Adding `README` to packages

PecanProject / pecan

The Predictive Ecosystem Analyzer (PEcAn) is an integrated ecological bioinformatics toolbox.

www.pecanproject.org

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Adding `README` to packages #3100

Closed meetagrawal09 closed 1 year ago

meetagrawal09 commented 1 year ago

Description

The PR aims to add a README file to all packages as part of prepping packages for CRAN This PR fixes #3043

Review Time Estimate

[ ] Immediately
[ ] Within one week
[X] When possible

Types of changes

[X] 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.
[ ] My name is in the list of CITATION.cff
[ ] I have updated the CHANGELOG.md.
[ ] I have updated the documentation accordingly.
[X] I have read the CONTRIBUTING document.
[ ] I have added tests to cover my changes.
[ ] All new and existing tests passed.

meetagrawal09 commented 1 year ago

The work on this pull request is in-progress. This PR will try to add a README to all the packages which already don't have one.

Currently working on adding these to pecan/models. I would need some help on the below issues :

What all sections do we require in the README for a model other than those which have been auto-generated here that is INSTALLATION and EXAMPLE
Where can I find relevant information for each of these sections ( I did look up some information at Link )

@Aariq, @mdietze, @infotroph if you can please help me out with this.

Aariq commented 1 year ago

Here's an example of installation instructions for PEcAn.BIOCRO:

You can install the development version of PEcAn.BIOCRO from r-universe like so:

# Enable repository from pecanproject
options(repos = c(
  pecanproject = 'https://pecanproject.r-universe.dev',
  CRAN = 'https://cloud.r-project.org'))
# Download and install PEcAn.BIOCRO in R
install.packages('PEcAn.BIOCRO')

Or you can install directly from GitHub with the remotes package like so:

library(remotes)
install_github('pecanproject/pecan',  subdir = "models/biocro")

Aariq commented 1 year ago

For the example section, you could see if the package has a vignette and include a simplified version or maybe just leave that section empty for now.

meetagrawal09 commented 1 year ago

@Aariq can you please have a look at this failing check. Description put up below.

Error(s) in re-building vignettes:
    ...
  --- re-building ‘betydb_access.Rmd’ using rmarkdown
  Error: processing vignette 'betydb_access.Rmd' failed with diagnostics:
  The function xfun::isFALSE() will be deprecated in the future. Please consider using base::isFALSE(x) or identical(x, FALSE) instead.
  --- failed re-building ‘betydb_access.Rmd’

  --- re-building ‘create_sites.geometry.Rmd’ using rmarkdown
  Error: processing vignette 'create_sites.geometry.Rmd' failed with diagnostics:
  The function xfun::isFALSE() will be deprecated in the future. Please consider using base::isFALSE(x) or identical(x, FALSE) instead.
  --- failed re-building ‘create_sites.geometry.Rmd’

meetagrawal09 commented 1 year ago

@Aariq I have added a README file to all the model packages. The below listed packages already contained a README file :

models/cable
models/jules
models/ldndc
models/linkages
models/maat
models/sibcasa
models/stics

Is there a need to update those just to follow a pattern like the newly added README files ( retaining their current data in relevant sections ) ?

Aariq commented 1 year ago

@Aariq can you please have a look at this failing check. Description put up below.

Error(s) in re-building vignettes:
    ...
  --- re-building ‘betydb_access.Rmd’ using rmarkdown
  Error: processing vignette 'betydb_access.Rmd' failed with diagnostics:
  The function xfun::isFALSE() will be deprecated in the future. Please consider using base::isFALSE(x) or identical(x, FALSE) instead.
  --- failed re-building ‘betydb_access.Rmd’

  --- re-building ‘create_sites.geometry.Rmd’ using rmarkdown
  Error: processing vignette 'create_sites.geometry.Rmd' failed with diagnostics:
  The function xfun::isFALSE() will be deprecated in the future. Please consider using base::isFALSE(x) or identical(x, FALSE) instead.
  --- failed re-building ‘create_sites.geometry.Rmd’

Sorry, I have no clue. xfun::isFALSE() doesn't appear in those vignettes, and xfun isn't even a direct dependency, so must be buried in a function somewhere. My guess is it isn't something we can fix.

meetagrawal09 commented 1 year ago

I've added a README to all the packages Would like to get a review on this PR

meetagrawal09 commented 1 year ago

@mdietze this PR is ready for a merge.