mi3nts / mints-aq-reports

Repository for generation of MINTS automated reports
https://mi3nts.github.io/mints-aq-reports/
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Parametrize Notebook Templates #12

Open john-waczak opened 1 year ago

john-waczak commented 1 year ago

Once we have demo notebooks for each analysis style, we should augment them with a set of parameters that can be passed in at execution time via papermill. For starters these should include:

We should also update the quarto metadata to use the supplied device_name parameter when generating the title for each report. The device_name parameter should also be injected into the output notebook filename to keep things easy.

john-waczak commented 1 year ago

This discussion looks relevant for setting up a slurm job array with a bunch of papermill tasks

john-waczak commented 1 year ago

This link provides a nice tutorial for configuring slurm job arrays. The easiest thing to do will probably be to have a script we can run that will generate generate the papermill parameter files as well as a slurm config file. That config file can contain the path of the parameter file as well as the output file path we want to use.