Required cobra version is not installed correctly

[ChristianLieven]

After updating cookiecutter:

pip install cookiecutter --upgrade

and then trying to create a new memote project:

cookiecutter gh:biosustain/cookiecutter-memote

I get the following import error:

copying '/Users/clie/Desktop/Side_Projects/Memote/Ecoli_Model_collection/iJR904/iJR904.xml' -> 'iJR904.xml' Initialized empty Git repository in /Users/clie/Desktop/Side_Projects/Memote/memote-e-coli/.git/ Traceback (most recent call last): File ".git/hooks/pre-commit", line 30, in <module> from cobra.io import read_sbml_model, save_yaml_model ImportError: cannot import name save_yaml_model ERROR: Stopping generation because post_gen_project hook script didn't exit successfully Hook script failed (exit status: 1)

I couldn't fix this even by grabbing the feat/yaml-io branch:

pip install -U git+https://github.com/opencobra/cobrapy.git@feat/yaml-io#egg=cobra --upgrade

Which resulted in:

(test-memote)nnfcb-l0232:cobrapy clie$ python
Python 2.7.10 (default, Jul 14 2015, 19:46:27) 
>>> from cobra.io import save_yaml_model
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: cannot import name save_yaml_model

[Midnighter]

Strange, that should have been the right path.

[Midnighter]

The cookiecutter actually doesn't install anything itself. So packages need to be available in the environment before running cookiecutter. This is usually not a problem since you would install memote (with dependencies) and then run memote new.

So if you install it first in your virtualenv:

pip install https://github.com/opencobra/cobrapy/archive/feat/yaml-io.zip

Everything should run as expected.

[ChristianLieven]

I guess that's where I was a bit confused. I'll give this a try and report back!

[Midnighter]

In future, everything will be solved by installing memote and its dependencies.