RDFLIB issues...

[dnkennedy]

So, I had the most recent rdflib (as of this writing):

% pip show rdflib
Name: rdflib
Version: 7.0.0
Summary: RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.

Home-page: https://github.com/RDFLib/rdflib

Author: Daniel 'eikeon' Krech
Author-email: eikeon@eikeon.com
License: BSD-3-Clause
Location: /Users/kennedyd/opt/anaconda3/envs/segstats_jsonld/lib/python3.11/site-packages
Requires: isodate, pyparsing
Required-by: prov, pynidm

And a the current pynidm:

% pip show pynidm
Name: pynidm
Version: 4.1.0
Summary: PYNIDM: a Python NIDM library and tools

Home-page: https://github.com/incf-nidash/PyNIDM

Author: INCF-NIDASH developers
Author-email: incf-nidash-nidm@googlegroups.com
License: Apache-2.0
Location: /Users/kennedyd/opt/anaconda3/envs/segstats_jsonld/lib/python3.11/site-packages
Requires: click, click-option-group, cognitiveatlas, datalad, etelemetry, numpy, ontquery, pandas, patsy, prov, pybids, pydot, pygithub, pyld, python-dateutil, rapidfuzz, rdflib, requests, scikit-learn, scipy, statsmodels, tabulate, validators
Required-by: segstats-jsonld

But I get (hundreds) of the following error:

caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info

Traceback (most recent call last):
File "/Users/kennedyd/opt/anaconda3/envs/segstats_jsonld/lib/python3.11/site-packages/rdflib/namespace/init.py", line 691, in _store_bind
return self.store.bind(prefix, namespace, override=override)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'

With @dbkeator 's help, I backed my rdflib back out to 6.3.2, which worked for him. And that removed my rdflib errors.

How do we deal with this for others?????

[dnkennedy]

Just poking at this again, since I'm really not a fan of manually having users have to back out their rdflib. Can't the 'environment' deal with this somehow? or pynidm comply with the current rdflib??? And I'm getting these messages still, and I'm trying to get this tool (starting with asegstats2nidm) used in other platforms (such as BrainLife) where all these messages are very unseemly...

[yarikoptic]

me poking around too now and having the same issue

❯ python -c 'from segstats_jsonld.fs_to_nidm import main'
RDFLib Version: 5.0.1
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'
caught a TypeError, retrying call to <class 'rdflib.plugins.memory.IOMemory'>.bind without override, see https://github.com/RDFLib/rdflib/issues/1880 for more info
Traceback (most recent call last):
  File "/home/yoh/proj/repronim/segstats_jsonld/venv/dev3/lib/python3.12/site-packages/rdflib/namespace/__init__.py", line 636, in _store_bind
    return self.store.bind(prefix, namespace, override=override)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: IOMemory.bind() got an unexpected keyword argument 'override'

[yarikoptic]

this warning seems to be of no consequence for us for operation, submitting upstream

• Downgrade log message about plugin without override argument to debug from warning RDFLib/rdflib#3063

[yarikoptic]

I think upgrade of librdf to current 7.1.3, conflicting with prov which needed before 7, also got rid of that warning... duct logs will be pushed to https://github.com/ReproNim/OpenNeuroDerivatives-NIDM