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From readbeyond/aeneas#176 (comment) :

Just an idea, maybe not a good one: you could make python 'stubs' for the aeneas commands that live in the aeneas-vagrant folder. These would only forward the arguments to the real aeneas commands in the VM via 'vagrant ssh -c.' I think 'vagrant ssh -c' is not set up to print stderr to the terminal from the VM child process, only stdin. Not quite sure though. Like this, it's really almost like having aeneas installed natively.. I had difficulties installed aeneas natively on ubuntu 16.04 (such issues are understandable). Although, it's probably confusing for the user that they can't specify input files outside of the aeneas-vagrant folder. Ah, forget it. If I have a better idea I'll let you know. :-)

When I set up the VM according to your instructions (on Ubuntu 16.04), I noticed the aeneas commands weren't available on the terminal until I ran 'sudo pip install aeneas --upgrade'

==> default: Waiting for machine to boot. This may take a few minutes...
default: SSH address: 127.0.0.1:2222
default: SSH username: vagrant
default: SSH auth method: private key
default:
default: Vagrant insecure key detected. Vagrant will automatically replace
default: this with a newly generated keypair for better security.
default:
default: Inserting generated public key within guest...
default: Removing insecure key from the guest if it's present...
default: Key inserted! Disconnecting and reconnecting using new SSH key...
==> default: Machine booted and ready!
==> default: Checking for guest additions in VM...
default: No guest additions were detected on the base box for this VM! Guest
default: additions are required for forwarded ports, shared folders, host only
default: networking, and more. If SSH fails on this machine, please install
default: the guest additions and repackage the box to continue.
default:
default: This is not an error message; everything may continue to work properly,
default: in which case you may ignore this message.
==> default: Installing rsync to the VM...
==> default: Rsyncing folder: /cygdrive/d/Aeneas/aeneas-vagrant/ => /vagrant
There was an error when attempting to rsync a synced folder.
Please inspect the error message below for more info.

Host path: /cygdrive/d/Aeneas/aeneas-vagrant/
Guest path: /vagrant
Command: "rsync" "--verbose" "--archive" "--delete" "-z" "--copy-links" "--chmod=ugo=rwX" "--no-perms" "--no-owner" "--no-group" "--rsync-path" "sudo rsync" "-e" "ssh -p 2222 -o LogLevel=FATAL -o IdentitiesOnly=yes -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i 'D:/Aeneas/aeneas-vagrant/.vagrant/machines/default/virtualbox/private_key'" "--exclude" ".vagrant/" "/cygdrive/d/Aeneas/aeneas-vagrant/" "[email protected]:/vagrant"
Error: [email protected]: Permission denied (publickey).
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: error in rsync protocol data stream (code 12) at io.c(228) [sender=3.2.3]