You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Consequently, the README file was improved to cover these new developments and the new preprint on SBSCL.
Several efficiency improvements to the numerical solvers (the AbstractDESSolver and the Rosenbrock solver), e.g., avoiding unnecessary conversion of double values to BigDecimal objects and by reducing some nested loops in the Rosenbrock solver: Thanks to Leonhard Markert.
Testing against constraint-based models from the BiGG Models Database has been improved. The new functionality enables saving simulation results in a CSV file. For testing purposes, simulation results were generated with COBRApy to benchmark SBSCL. These automated tests were incorporated into the continuous integration.
Improvements to the Java™ documentation by using correct reaction arrows and italicizing variable names, improvement of source-code expressions, where needed.
Bug Fixes
Bump dependencies on third-party software:
JUnit from version 4.11 to 4.13.1
JavaDoc from version 2.10.2 to 3.2.0
Fix of several error-prone issues and minor source-code improvements, exploiting more recent Java™ language features (such as using the diamond operator or no longer needed conversions of basic data types to their corresponding objects): Thanks to Leonhard Markert.
Fix of the SBML test suite download script (detected a wrong directory path and made the Bash less strict to improve the efficiency of automated testing): Thanks to Leonhard Markert.
Code cleaning (e.g., removing unnecessary public declarations from interface methods): Thanks to Leonhard Markert.
Cleaning up remainders of earlier libSBML dependency within the fern package, such as removing unnecessary casts to int, long, or SBML data types within iteration: Thanks to Leonhard Markert.
Minor improvement to the output while testing (proper display of directory structures).
Additions to the .gitignore file.
Additions of missing @Override tags and removal of unnecessary import statements within the fern package