Notebooks errors (list)

[thomcsmits]

I've went through the instructions for setting up the notebooks.

macOS 13.4, conda 24.3.0

I ran each notebook to see if any errors occurred.

Each notebook prompted for the install of anywidget and starlette (see also #343). After installing both (starlette=0.27.0, anywidget=0.9.10), the following errors remained. The widgets only showed after resetting the kernel for anywidgets.

All notebooks

• [ ] cellbrowser_to_vitessce_config_conversion.ipynb
  • [ ] (Cell 3) ValueError: CellBrowser config is not valid. Please check the error message above.
• [ ] config_to_python.ipynb
• [ ] data_conversion.ipynb
  • [ ] (Cell 1) ImportError: cannot import name 'SnapWrapper' from 'vitessce'
• [ ] data_export_files.ipynb
  • [ ] (Cell 1) ImportError: cannot import name 'VitessceWidget' from 'vitessce'
• [ ] data_export_s3.ipynb
  • [ ] (Cell 1) ImportError: cannot import name 'VitessceWidget' from 'vitessce'
• [ ] web_app_brain.ipynb
  • [ ] (Cell 3) FutureWarning: Moving element from .uns['neighbors']['distances'] to .obsp['distances'].
  • [ ] (Cell 3) FutureWarning: Moving element from .uns['neighbors']['connectivities'] to .obsp['connectivities']
  • [ ] (Cell 4) FutureWarning: Series._getitem_ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use ser.iloc[pos]
  • [ ] (Cell 4) FutureWarning: Series._getitem_ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use ser.iloc[pos]
  • [ ] (Cell 7) TypeError: stat: path should be string, bytes, os.PathLike or integer, not AnnData
• [ ] widget_brain_with_base_dir.ipynb
  • [ ] (Cell 4) FutureWarning: Moving element from .uns['neighbors']['distances'] to .obsp['distances'].
  • [ ] (Cell 4) FutureWarning: Moving element from .uns['neighbors']['connectivities'] to .obsp['connectivities']
  • [ ] (Cell 5) FutureWarning: Series._getitem_ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use ser.iloc[pos]
  • [ ] (Cell 5) FutureWarning: Series._getitem_ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use ser.iloc[pos]
• [ ] widget_brain.ipynb
  • [ ] (Cell 3) FutureWarning: Moving element from .uns['neighbors']['distances'] to .obsp['distances'].
  • [ ] (Cell 3) FutureWarning: Moving element from .uns['neighbors']['connectivities'] to .obsp['connectivities']
  • [ ] (Cell 4) FutureWarning: Series._getitem_ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use ser.iloc[pos]
  • [ ] (Cell 4) FutureWarning: Series._getitem_ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use ser.iloc[pos]
• [ ] widget_from_dict.ipynb
• [ ] widget_genomic_profiles.ipynb
  • [ ] (Cell 2) ValueError: Line 1: Not a Matrix Market file. Missing banner.
• [ ] widget_imaging.ipynb
• [ ] widget_imaging_beta.ipynb
• [ ] widget_imaging_segmentation.ipynb
• [ ] widget_loom.ipynb
  • [ ] (Cell 3) Argument obsm_names has been deprecated in favour of obsm_mapping. In 0.9 this will be an error.
  • [ ] (Cell 5) FutureWarning: X.dtype being converted to np.float32 from uint16. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass AnnData(X, dtype=X.dtype, ...) to get the future behavour.
• [ ] widget_on_colab.ipynb
• [ ] widget_pbmc.ipynb
  • [ ] (Cell 3) FutureWarning: Moving element from .uns['neighbors']['distances'] to .obsp['distances'].
  • [ ] (Cell 3) FutureWarning: Moving element from .uns['neighbors']['connectivities'] to .obsp['connectivities']
• [ ] widget_pbmc_remote.ipynb
• [ ] widget_shortcut.ipynb
  • [ ] (Cell 3) FutureWarning: Moving element from .uns['neighbors']['distances'] to .obsp['distances'].
  • [ ] (Cell 3) FutureWarning: Moving element from .uns['neighbors']['connectivities'] to .obsp['connectivities']
  • [ ] (Cell 4) FutureWarning: Series._getitem_ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use ser.iloc[pos]
  • [ ] (Cell 4) FutureWarning: Series._getitem_ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use ser.iloc[pos]
  • [ ] (Cell 6) TypeError: stat: path should be string, bytes, os.PathLike or integer, not AnnData

Broken notebooks

• cellbrowser_to_vitessce_config_conversion.ipynb
• data_conversion.ipynb
• data_export_files.ipynb
• widget_shortcut.ipynb
• widget_genomic_profiles.ipynb
• data_export_s3.ipynb