Notebook flake fixes

[ceball]

I'm testing a notebook linting tool. These are the issues it found in the doc/ directory, running it with python3.

It's not clear to me that everything it's found is correct, e.g.

• Is there a notebook about pandas that doesn't use pandas? Or is it because you need to import pandas to get features of the pandas backend?
• Do notebooks work in python 2 and python 3 with both the print statement and function? One notebook had both in.
• Are some things in notebooks deliberately imported and unused?

This is what I ran:

pip install pytest-nbsmoke
pytest --tb=short --nbsmoke-lint doc/

--tb=short is necessary because currently the combined pytest/nbconvert output is huge, unfortunately.

If I run nbsmoke on examples/, I get a lot more to fix. But first I wanted to see how you feel about these changes...

[ceball]

From running on examples/, I noticed two things: (1) you guys have done an unbelievable amount of work (!), and (2) you like to import numpy but not use it ;)

$ pytest --nbsmoke-lint examples/
===================================================== test session starts =====================================================
platform darwin -- Python 3.6.3, pytest-3.2.3, py-1.4.34, pluggy-0.4.0
rootdir: /Users/cball/code/ioam/holoviews3, inifile:
plugins: nbsmoke-0.1.5
collected 201 items                                                                                                            

examples/gallery/demos/bokeh/area_chart.ipynb .
examples/gallery/demos/bokeh/autompg_histogram.ipynb F
examples/gallery/demos/bokeh/bachelors_degrees_by_gender.ipynb F
examples/gallery/demos/bokeh/bars_economic.ipynb F
examples/gallery/demos/bokeh/boxplot_chart.ipynb F
examples/gallery/demos/bokeh/dot_example.ipynb F
examples/gallery/demos/bokeh/dragon_curve.ipynb .
examples/gallery/demos/bokeh/dropdown_economic.ipynb F
examples/gallery/demos/bokeh/histogram_example.ipynb .
examples/gallery/demos/bokeh/iris_density_grid.ipynb F
examples/gallery/demos/bokeh/iris_example.ipynb F
examples/gallery/demos/bokeh/iris_splom_example.ipynb F
examples/gallery/demos/bokeh/legend_example.ipynb .
examples/gallery/demos/bokeh/lesmis_example.ipynb .
examples/gallery/demos/bokeh/lorenz_attractor_example.ipynb .
examples/gallery/demos/bokeh/mandelbrot_section.ipynb .
examples/gallery/demos/bokeh/measles_example.ipynb .
examples/gallery/demos/bokeh/network_graph.ipynb .
examples/gallery/demos/bokeh/quiver_demo.ipynb .
examples/gallery/demos/bokeh/scatter_economic.ipynb F
examples/gallery/demos/bokeh/square_limit.ipynb .
examples/gallery/demos/bokeh/step_chart.ipynb F
examples/gallery/demos/bokeh/stocks_example.ipynb .
examples/gallery/demos/bokeh/texas_choropleth_example.ipynb F
examples/gallery/demos/bokeh/topographic_hillshading.ipynb F
examples/gallery/demos/bokeh/us_unemployment.ipynb .
examples/gallery/demos/bokeh/verhulst_mandelbrot.ipynb .
examples/gallery/demos/matplotlib/area_chart.ipynb .
examples/gallery/demos/matplotlib/autompg_histogram.ipynb F
examples/gallery/demos/matplotlib/bachelors_degrees_by_gender.ipynb F
examples/gallery/demos/matplotlib/bars_economic.ipynb F
examples/gallery/demos/matplotlib/boxplot_chart.ipynb F
examples/gallery/demos/matplotlib/dragon_curve.ipynb .
examples/gallery/demos/matplotlib/dropdown_economic.ipynb F
examples/gallery/demos/matplotlib/histogram_example.ipynb .
examples/gallery/demos/matplotlib/iris_density_grid.ipynb F
examples/gallery/demos/matplotlib/iris_example.ipynb F
examples/gallery/demos/matplotlib/iris_splom_example.ipynb F
examples/gallery/demos/matplotlib/legend_example.ipynb .
examples/gallery/demos/matplotlib/lorenz_attractor_example.ipynb .
examples/gallery/demos/matplotlib/mandelbrot_section.ipynb .
examples/gallery/demos/matplotlib/measles_example.ipynb .
examples/gallery/demos/matplotlib/network_graph.ipynb .
examples/gallery/demos/matplotlib/polar_scatter_demo.ipynb .
examples/gallery/demos/matplotlib/quiver_demo.ipynb .
examples/gallery/demos/matplotlib/scatter_economic.ipynb F
examples/gallery/demos/matplotlib/square_limit.ipynb .
examples/gallery/demos/matplotlib/step_chart.ipynb F
examples/gallery/demos/matplotlib/stocks_example.ipynb .
examples/gallery/demos/matplotlib/surface_3d.ipynb .
examples/gallery/demos/matplotlib/texas_choropleth_example.ipynb F
examples/gallery/demos/matplotlib/topographic_hillshading.ipynb F
examples/gallery/demos/matplotlib/trisurf3d_demo.ipynb .
examples/gallery/demos/matplotlib/us_unemployment.ipynb .
examples/gallery/demos/matplotlib/verhulst_mandelbrot.ipynb .
examples/gallery/demos/plotly/surface_3d.ipynb .
examples/gallery/demos/plotly/trisurf3d_demo.ipynb .
examples/getting_started/1-Introduction.ipynb .
examples/getting_started/2-Customization.ipynb .
examples/getting_started/3-Tabular_Datasets.ipynb .
examples/getting_started/4-Gridded_Datasets.ipynb F
examples/getting_started/5-Live_Data.ipynb .
examples/reference/containers/bokeh/DynamicMap.ipynb .
examples/reference/containers/bokeh/GridSpace.ipynb .
examples/reference/containers/bokeh/HoloMap.ipynb .
examples/reference/containers/bokeh/Layout.ipynb .
examples/reference/containers/bokeh/NdLayout.ipynb .
examples/reference/containers/bokeh/NdOverlay.ipynb .
examples/reference/containers/bokeh/Overlay.ipynb .
examples/reference/containers/matplotlib/DynamicMap.ipynb .
examples/reference/containers/matplotlib/GridSpace.ipynb .
examples/reference/containers/matplotlib/HoloMap.ipynb .
examples/reference/containers/matplotlib/Layout.ipynb .
examples/reference/containers/matplotlib/NdLayout.ipynb .
examples/reference/containers/matplotlib/NdOverlay.ipynb .
examples/reference/containers/matplotlib/Overlay.ipynb .
examples/reference/elements/bokeh/Area.ipynb .
examples/reference/elements/bokeh/Arrow.ipynb .
examples/reference/elements/bokeh/Bars.ipynb .
examples/reference/elements/bokeh/Bivariate.ipynb .
examples/reference/elements/bokeh/Bounds.ipynb F
examples/reference/elements/bokeh/Box.ipynb .
examples/reference/elements/bokeh/BoxWhisker.ipynb .
examples/reference/elements/bokeh/Contours.ipynb .
examples/reference/elements/bokeh/Curve.ipynb .
examples/reference/elements/bokeh/Distribution.ipynb .
examples/reference/elements/bokeh/Ellipse.ipynb .
examples/reference/elements/bokeh/ErrorBars.ipynb .
examples/reference/elements/bokeh/Graph.ipynb F
examples/reference/elements/bokeh/HLine.ipynb .
examples/reference/elements/bokeh/HSV.ipynb .
examples/reference/elements/bokeh/HeatMap.ipynb .
examples/reference/elements/bokeh/Histogram.ipynb .
examples/reference/elements/bokeh/Image.ipynb .
examples/reference/elements/bokeh/ItemTable.ipynb F
examples/reference/elements/bokeh/Path.ipynb .
examples/reference/elements/bokeh/Points.ipynb .
examples/reference/elements/bokeh/Polygons.ipynb .
examples/reference/elements/bokeh/QuadMesh.ipynb .
examples/reference/elements/bokeh/RGB.ipynb .
examples/reference/elements/bokeh/Raster.ipynb .
examples/reference/elements/bokeh/Scatter.ipynb .
examples/reference/elements/bokeh/Spikes.ipynb .
examples/reference/elements/bokeh/Spline.ipynb F
examples/reference/elements/bokeh/Spread.ipynb .
examples/reference/elements/bokeh/Table.ipynb F
examples/reference/elements/bokeh/Text.ipynb .
examples/reference/elements/bokeh/VLine.ipynb .
examples/reference/elements/bokeh/VectorField.ipynb .
examples/reference/elements/matplotlib/Area.ipynb .
examples/reference/elements/matplotlib/Arrow.ipynb .
examples/reference/elements/matplotlib/Bars.ipynb .
examples/reference/elements/matplotlib/Bivariate.ipynb .
examples/reference/elements/matplotlib/Bounds.ipynb F
examples/reference/elements/matplotlib/Box.ipynb .
examples/reference/elements/matplotlib/BoxWhisker.ipynb .
examples/reference/elements/matplotlib/Contours.ipynb .
examples/reference/elements/matplotlib/Curve.ipynb .
examples/reference/elements/matplotlib/Distribution.ipynb .
examples/reference/elements/matplotlib/Ellipse.ipynb .
examples/reference/elements/matplotlib/ErrorBars.ipynb .
examples/reference/elements/matplotlib/Graph.ipynb F
examples/reference/elements/matplotlib/HLine.ipynb .
examples/reference/elements/matplotlib/HSV.ipynb .
examples/reference/elements/matplotlib/HeatMap.ipynb .
examples/reference/elements/matplotlib/Histogram.ipynb .
examples/reference/elements/matplotlib/Image.ipynb .
examples/reference/elements/matplotlib/ItemTable.ipynb F
examples/reference/elements/matplotlib/Path.ipynb .
examples/reference/elements/matplotlib/Points.ipynb .
examples/reference/elements/matplotlib/Polygons.ipynb .
examples/reference/elements/matplotlib/QuadMesh.ipynb .
examples/reference/elements/matplotlib/RGB.ipynb .
examples/reference/elements/matplotlib/Raster.ipynb .
examples/reference/elements/matplotlib/Scatter.ipynb .
examples/reference/elements/matplotlib/Scatter3D.ipynb .
examples/reference/elements/matplotlib/Spikes.ipynb .
examples/reference/elements/matplotlib/Spline.ipynb F
examples/reference/elements/matplotlib/Spread.ipynb .
examples/reference/elements/matplotlib/Surface.ipynb .
examples/reference/elements/matplotlib/Table.ipynb F
examples/reference/elements/matplotlib/Text.ipynb .
examples/reference/elements/matplotlib/Trisurface.ipynb .
examples/reference/elements/matplotlib/VLine.ipynb .
examples/reference/elements/matplotlib/VectorField.ipynb .
examples/reference/elements/plotly/BoxWhiskers.ipynb .
examples/reference/elements/plotly/Curve.ipynb .
examples/reference/elements/plotly/Distribution.ipynb .
examples/reference/elements/plotly/ErrorBars.ipynb .
examples/reference/elements/plotly/HeatMap.ipynb .
examples/reference/elements/plotly/Image.ipynb .
examples/reference/elements/plotly/ItemTable.ipynb F
examples/reference/elements/plotly/Points.ipynb .
examples/reference/elements/plotly/Raster.ipynb .
examples/reference/elements/plotly/Scatter.ipynb .
examples/reference/elements/plotly/Scatter3D.ipynb .
examples/reference/elements/plotly/Surface.ipynb .
examples/reference/elements/plotly/Table.ipynb F
examples/reference/elements/plotly/Trisurface.ipynb .
examples/reference/features/bokeh/table_hooks_example.ipynb F
examples/reference/streams/bokeh/Bounds.ipynb .
examples/reference/streams/bokeh/BoundsX.ipynb .
examples/reference/streams/bokeh/BoundsY.ipynb .
examples/reference/streams/bokeh/PointerX.ipynb F
examples/reference/streams/bokeh/PointerXY.ipynb .
examples/reference/streams/bokeh/RangeXY.ipynb F
examples/reference/streams/bokeh/Selection1D.ipynb .
examples/reference/streams/bokeh/Selection1D_paired.ipynb .
examples/reference/streams/bokeh/Selection1D_points.ipynb .
examples/reference/streams/bokeh/Selection1D_tap.ipynb .
examples/reference/streams/bokeh/Tap.ipynb F
examples/topics/geometry/lsystems.ipynb .
examples/topics/geometry/square_limit.ipynb .
examples/topics/simulation/boids.ipynb .
examples/topics/simulation/hipster_dynamics.ipynb .
examples/topics/simulation/sri_model.ipynb F
examples/user_guide/01-Annotating_Data.ipynb F
examples/user_guide/02-Composing_Elements.ipynb .
examples/user_guide/03-Customizing_Plots.ipynb .
examples/user_guide/04-Dimensioned_Containers.ipynb F
examples/user_guide/05-Building_Composite_Objects.ipynb .
examples/user_guide/06-Live_Data.ipynb .
examples/user_guide/07-Tabular_Datasets.ipynb .
examples/user_guide/08-Gridded_Datasets.ipynb F
examples/user_guide/09-Indexing_and_Selecting_Data.ipynb .
examples/user_guide/10-Transforming_Elements.ipynb .
examples/user_guide/11-Responding_to_Events.ipynb F
examples/user_guide/12-Custom_Interactivity.ipynb .
examples/user_guide/13-Data_Pipelines.ipynb F
examples/user_guide/14-Large_Data.ipynb F
examples/user_guide/15-Streaming_Data.ipynb .
examples/user_guide/16-Dashboards.ipynb F
examples/user_guide/Continuous_Coordinates.ipynb .
examples/user_guide/Deploying_Bokeh_Apps.ipynb .
examples/user_guide/Exporting_and_Archiving.ipynb F
examples/user_guide/Installing_and_Configuring.ipynb .
examples/user_guide/Network_Graphs.ipynb F
examples/user_guide/Plots_and_Renderers.ipynb F
examples/user_guide/Plotting_with_Bokeh.ipynb .
examples/user_guide/Plotting_with_Matplotlib.ipynb .
examples/user_guide/Tips_and_Tricks.ipynb F
[...]
=========================================== 54 failed, 147 passed in 28.52 seconds ============================================

[jbednar]

• In general, I'd be surprised if a notebook imported something for its use as a side effect; I don't think any of those would be intentional.
• Pandas shouldn't have to be imported in the notebook to be used; it's imported with try/except whether or not a notebook imports it.
• All uses of print should be with parentheses, to work in py2 and 3. Extra imports of numpy can surely be deleted.

[jbednar]

None of those look controversial to me!

[jlstevens]

The changes I see in the diffs all look helpful. Thanks!

[philippjfr]

Agreed, happy to merge this. Looks like there are more failures than fixes though. Do you want to make the other fixes too or should we just go ahead and merge this?

[ceball]

I'd merge this, saying it relates to doc only.

I'll do examples next, separately.

[philippjfr]

Great thanks for doing this!

[github-actions]

This pull request has been automatically locked since there has not been any recent activity after it was closed. Please open a new issue for related bugs.