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Bump required R version to R 4.0.0 #584

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Bump required R version to R 4.0.0 #584

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dfc43ad
Bump required R version to R 4.0.0
hadley Nov 7, 2024
5bc1ac7
`use_tidy_github_actions()`
hadley Nov 7, 2024
5d805b3
Restore accidentally deleted code
hadley Nov 8, 2024
a74b364
Merged origin/main into R-4.0.0
hadley Nov 8, 2024
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27 changes: 14 additions & 13 deletions .github/workflows/R-CMD-check.yaml
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Expand Up @@ -10,7 +10,9 @@ on:
pull_request:
branches: [main, master]

name: R-CMD-check
name: R-CMD-check.yaml

permissions: read-all

jobs:
R-CMD-check:
Expand All @@ -25,24 +27,22 @@ jobs:
- {os: macos-latest, r: 'release'}

- {os: windows-latest, r: 'release'}
# Use 3.6 to trigger usage of RTools35
- {os: windows-latest, r: '3.6'}
# use 4.1 to check with rtools40's older compiler
- {os: windows-latest, r: '4.1'}

- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
- {os: ubuntu-latest, r: 'release'}
- {os: ubuntu-latest, r: 'oldrel-1'}
- {os: ubuntu-latest, r: 'oldrel-2'}
- {os: ubuntu-latest, r: 'oldrel-3'}
- {os: ubuntu-latest, r: 'oldrel-4'}
# use 4.0 or 4.1 to check with rtools40's older compiler
- {os: windows-latest, r: 'oldrel-4'}

- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
- {os: ubuntu-latest, r: 'release'}
- {os: ubuntu-latest, r: 'oldrel-1'}
- {os: ubuntu-latest, r: 'oldrel-2'}
- {os: ubuntu-latest, r: 'oldrel-3'}
- {os: ubuntu-latest, r: 'oldrel-4'}

env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-pandoc@v2

Expand All @@ -60,3 +60,4 @@ jobs:
- uses: r-lib/actions/check-r-package@v2
with:
upload-snapshots: true
build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
8 changes: 5 additions & 3 deletions .github/workflows/pkgdown.yaml
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Expand Up @@ -9,7 +9,9 @@ on:
types: [published]
workflow_dispatch:

name: pkgdown
name: pkgdown.yaml

permissions: read-all

jobs:
pkgdown:
Expand All @@ -22,7 +24,7 @@ jobs:
permissions:
contents: write
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-pandoc@v2

Expand All @@ -41,7 +43,7 @@ jobs:

- name: Deploy to GitHub pages 🚀
if: github.event_name != 'pull_request'
uses: JamesIves/github-pages-deploy-action@v4.4.1
uses: JamesIves/github-pages-deploy-action@v4.5.0
with:
clean: false
branch: gh-pages
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12 changes: 9 additions & 3 deletions .github/workflows/pr-commands.yaml
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Expand Up @@ -4,7 +4,9 @@ on:
issue_comment:
types: [created]

name: Commands
name: pr-commands.yaml

permissions: read-all

jobs:
document:
Expand All @@ -13,8 +15,10 @@ jobs:
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
permissions:
contents: write
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: r-lib/actions/pr-fetch@v2
with:
Expand Down Expand Up @@ -50,8 +54,10 @@ jobs:
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
permissions:
contents: write
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: r-lib/actions/pr-fetch@v2
with:
Expand Down
24 changes: 18 additions & 6 deletions .github/workflows/test-coverage.yaml
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Expand Up @@ -6,7 +6,9 @@ on:
pull_request:
branches: [main, master]

name: test-coverage
name: test-coverage.yaml

permissions: read-all

jobs:
test-coverage:
Expand All @@ -15,14 +17,15 @@ jobs:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true

- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::covr, any::xml2
needs: coverage

- name: Setup
Expand All @@ -32,23 +35,32 @@ jobs:

- name: Test coverage
run: |
covr::codecov(
cov <- covr::package_coverage(
quiet = FALSE,
clean = FALSE,
install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
)
covr::to_cobertura(cov)
shell: Rscript {0}

- uses: codecov/codecov-action@v4
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What is the advantage of using the codecov-action vs having covr upload to codecov directly?

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I don't know 😞 I just updated using our standard scripts. @gaborcsardi might know.

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covr uses the old protocol, which does not support organization level codecov tokens.

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🤔

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@jimhester jimhester Nov 8, 2024 •
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Hmm, I guess due to this https://codecovpro.zendesk.com/hc/en-us/articles/21567817259163-Error-finding-token-when-trying-to-upload, but I have always just added the codecov app and never had any problems with the automatic token.

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@gaborcsardi gaborcsardi Nov 8, 2024 •
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Well, you don't have any problems if you don't look at the results. :) Upload failures do not fail the workflow run, so you typically do not notice them:

[1] "Rate limit reached. Please upload with the Codecov repository upload token to resolve issue. Expected time to availability: 1300s."

https://github.com/r-lib/covr/actions/runs/11729639825/job/32675733827#step:6:88

The last successful upload for covr was ~7 months ago:
https://app.codecov.io/gh/r-lib/covr/commits

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I seem to no longer have access to the admin settings for this repo, so can't comment on if codecov app is still installed for this repo or the r-lib org in general.

But I don't really like going through the cobutura codepath for repositories by default, it adds some additional complexity and also a xml2 dependency. Additionally the output is really geared towards more java style classes, and doesn't perfectly align with R package organization. Additionally doesn't relying on secrets mean that forks are no longer supported?

I am not sure why the existing path would work differently with organization tokens vs the action? Aren't they both changing the secret into an environment variable in the same way?

with:
fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
file: ./cobertura.xml
plugin: noop
disable_search: true
token: ${{ secrets.CODECOV_TOKEN }}

- name: Show testthat output
if: always()
run: |
## --------------------------------------------------------------------
find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash

- name: Upload test results
if: failure()
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: coverage-test-failures
path: ${{ runner.temp }}/package
2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -42,7 +42,7 @@ Description: Track and report code coverage for your package and (optionally)
URL: https://covr.r-lib.org, https://github.com/r-lib/covr
BugReports: https://github.com/r-lib/covr/issues
Depends:
R (>= 3.1.0),
R (>= 4.0.0),
methods
Imports:
digest,
Expand Down
4 changes: 0 additions & 4 deletions R/utils.R
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Expand Up @@ -200,10 +200,6 @@ per_line <- function(coverage) {
class = "line_coverages")
}

if (getRversion() < "3.2.0") {
isNamespaceLoaded <- function(x) x %in% loadedNamespaces()
}

is_windows <- function() {
.Platform$OS.type == "windows"
}
Expand Down
4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -2,7 +2,7 @@

<!-- badges: start -->
[![R-CMD-check](https://github.com/r-lib/covr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/r-lib/covr/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/r-lib/covr/branch/master/graph/badge.svg)](https://app.codecov.io/gh/r-lib/covr?branch=master)
[![Codecov test coverage](https://codecov.io/gh/r-lib/covr/graph/badge.svg)](https://app.codecov.io/gh/r-lib/covr)
[![CRAN version](http://www.r-pkg.org/badges/version/covr)](https://cran.r-project.org/package=covr)
<!-- badges: end -->

Expand All @@ -18,7 +18,7 @@ install.packages("covr")
devtools::install_github("r-lib/covr")
```

The easiest way to setup covr on [Github Actions](https://github.com/r-lib/actions/tree/v2-branch/examples#test-coverage-workflow)
The easiest way to setup covr on [Github Actions](https://github.com/r-lib/actions/tree/v2-branch/examples#test-coverage-workflow)
is with [usethis](https://github.com/r-lib/usethis).

```r
Expand Down
12 changes: 0 additions & 12 deletions tests/testthat/test-utils.R
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Expand Up @@ -30,18 +30,6 @@ test_that("it works as expected", {
})

context("get_source_filename")
test_that("it works", {
# R 4.0.0 changes this behavior so `getSrcFilename()` will actually return
# "test-utils.R"

skip_if(getRversion() >= "4.0.0")

x <- eval(bquote(function() 1))

expect_identical(getSrcFilename(x), character())
expect_identical(get_source_filename(x), "")
})

test_that("per_line removes blank lines and lines with only punctuation (#387)", {
skip_on_cran()

Expand Down
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