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upgrade checklist GHA
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‎.github/CODE_OF_CONDUCT.md‎

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@@ -8,7 +8,7 @@ We are committed to making participation in this project a harassment-free exper
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everyone, regardless of level of experience, gender, gender identity and expression,
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sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
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Examples of unacceptable behavior by participants include the use of sexual language or
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Examples of unacceptable behaviour by participants include the use of sexual language or
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imagery, derogatory comments or personal attacks, trolling, public or private harassment,
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insults, or other unprofessional conduct.
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Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed
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from the project team.
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Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by
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Instances of abusive, harassing, or otherwise unacceptable behaviour may be reported by
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opening an issue or contacting one or more of the project maintainers.
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This Code of Conduct is adapted from the Contributor Covenant

‎.github/CONTRIBUTING.md‎

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### Fixing typos
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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.
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E.g. edit a roxygen comment in a `.R` file below `R/`, not in an `.Rd` file below `man/`.
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E.g. edit a `roxygen2` comment in a `.R` file below `R/`, not in an `.Rd` file below `man/`.
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### Prerequisites
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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.
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If you’ve found a bug, create an associated issue and illustrate the bug with a minimal [reprex](https://www.tidyverse.org/help/#reprex).
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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).
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### Pull request process
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* We recommend that you create a Git branch for each pull request (PR).
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* Look at the GitHub Actions build status before and after making changes.
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The `README` should contain badges for any continuous integration services used by the package.
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* We require the tidyverse [style guide](http://style.tidyverse.org).
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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.
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* We use [roxygen2](https://cran.r-project.org/package=roxygen2).
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* We use [testthat](https://cran.r-project.org/package=testthat).
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* We require the `tidyverse` [style guide](http://style.tidyverse.org).
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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.
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* We use [`roxygen2`](https://cran.r-project.org/package=roxygen2).
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* We use [`testthat`](https://cran.r-project.org/package=testthat).
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Contributions with test cases included are easier to accept.
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* 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).
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### Thanks for contributing!
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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
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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

‎.github/workflows/check_on_branch.yml‎

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- master
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- ghpages
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name: "check package"
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name: "check package with checklist"
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jobs:
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check-package:
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runs-on: ubuntu-latest
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name: "check package"
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: read
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steps:
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- uses: inbo/actions/check_pkg@master
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with:
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token: ${{ secrets.PAT }}
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- uses: inbo/actions/check_pkg@main

‎.github/workflows/check_on_different_r_os.yml‎

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config:
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- {os: macOS-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-22.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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_R_CHECK_SYSTEM_CLOCK_: false
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RSPM: ${{ matrix.config.rspm }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-r@master
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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extra-repositories: https://inbo.r-universe.dev
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- uses: r-lib/actions/setup-pandoc@master
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- uses: r-lib/actions/setup-pandoc@v2
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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if: runner.os != 'Windows'
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uses: actions/cache@v1
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install system dependencies
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if: runner.os == 'Linux'
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env:
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RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
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run: |
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Rscript -e "remotes::install_github('r-hub/sysreqs')"
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sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
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sudo -s eval "$sysreqs"
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sudo apt-get install -y libcurl4-openssl-dev
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- name: Install dependencies
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run: |
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("rcmdcheck")
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shell: Rscript {0}
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- name: Session info
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run: |
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options(width = 100)
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pkgs <- installed.packages()[, "Package"]
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sessioninfo::session_info(pkgs, include_base = TRUE)
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shell: Rscript {0}
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- name: Check
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env:
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_R_CHECK_CRAN_INCOMING_: false
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run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
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shell: Rscript {0}
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- name: Show testthat output
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if: always()
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run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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extra-packages: any::rcmdcheck
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needs: check
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@master
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- uses: r-lib/actions/check-r-package@v2
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with:
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name: ${{ runner.os }}-r${{ matrix.config.r }}-results
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path: check
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retention-days: 5
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error-on: '"error"'

‎.github/workflows/check_on_main.yml‎

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branches:
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- main
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- master
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schedule:
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- cron: '6 0 15 * *'
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permissions:
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contents: write
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name: "check package on main"
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name: "check package on main with checklist"
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jobs:
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check-package:
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runs-on: ubuntu-latest
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name: "check package"
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: inbo/actions/check_pkg@master
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with:
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token: ${{ secrets.PAT }}
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- uses: inbo/actions/check_pkg@main

‎.github/workflows/release.yml‎

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name: Releases
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on:
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push:
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tags:
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- 'v*'
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name: Create Release
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- v*
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workflow_run:
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workflows: ["check package on main"]
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types:
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- completed
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jobs:
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build:
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name: Create Release
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- name: Checkout code
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uses: actions/checkout@v2
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- uses: actions/checkout@v3
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- name: Get tag message
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run: |
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TAG_BODY=$(git tag --contains ${{ github.sha }} -n100 | awk '(NR>1)')
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echo "::set-output name=TAG_BODY::$TAG_BODY"
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TAG=$(git tag --contains $(git rev-parse HEAD))
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TAG_BODY=$(git tag --contains $(git rev-parse HEAD) -n100 | awk '(NR>2)')
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echo "TAG=$TAG" >> $GITHUB_OUTPUT
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echo "TAG_BODY=$TAG_BODY" >> $GITHUB_OUTPUT
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id: tag-body
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- name: Create Release
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id: create_release
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uses: actions/create-release@v1
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- uses: ncipollo/release-action@v1
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with:
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tag_name: ${{ github.ref }}
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release_name: Release ${{ github.ref }}
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name: Release ${{ steps.tag-body.outputs.TAG }}
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tag: ${{ steps.tag-body.outputs.TAG }}
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body: ${{ steps.tag-body.outputs.TAG_BODY }}
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draft: false
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prerelease: false

‎.gitignore‎

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*.dbf
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*.doc*
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*.gddoc
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*.gdsheet
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*.gpkg
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*.html
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*.mdb
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*.shp*
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*.shx
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*.xls*
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*_files
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.DS_Store
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.httr-oauth
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.RData
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.Renviron
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.Rhistory
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.Rproj.user
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.Ruserdata
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*.html
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.httr-oauth
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docs
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libs
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output
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renv/library

‎_pkgdown.yml‎

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href: https://www.facebook.com/pg/INBOVlaanderen
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authors:
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Research Institute for Nature and Forest:
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Research Institute for Nature and Forest (INBO):
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href: "https://www.vlaanderen.be/inbo/en-gb"
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html: "<img src='https://inbo.github.io/checklist/reference/figures/logo-en.png' height=24>"

‎codecov.yml‎

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comment: true
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coverage:
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precision: 2
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precision: 1
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round: down
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range: "70...100"
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status:
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project:
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default:
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target: auto
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threshold: 0%
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informational: false
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patch:
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default:
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target: auto
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threshold: 0%
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threshold: 10%
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informational: true
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project:
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default:
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target: auto
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threshold: 1%
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informational: false

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