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use utils/submodule in setup.py...
use utils/submodule in setup.py `setup.py anything` will halt with an informative error if the submodules are unclean. It will fetch the submodules if they are entirely absent. Nothing will happen if it is not a git repo.

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README_STARTUP
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This is the IPython startup directory
.py and .ipy files in this directory will be run *prior* to any code or files specified
via the exec_lines or exec_files configurables whenever you load this profile.
Files will be run in lexicographical order, so you can control the execution order of files
with a prefix, e.g.::
00-first.py
50-middle.py
99-last.ipy