Error: datashader.bundling

[fcorowe]

Thanks for the package. The maps look awesome.

I am having a problem running the code provided on the website. Specifically I am struggling to run the following line:

hbundle <- edge_bundle_hammer(g, xy, bw = 0.7, decay = 0.5)

It returns this error: Error: Python module datashader.bundling was not found.

I checked I have this datashader installed and it is:

(flowmap) MacBook-Pro-5:flow-map_edgebundle franciscorowe$ conda list
# packages in environment at /Users/franciscorowe/opt/anaconda3/envs/flowmap:
#
# Name                    Version                   Build  Channel
brotli                    1.0.9                    pypi_0    pypi
brotli-python             1.0.9           py311h814d153_9    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
ca-certificates           2023.7.22            h8857fd0_0    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
charset-normalizer        3.2.0              pyhd8ed1ab_0    conda-forge
click                     8.1.6           unix_pyh707e725_0    conda-forge
cloudpickle               2.2.1              pyhd8ed1ab_0    conda-forge
colorcet                  3.0.1              pyhd8ed1ab_0    conda-forge
dask-core                 2023.8.0           pyhd8ed1ab_0    conda-forge
**datashader**               0.15.2             pyhd8ed1ab_0    conda-forge
....

Yet, I get the same error when I run the line of code above.

Any advice on this issue would be appreciated, or general advice on how to get the package working.

My computational set up is:

R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

[schochastics]

Debugging datashader is always tricky for me. Did you use the automatic install shown here: https://github.com/schochastics/edgebundle/blob/main/R/bundle_hammer.R#L62-L68

Or did you install it manually?

[fcorowe]

I did try both options - same result

[fcorowe]

This is the message I get:

hbundle <- edge_bundle_hammer(g, xy, bw = 0.7, decay = 0.5)
List of 20
 $ python              : chr "/usr/bin/python3"
 $ libpython           : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/lib/python3.9/config-3.9-"| __truncated__
 $ pythonhome          : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9:/Library/Developer/Comman"| __truncated__
 $ pythonpath          : chr "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/reticulate/config:/Library/Developer/Comma"| __truncated__
 $ prefix              : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ exec_prefix         : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ base_exec_prefix    : chr "/Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9"
 $ virtualenv          : chr ""
 $ virtualenv_activate : chr ""
 $ version_string      : chr "3.9.6 (default, May  7 2023, 23:32:44)  [Clang 14.0.3 (clang-1403.0.22.14.1)]"
 $ version             : chr "3.9"
 $ architecture        : chr "64bit"
 $ anaconda            : logi FALSE
 $ conda               : chr "False"
 $ numpy               : NULL
 $ required_module     : chr "datashader"
 $ required_module_path: NULL
 $ available           : logi TRUE
 $ python_versions     : chr "/usr/bin/python3"
 $ forced              : chr "RETICULATE_PYTHON_FALLBACK"
 - attr(*, "class")= chr "py_config"
Error: Python module datashader.bundling was not found.

Detected Python configuration:

[fcorowe]

Also I tried it two machines: a Mac Studio, and a Mac Pro. The output above is from the Mac Studio which I trust less as I can't list the modules that are installed on the version of Python. Nonetheless, I can't get the package to work on my Mac Pro either.

[schochastics]

what happens when you run install_bundle_py?

[prochlorothrix]

what happens when you run install_bundle_py?

I had the same issue on Ubuntu 22.04 and running install_bundle_py() fixed it.

[schochastics]

I'd recommend switching to ggraph for edgebundling. Most of the algorithms implemented here are now ported in a better way to that package

[fcorowe]

Hi @schochastics, could you please elaborate on what exactly is the suggestion. Is it to use this package: https://ggraph.data-imaginist.com/reference/geom_conn_bundle.html instead of yours?

[schochastics]

@fcorowe Yes, most functionality was ported to ggraph and is available under geom_edge_bundle_* see the release blog post: https://www.data-imaginist.com/posts/2024-02-15-ggraph-2-2-0/