples_dir / "sbmlsim",
+        )
+
+    # ----------------------
+    # L1V4 Parameter Fitting
+    # ----------------------
+    # working_dir = base_path / "l1v4_parameter_fitting"
+    # for name, sedml_file in [
+    #     # "Elowitz_Nature2000.xml",
+    # ]:
+    #     execute_sedml(
+    #         working_dir=working_dir,
+    #         path=working_dir / sedml_file
+    #     )