phuse-org/devops

Home of the Pharma DevOps Working Group, providing everything you need for R and Python codebases used for clinical reporting

devops's Issues

The validator doesn't work due to a font issue

Currently this doesn't work due to an issue with the gh-action: https://phuse-org.github.io/devops/content/cicdworkflows-enhanced/posts/validate/validate.html

This needs to be closed: insightsengineering/thevalidatoR#66

Add existing admiral content

Using the admiral content as a starter for a pan-packages set of guidance.

depends on #2

Could we identify an incoming package to work through the site contents with?

Discussed in #24

^{Originally posted by epijim May 6, 2024}
@bms63 suggested admiralobesity? @cicdguy agreed.

Submit phuse abstract

Aim to submit abstract to PHUSE US Connect about this working group, and with content from the landscaping of where we are today with CICD

Itemizing capabilities

After an initial look, the simplest use case seems to be very well covered by usethis::use_github_action, which drastically simplifies the maintenance and setup.

I'd consider any deviation from this should show some considerable value-add since it immediately means breaking with very widely used best practices.

I'm going to kick off the discussion with what I see as the matrix of actions that we might consider. Feel free to suggest additional behaviors and the scopes where they should apply.

behavior	scope	tool/action
R CMD check	minimum	usethis::use_github_action("check-standard")
	recommended	usethis::use_github_action("check-full")
Documentation	all	usethis::use_github_action("pkgdown")
Testing & Coverage	all	usethis::use_github_action("test-coverage")

Integrate into pharamverse.org

Discuss with technical working group (who have pharmaverse website) how we can integrate this project.

Pick quarto template and add to this repo

Dinakar mentioned he had a great new template. Aim is to get this into main.

@dinakar - as the first bit of code going in, I'll defer to you if you want to add branch protections (maybe not needed yet as the site isn't public?)

Do we want folks to be able to comment on the site? I feel like that should be disabled?

(from Ben)

Define a 'minimum' and 'recommended' list

Early feedback from one pharmaverse package we we need to separate out the packages from what are really the core CICD needed to have a robust release, and what are nice to haves.

Aim in this issue is to define our initial list (updating here in the desc:

Minimum

• Generate and deploy documentation to a location outside main branch when main updated (to prevent repo bloat from artifacts)
• Ensure man pages are always upto date on main and devel
• Check links on PR to main, to ensure docs have working links each time a release is made
• Check unit tests using container with CRAN + leading edge of r-universe pharmaverse page
• Report code coverage of main and display as badge in repo

Suggested

• Ability to fail PR to main if code coverage below certain value
• lint R code to help with consistency | run styler
• Check unit tests using container with CRAN + specific cohort of related R packages
• Generate an example validation report against rocker + pharmaverse when a tag/release is made
• Render README
• Check spelling

Need to add example on how to use R CMD CHECK against bleeding edge repos

Currently we have:

How do I set it up?

Below is an example of using this gh-action whenever someone tries to make PR into your main or devel branch or updates the branch. We recomend you use this on both main and devel branches, as it will help you catch issues before they get into your main branch.

name: Run R-CMD-check
# sourced from phuse-org/devops-toolkit

on:
  pull_request:
    types:
      - opened
      - synchronize
      - reopened
      - ready_for_review
    branches:
      - main
  push:
    branches:
      - main
  workflow_dispatch:

jobs:
  check:
    name: Check
    uses: phuse-org/devops-toolkit/.github/workflows/R-CMD-check.yml@main

The deets

Advanced use

TODO: Add here how to also run against pharmaverse's r-universe latest & the latest release of PPM packages.

Where to 'store' gh-actions in our list

Currently we recommend and maintain gh-actions in two locations:

• insightsengineering/r.pkg.template/.github/workflows
• pharmaverse/admiralci

This needs be simplified - as it's confusing to look at the huge battery of CICD on Nest and admiral, and understand why they did things slightly differently, and which CICD is really needed and why.

@cicdguy and @bms63 my suggestion is:

• Can we avoid duplicating CICD that already works? e.g. content in the tic package (https://docs.ropensci.org/tic/) and only if a gh-action is missing
• Place all our gh-actions in a repo pharmaverse/cicd?

Dinakar - what are our thoughts?

codecoverage isn't what the action actually does

https://phuse-org.github.io/devops/content/cicdworkflows-minimum/posts/code-coverage.html

Pull together list of relevant content

• trainings (phuse)
• other packages tools
• generic non-pharma tools

And add into #3

giscus works locally, but not on the deployed site!