[Neurodebian-devel] nipype and python-pydot incompatibility

[Yaroslav Halchenko]

On Thu, 08 Mar 2018, Alex Waite wrote:
> pkg_resources.DistributionNotFound: The 'pydot>=1.2.3' distribution was not
> found and is required by nipype

doh -- thanks for the email and for the buzz about me not replying ;)

> This problem is with both nipype 0.14.0-1~nd90+1 and 1.0.1-1~nd90+1

> python-pydot 1.2.3 is available in testing but not stable.

> At very least, I think nipype should depend on >= 1.2.3 python-pydot.

> But, reading about python-pydotplus (also depended on by the nipype package)
> seems to imply that it is a pseudo successor to python-pydot? It's a dep, so
> I wasn't able to remove it, but perhaps python-pydotplus is a enough and
> python-pydot can be removed as a dep and conflict with <1.2.3?

python-pydotplus provides its own pydotplus module 

nipype seems to be not using any of them directly:

$> git grep pydot
doc/users/install.rst:    'doc': ['Sphinx>=1.4', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],
nipype/info.py:    'pydotplus',
nipype/info.py:    'pydot>=%s' % PYDOT_MIN_VERSION,
nipype/info.py:    'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],
nipype/pipeline/engine/utils.py:    nx.drawing.nx_pydot.write_dot(pklgraph, simple_dot)
requirements.txt:pydotplus
requirements.txt:pydot>=1.2.3
rtd_requirements.txt:pydotplus
rtd_requirements.txt:pydot>=1.2.3

and overall the question is more for upstream:
https://github.com/nipy/nipype/issues/2494

> Thoughts? I don't use these packages personally, so it's all just
> conjecture.

even disregarding either backport of pydot works out I think I should
remove listing of those in info.py altogether so tools do not crash when pydot,
needed only for one specific option/use-case is not available 


> ---Alex

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-- 
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
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