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biocommons / biocommons.seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences
Apache License 2.0
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Remove namespace warning #106

Open holtgrewe opened 1 year ago

holtgrewe commented 1 year ago

The following namespace warning occurs when running tests. One probably has to migrate to "new style namespaces". The matplotlib library has a similar issue albeit not resolved this yet.

============================================================================================================================== warnings summary ===============================================================================================================================
../../../../opt/miniconda3/envs/seqrepo/lib/python3.8/site-packages/pkg_resources/__init__.py:121
../../../../opt/miniconda3/envs/seqrepo/lib/python3.8/site-packages/pkg_resources/__init__.py:121
  /opt/miniconda3/envs/seqrepo/lib/python3.8/site-packages/pkg_resources/__init__.py:121: DeprecationWarning: pkg_resources is deprecated as an API
    warnings.warn("pkg_resources is deprecated as an API", DeprecationWarning)

../../../../opt/miniconda3/envs/seqrepo/lib/python3.8/site-packages/biocommons/__init__.py:3
../../../../opt/miniconda3/envs/seqrepo/lib/python3.8/site-packages/biocommons/__init__.py:3
  /opt/miniconda3/envs/seqrepo/lib/python3.8/site-packages/biocommons/__init__.py:3: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('biocommons')`.
  Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
    pkg_resources.declare_namespace(__name__)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
github-actions[bot] commented 1 year ago

This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.

github-actions[bot] commented 1 year ago

This issue was closed because it has been stalled for 7 days with no activity.

jsstevenson commented 3 months ago

I believe this was fixed in #149. I'm going to remove the bug label which will allow stalebot to close this issue automatically after a while, but we can restore it if I'm wrong.