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

Status: Open.

#167 In biosimulators/Biosimulators_utils;

· jcschaff opened on Aug 6, 2026

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

Status: Open.

#163 In biosimulators/Biosimulators_utils;

· dweindl opened on Dec 9, 2025

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

Status: Open.

#162 In biosimulators/Biosimulators_utils;

· dweindl opened on Dec 9, 2025

Creation of PDFs gets colors of graphs wrong

Status: Open.

#157 In biosimulators/Biosimulators_utils;

· luciansmith opened on Dec 12, 2024

ModuleNotFoundError libsbml

Status: Open.

#156 In biosimulators/Biosimulators_utils;

· stellaprins opened on Nov 13, 2024

Allow XPath references to model objects, not just attributes

Status: Open.

#144 In biosimulators/Biosimulators_utils;

· luciansmith opened on Jun 29, 2023

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

bugSomething isn't workingSomething isn't working

discussion

enhancementNew feature or requestNew feature or request

future

Status: Open.

#143 In biosimulators/Biosimulators_utils;

· CodeByDrescher opened on Jun 26, 2023

Warn about duplicate figure names (or fix)

Status: Open.

#141 In biosimulators/Biosimulators_utils;

· luciansmith opened on Jun 14, 2023

dependency on capturer

Status: Open.

#135 In biosimulators/Biosimulators_utils;

· fbergmann opened on May 3, 2023

Subdirectories in OMEX files not working

Status: Open.

#131 In biosimulators/Biosimulators_utils;

· luciansmith opened on Apr 3, 2023

Use tolerances even when changing simulation algorithm.

Status: Open.

#130 In biosimulators/Biosimulators_utils;

· luciansmith opened on Apr 3, 2023

Fix failing XPP validation tests

Status: Open.

#127 In biosimulators/Biosimulators_utils;

· luciansmith opened on Mar 29, 2023