Issues

• SED-ML validation checks setValue/change targets against the last model in the document instead of the referenced model

  biosimulators/Biosimulators_utils#167 · Filter by author jcschaff opened on Aug 6, 2026

• DeprecationWarning: Data type alias 'a' was deprecated in NumPy 2.0. Use the 'S' alias instead.

  biosimulators/Biosimulators_utils#163 · Filter by author dweindl opened on Dec 9, 2025

• DeprecationWarning: 'imghdr' is deprecated and slated for removal in Python 3.13

  biosimulators/Biosimulators_utils#162 · Filter by author dweindl opened on Dec 9, 2025

• Creation of PDFs gets colors of graphs wrong

  biosimulators/Biosimulators_utils#157 · Filter by author luciansmith opened on Dec 12, 2024

• ModuleNotFoundError libsbml

  biosimulators/Biosimulators_utils#156 · Filter by author stellaprins opened on Nov 13, 2024

• Allow XPath references to model objects, not just attributes

  biosimulators/Biosimulators_utils#144 · Filter by author luciansmith opened on Jun 29, 2023

• Capturer clashes with Pycharm due to rebinding of io.FileIO based sys.stdout and sys.stderr streams

  bugdiscussionenhancementfuture
  biosimulators/Biosimulators_utils#143 · Filter by author CodeByDrescher opened on Jun 26, 2023
  

• Warn about duplicate figure names (or fix)

  biosimulators/Biosimulators_utils#141 · Filter by author luciansmith opened on Jun 14, 2023
  1

• dependency on capturer

  biosimulators/Biosimulators_utils#135 · Filter by author fbergmann opened on May 3, 2023
  2

• Subdirectories in OMEX files not working

  biosimulators/Biosimulators_utils#131 · Filter by author luciansmith opened on Apr 3, 2023

• Use tolerances even when changing simulation algorithm.

  biosimulators/Biosimulators_utils#130 · Filter by author luciansmith opened on Apr 3, 2023

• Fix failing XPP validation tests

  biosimulators/Biosimulators_utils#127 · Filter by author luciansmith opened on Mar 29, 2023

• Incorrect validation error for tasks that reference models.

  biosimulators/Biosimulators_utils#124 · Filter by author luciansmith opened on Dec 8, 2022

• infix math doesn't follow Python conventions

  biosimulators/Biosimulators_utils#120 · Filter by author luciansmith opened on Oct 18, 2022
  1

• Biosimulators_utils is incompatible with numpy>=1.23.0

  biosimulators/Biosimulators_utils#115 · Filter by author CodeByDrescher opened on Sep 1, 2022
  

• Round-tripping created OMEX files gives a warning

  biosimulators/Biosimulators_utils#114 · Filter by author luciansmith opened on Aug 2, 2022

• Raise Issue with CellML team regarding incorrect schema

  biosimulators/Biosimulators_utils#110 · Filter by author bilalshaikh42 opened on Apr 12, 2022
  3

• Encode additional features of XPP ODE files into SED-ML

  futureModeling format
  biosimulators/Biosimulators_utils#101 · Filter by author jonrkarr opened on Feb 18, 2022

• Convert data models to subclasses of dataclass

  enhancementfuture
  biosimulators/Biosimulators_utils#79 · Filter by author jonrkarr opened on Dec 8, 2021

• Where possible return unit information with get_parameters_variables_outputs_for_simulation

  enhancementModeling format
  biosimulators/Biosimulators_utils#69 · Filter by author jonrkarr opened on Oct 10, 2021
  3

• Support additional actions of BNGL format

  Modeling format
  biosimulators/Biosimulators_utils#64 · Filter by author jonrkarr opened on Sep 22, 2021

• Add validation rules for SED-ML L1V4

  SED-ML
  biosimulators/Biosimulators_utils#59 · Filter by author jonrkarr opened on Aug 9, 2021

• Improve support for ZGINML format

  enhancementModeling format
  biosimulators/Biosimulators_utils#56 · Filter by author jonrkarr opened on Jul 9, 2021

• Update BioNetGen requirement when installation fixed

  Modeling format
  biosimulators/Biosimulators_utils#55 · Filter by author jonrkarr opened on Jul 7, 2021

• Use new Smoldyn features that will be added to 2.67

  enhancementModeling format
  biosimulators/Biosimulators_utils#53 · Filter by author jonrkarr opened on Jun 23, 2021