If a module using versioneer is imported from in a pythonw.exe, then a console window is visible for each call to git.exe/git.cmd. The subprocess.Popen call should set the startupinfo argument.

This code will open a console window when executed by pythonw.exe:

import subprocess
command = ['git', '--help']
subprocess.Popen(command).wait()

This code does not open a console window:

import subprocess
command = ['git', '--help']
startupinfo = subprocess.STARTUPINFO()
startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
subprocess.Popen(command, startupinfo=startupinfo).wait()

subprocess.STARTUPINFO is only available on windows.