SBML Test Suite version 3.3.0 released
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Michael Hucka
Dec 13, 2017, 1:22:35 PM12/13/17
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The SBML Team is pleased to announce the full release of version 3.3.0 of the SBML Test Suite. You can download it now from GitHub:
https://github.com/sbmlteam/sbml-test-suite/releases/tag/3.3.0
This release brings many updates and some changes. The following is a list of the highlights; a more detailed accounting of the changes can be found in the NEWS.md file at
https://github.com/sbmlteam/sbml-test-suite/blob/master/NEWS.md
Here is a list of some highlights:
* This release contains hundreds of new semantic test cases, numbers 01219-1780, written by Lucian Smith. (Note: if your simulator uses libSBML, you will need at least libSBML version 5.15.0 to run these tests.) As before, the SBML Test Runner only uses the semantic test cases (and bundles them), but stochastic and syntactic test cases are also available as separate downloadable archives.
* A few things have been cleaned up in past tests. Examples include model identifiers of a few test models that were misleading (now fixed), and a few tests that were designed to test species in multiple compartments were at some point accidentally changed so that all the species were put into a single compartment (they have been redistributed appropriately now).
* With the addition of FBC v2 tests, the 'packagesPresent' line in the .m file can now include fbc_v1 or fbc_v2, depending on which version of the test it is. The original fbc tag is still present. In addition, a new FBC test tag 'fbc:NonStrict' is now provided for FBC v2 models where the 'strict' flag has been set to 'false'.
* There is a new installer for the SBML Test Runner for macOS X.
* The Test Runner's algorithm for comparing test results and displaying the differences between expected and actual result values now properly ignores column ordering. Also, it now considers it an error if the results do not have the expected number of rows. Thanks to Leandro Watanabe and Chris Myers (U. Utah) and Lucian Smith for reporting the problems.
* The Test Runner now allows the combination of filters that include, simultaneously, tags, problematic test cases, and only supported test cases. Thanks to Chris Myers for raising the issue and testing the implementation.
* The SBML Test Runner now monitors for file changes in the currently-displayed test case. If the application's output '.csv' file is changed outside the runner (e.g., by manually editing the file), it should now notice the changes and update the display. In addition, the Test Runner also monitors the test case settings file, to detect changes that developers may make while experimenting with test case definitions. A setting in the preferences dialog allows this feature to be turned on and off.
* This release of the SBML Test Runner works around a crashing bug caused by an SWT-GTK issue that manifests itself on Ubuntu 16.
* This release of the SBML Test Runner works around a font scaling issue that manifests itself on Windows when using display scaling of 150%.
* The default value of the "Always check for new versions of test cases when application starts" preference option is now "yes" instead of "no" for new users. Users who have used the previous version of the Test Runner will not be affected; this only affects new users of the Test Runner.
* The File -> Exit menu item should now work on Windows. Thanks to Thomas Hamm for reporting that it did nothing before. Missing keyboard shortcuts on Windows are now available in the latest version.
* The Test Runner features various other small fixes and improvements.
* The SBML Test Suite home repository has been moved to GitHub (https://github.com/sbmlteam/sbml-test-suite).
* The issue tracker for the Test Suite is now the GitHub tracker (https://github.com/sbmlteam/sbml-test-suite/issues).
Mike
https://github.com/sbmlteam/sbml-test-suite/releases/tag/3.3.0
This release brings many updates and some changes. The following is a list of the highlights; a more detailed accounting of the changes can be found in the NEWS.md file at
https://github.com/sbmlteam/sbml-test-suite/blob/master/NEWS.md
Here is a list of some highlights:
* This release contains hundreds of new semantic test cases, numbers 01219-1780, written by Lucian Smith. (Note: if your simulator uses libSBML, you will need at least libSBML version 5.15.0 to run these tests.) As before, the SBML Test Runner only uses the semantic test cases (and bundles them), but stochastic and syntactic test cases are also available as separate downloadable archives.
* A few things have been cleaned up in past tests. Examples include model identifiers of a few test models that were misleading (now fixed), and a few tests that were designed to test species in multiple compartments were at some point accidentally changed so that all the species were put into a single compartment (they have been redistributed appropriately now).
* With the addition of FBC v2 tests, the 'packagesPresent' line in the .m file can now include fbc_v1 or fbc_v2, depending on which version of the test it is. The original fbc tag is still present. In addition, a new FBC test tag 'fbc:NonStrict' is now provided for FBC v2 models where the 'strict' flag has been set to 'false'.
* There is a new installer for the SBML Test Runner for macOS X.
* The Test Runner's algorithm for comparing test results and displaying the differences between expected and actual result values now properly ignores column ordering. Also, it now considers it an error if the results do not have the expected number of rows. Thanks to Leandro Watanabe and Chris Myers (U. Utah) and Lucian Smith for reporting the problems.
* The Test Runner now allows the combination of filters that include, simultaneously, tags, problematic test cases, and only supported test cases. Thanks to Chris Myers for raising the issue and testing the implementation.
* The SBML Test Runner now monitors for file changes in the currently-displayed test case. If the application's output '.csv' file is changed outside the runner (e.g., by manually editing the file), it should now notice the changes and update the display. In addition, the Test Runner also monitors the test case settings file, to detect changes that developers may make while experimenting with test case definitions. A setting in the preferences dialog allows this feature to be turned on and off.
* This release of the SBML Test Runner works around a crashing bug caused by an SWT-GTK issue that manifests itself on Ubuntu 16.
* This release of the SBML Test Runner works around a font scaling issue that manifests itself on Windows when using display scaling of 150%.
* The default value of the "Always check for new versions of test cases when application starts" preference option is now "yes" instead of "no" for new users. Users who have used the previous version of the Test Runner will not be affected; this only affects new users of the Test Runner.
* The File -> Exit menu item should now work on Windows. Thanks to Thomas Hamm for reporting that it did nothing before. Missing keyboard shortcuts on Windows are now available in the latest version.
* The Test Runner features various other small fixes and improvements.
* The SBML Test Suite home repository has been moved to GitHub (https://github.com/sbmlteam/sbml-test-suite).
* The issue tracker for the Test Suite is now the GitHub tracker (https://github.com/sbmlteam/sbml-test-suite/issues).
Mike
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