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Separating python and r kernels into their own conda envs #23

Merged
merged 9 commits into from
Mar 9, 2023
Merged

Separating python and r kernels into their own conda envs #23

merged 9 commits into from
Mar 9, 2023

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SandyRogers
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@SandyRogers SandyRogers commented Mar 3, 2023 •
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This PR:

  • creates 2 conda environments (one for Python, one for R), and installs them as Jupyter Kernels for the Notebooks.
    • this helps with clashing dependencies
    • the kernels are managed by nb_conda_kernels
  • adds a stub notebook for R so that it is easier to contribute a new R-based notebook
  • adds static rendering of the R notebooks so that they appear on docs.mgnify.org
  • improves the management of the mgnifyr cache file

TODO:

  • the test for using jupyter lab in shinyproxy is intermittently failing when running in headless mode.

@SandyRogers SandyRogers marked this pull request as ready for review March 9, 2023 13:49
@SandyRogers SandyRogers changed the title [wip] separating python and r kernels into their own conda envs Separating python and r kernels into their own conda envs Mar 9, 2023
@SandyRogers SandyRogers merged commit 7ba7234 into main Mar 9, 2023
@SandyRogers SandyRogers deleted the kernel-envs branch March 9, 2023 13:54
SHillman836 pushed a commit to SHillman836/notebooks that referenced this pull request Jul 10, 2024
@SandyRogers
Separating python and r kernels into their own conda envs (EBI-Metage…
5809641 
…nomics#23)

* [wip] separating python and r kernels into otheir wn conda envs

* keep R conda env activated for all R dependency steps

* updates jl extensions to target ES2018

* separates r and python kernels into different conda envs

* adds missing matplotlib dependency

* adds static rendering of R notebooks

* updates tests to use separated conda env names

* allows test retries even if setup handler fails
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@SandyRogers