Exclude pycache when copying packet inputs and outputs.

[plietar]

Python tends to produce a lot of __pycache__ folders. These can be found both in a report's source directory, if the user ran the entrypoint script outside of an orderly context, and in the packet's working directory after executing the packet.

There is never a good reason to include these in packets and we can exclude them unconditionally, both when copying files in and out of a packet's working directory.

As a side-effect of now using the same function to copy files in and out of a packet, this commit also fixes the use of directory in a report's source directory. Previously we were attempting to call shutil.copy2 on every entry, which would fail on directories.

[richfitz]

LGTM - do we need to exclude .pyc files or are these never found out of the cache directory any more?

[plietar]

do we need to exclude .pyc files or are these never found out of the cache directory any more?

Seems like as of Python 3.2 they are always in the pycache directory, so this should be enough.

https://docs.python.org/dev/whatsnew/3.2.html#pep-3147-pyc-repository-directories

to prevent all of these new files from cluttering source directories, the pyc files are now collected in a __pycache__ directory stored under the package directory.