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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
The text was updated successfully, but these errors were encountered:
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
The text was updated successfully, but these errors were encountered: