Fix build breakages and a couple other cleanup items.

* Move pych --testing call to test_python.bash script. It should work now, since
  the test_python.bash script correctly configures the environment.
* Throw -W when building sphinx docs.
* Fix errors that showed up with -W (mostly just indentation).
* Use portable open command in top level makefile "doc" recipe.

paired w/ @lydia-duncan