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% abcd --remote abcd@gc121mac1 iron.db --store MDPHONON_128.xyz
OSError: [Errno 7] Argument list too long

It looks like the whole file gets added to the remote command as a b64 encoded string, which will be too large for many shells. Perhaps the file contents need to be piped to a listening server instead?

If no directory is set when running the command it is left blank in the config file. This causes abcd to always look in the working directory which often fails.

It would be nice if re-running the command would also pick up the current value and allow it to be changed.

Since the backends are standard, this is probably already possible. However, some documentation and examples would be good to show that abcd can be used within scripts to interact with ase objects. It could be something like:

import abcd

my_db = abcd.Database('something.db')

for atoms_object in my_db.query('energy<-3460.93272745'):
    new_atoms = do_something(atoms_object)
    my_db.store(new_atoms)

Could be changed to use a single file, or files in a single directory. Also consider conforming to freedesktop specification of XDG_CONFIG_HOME (i.e. ~/.config/) on Linux.

one should be able to use any installed backend at any time. Remote repositories should be remembered or be able to be bookmarked so that they appear in the list of available databases. Bookmarks could also be used to give shortened names to databases. For example:

usage: abcd [db-name] [selection] [options]
Hello. Databases you have access to:
>> asedb
   [my] my_first_db.db
   [short] long_name_for_database.db
   >> remote.ac.uk
      [collab] [email protected]:shared.db
      [collab2] [email protected]:shared_2.db
>> mongodb
   [db1] database_one
   database_no_short_name

I've seen a few prints itertiems and basestrs. Likely just needs someone to find all the incompatibilities and make them compatible with Python 2 and 3. The other option is a compatibility layer like six.

Documentation should be updated to indicate which versions are supported.