rdflib and other pip incompatibilities

[turbomam]

I believe rdflib conflicts are already under discussion in the LinkML community? The click conflict is new to me. I've been doing some of my development on an Ubuntu 20 desktop recently.

(venv) mark@nuc-two-ups:~/gitrepos/linkml-model-enrichment$ pip install -r requirements.txt

... ERROR: linkml-runtime 1.1.2 has requirement rdflib~=5.0, but you'll have rdflib 6.0.2 which is incompatible. ERROR: sparqlslurper 0.4.1 has requirement rdflib~=5.0, but you'll have rdflib 6.0.2 which is incompatible. ERROR: pyshexc 0.8.3 has requirement rdflib~=5.0, but you'll have rdflib 6.0.2 which is incompatible. ERROR: pyshex 0.7.20 has requirement rdflib~=5.0, but you'll have rdflib 6.0.2 which is incompatible. ERROR: linkml 1.1.9 has requirement click~=7.0, but you'll have click 8.0.3 which is incompatible. ERROR: linkml 1.1.9 has requirement rdflib~=5.0, but you'll have rdflib 6.0.2 which is incompatible. ERROR: funowl 0.1.9 has requirement rdflib>=5.0.0,~=5.0, but you'll have rdflib 6.0.2 which is incompatible. ...

[turbomam]

It looks like the apt package manager installed some packages system-wide

pip3 freeze > installed.txt
pip3 uninstall -r installed.txt

... Found existing installation: appdirs 1.4.3 Not uninstalling appdirs at /usr/lib/python3/dist-packages, outside environment /usr ...

[turbomam]

tried pip3 install linkml instead. Installed linkml, -runtime, etc. and click.

[turbomam]

linkml-model-enrichment$ python3.9 -m venv venv
linkml-model-enrichment$ source venv/bin/activate
linkml-model-enrichment$ pip list

Package Version pip 20.0.2 pkg-resources 0.0.0
setuptools 44.0.0

[turbomam]

pip install wheel doesn't hurt

[turbomam]

Surprise

linkml-model-enrichment$ pip list | grep linkml

linkml 1.1.9
linkml-runtime 1.1.2
linkml-runtime-api 0.0.4

linkml-model-enrichment$ pip list | grep click

click 8.0.3
click-log 0.3.2
sphinx-click 3.0.1

linkml-model-enrichment$ pip list | grep rdf

rdflib 6.0.2
rdflib-jsonld 0.6.1
rdflib-pyldmod-compat 0.1.2

[turbomam]

linkml-model-enrichment$ tsv2linkml --output ../synbio-schema/util/query_results/synbio_part.yaml --class_name synbio_part ../synbio-schema/util/query_results/parts.tsv

Traceback (most recent call last): File "/home/mark/gitrepos/linkml-model-enrichment/venv/lib/python3.9/site-packages/pkg_resources/init.py", line 568, in _build_master ws.require(requires) File "/home/mark/gitrepos/linkml-model-enrichment/venv/lib/python3.9/site-packages/pkg_resources/init.py", line 886, in require needed = self.resolve(parse_requirements(requirements)) File "/home/mark/gitrepos/linkml-model-enrichment/venv/lib/python3.9/site-packages/pkg_resources/init.py", line 777, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (rdflib 6.0.2 (/home/mark/gitrepos/linkml-model-enrichment/venv/lib/python3.9/site-packages), Requirement.parse('rdflib>=5.0.0,~=5.0'), {'funowl'})

[turbomam]

commented out every line in requirements.txt, and linkml-model-enrichment worked. Will have to add some back in for XXX

[sierra-moxon]

@turbomam - I think I can close this as its pre-rdflib 6.0 migration? Please of course reopen if its still an issue.