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.
[ ] (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
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
ser.iloc[pos]ser.iloc[pos]ser.iloc[pos]ser.iloc[pos]ser.iloc[pos]ser.iloc[pos]obsm_mapping. In 0.9 this will be an error.AnnData(X, dtype=X.dtype, ...)to get the future behavour.ser.iloc[pos]ser.iloc[pos]Broken notebooks