generated from pharmaverse/admiraltemplate
-
Notifications
You must be signed in to change notification settings - Fork 4
/
Copy pathREADME.Rmd
172 lines (118 loc) · 7.68 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
---
title: "CI/CD Workflows for Admiral R Packages"
output: md_document
date: '2022-08-03'
---
<!-- Please do not edit the README.md file as it is auto-generated. Only edit the README.Rmd file -->
```{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
{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 tends to be use by other packages (`oak` package for example). A global repository at Pharmaverse organization level will be set-up to host all common workflows for pharmaverse packages (Beyond Admiral uses cases).
This package will then probably be replaced by this global Pharmaverse repository in the future. -->
- 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.
<!-- TODO: update common.inactive taking the one from admiral because it's quite outdated .. -->
## 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:
### Actions Tab
Alternatively, you can check on the workflows on the Actions tab in the repository as well:
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)