zenodo information added

.zenodo.json

@@ -0,0 +1,31 @@
+{
+  "upload_type": "software",
+  "title": "sbmlsim: SBML simulation made easy",
+  "creators": [
+    {
+      "orcid": "0000-0003-1725-179X",
+      "affiliation": "Humboldt-University Berlin, Institute for Theoretical Biology, Berlin",
+      "name": "König, Matthias"
+    }
+  ],
+  "description": "<p><code>sbmlsim</code> is a collection of python utilities to simplify simulations with <a href=\"http://www.sbml.org\">SBML</a> models implemented on top of <code><a href=\"http://libroadrunner.org/\">roadrunner</a></code> and other libraries with source code available from <a href=\"https://github.com/matthiaskoenig/sbmlsim\">https://github.com/matthiaskoenig/sbmlsim</a></p>\n<p>Features include among others<ul><li>simulation experiments</li><li>simulation reports</a></li><li>parameter fitting</li></ul></p>\n<p>The documentation is available on <a href=\"https://sbmlsim.readthedocs.io\">https://sbmlsim.readthedocs.io</a></p>\n<p>If you have any questions or issues please <a href=\"https://github.com/matthiaskoenig/sbmlsim/issues\">open an issue</a></p>\n<h2>Funding</h2><p>Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (<strong>LiSyM</strong>, grant number 031L0054) and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 <strong><a href=\"https://qualiperf.de\">QuaLiPerF</a></strong> (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach)\" by grant number 436883643. Matthias König has received funds from the EOSCsecretariat.eu which has received funding from the European Union's Horizon Programme call H2020-INFRAEOSC-05-2018-2019, grant Agreement number 831644.</p>",
+  "access_right": "open",
+  "license": "LGPL-3.0",
+  "keywords": [
+    "modeling",
+    "standardization",
+    "SBML",
+    "SED-ML",
+    "COMBINE"
+  ],
+  "communities": [
+    {
+      "identifier": "eoscsecretariat"
+    }
+  ],
+  "grants": [
+    {
+      "id": "831644"
+    }
+  ]
+}

README.rst

@@ -34,7 +34,7 @@ sbmlsim: SBML simulation made easy
    :alt: Black
 
 
-sbmlsim is a collection of python utilities to to simplify simulations with
+sbmlsim is a collection of python utilities to simplify simulations with
 `SBML <http://www.sbml.org>`__ models implemented on top of
 `roadrunner <http://libroadrunner.org/>`__. Source code is available from
 `https://github.com/matthiaskoenig/sbmlsim <https://github.com/matthiaskoenig/sbmlsim>`__.

release-notes/0.2.1.md

@@ -0,0 +1,3 @@
+# Release notes for sbmlsim 0.2.1
+- bugfix release
+- zenodo information for EOSC

setup.cfg

@@ -30,23 +30,26 @@ classifiers =
 	Operating System :: OS Independent
 	Programming Language :: Python :: 3.7
 	Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
 	Programming Language :: Python :: Implementation :: CPython
 	Topic :: Scientific/Engineering
 	Topic :: Scientific/Engineering :: Bio-Informatics
 license = LGPL-3.0
-description = sbmlsim are utilities for simulation of SBML.
+description = sbmlsim are utilities for the simulation of SBML models.
 long_description = file: README.rst
 long_description_content_type = text/x-rst
 keywords =
 	modeling
 	standardization
 	SBML
+    SED-ML
+    COMBINE
 
 [options]
 zip_safe = True
 python_requires = >=3.7
 install_requires =
-	sbmlutils>=0.5.1
+	sbmlutils>=0.5.4
 	numpy>=1.21
 	depinfo>=0.1.7
 	scipy>=1.7

src/sbmlsim/combine/mathml.py

@@ -81,7 +81,7 @@ def expr_from_formula(formula: str):
 
 
 def evaluate(astnode: libsbml.ASTNode, variables: Dict):
-    """Evaluate the astnode with values """
+    """Evaluate the astnode with values"""
     expr = parse_astnode(astnode)
     f = lambdify(args=list(expr.free_symbols), expr=expr)
     res = f(**variables)

src/sbmlsim/combine/omex.py

@@ -42,7 +42,7 @@ def __init__(
 
 
 class Entry:
-    """ Helper class to store content to create an OmexEntry."""
+    """Helper class to store content to create an OmexEntry."""
 
     def __init__(
         self,

src/sbmlsim/combine/sedml/data.py

@@ -19,7 +19,7 @@
 
 
 class DataDescriptionParser(object):
-    """ Class for parsing DataDescriptions. """
+    """Class for parsing DataDescriptions."""
 
     FORMAT_URN = "urn:sedml:format:"
     FORMAT_NUML = "urn:sedml:format:numl"

src/sbmlsim/combine/sedml/kisao.py

@@ -169,7 +169,7 @@ def integrator_from_kisao(kisao):
 
 
 def algorithm_parameter_to_parameter_key(par):
-    """ Resolve the mapping between parameter keys and roadrunner integrator keys."""
+    """Resolve the mapping between parameter keys and roadrunner integrator keys."""
     ParameterKey = namedtuple("ParameterKey", "key value dtype")
     kisao = par.getKisaoID()
     value = par.getValue()

src/sbmlsim/combine/sedml/parser.py

@@ -97,7 +97,7 @@
 import warnings
 from collections import OrderedDict, namedtuple
 from pathlib import Path
-from typing import Dict, List, Union, Optional
+from typing import Dict, List, Optional, Union
 
 import libsedml
 import numpy as np
@@ -106,12 +106,12 @@
 from sbmlsim.combine.sedml.io import read_sedml
 from sbmlsim.combine.sedml.kisao import is_supported_algorithm_for_simulation_type
 from sbmlsim.combine.sedml.task import Stack, TaskNode, TaskTree
-from sbmlsim.data import DataSet, Data
+from sbmlsim.data import Data, DataSet
 from sbmlsim.experiment import ExperimentDict, SimulationExperiment
 from sbmlsim.model import model_resources
 from sbmlsim.model.model import AbstractModel
-from sbmlsim.plot import Figure, Plot, Axis, Curve
-from sbmlsim.simulation import ScanSim, TimecourseSim, Timecourse, AbstractSim
+from sbmlsim.plot import Axis, Curve, Figure, Plot
+from sbmlsim.simulation import AbstractSim, ScanSim, Timecourse, TimecourseSim
 from sbmlsim.task import Task
 from sbmlsim.units import UnitRegistry
 
@@ -139,7 +139,7 @@ def experiment_from_omex(omex_path: Path):
 
 
 class SEDMLParser(object):
-    """ Parsing SED-ML in internal format."""
+    """Parsing SED-ML in internal format."""
 
     def __init__(self, sed_doc: libsedml.SedDocument, working_dir: Path):
         """Parses information from SedDocument."""
@@ -255,7 +255,6 @@ def f_figures(obj) -> Dict[str, Figure]:
                         curve.y._register_data()
                     # FIXME: also for xerr and yerr
 
-
     # --- MODELS ---
     @staticmethod
     def parse_xpath_target(xpath: str) -> str:
@@ -431,7 +430,7 @@ def parse_change(self, sed_change: libsedml.SedChange) -> Dict:
             return {}
 
     def parse_simulation(self, sed_sim: libsedml.SedSimulation) -> Union[TimecourseSim]:
-        """ Parse simulation information."""
+        """Parse simulation information."""
         sim_type = sed_sim.getTypeCode()
         algorithm = sed_sim.getAlgorithm()
         if algorithm is None:
@@ -466,10 +465,10 @@ def parse_simulation(self, sed_sim: libsedml.SedSimulation) -> Union[TimecourseS
                     Timecourse(
                         start=initial_time,
                         end=output_end_time,
-                        steps=number_of_points-1,
+                        steps=number_of_points - 1,
                     ),
                 ],
-                time_offset=output_start_time
+                time_offset=output_start_time,
             )
             return tcsim
 
@@ -492,7 +491,7 @@ def parse_simulation(self, sed_sim: libsedml.SedSimulation) -> Union[TimecourseS
         # TODO/FIXME: handle all the algorithm parameters as integrator parameters
 
     def parse_task(self, sed_task: libsedml.SedAbstractTask) -> Task:
-        """ Parse arbitrary task (repeated or simple, or simple repeated)."""
+        """Parse arbitrary task (repeated or simple, or simple repeated)."""
         # If no DataGenerator references the task, no execution is necessary
         dgs = self.data_generators_for_task(sed_task)
         if len(dgs) == 0:
@@ -569,13 +568,11 @@ def _parse_simple_repeated_task(self, node: TaskNode):
         #         forLines.append("{}.extend({})".format(task.getId(), t.getId()))
 
     def parse_figure(self, sed_output: libsedml.SedOutput) -> Figure:
-        """ Parse simulation information."""
+        """Parse simulation information."""
         type_code = sed_output.getTypeCode()
         if type_code == libsedml.SEDML_OUTPUT_PLOT2D:
             sed_plot2d: libsedml.SedPlot = sed_output
-            plots = [
-                self.parse_plot2d(sed_plot2d)
-            ]
+            plots = [self.parse_plot2d(sed_plot2d)]
             f = Figure(
                 experiment=None,
                 sid=sed_plot2d.getId(),
@@ -657,11 +654,7 @@ def data_from_datagenerator(self, sed_dg_ref: Optional[str]) -> Optional[Data]:
         elif sed_var.isSetTarget():
             index = self.parse_xpath_target(sed_var.getTarget())
 
-        return Data(
-            experiment=self.exp_class,
-            index=index,
-            task=task_id
-        )
+        return Data(experiment=self.exp_class, index=index, task=task_id)
 
     def _parse_repeated_task(self, node: TaskNode):
         print("repeated task")
@@ -673,7 +666,7 @@ def data_generators_for_task(
         self,
         sed_task: libsedml.SedTask,
     ) -> List[libsedml.SedDataGenerator]:
-        """ Get the DataGenerators which reference the given task."""
+        """Get the DataGenerators which reference the given task."""
         sed_dgs = []
         for (
             sed_dg
@@ -711,7 +704,7 @@ def selections_for_task(self, sed_task: libsedml.SedTask):
 
     @staticmethod
     def get_ordered_subtasks(sed_task: libsedml.SedTask) -> List[libsedml.SedTask]:
-        """ Ordered list of subtasks for task."""
+        """Ordered list of subtasks for task."""
         subtasks = sed_task.getListOfSubTasks()
         subtask_order = [st.getOrder() for st in subtasks]
 

src/sbmlsim/combine/sedml/task.py

@@ -2,7 +2,7 @@
 
 
 class TaskNode(object):
-    """Tree implementation of task tree. """
+    """Tree implementation of task tree."""
 
     def __init__(self, task: libsedml.SedAbstractTask, depth: int):
         self.task = task
@@ -28,7 +28,7 @@ def info(self) -> str:
         return f"<[{self.depth}] {self.task.getId()} ({self.task.getElementName()})>"
 
     def __iter__(self):
-        """ Depth-first iterator which yields TaskNodes."""
+        """Depth-first iterator which yields TaskNodes."""
         yield self
         for child in self.children:
             for node in child:
@@ -39,7 +39,7 @@ def __repr__(self) -> str:
 
 
 class Stack(object):
-    """ Stack implementation for nodes."""
+    """Stack implementation for nodes."""
 
     def __init__(self):
         self.items = []
@@ -99,7 +99,7 @@ def add_children(node):
 
     @staticmethod
     def parse_task_tree(doc: libsedml.SedDocument, tree: TaskNode):
-        """ Python code generation from task tree. """
+        """Python code generation from task tree."""
 
 
 class Test(object):

src/sbmlsim/combine/sedml/tesedml.py

@@ -410,7 +410,7 @@ def executeCombineArchive(
 
 
 class SEDMLCodeFactory(object):
-    """ Code Factory generating executable code."""
+    """Code Factory generating executable code."""
 
     # template location
     TEMPLATE_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "templates")
@@ -748,7 +748,7 @@ def taskToPython(doc, task):
         return SEDMLCodeFactory.taskTreeToPython(doc, tree=taskTree)
 
     class TaskNode(object):
-        """ Tree implementation of task tree. """
+        """Tree implementation of task tree."""
 
         def __init__(self, task, depth):
             self.task = task
@@ -780,14 +780,14 @@ def info(self):
             )
 
         def __iter__(self):
-            """ Depth-first iterator which yields TaskNodes."""
+            """Depth-first iterator which yields TaskNodes."""
             yield self
             for child in self.children:
                 for node in child:
                     yield node
 
     class Stack(object):
-        """ Stack implementation for nodes."""
+        """Stack implementation for nodes."""
 
         def __init__(self):
             self.items = []
@@ -843,7 +843,7 @@ def add_children(node):
 
     @staticmethod
     def getOrderedSubtasks(task):
-        """ Ordered list of subtasks for task."""
+        """Ordered list of subtasks for task."""
         subtasks = task.getListOfSubTasks()
         subtaskOrder = [st.getOrder() for st in subtasks]
         # sort by order, if all subtasks have order (not required)
@@ -853,7 +853,7 @@ def getOrderedSubtasks(task):
 
     @staticmethod
     def taskTreeToPython(doc, tree):
-        """ Python code generation from task tree. """
+        """Python code generation from task tree."""
 
         # go forward through task tree
         lines = []
@@ -1424,7 +1424,7 @@ def getIntegratorNameForKisaoID(kid):
 
     @staticmethod
     def algorithmParameterToParameterKey(par):
-        """ Resolve the mapping between parameter keys and roadrunner integrator keys."""
+        """Resolve the mapping between parameter keys and roadrunner integrator keys."""
         ParameterKey = namedtuple("ParameterKey", "key value dtype")
         kid = par.getKisaoID()
         value = par.getValue()
@@ -1672,7 +1672,7 @@ def dataGeneratorToPython(doc, generator):
         return "\n".join(lines)
 
     def outputToPython(self, doc, output):
-        """ Create output """
+        """Create output"""
         lines = []
         typeCode = output.getTypeCode()
         if typeCode == libsedml.SEDML_OUTPUT_REPORT:
@@ -2019,7 +2019,7 @@ def outputPlot3DToPython(self, doc, output):
 
 ##################################################################################################
 class SEDMLTools(object):
-    """ Helper functions to work with sedml. """
+    """Helper functions to work with sedml."""
 
     INPUT_TYPE_STR = "SEDML_STRING"
     INPUT_TYPE_FILE_SEDML = "SEDML_FILE"
@@ -2227,7 +2227,7 @@ def terminate_trace(trace):
 
 
 def fix_endpoints(x, y, color, tag, fig):
-    """ Adds endpoint markers wherever there is a discontinuity in the data."""
+    """Adds endpoint markers wherever there is a discontinuity in the data."""
     warnings.warn("don't use this", DeprecationWarning)
     # expect x and y to be 1d
     if len(x.shape) > 1:
@@ -2287,7 +2287,7 @@ def fix_endpoints(x, y, color, tag, fig):
     from tellurium.tests.testdata import OMEX_TEST_DIR, SEDML_TEST_DIR
 
     def testInput(sedmlInput):
-        """ Test function run on inputStr. """
+        """Test function run on inputStr."""
         print("\n", "*" * 100)
         print(sedmlInput)
         print("*" * 100)

src/sbmlsim/data.py

@@ -369,7 +369,9 @@ def from_df(
                                 if f"mean_{err_key}" in df.columns:
                                     # remove existing mean_sd column
                                     del df[f"mean_{err_key}"]
-                                    logger.warning(f"Removing existing column: `mean_{err_key}`from DataSet.")
+                                    logger.warning(
+                                        f"Removing existing column: `mean_{err_key}`from DataSet."
+                                    )
 
                                 df.rename(
                                     columns={f"{err_key}": f"mean_{err_key}"},

src/sbmlsim/examples/example_timecourse.py

@@ -9,7 +9,7 @@
 
 
 def run_timecourse_examples():
-    """ Run various timecourses. """
+    """Run various timecourses."""
     simulator = Simulator(MODEL_REPRESSILATOR)
 
     # 1. simple timecourse simulation

src/sbmlsim/examples/example_units.py

@@ -14,7 +14,7 @@
 
 
 def run_demo_example():
-    """ Run various timecourses. """
+    """Run various timecourses."""
     simulator = Simulator(MODEL_DEMO)
     # build quantities using the unit registry for the model
     Q_ = simulator.Q_