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Merge pull request #92 from inbo/hotfix
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ThierryO committed May 8, 2023
2 parents 33fdf6c + ede353a commit 63e582a
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16 changes: 8 additions & 8 deletions .Rbuildignore
@@ -1,21 +1,21 @@
^_pkgdown.yml$
CODE_OF_CONDUCT.md
CONTRIBUTING.md
Dockerfile
^.*\.Rproj$
^CITATION\.cff$
^LICENSE.md$
^README\.Rmd$
^\.Rproj\.user$
^\.github$
^\.httr-oauth$
^\.Rproj\.user$
^\.zenodo\.json$
^_pkgdown.yml$
^checklist.yml$
^CITATION\.cff$
^codecov\.yml$
^data-raw$
^docs$
^LICENSE.md$
^man-roxygen$
^pkgdown$
^README\.Rmd$
CODE_OF_CONDUCT.md
CONTRIBUTING.md
create_docker.sh
docker
Dockerfile
docs
4 changes: 2 additions & 2 deletions .github/CODE_OF_CONDUCT.md
Expand Up @@ -8,7 +8,7 @@ We are committed to making participation in this project a harassment-free exper
everyone, regardless of level of experience, gender, gender identity and expression,
sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.

Examples of unacceptable behavior by participants include the use of sexual language or
Examples of unacceptable behaviour by participants include the use of sexual language or
imagery, derogatory comments or personal attacks, trolling, public or private harassment,
insults, or other unprofessional conduct.

Expand All @@ -17,7 +17,7 @@ commits, code, wiki edits, issues, and other contributions that are not aligned
Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed
from the project team.

Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by
Instances of abusive, harassing, or otherwise unacceptable behaviour may be reported by
opening an issue or contacting one or more of the project maintainers.

This Code of Conduct is adapted from the Contributor Covenant
Expand Down
14 changes: 7 additions & 7 deletions .github/CONTRIBUTING.md
Expand Up @@ -3,22 +3,22 @@
### Fixing typos

Small typos or grammatical errors in documentation may be edited directly using the GitHub web interface, so long as the changes are made in the _source_ file.
E.g. edit a roxygen comment in a `.R` file below `R/`, not in an `.Rd` file below `man/`.
E.g. edit a `roxygen2` comment in a `.R` file below `R/`, not in an `.Rd` file below `man/`.

### Prerequisites

Before you make a substantial pull request, you should always file an issue and make sure someone from the team agrees that it’s a problem.
If you’ve found a bug, create an associated issue and illustrate the bug with a minimal [reprex](https://www.tidyverse.org/help/#reprex).
If you’ve found a bug, create an associated issue and illustrate the bug with a minimal [reproducible example](https://www.tidyverse.org/help/#reprex).

### Pull request process

* We recommend that you create a Git branch for each pull request (PR).
* Look at the GitHub Actions build status before and after making changes.
The `README` should contain badges for any continuous integration services used by the package.
* We require the tidyverse [style guide](http://style.tidyverse.org).
You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.
* We use [roxygen2](https://cran.r-project.org/package=roxygen2).
* We use [testthat](https://cran.r-project.org/package=testthat).
* We require the `tidyverse` [style guide](http://style.tidyverse.org).
You can use the [`styler`](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.
* We use [`roxygen2`](https://cran.r-project.org/package=roxygen2).
* We use [`testthat`](https://cran.r-project.org/package=testthat).
Contributions with test cases included are easier to accept.
* For user-facing changes, add a bullet to the top of `NEWS.md` below the current development version header describing the changes made followed by your GitHub username, and links to relevant issue(s)/PR(s).

Expand All @@ -36,4 +36,4 @@ email is totally warranted if it's a sensitive problem of any kind.

### Thanks for contributing!

This contributing guide is adapted from the tidyverse contributing guide available at https://raw.githubusercontent.com/r-lib/usethis/master/inst/templates/tidy-contributing.md
This contributing guide is adapted from the `tidyverse` contributing guide available at https://raw.githubusercontent.com/r-lib/usethis/master/inst/templates/tidy-contributing.md
11 changes: 5 additions & 6 deletions .github/workflows/check_on_branch.yml
Expand Up @@ -5,17 +5,16 @@ on:
- master
- ghpages

name: "check package"
name: "check package with checklist"

jobs:
check-package:
runs-on: ubuntu-latest
name: "check package"
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
permissions:
contents: read
steps:
- uses: inbo/actions/check_pkg@master
with:
token: ${{ secrets.PAT }}
aptget: libpoppler-cpp-dev
- uses: inbo/actions/check_pkg@checklist-0.3.2
74 changes: 11 additions & 63 deletions .github/workflows/check_on_different_r_os.yml
Expand Up @@ -22,83 +22,31 @@ jobs:
config:
- {os: macOS-latest, r: 'release'}
- {os: windows-latest, r: 'release'}
- {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-22.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}

env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
_R_CHECK_SYSTEM_CLOCK_: false
RSPM: ${{ matrix.config.rspm }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- uses: r-lib/actions/setup-r@master
- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
extra-repositories: https://inbo.r-universe.dev

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

- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}
- uses: r-lib/actions/setup-r-dependencies@v2

- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v1
- uses: r-lib/actions/check-r-package@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
extra-packages: any::rcmdcheck

- name: Install MacOS system dependencies
if: runner.os == 'macOS'
run: |
brew install xquartz
- name: Install system dependencies
if: runner.os == 'Linux'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
run: |
Rscript -e "remotes::install_github('r-hub/sysreqs')"
sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
sudo -s eval "$sysreqs"
sudo apt-get install -y libcurl4-openssl-dev
- name: Install dependencies
run: |
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("rcmdcheck")
shell: Rscript {0}

- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}

- name: Check
env:
_R_CHECK_CRAN_INCOMING_: false
run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
shell: Rscript {0}

- name: Show testthat output
if: always()
run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash

- name: Upload check results
if: failure()
uses: actions/upload-artifact@master
- uses: r-lib/actions/check-r-package@v2
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
path: check
retention-days: 5
error-on: '"error"'
13 changes: 5 additions & 8 deletions .github/workflows/check_on_main.yml
Expand Up @@ -3,20 +3,17 @@ on:
branches:
- main
- master
schedule:
- cron: '6 0 15 * *'
permissions:
contents: write

name: "check package on main"
name: "check package on main with checklist"

jobs:
check-package:
runs-on: ubuntu-latest
name: "check package"
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: inbo/actions/check_pkg@master
with:
token: ${{ secrets.PAT }}
aptget: libpoppler-cpp-dev
- uses: inbo/actions/check_pkg@checklist-0.3.2
9 changes: 8 additions & 1 deletion .github/workflows/examples.yml
Expand Up @@ -5,6 +5,9 @@ on:
- master

name: test-inbomd-examples
permissions:
contents: write

jobs:
test-examples:
runs-on: ubuntu-latest
Expand All @@ -13,7 +16,11 @@ jobs:
- name: checkout
uses: actions/checkout@v2
- name: build examples
uses: inbo/actions/render_inbomd@master
uses: inbo/actions/render_inbomd@inbomd-0.6.0
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
EXAMPLE_BRANCH: main

- name: push gh-pages
if: ${{ github.event_name == 'push' }}
run: |
Expand Down
35 changes: 18 additions & 17 deletions .github/workflows/release.yml
@@ -1,30 +1,31 @@
name: Releases

on:
push:
tags:
- 'v*'

name: Create Release
- v*
workflow_run:
workflows: ["check package on main"]
types:
- completed

jobs:

build:
name: Create Release
runs-on: ubuntu-latest
permissions:
contents: write
steps:
- name: Checkout code
uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Get tag message
run: |
TAG_BODY=$(git tag --contains ${{ github.sha }} -n100 | awk '(NR>1)')
echo "::set-output name=TAG_BODY::$TAG_BODY"
TAG=$(git tag --contains $(git rev-parse HEAD))
TAG_BODY=$(git tag --contains {{ github.sha }} -n100 | awk '(NR>1)')
echo "TAG=$TAG" >> $GITHUB_OUTPUT
echo "TAG_BODY=$TAG_BODY" >> $GITHUB_OUTPUT
id: tag-body
- name: Create Release
id: create_release
uses: actions/create-release@v1
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- uses: ncipollo/release-action@v1
with:
tag_name: ${{ github.ref }}
release_name: Release ${{ github.ref }}
name: Release ${{ steps.tag-body.outputs.TAG }}
tag: ${{ steps.tag-body.outputs.TAG }}
body: ${{ steps.tag-body.outputs.TAG_BODY }}
draft: false
prerelease: false
23 changes: 18 additions & 5 deletions .gitignore
@@ -1,12 +1,25 @@
*.dbf
*.doc*
*.gddoc
*.gdsheet
*.gpkg
*.html
*.log
*.mdb
*.shp*
*.shx
*.synctex.gz
*.toc
*.xls*
*_files
.DS_Store
.httr-oauth
.RData
.Rhistory
.Rproj.user
.Ruserdata
*.html
*.log
*.synctex.gz
*.toc
.httr-oauth
docs
inst/doc
libs
output
renv/library

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