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I added new Shell Command option to support your request. I'm not sure how Shell Command should look like. If bash is available as global command everything should work properly with example from Settings page. Please try and let me know.
At last build Microsoft introduced a way to execute linux on windows.
Would it be possible to use the python installed on linux from atom?
NOTE: to execute a python script from the windows shell one would have to:
bash -c "python script.py"
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