Reflect changes in new P2Rank version in tutorials

[skodapetr]

For example -conservation_dir param was replaced with -conservation_dirs.
I do not have full list of changes.
We should also update the results for model.

[davidjakubec]

Hi,

I think that this Issue is part of a broader problem with the documentation/tutorials being distributed through several channels (e.g., prank -h, @rdk/p2rank README, this wiki) . This is related to issues rdk/p2rank#47 and rdk/p2rank#48 in @rdk/p2rank. As a new user, it is not clear which of the documentations is up-to-date and which should I follow. For example, should I use -m or -model and what does the option actually do in combination with -c? Should I specify the file extension .groovy when selecting a configuration? These are some of the questions I was left wondering. Though they may seem stupid or harmless, they may not be so, as p2rank does not validate the input arguments (rdk/p2rank#36) -- therefore, if a user does not use the correct, up-to-date option/argument name, no error is displayed and they won't find out unless they check the logs (and they will then only identify the issue if they know what to look for). The -conservation_dirs issue described here is a specific example of this: if the old -conservation_dir option is used, the specified directory is not used in any way.

I think it would make sense to have a discussion about what each documentation channel should entail -- e.g., should @rdk/p2rank be self-contained, or should it point to the wiki for turorials? Or, if there are no human resources to keep several documentations up-to-date, I think it would make sense to at least get rid of the obsolete/redundant pages.

David

[skodapetr]

We agreed that the documentation should reflect, and explicitly state, the last release.