Test running compiled SINGE on macOS

[agitter]

This pull request contains initial work to install and run SINGE on macOS. It uses GitHub Actions to avoid cluttering the Travis CI configuration further.

The main error is that the compiled MATLAB executables are not cross-platform. I added a note to the readme describing this (edd02a6). Running them on macOS gives the error:
./run_SINGE_GLG_Test.sh: line 30: ./SINGE_GLG_Test: cannot execute binary file

The solution would be to compile another version of the executables on macOS and host them alongside the Linux executables. In the meantime, macOS (and Windows) users can run SINGE through MATLAB if they have a MATLAB license or through Docker.

[agitter]

I updated the SINGE.sh script to detect the operating system. It checks for macOS and assumes Linux otherwise. When macOS is detected, it adds the _mac suffix to the wrapper scripts for the compiled MATLAB code so that the OS-specific script is used.

This works in our Linux Travis CI test and the macOS GitHub Actions test. You can see in the script output that the correct OS is recognized:

• Linux https://travis-ci.com/github/gitter-lab/SINGE/builds/173157059#L378
• macOS https://github.com/gitter-lab/SINGE/runs/811229038#step:7:13

I'll add a little more documentation, and then this will be ready for review.

[atuldeshpande]

I think we should document somewhere whether the macOS sanity test compares against the test matrices and the final network. (There might be dependence on OS in the random number generation).

[agitter]

Currently this test does not compare the edge weights or gene scores against the reference data. It prints the gene scores in the build log for manual inspection.

I can add the test cases before merging to assess any OS-specific behavior. That would be good for us to know about and alert users about.

[agitter]

@atuldeshpande the macOS workflow now runs the script that compares the new generated output with the stored reference output. I also described what tests are run in the readme.

The OS-specific differences are minor:

Comparing SINGE_Gene_Influence.txt
files are identical
Comparing SINGE_Ranked_Edge_List.txt
files are identical
Comparing sparse adjacency matrices
Spare matrices in Output/AdjMatrix_data1_X_SCODE_datapmat_ID_541_lambda_0p01_replicate_1.mat and tests/reference/latest/AdjMatrix_data1_X_SCODE_datapmat_ID_541_lambda_0p01_replicate_1.mat have different values
Maximum absolute difference: 0.0001509642757788754
Spare matrices in Output/AdjMatrix_data1_X_SCODE_datapmat_ID_541_lambda_0p01_replicate_2.mat and tests/reference/latest/AdjMatrix_data1_X_SCODE_datapmat_ID_541_lambda_0p01_replicate_2.mat have different values
Maximum absolute difference: 0.005782771667936615
Spare matrices in Output/AdjMatrix_data1_X_SCODE_datapmat_ID_542_lambda_0p01_replicate_1.mat and tests/reference/latest/AdjMatrix_data1_X_SCODE_datapmat_ID_542_lambda_0p01_replicate_1.mat have different values
Maximum absolute difference: 0.00011594663658021087
Spare matrices in Output/AdjMatrix_data1_X_SCODE_datapmat_ID_542_lambda_0p01_replicate_2.mat and tests/reference/latest/AdjMatrix_data1_X_SCODE_datapmat_ID_542_lambda_0p01_replicate_2.mat have different values
Maximum absolute difference: 0.00014391767285104606

The gene and edge scores match up to 5 significant figures. However, some values in the individual adjacency matrices fail the numpy.allclose test, which has a relative and an absolute tolerance.

Should we relax the test case? Or relax it only for the macOS test but leave it more stringent in Linux?

[agitter]

I generalized the test script so that it can take an optional tolerance argument. The macOS test now uses a more permissive threshold, and the Linux test uses the defaults, which are more strict. All tests are passing.