add debug snakefile and directory

[zhiqianx]

Added debug snakefile to test for the weird behavior of ML analysis code is issue #98

[agitter]

I tested this locally on my Windows 10 machine in the spras conda environment

git checkout zhiqianx/master
cd ML_debug/
snakemake --cores 1

These are the output images, which all look distinct as expected.

There was this warning

ML_debug\Snakefile:29: UserWarning: Starting a Matplotlib GUI outside of the main thread will likely fail.

I believe we need to add

plt.switch_backend('Agg')

after importing pyplot to remove that.

When I instead run with multiple cores I can't even generate output successfully

snakemake --cores 3
WARNING: QApplication was not created in the main() thread.
WARNING: QApplication was not created in the main() thread.
qt.qpa.plugin: Could not find the Qt platform plugin "windows" in ""
qt.qpa.plugin: Could not find the Qt platform plugin "windows" in ""
qt.qpa.plugin: Could not find the Qt platform plugin "windows" in ""
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Maybe this gives a clue to the error? @zhiqianx are you to run this example with 3 cores?