NCAR / manage_externals

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Bugfix: timeout limit for subprocesses

For security reasons svn and git do not use standard in/out/error to request
and process authentication. Instead, they use lower level system interfaces.
Python calling a subprocess can only interact with stdio, and can not intercept
or detect the lower level calls. On some systems, these requests are visible
to the user, on some systems they are not. When subprocess commands expect user
input they will wait and manage_externals appears to hang.

Change the subprocess calls to polling the running process and checking the
current run time. If the run time exceeds a timeout limit, then we display an
error message suggesting that the user verify authentication and then declare a
fatal error.

The default timeout interval of 5 minutes is probably too long and can be
shortened. But since svn requires network interaction and some large checkouts
can take a long time, this is a 'conservative' initial value.

Breakup up the subprocess call routine so it is easier to understand.

Testing:
  make test - python2/python3 - all tests pass.
  manually test with very short timeout to ensure error message is raised.

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