AttributeError: module 'umap.plot' has no attribute 'output_notebook'
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Description
import umap
import umap.plot
umap.__version__
'0.4.2'.
After import umap in Jupyter notebook I get the same issue as in https://github.com/lmcinnes/umap/issues/321. I assumed that with version >0.4 it should have been resolved. Am I doing something wrong?
umap.plot.output_notebook()
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-2-c970ec05c096> in <module>
----> 1 umap.plot.output_notebook()
AttributeError: module 'umap.plot' has no attribute 'output_notebook'
And I indeed do not see 'output_notebook'
dir(umap.plot)
['Patch',
'__builtins__',
'__cached__',
'__doc__',
'__file__',
'__loader__',
'__name__',
'__package__',
'__spec__',
'_blue',
'_datashade_points',
'_diagnostic_types',
'_embed_datashader_in_an_axis',
'_get_extent',
'_green',
'_matplotlib_points',
'_nhood_compare',
'_nhood_search',
'_red',
'_select_font_color',
'_themes',
'_to_hex',
'bd',
'bpl',
'btr',
'colorcet',
'connectivity',
'darkblue_cmap',
'darkgreen_cmap',
'darkpurple_cmap',
'darkred_cmap',
'deheap_sort',
'diagnostic',
'ds',
'fire_cmap',
'hd',
'hv',
'initialise_search',
'initialized_nnd_search',
'interactive',
'matplotlib',
'np',
'numba',
'pd',
'plt',
'points',
'show',
'show_interactive',
'show_static',
'sklearn',
'submatrix',
'tf',
'warn']
As a workaround I use the function directly from bokeh
from bokeh.plotting import show, save, output_notebook, output_file
p = umap.plot.interactive(mapper, labels=labels, hover_data=hover_data)
And then I have to run the show command twice
output_notebook()
show(p)
In order not to get this error
RuntimeError: Models must be owned by only a single document, Circle(id='1036', ...) is already in a doc
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the issue in a Jupyter notebook with umap.plot.interactive and the Bokeh output_notebook workaround described in the report. Read the umap.plot interactive path and check how notebook output is initialized; done means output_notebook is available or clearly documented, and displaying the plot no longer requires repeated show calls or triggers the duplicate-document error.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- data-visualization, machine-learning
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100