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nhoffman / bioy

Tools for NGS sequence analysis and bacterial classification
GNU General Public License v3.0
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package import fails when installed with pip install --no-deps #40

Open nhoffman opened 8 years ago

nhoffman commented 8 years ago

It should be possible to use modules that don't depend on non-stdlib packages - for example, sequtils

nhoffman commented 8 years ago

Ok, the problem seems to be that bioy_pkg/init.py imports 'utils' - but the root of the problem is that the CLI is implemented in init - Chris - can you please put it back where it was (presumably in subcommands/init.py)? Looks like this was done around commit 3e7c87c5. In general, init should contain (and import) as little as possible. I want to be able to install with pip install --no-deps and then be able to do python -c 'from bioy_pkg import sequtils' (for example). Only modules with a specific need for non-stdlib dependencies should fail in their absence at runtime.

nhoffman commented 8 years ago

please work in 040-allow-no-deps

crosenth commented 8 years ago

Interesting, I guess I wasn't expecting that kind of usage. Can you give me the CLI commands to reproduce exactly what is not working?

crosenth commented 8 years ago

^ I ask because running 'python -c 'from bioy_pkg import sequtils' on a fresh pip install --no-deps bioy works okay for me on quoll.