Added new Rmd template for basic PEcAn workflow to PEcAn.all package

[dlebauer]

Description

Added a template for a basic PEcAn workflow.

Motivation and Context

Will help users make the transition from Web to interactive R session by adding an Rmarkdown template that users can use to create a new workflow from within the Rstudio interface.

I didn't know where to put the documentation, but it would be

In Rstudio with the PEcAn.all package loaded

library(PEcAn.all)

• File --> new file --> Rmarkdown --> From Template
• Choose the PEcAn workflow template.
• You can start with a pecan.xml file from the web interface or the tests/ directory and modify as needed

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My change requires a change to the documentation.
• I have updated the CHANGELOG.md.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.

[tonygardella]

Super useful! Need the do.conversions and Traits step.

[tonygardella]

Do conversions:

settings <- PEcAn.utils::do_conversions(settings)

Traits:

settings <- PEcAn.DB::runModule.get.trait.data(settings)
PEcAn.settings::write.settings(settings, outputfile='pecan.TRAIT.xml')

[mdietze]

Let's discuss this at next week's meeting. We had previously worked hard to migrate from having 3 different versions of workflow.R to having having a single canonical version because having multiple workflows was causing a ton of problems both for development (having to implement the same thing in multiple places) and debugging (failing to implement the same thing in multiple places). The fact that @tonygardella already identified such a discrepancy within the originating PR is pretty indicative that the proposed addition will revert us to that condition again.

[dlebauer]

@mdietze I thought about discussing first but wanted to put this up there as a starting point.

Perhaps if we really make this bare-bones and/or automatically parse lines from workflow.R during one of the make steps, we could keep them consistent. But I think that having an Rmd template is a fundamentally different use case than having an automated R script. The scripts/workflow*.R files are not user friendly for interactively debuging a workflow, or for keeping track of science methods and rationale , notes etc. and ultimately publishing a workflow as a reproducible(ish?) analysis. The status and if/else get in the way.

PS we currently have four workflow scripts ...

[tonygardella]

@dlebauer I'll bring this up next week in the weekly discussion. I ultimately think we just need a page in documentation outlining how to move to using pecan through Rstudio/R.

[infotroph]

Without prejudice to the good points above about whether we want multiple workflows, a suggestion: If we do want this template, Would it make sense for it to live in PEcAn.workflow instead of PEcAn.all?

[tonygardella]

@dlebauer @infotroph @mdietze I'm going to close this and open this as an issue for discussion. I like the idea of having a template to make it easy for people to run pecan outside of the web interface and perhaps direct people on where people can customize their runs. However, I don't like the idea of having to maintain multiple workflow scripts.

I personally think we should have this live in documentation as a page describing and breaking down workflow.R so people can do a basic run from the command line or from within R studio.

[dlebauer]

I am re-opening because I don't think that the underlying problem has been resolved.

[github-actions]

This PR is stale because it has been open 365 days with no activity.

[infotroph]

@dlebauer OK to close this now that we have Rmd demos?

[dlebauer]

It's different than a demo

[infotroph]

Then please make changes to address the comments from eight years ago, all of which seem like reasonable requests to me.

[dlebauer]

@infotroph ok will implement Tony's suggestions to add:

settings <- PEcAn.utils::do_conversions(settings)

settings <- PEcAn.DB::runModule.get.trait.data(settings)
PEcAn.settings::write.settings(settings, outputfile = 'pecan.TRAIT.xml')

And to be consistent with other demos will migrate to qmd.

There are other suggestions and ideas from long ago, but I am not sure if any necessary - this is distinct from the demo / tutorials, and is neither documentation nor a script.