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mrc-ide / priority-pathogens

https://mrc-ide.github.io/priority-pathogens/
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Migrate to orderly2 #7

Closed sangeetabhatia03 closed 1 year ago

sangeetabhatia03 commented 1 year ago

This PR migrates the source tree to orderly2. To test this,

  1. First install orderly2 following the instructions here https://github.com/mrc-ide/orderly2
  2. Then, copy a couple of ebola databases to the db_extraction folder under src. If you copy Sabine's and mine, you don't have to edit anything else but if you choose to copy others, edit the lines 9 and 10 in src/db_extraction/orderly.R to the filenames you have copied over.
  3. Then start a R session in priority-pathogens and run orderly2::orderly_run("db_extraction")
  4. If this runs without any problems, then we can safely conclude that the migration has been successful. The other task in the source tree was not set up to run as an orderly task.