neurdflib does not appear to fulfill prov dependency requirement

[liamtimms]

Summary

Hi, apologies if this is not the right place to ask however I seem to be running into an issue with a dependencies in setting up nipype. I am installing neurdflib as dependency for nipype and I can see that this includes the rdflib files in the python3.7/site-packages/rdflib directory.

ls site-packages/rdflib/

__init__.py    events.py      parser.py  resource.py    util.py
__pycache__    exceptions.py  paths.py   serializer.py  void.py
collection.py  extras         plugin.py  store.py
compare.py     graph.py       plugins    term.py
compat.py      namespace.py   query.py   tools

Actual behavior

However, when attempting to run a selectfiles node in a work flow the following crash-file is produced (as examined via !nipypecli crash command n a jupyter-lab notebook):

  File "/usr/bin/nipypecli", line 6, in <module>
    from pkg_resources import load_entry_point
  File "/usr/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3250, in <module>
    @_call_aside
  File "/usr/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3234, in _call_aside
    f(*args, **kwargs)
  File "/usr/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3263, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/usr/lib/python3.7/site-packages/pkg_resources/__init__.py", line 583, in _build_master
    ws.require(__requires__)
  File "/usr/lib/python3.7/site-packages/pkg_resources/__init__.py", line 900, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/usr/lib/python3.7/site-packages/pkg_resources/__init__.py", line 786, in resolve
    raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'rdflib>=4.2.1' distribution was not found and is required by prov

Expected behavior

That as neurdflib is simply a patched version of rdflib, prov would be able to use neurdflib to satisfy the dependency requirement.

How to replicate the behavior

I am unsure if this is an effect of my specific setup as detailed below. It happens consistently while having neurdflib and prov installed but was not a problem in an older installation using the same workflow.

Script/Workflow details

A simple workflow starting with selectfiles node. This code was working in an older environment.

Platform details:

python -c "import nipype; from pprint import pprint; pprint(nipype.get_info())"

{'commit_hash': '%h',
 'commit_source': 'archive substitution',
 'networkx_version': '2.3',
 'nibabel_version': '2.5.1',
 'nipype_version': '1.2.2',
 'numpy_version': '1.17.2',
 'pkg_path': '/usr/lib/python3.7/site-packages/nipype',
 'scipy_version': '1.3.1',
 'sys_executable': '/usr/bin/python',
 'sys_platform': 'linux',
 'sys_version': '3.7.4 (default, Jul 16 2019, 07:12:58) \n[GCC 9.1.0]',
 'traits_version': '5.1.2'}

jupyter-lab --version

1.1.3

Execution environment

Have not yet learned Docker, currently running linux in a virtual machine for access to neuroimaging suites.

[satra]

@liamtimms - this is an unfortunate dependency since we are waiting on a PR being merged into rdflib. however, this hacked patch has an order effect. so you have to first install prov and then install neurdflib.

[liamtimms]

Hi, just following up on this: I was able to get it working using the install sequence you prescribed. Definitely not best practice but it seems to work for now.