Issue #22 enum anno evo

[turbomam]

• Switch to poetry
• check in some enum annotation and curation code that was developed elsewhere

I have moved the previou setup.py-oriented files including the Makefile to ./pre_poetry

There is a nested loop over the same iterable (requested_pvs_names) in linkml_model_enrichment/annotators/enum_annotator.py that has to be dealt with

[turbomam]

Fails GH actions checks because that requires the requirements.txt. How to move the GH actions to poetry? Will work on that.

[turbomam]

tried testing within poetry:

poetry run pytest

======================================================================================== test session starts ========================================================================================= platform darwin -- Python 3.9.9, pytest-6.2.5, py-1.11.0, pluggy-1.0.0 rootdir: /Users/MAM/Documents/gitrepos/linkml-model-enrichment collected 17 items / 1 error / 16 selected

=============================================================================================== ERRORS =============================================================================================== __ ERROR collecting tests/test_combined_tsv_enum.py __ ImportError while importing test module '/Users/MAM/Documents/gitrepos/linkml-model-enrichment/tests/test_combined_tsv_enum.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: /usr/local/Cellar/python@3.9/3.9.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/init.py:127: in import_module return _bootstrap._gcd_import(name[level:], package, level) tests/test_combined_tsv_enum.py:9: in from linkml_model_enrichment.annotators.enum_annotator import all_enums_to_ols E ImportError: cannot import name 'all_enums_to_ols' from 'linkml_model_enrichment.annotators.enum_annotator' (/Users/MAM/Documents/gitrepos/linkml-model-enrichment/linkml_model_enrichment/annotators/enum_annotator.py) ========================================================================================== warnings summary ========================================================================================== ../../../Library/Caches/pypoetry/virtualenvs/linkml-model-enrichment-ni1l8Qyw-py3.9/lib/python3.9/site-packages/rdflib_jsonld/init.py:9 /Users/MAM/Library/Caches/pypoetry/virtualenvs/linkml-model-enrichment-ni1l8Qyw-py3.9/lib/python3.9/site-packages/rdflib_jsonld/init.py:9: DeprecationWarning: The rdflib-jsonld package has been integrated into rdflib as of rdflib==6.0.0. Please remove rdflib-jsonld from your project's dependencies. warnings.warn(

../../../Library/Caches/pypoetry/virtualenvs/linkml-model-enrichment-ni1l8Qyw-py3.9/lib/python3.9/site-packages/funowl/base/cast_function.py:2 /Users/MAM/Library/Caches/pypoetry/virtualenvs/linkml-model-enrichment-ni1l8Qyw-py3.9/lib/python3.9/site-packages/funowl/base/cast_function.py:2: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.10 it will stop working from collections import Iterable, UserList

-- Docs: https://docs.pytest.org/en/stable/warnings.html ====================================================================================== short test summary info ======================================================================================= ERROR tests/test_combined_tsv_enum.py !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ==================================================================================== 2 warnings, 1 error in 2.69s ==================================================================================== MAM@MAM-M74 linkml-model-enrichment %