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2 changes: 1 addition & 1 deletion .github/workflows/rworkflows_static.yml
Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,7 @@ jobs:
echo "NOT_CRAN=${{ !env.as_cran }}" >> $GITHUB_ENV
shell: bash {0}
- name: ⏬ Checkout repository
uses: actions/checkout@v4
uses: actions/checkout@v6
- name: "\U0001F40D Setup Miniconda"
if: env.miniforge_variant != 'false'
uses: conda-incubator/setup-miniconda@v4
Expand Down
33 changes: 32 additions & 1 deletion NEWS.md
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,8 @@
resources:
- Add `testthat::skip_if_offline()` to all tests whose call stacks may
reach the internet (`test-check_bioc_version.R`, `test-fill_description.R`,
`test-get_authors.R`, `test-get_hex.R`, `test-infer_deps.R`).
`test-get_authors.R`, `test-get_hex.R`, `test-infer_biocviews.R`,
`test-infer_deps.R`).
- Move the existing offline guard up in `test-construct_cont.R` so that
the `versions_explicit = TRUE` branch (which calls `bioc_r_versions()`)
is also skipped when offline.
Expand All @@ -35,6 +36,17 @@
degrade gracefully when offline.
* Add `curl` to `Suggests` to support the new offline guards in examples
and vignettes.
* Vignettes: replace `read.dcf("../DESCRIPTION", ...)` with
`utils::packageDescription("rworkflows", ...)` so the setup chunks no
longer fail under `R CMD check`'s `tools::checkVignettes()`, which
tangles each vignette to a `.R` file and sources it from a temp working
directory where `../DESCRIPTION` does not resolve. The same change is
applied to `inst/templates/{templateR,docker}.Rmd` via a `__PKG__`
placeholder that `use_vignette_getstarted()` / `use_vignette_docker()`
substitute at write time.
* `use_vignette_getstarted()` / `use_vignette_docker()`: raise a clear
error when `package` is `NULL` or empty (previously they silently
produced a malformed file).

## Miscellaneous

Expand All @@ -43,9 +55,28 @@
the action runtime to Node.js 24, which is supported by GitHub-hosted
runners but requires self-hosted runners on a recent `actions/runner`
release.
* Bump `actions/checkout` from `@v4` to `@v6` (the bundled example

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workflow goes from `@v3`). v5 moved the runtime to Node.js 24 (requires
runner >= v2.327.1, satisfied by all GitHub-hosted runners) and v6
persists git auth credentials to a separate `.gitauth` file instead of
`.git/config`; neither change affects this action.
* Forward the `ncpus` input to `grimbough/bioc-actions/setup-bioc@v1` (as
its `Ncpus` input) so non-Linux R installs use the configured parallel
job count instead of the action's default of 3.
* Tests: replace `is_gha()` gates that were guarding internet access
with host-specific `skip_if_offline(host=...)` calls
(`bioconductor.org`, `github.com`, `raw.githubusercontent.com`,
`ghcr.io`) so individual tests skip when their actual remote is
unreachable. This includes the `get_description` Bioc-repo block,
which previously gated on `is_gha() | is_rstudio()` to dodge CRAN
flakiness (#65); it now skips on `bioconductor.org` instead. Each
`skip_if_offline()` is then wrapped in `if (!is_gha())` so GitHub
Actions exercises the network path regardless of the offline probe;
developer machines and CRAN's check farm continue to skip when the
named host is unreachable. `is_gha()` is also retained for the
`construct_conda_yml` env-creation block, where the test is
genuinely GHA-only (creates and leaves a conda env behind, so should
not run on developer machines).

# rworkflows 1.0.11

Expand Down Expand Up @@ -93,7 +124,7 @@

## New features

* New arg for number of cores to use for R package installation (`ncpus`).

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* Add `CODECOV_TOKEN` and `ncpus` to `rworkflows.yml` template.
* Update to `actions/cache@v4` as v3 is marked for deprecation.
## Documentation
Expand Down Expand Up @@ -169,7 +200,7 @@
* Synchronise `rworkflows` package versioning with `rworkflows` action
Release versioning.
* `use_vignette_docker`/`use_vignette_getstarted`
- Autofill `package` arg if not provided.

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## Bug fixes

Expand All @@ -187,7 +218,7 @@

* Add step to enable conda envs: #78
- Add subfunction: `gha_python_versions()` within `construct_runners`
- Add new *action.yml* args:

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[spelling] possible misspelling: args
- `miniforge_variant`
- `miniforge_version`
- `activate_environment`
Expand Down
9 changes: 8 additions & 1 deletion R/use_vignette_docker.R
Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,12 @@ use_vignette_docker <- function(package = names(get_description()),
verbose=TRUE){
# devoptera::args2vars(use_vignette_docker, reassign = TRUE)

force(package)
if (length(package) != 1L || is.na(package) || !nzchar(package)) {
stop("`package` must be a non-empty string. ",
"Could not be inferred from a local DESCRIPTION; ",
"pass `package` explicitly.")
}
#### Check if file exists already ####
if(file.exists(path) &
isFALSE(force_new)){
Expand All @@ -82,8 +88,9 @@ use_vignette_docker <- function(package = names(get_description()),
package = "rworkflows")
#### Edit the yaml header ###
l <- readLines(template_path)
l <- gsub("__PKG__", package, l, fixed = TRUE)
yml_lines <- seq(grep("---",l)[1],
rev(grep("---",l))[1] )
rev(grep("---",l))[1] )
yml <- yaml::read_yaml(text = l[yml_lines])
#### Set params ####
## cont
Expand Down
8 changes: 7 additions & 1 deletion R/use_vignette_getstarted.R
Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,11 @@ use_vignette_getstarted <- function(package = names(get_description()),
# devoptera::args2vars(use_vignette_getstarted, reassign = TRUE)

force(package)
if (length(package) != 1L || is.na(package) || !nzchar(package)) {
stop("`package` must be a non-empty string. ",
"Could not be inferred from a local DESCRIPTION; ",
"pass `package` explicitly.")
}
#### Check if file exists already ####
if(file.exists(path) &
isFALSE(force_new)){
Expand All @@ -38,8 +43,9 @@ use_vignette_getstarted <- function(package = names(get_description()),
package = "rworkflows")
#### Edit the yaml header ###
l <- readLines(template_path)
l <- gsub("__PKG__", package, l, fixed = TRUE)
yml_lines <- seq(grep("---",l)[1],
rev(grep("---",l))[1] )
rev(grep("---",l))[1] )
yml <- yaml::read_yaml(text = l[yml_lines])
## vignette title
yml$title <- title
Expand Down
2 changes: 1 addition & 1 deletion action.yml
Original file line number Diff line number Diff line change
Expand Up @@ -219,7 +219,7 @@ runs:

## Checkout before Miniconda so that environment_file can reference repo files
- name: ⏬ Checkout repository
uses: actions/checkout@v4
uses: actions/checkout@v6

- name: 🐍 Setup Miniconda
if: inputs.miniforge_variant != 'false'
Expand Down
2 changes: 1 addition & 1 deletion inst/example/check_rworkflows-merged.yml
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ jobs:
run: |
curl -fsSL https://deb.nodesource.com/setup_18.x | sudo -E bash -
sudo apt-get install -y nodejs
- uses: actions/checkout@v3
- uses: actions/checkout@v6
- uses: ./rworkflows-merged
with:
run_bioccheck: true
Expand Down
4 changes: 2 additions & 2 deletions inst/templates/docker.Rmd
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
---
title: "Docker/Singularity Containers"
author: "<h4>Authors: <i>`r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`</i></h4>"
author: "<h4>Authors: <i>`r auths <- eval(parse(text = gsub('person','c',utils::packageDescription('__PKG__', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`</i></h4>"
date: "<h4>Vignette updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h4>"
output:
BiocStyle::html_document:
Expand All @@ -24,16 +24,16 @@

```{r setup, include=FALSE}
#### Package name ####
PKG <- read.dcf("../DESCRIPTION", fields = "Package")[1]
PKG <- "__PKG__"

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[lintr] Variable and function name style should match snake_case or symbols.

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[lintr] Variable and function name style should match snake_case or symbols.
library(PKG, character.only = TRUE)
## Docker containers must be lowercase
pkg <- tolower(PKG)
#### Username of DockerHub account ####
docker_org <- params$docker_org
docker_registry <- params$docker_registry

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[lintr] Remove trailing whitespace.

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[lintr] Remove trailing whitespace.
cont <- params$cont

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[lintr] Remove trailing whitespace.

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[lintr] Remove trailing whitespace.
docker_url <- if(grepl("ghcr.io",docker_registry)){

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paste("https://ghcr.io",cont,sep="/")

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} else {
paste("https://hub.docker.com/repository/docker",docker_org,pkg,sep="/")
}
Expand Down
4 changes: 2 additions & 2 deletions inst/templates/templateR.Rmd
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
---
title: "Get Started"
author: "<h4>Authors: <i>`r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`</i></h4>"
author: "<h4>Authors: <i>`r auths <- eval(parse(text = gsub('person','c',utils::packageDescription('__PKG__', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`</i></h4>"
date: "<h4>Vignette updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h4>"
output:
BiocStyle::html_document
Expand All @@ -12,7 +12,7 @@ vignette: >


```{r, echo=FALSE, include=FALSE}
pkg <- read.dcf("../DESCRIPTION", fields = "Package")[1]
pkg <- "__PKG__"
library(pkg, character.only = TRUE)
```

Expand Down
3 changes: 1 addition & 2 deletions tests/testthat/test-bioc_r_versions.R
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
test_that("bioc_r_versions works", {
## Don't run on CRAN servers due to ongoing internet connectivity issues
if(!is_gha()) testthat::skip_if_offline()
if (!is_gha()) testthat::skip_if_offline(host = "bioconductor.org")

ver1 <- bioc_r_versions(bioc_version="devel")
testthat::expect_true(ver1$bioc>="3.17")
Expand Down
3 changes: 1 addition & 2 deletions tests/testthat/test-check_bioc_version.R
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
test_that("check_bioc_version works", {
## Skip if offline: relies on bioc_r_versions() which fetches a remote yaml
if(!is_gha()) testthat::skip_if_offline()
if (!is_gha()) testthat::skip_if_offline(host = "bioconductor.org")

testthat::expect_equal(
check_bioc_version(bioc = "3.17"),
Expand Down
6 changes: 1 addition & 5 deletions tests/testthat/test-check_cont.R
Original file line number Diff line number Diff line change
@@ -1,9 +1,5 @@
test_that("check_cont works", {
## Don't run on CRAN servers due to ongoing internet connectivity issues
if(!is_gha()) {
testthat::skip_if_offline()
testthat::skip_on_cran()
}
if (!is_gha()) testthat::skip_if_offline(host = "ghcr.io")

testthat::expect_no_warning(
check_cont(cont = "bioconductor/bioconductor_docker:devel")
Expand Down
3 changes: 1 addition & 2 deletions tests/testthat/test-check_r_version.R
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
test_that("check_r_version works", {
## Don't run on CRAN servers due to ongoing internet connectivity issues
if(!is_gha()) testthat::skip_if_offline()
if (!is_gha()) testthat::skip_if_offline(host = "bioconductor.org")

testthat::expect_equal(
check_r_version(r = "4.1"),
Expand Down
5 changes: 2 additions & 3 deletions tests/testthat/test-construct_conda_yml.R
Original file line number Diff line number Diff line change
Expand Up @@ -46,9 +46,8 @@ test_that("construct_conda_yml works", {
return_path = TRUE,
save_path = save_path)
testthat::expect_true(file.exists(path2))

## Don't run on CRAN servers due to ongoing internet connectivity issues
if(!is_gha()) testthat::skip_if_offline()

if (!is_gha()) testthat::skip_if_offline(host = "conda.anaconda.org")

# conda <- conda_path()
out <- reticulate::conda_create(environment = path2,
Expand Down
4 changes: 1 addition & 3 deletions tests/testthat/test-construct_cont.R
Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,7 @@ test_that("construct_cont works", {
testthat::expect_equal(cont2[[1]],
paste0(default_registry,"bioconductor/bioconductor_docker:",default_tag))

## Don't run on CRAN servers due to ongoing internet connectivity issues
## (versions_explicit=TRUE / run_check_cont=TRUE both require internet)
if(!is_gha()) testthat::skip_if_offline()
if (!is_gha()) testthat::skip_if_offline(host = "bioconductor.org")

cont3 <- construct_cont(versions_explicit = TRUE)
testthat::expect_true(grepl("bioconductor/bioconductor_docker:RELEASE_*",
Expand Down
3 changes: 1 addition & 2 deletions tests/testthat/test-construct_runners.R
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
test_that("construct_runners works", {
## Don't run on CRAN servers due to ongoing internet connectivity issues
if(!is_gha()) testthat::skip_if_offline()
if (!is_gha()) testthat::skip_if_offline(host = "bioconductor.org")

#### Set up tests ####
run_tests <- function(runners){
Expand Down
3 changes: 1 addition & 2 deletions tests/testthat/test-fill_description.R
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
test_that("fill_description works", {
## Skip if offline: downloads a DESCRIPTION file from GitHub
if(!is_gha()) testthat::skip_if_offline()
if (!is_gha()) testthat::skip_if_offline(host = "github.com")

url <- "https://github.com/neurogenomics/templateR/raw/master/DESCRIPTION"
path <- tempfile(pattern = "DESCRIPTION")
Expand Down
3 changes: 1 addition & 2 deletions tests/testthat/test-get_authors.R
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
test_that("get_authors works", {
## Skip if offline: get_description() may fall back to GitHub for refs
if(!is_gha()) testthat::skip_if_offline()
if (!is_gha()) testthat::skip_if_offline(host = "github.com")

true_auths <- "Brian Schilder, Alan Murphy, Hiranyamaya (Hiru) Dash, Nathan Skene"
#### ref is NULL ####
Expand Down
71 changes: 32 additions & 39 deletions tests/testthat/test-get_description.R
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
skip_if_offline()
if (!is_gha()) testthat::skip_if_offline(host = "github.com")
test_that("get_description works", {

run_tests <- function(dl){
Expand All @@ -22,8 +22,8 @@ test_that("get_description works", {
paths="typo")
d6 <- get_description(refs=NULL,
paths="typo")
d7 <- get_description(refs=NULL,
paths=here::here("DESCRIPTION")
d7 <- get_description(refs=NULL,
paths=system.file("DESCRIPTION", package="rworkflows")
)
d8 <- get_description(refs=c("stats","data.table"),
paths=NULL)
Expand Down Expand Up @@ -56,43 +56,36 @@ test_that("get_description works", {
testthat::expect_null(d6[[1]])


if(is_gha() && testthat::is_testing()){
testthat::expect_equal(d7[[1]],
d1[[1]])
} else{
message("Skipping test.")
}

testthat::expect_equal(d7[[1]],
d1[[1]])

#### Search CRAN/Bioc repos ####
## Don't run on CRAN due to issues on their server:
## https://github.com/neurogenomics/rworkflows/issues/65
if (is_gha() | is_rstudio()) {
#### Run first time ####
d13a <- get_description(refs="ABSSeq",
db = rworkflows::biocpkgtools_db,
use_repos = TRUE)
testthat::expect_equal(d13a[[1]],
d1[[1]])
#### Rerun to use stored DESCRITPION files ####
d13b <- get_description(refs="ABSSeq",
db = rworkflows::biocpkgtools_db,
use_repos = TRUE)
testthat::expect_equal(d13b[[1]],
d1[[1]])
#### Unable to find pkg info ####
testthat::expect_null(
get_description(refs="typooo",
db = rworkflows::biocpkgtools_db,
use_repos = TRUE)
)
#### Gather remote data ####
d13c <- get_description(refs="ABSSeq",
db = NULL,
use_repos = TRUE,
repo = "BioCsoft")
testthat::expect_equal(d13c[[1]],
d1[[1]])
}
if (!is_gha()) testthat::skip_if_offline(host = "bioconductor.org")
#### Run first time ####
d13a <- get_description(refs="ABSSeq",
db = rworkflows::biocpkgtools_db,
use_repos = TRUE)
testthat::expect_equal(d13a[[1]],
d1[[1]])
#### Rerun to use stored DESCRITPION files ####
d13b <- get_description(refs="ABSSeq",
db = rworkflows::biocpkgtools_db,
use_repos = TRUE)
testthat::expect_equal(d13b[[1]],
d1[[1]])
#### Unable to find pkg info ####
testthat::expect_null(
get_description(refs="typooo",
db = rworkflows::biocpkgtools_db,
use_repos = TRUE)
)
#### Gather remote data ####
d13c <- get_description(refs="ABSSeq",
db = NULL,
use_repos = TRUE,
repo = "BioCsoft")
testthat::expect_equal(d13c[[1]],
d1[[1]])
#### Search GitHub repos ####
d14 <- get_description(refs="neurogenomics/orthogene",
paths=NULL,
Expand Down
17 changes: 6 additions & 11 deletions tests/testthat/test-get_hex.R
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
test_that("get_hex works", {
## Skip if offline: get_hex() validates URLs over the network
if(!is_gha()) testthat::skip_if_offline()
if (!is_gha()) testthat::skip_if_offline(host = "github.com")

#### When repo name provided ####
hex1 <- get_hex(refs="neurogenomics/rworkflows")
Expand All @@ -9,14 +8,10 @@ test_that("get_hex works", {
testthat::expect_equal(hex2$rworkflows,
hex1$`neurogenomics/rworkflows`)
#### When DESCRIPTION path provided ####
hex3 <- get_hex(refs=NULL,
paths=here::here("DESCRIPTION"))
if(is_gha() && testthat::is_testing()){
testthat::expect_equal(hex3[[1]],
hex1[[1]])
} else {
message("Skipping test.")
}
hex3 <- get_hex(refs=NULL,
paths=system.file("DESCRIPTION", package="rworkflows"))
testthat::expect_equal(hex3[[1]],
hex1[[1]])
#### When neither refs nor paths provided ####
hex4 <- get_hex(refs=NULL,
paths=NULL)
Expand All @@ -41,7 +36,7 @@ test_that("get_hex works", {
hex1[[1]])
#### When paths length > refs length ####
hex7 <- get_hex(refs="neurogenomics/rworkflows",
paths = rep(here::here("DESCRIPTION"),2))
paths = rep(system.file("DESCRIPTION", package="rworkflows"),2))
testthat::expect_equal(hex7[[1]],
hex1[[1]])
#### Can't find URL: but URL inferred ####
Expand Down
2 changes: 1 addition & 1 deletion tests/testthat/test-get_yaml.R
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
test_that("get_yaml works", {
if(!is_gha()) testthat::skip_if_offline()
if (!is_gha()) testthat::skip_if_offline(host = "github.com")

testthat::expect_type(
rworkflows:::get_yaml(template = "rworkflows"),
Expand Down
3 changes: 1 addition & 2 deletions tests/testthat/test-gha_python_versions.R
Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
test_that("gha_python_versions works", {
## Don't run on CRAN servers due to ongoing internet connectivity issues
if(!is_gha()) testthat::skip_if_offline()
if (!is_gha()) testthat::skip_if_offline(host = "raw.githubusercontent.com")

testthat::expect_equal(gha_python_versions(python_version = "3.11"),"3.11")
testthat::expect_equal(gha_python_versions(python_version = "3.x"),"3.x")
Expand Down
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