SINGE shell script and separation of GLG_Instance and Aggregate functions

[atuldeshpande]

Closes #17

This pull request creates a shell script to emulate the standalone SINGE function which calls the GLG_Instance executable followed by Aggregate executable.
Requires compilation of the code/GLG_Instance.m and code/Aggregate.m. "v94" in the standalone_SCINGE.sh should be replaced by the name of the folder containing the runtime libraries.

[agitter]

What changed in data1/tf.mat? Can we avoid changing the input data in this pull request?

Do we want to still keep SCINGE_Example.m or is that stale now? The main reason to keep it would be to give an example for users who want to run SINGE locally and directly through MATLAB instead of using the compiled code, right?

Can we rename SCINGE.m and any other source files that use the old name in this pull request?

Do we want to change test cases to run standalone_SCINGE.sh on the sample data? That's the primary workflow now. We could also test that and the compiled SCINGE_Example.

[atuldeshpande]

We can run the equivalent of SINGE_Example.m by running the following command:
./standalone_SCINGE.sh data1/X_SCODE_data.mat data1/tf.mat testOutput tests/example_hyperparameters.txt

Perhaps we can include the above in the README.md?

[agitter]

Perhaps we can include the above in the README.md?

Yes, let's add that command to the readme when we document how to use this new script and updated our input parameter descriptions.

[agitter]

I finished a round of changes to the compile script, Dockerfile, and Docker-based tests. I'll see what errors appear when these tests run.

I restored SINGE_Example.m. I'd like to keep this as example usage for anyone who wants to use SINGE directly through MATLAB. We'll have to document both options (MATLAB and script) in the readme.

[agitter]

I had to specify the MATLAB runtime path in the standalone script so that it could find the runtime in the Docker container. Should we make that another argument to the script? The location will vary for different users.

[atuldeshpande]

If someone provides the argument -lambda, will it be truncated as ambda?

Yes. That's how it will handle currently.

[agitter]

The new parameter parser broke the support for one of the date formats:

Error using parseParams (line 47)
The value of 'date' is invalid. It must satisfy the function: @(x)any(ismember({datestr(datenum(x),['mm/dd/yyyy']),datestr(datenum(x))},x)).
Error in SINGE_GLG_Test (line 9)

See https://travis-ci.com/gitter-lab/SINGE/builds/126320790#L698

[agitter]

@atuldeshpande it looks like the error here https://travis-ci.com/gitter-lab/SINGE/jobs/235318717#L989 is being caused by SINGE.m. The call to SINGE_GLG_Test doesn't pass the output directory so it defaults to Output. That causes SINGE_Aggregate to crash if a non-default output directory is used.