insightsengineering / teal.modules.hermes

RNA-seq analysis modules to add to a teal application
https://insightsengineering.github.io/teal.modules.hermes/
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Review `tmhermes` documentation before release #307

Closed donyunardi closed 1 year ago

donyunardi commented 1 year ago

Summary

Related with insightsengineering/nestdevs-tasks#25 and also: https://github.com/insightsengineering/teal.modules.hermes/pull/294 In preparation to release, we need to review/assess all documentation in the package.

Acceptance Criteria

donyunardi commented 1 year ago

Closing this issue as chunks is not used in this module.

Confirmed that the chunks mentioned here is just a design files and not part of R package (see comment here).

@danielinteractive please update the mentioned design files to use qenv if needed and remove any reference to chunks to avoid future confusion.

donyunardi commented 1 year ago

Sorry, reopen this again. Even though chunks is out of the picture, we still need to release this due to update during the refactor: https://github.com/insightsengineering/teal.modules.hermes/pull/294

m7pr commented 1 year ago

Hey @gogonzo I did review this package. There is no use of teal.code::chunks in examples, regular code nor vignettes. The only place this is used is a design/ folder (those two files https://github.com/search?q=org%3Ainsightsengineering+repo%3Ainsightsengineering%2Fteal.modules.hermes++chunks&type=code) but this folder is listed in .Rbuildignore so it's not a part of the package.

Also no need to add teal.code to dependencies in DESCRIPTION

gogonzo commented 1 year ago

This design directory should be either removed or chunks should be replaced by qenv. chunks will disappear forever. @danielinteractive please select what you prefer

danielinteractive commented 1 year ago

@gogonzo the point is that design folder contains many outdated things, it is a memory of the project. Therefore you can consider this as it does not have to work at all, but it can be helpful later for us when understanding the history. so we can just keep it like it is. as mentioned, it is not part of the R package.

gogonzo commented 1 year ago

@gogonzo the point is that design folder contains many outdated things, it is a memory of the project. Therefore you can consider this as it does not have to work at all, but it can be helpful later for us when understanding the history. so we can just keep it like it is. as mentioned, it is not part of the R package.

Fair enough. Danke schön!

m7pr commented 1 year ago

so I guess we can close this issue