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https://github.com/pharmaverse/admiralci

CI/CD workflows used across the admiral family of packages
https://github.com/pharmaverse/admiralci

actions admiral cicd clinical-trials r-package workflows

Last synced: 11 days ago
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CI/CD workflows used across the admiral family of packages

Host: GitHub
URL: https://github.com/pharmaverse/admiralci
Owner: pharmaverse
License: other
Created: 2022-07-28T15:48:59.000Z (over 2 years ago)
Default Branch: main
Last Pushed: 2024-07-23T12:56:48.000Z (5 months ago)
Last Synced: 2024-07-24T08:07:53.056Z (5 months ago)
Topics: actions, admiral, cicd, clinical-trials, r-package, workflows
Language: R
Homepage: https://pharmaverse.github.io/admiralci
Size: 10.1 MB
Stars: 13
Watchers: 3
Forks: 4
Open Issues: 11
Metadata Files:
- Readme: README.Rmd
- License: LICENSE.md
- Codeowners: .github/CODEOWNERS

Awesome Lists containing this project

README

        ---

title: "CI/CD Workflows for Admiral R Packages"

output: md_document

date: '2022-08-03'

---

```{r setup, include=FALSE}

knitr::opts_chunk$set(echo = TRUE)

link <- function(text, url) {

  return(

    paste0(

      "[", text, "]",

      "(", url, ")"

    )

  )

}

dyn_link <- function(text,

                     base_url,

                     relative_url = "",

                     # Change to TRUE when admiral adopts multiversion docs

                     is_multiversion = FALSE,

                     multiversion_default_ref = "main") {

  url <- paste(base_url, relative_url, sep = "/")

  if (is_multiversion) {

    url <- paste(

      base_url,

      Sys.getenv("BRANCH_NAME", multiversion_default_ref),

      relative_url,

      sep = "/"

    )

  }

  return(link(text, url))

}

# Other variables

admiralci_homepage <- "https://pharmaverse.github.io/admiralci"

```

# Purpose of admiralci

![](man/figures/admiralci_hex.png){width=30% height=30%}

This repository contains GitHub Actions continuous integration/continuous delivery (CI/CD) workflows, most of which are used by [`admiral`](https://github.com/pharmaverse/admiral) and its extensions.

Workflows defined here are responsible for assuring high package quality standards without compromising performance, security, or reproducibility.

Please refer to the [`.github/workflows`](.github/workflows) directory to view the source code for the GitHub Actions workflows.

Notes :

- Some workflows are using github actions from [InsightsEngineering](https://github.com/insightsengineering/) group.

- Most of the workflows are sharing the same steps (see [Common workflows structure](https://pharmaverse.github.io/admiralci/articles/common_structure.html)) (boilerplate code)

# Available workflows

## Workflows triggered by Admiral MR (feature branch to main branch)

### Check Templates

- [Link to workflow code (yml file)](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/check-templates.yml)

- [Link to the documentation](`r paste0(admiralci_homepage, "/articles/check-templates.html")`)

### Lintr

- [Link to workflow code (yml file)](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/lintr.yml)

- [Link to the documentation](`r paste0(admiralci_homepage, "/articles/lintr.html")`)

### Man Pages

- [Link to workflow code (yml file)](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/man-pages.yml)

- [Link to the documentation](`r paste0(admiralci_homepage, "/articles/man-pages.html")`)

### R CMD CHECKS

- [Link to workflow code (yml file)](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/r-cmd-check.yml)

- [Link to the documentation](`r paste0(admiralci_homepage, "/articles/r-cmd-checks.html")`)

### Check Templates

- [Link to workflow code (yml file)](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/spellchecks.yml)

- [Link to the documentation](`r paste0(admiralci_homepage, "/articles/spellchecks.html")`)

### Code Coverage

- [Link to workflow code (yml file)](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/code-coverage.yml)

- [Link to the documentation](`r paste0(admiralci_homepage, "/articles/code-coverage.html")`)

### Readme Render

- [Link to workflow code (yml file)](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/readme-render.yml)

- [Link to the documentation](`r paste0(admiralci_homepage, "/articles/readme-render.html")`)

### Style

- [Link to workflow code (yml file)](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/style.yml)

- [Link to the documentation](`r paste0(admiralci_homepage, "/articles/style.html")`)

## Workflows trigger by a new release

### Validation

- [Link to workflow code (yml file)](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/r-pkg-validation.yml)

- [Link to the documentation](`r paste0(admiralci_homepage, "/articles/validation.html")`)

### Pkgdown

- [Link to workflow code (yml file)](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/pkgdown.yml)

- [Link to the documentation](`r paste0(admiralci_homepage, "/articles/pkgdown.html")`)

## cron workflows

### Push Docker Image

- [Link to workflow code (yml file)](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/push-docker-image.yml)

- [Link to the documentation](`r paste0(admiralci_homepage, "/articles/push-docker.html")`)

### Cran Status

- [Link to workflow code (yml file)](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/cran-status.yml)

- [Link to the documentation](`r paste0(admiralci_homepage, "/articles/cran-status.html")`)

### Check R Tags

- [Link to workflow code (yml file)](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/check-r-tags.yml)

- [Link to the documentation](`r paste0(admiralci_homepage, "/articles/check-r-tags.html")`)

# How to use these workflows?

## Reuse (recommended)

You could add just _one_ file called `.github/workflows/common.yml` to directly import these workflows while receiving the latest updates and enhancements, given that the workflows defined in this repository are reusable via the [`workflow_call`][workflow_call] GitHub Actions event.

The contents of the `.github/workflows/common.yml` file are available in the [`common.yml.inactive`](https://github.com/pharmaverse/admiralci/blob/main/.github/workflows/common.yml.inactive) file in this repository. Feature flags in the form of `workflow_call` inputs are available for customization purposes. Feature flags are documented in the same file - look for the `env:` and `with:` hashes in the file for feature flags.

## Copy as-is (not recommended)

Alternatively, if you want a high level of customization, you could simply copy the workflows as-is from this repository to your repository and modify them to your liking.

We do not recommand this approach. For example, you might miss some updated or even bugs fixes from `admiralci` workflows. If you need some updates in some existing workflows, please [raise an issue](https://github.com/pharmaverse/admiralci/issues).

## Where to see these workflows in action?

### Pull Request

At the bottom of a pull request, you can check on the status of each workflow:

![](man/figures/pr_workflows.jpg)

### Actions Tab

Alternatively, you can check on the workflows on the Actions tab in the repository as well:

![](man/figures/actions_tab_workflows.jpg)

Most of our workflows are using Github Marketplace actions, referenced bellow :

- [InsightsEngineering](https://github.com/insightsengineering)

- [r-lib-actions](https://github.com/r-lib/actions)

- [sd-action](https://github.com/marketplace/actions/staged-dependencies-action)

- [sd-repo](https://github.com/openpharma/staged.dependencies)

- [lychee](https://github.com/lycheeverse/lychee)

- [covr](https://covr.r-lib.org/)

- [lintr](https://lintr.r-lib.org/)

- [pkgdown](https://pkgdown.r-lib.org/)

- [multi-version-docs](https://github.com/marketplace/actions/r-pkgdown-multi-version-docs)

- [validation](https://github.com/marketplace/actions/r-package-validation-report)

- [spelling](https://docs.ropensci.org/spelling/)

- [styler](https://styler.r-lib.org/)

- [workflow_call](https://docs.github.com/en/actions/using-workflows/reusing-workflows)