T018: warning fixes / molecule images not showing #347
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mbackenkoehler
added
bug
Currently, the code snippet `import pypdb; from biopandas.pdb import PandasPdb` raises DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. pd_version = LooseVersion(pd.__version__). This is raised by `biopandas`, but only after importing `pypdb`. importing any of the two separately doesn't raise a warning. This is probably due to `pypdb` setting some global variables (for Pandas?) that then raise a warning from `biopandas`. Before applying the ultimate solution updating dependencies, for now, changing the order suppresses the warning.
This was an inconsequential bug that caused the PDB file to be downloaded twice. With this fix, it is only downloaded once.
This requires a newer version of RDKit, thus the pinned version was removed from `test_env.yml`; this still doesn't update RDKit to the latest version, due to pinning in other dependencies. Note that for this fix to work, you have to recreate your environment with the new `test_env.yml`, or update RDKit manually.
The warning "MDAnalysis/coordinates/PDB.py:1129: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0'" is caused by MDAnalysis, which is used by OpenCADD, which is used in the `extract_molecule_from_pdb_file` function in `utils/helpers/pdb.py`. Cause of the warning is that formal charges are not present in the PDB file. This is a common situation since many PDB files don't have formal charges assigned. However, this pinned version of MDAnalysis raises a warning in these situations, which is now suppressed by a context manager in this commit
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@AndreaVolkamer, @mbackenkoehler, is my update to this PR description correct? |
dominiquesydow
changed the title
…ings-and-images-not-showing T018: deprecation warnings and images not showing (#334)
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Corresponding changes in other notebooks will follow in a separate PR |
mbackenkoehler
deleted the
334-t018-deprecation-warnings-and-images-not-showing
branch
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This PR collects changes to solve #334