Resolves issues of SBMLTestSuite and FBA

draeger-lab / SBSCL

The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.

https://draeger-lab.github.io/SBSCL/

GNU Lesser General Public License v3.0

20 stars 13 forks source link

Resolves issues of SBMLTestSuite and FBA #40

Closed hemilpanchiwala closed 4 years ago

hemilpanchiwala commented 4 years ago

Major changes from this PR:

Adds a running wrapper for the SBML Test Runner that allows to check the results through the plot and compare the distance plots.
Adds testing by CompSimulator for the comp models in SBMLTestSuiteTest
Adds three new distance metrics in SBSCL.
- Maximum Absolute Distance
- Maximum Relative Distance
- Maximum Divergence Tolerance - The metric used by SBML Test Runner
Adds the newly added tests from SBML Test Suite.
Updates the INSTALL.md section for the SBML Test Runner.
Moves all the script files under the src/test/scripts folder. Updated the scripts files.
CobraSolver is refactored to FluxBalancedAnalysis.
Solves the issues with the FluxBalanceAnalysis so that all the FBC tests from SBML Test Suite now runs perfectly.
Fixes some other minor issues and some enhancement in the code

hemilpanchiwala commented 4 years ago

As a general recommendation, I'd suggest making use of the templates for code style from the JSBML project at https://github.com/sbmlteam/jsbml/tree/master/dev/. They can really help to automatically insert blank spaces, curly braces, and so forth, where forgotten.

Further comments were given in the code.

@draeger, I can just see their recommendations but can't add the templates as I am working on IntelliJ (even prefer), and the templates are only present for Eclipse.

draeger commented 4 years ago

As a general recommendation, I'd suggest making use of the templates for code style from the JSBML project at https://github.com/sbmlteam/jsbml/tree/master/dev/. They can really help to automatically insert blank spaces, curly braces, and so forth, where forgotten. Further comments were given in the code.

@draeger, I can just see their recommendations but can't add the templates as I am working on IntelliJ (even prefer), and the templates are only present for Eclipse.

Ok; so IntelliJ doesn't have an import for such files or doesn't come with comparable functions?

hemilpanchiwala commented 4 years ago

As a general recommendation, I'd suggest making use of the templates for code style from the JSBML project at https://github.com/sbmlteam/jsbml/tree/master/dev/. They can really help to automatically insert blank spaces, curly braces, and so forth, where forgotten. Further comments were given in the code.

@draeger, I can just see their recommendations but can't add the templates as I am working on IntelliJ (even prefer), and the templates are only present for Eclipse.

Ok; so IntelliJ doesn't have an import for such files or doesn't come with comparable functions?

I can just format the code as per the Java code style which is provided in IntelliJ given at this link.

hemilpanchiwala commented 4 years ago

change name of method. This is very unspecific. Use something like addBoundsEpsilon which states what the method is doing. updateBounds could do anything with the bounds. Also probably a good idea to define the eps locally here (because it is not used anywhere else).

@matthiaskoenig, but we have given get and set methods for the eps. So, I don't think we should declare it locally in the method.