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Merge pull request #42 from inbo/checklist
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Checklist
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ThierryO committed Jul 14, 2023
2 parents 723b990 + 2959ad8 commit c143e0d
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24 changes: 12 additions & 12 deletions .Rbuildignore
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@@ -1,29 +1,29 @@
.*_cache$
^_builds$
^_pkgdown.yml$
^_projects$
^_steps$
^.*\.png$
CONTRIBUTING.md
^.*\.Rproj$
^.*\.png$
^CITATION\.cff$
^CODE_OF_CONDUCT\.md$
^LICENSE.md$
^NEWS\.md$
^README\.Rmd$
^\.Rproj\.user$
^\.git$
^\.github$
^\.httr-oauth$
^\.lintr$
^\.Rproj\.user$
^\.travis\.yml$
^\.zenodo\.json$
^_builds$
^_pkgdown.yml$
^_projects$
^_steps$
^appveyor\.yml$
^checklist.yml$
^CITATION\.cff$
^CODE_OF_CONDUCT\.md$
^codecov\.yml$
^data-raw$
^docs$
^LICENSE.md$
^man-roxygen$
^man\-roxygen$
^NEWS\.md$
^pkgdown$
^README\.Rmd$
^wercker\.yml$
CONTRIBUTING.md
4 changes: 2 additions & 2 deletions .github/CODE_OF_CONDUCT.md
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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
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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
10 changes: 5 additions & 5 deletions .github/workflows/check_on_branch.yml
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Expand Up @@ -5,16 +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 }}
- uses: inbo/actions/check_pkg@main
70 changes: 11 additions & 59 deletions .github/workflows/check_on_different_r_os.yml
Original file line number Diff line number Diff line change
Expand Up @@ -22,78 +22,30 @@ 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, https://inla.r-inla-download.org/R/testing

- 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}

- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v1
- uses: r-lib/actions/setup-r-dependencies@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-

- 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
extra-packages: any::rcmdcheck
needs: check

- 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"'
12 changes: 5 additions & 7 deletions .github/workflows/check_on_main.yml
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Expand Up @@ -3,19 +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 }}
- uses: inbo/actions/check_pkg@main
49 changes: 28 additions & 21 deletions .github/workflows/release.yml
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@@ -1,30 +1,37 @@
name: Releases

on:
push:
tags:
- 'v*'

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

jobs:
build:
name: Create Release
prepare:
runs-on: ubuntu-latest
outputs:
tag: ${{ steps.gettag.outputs.tag }}
body: ${{ steps.gettag.outputs.body }}
steps:
- name: Checkout code
uses: actions/checkout@v2
- name: Get tag message
- uses: actions/checkout@v3
- name: Get tag
run: |
TAG_BODY=$(git tag --contains ${{ github.sha }} -n100 | awk '(NR>1)')
echo "::set-output name=TAG_BODY::$TAG_BODY"
id: tag-body
- name: Create Release
id: create_release
uses: actions/create-release@v1
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
git fetch --tags --force
TAG=$(git tag --contains $(git rev-parse HEAD))
echo "tag=$TAG" >> "$GITHUB_OUTPUT"
echo "body=$TAG_BODY" >> "$GITHUB_OUTPUT"
id: gettag
publish:
runs-on: ubuntu-latest
permissions:
contents: write
needs: prepare
steps:
- uses: ncipollo/release-action@v1
with:
tag_name: ${{ github.ref }}
release_name: Release ${{ github.ref }}
body: ${{ steps.tag-body.outputs.TAG_BODY }}
draft: false
prerelease: false
name: Release ${{needs.prepare.outputs.tag}}
tag: ${{needs.prepare.outputs.tag}}
body: ${{needs.prepare.outputs.body}}
27 changes: 21 additions & 6 deletions .gitignore
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@@ -1,12 +1,27 @@
_builds
_projects
_steps
.httr-oauth
*.dbf
*.doc*
*.gddoc
*.gdsheet
*.gpkg
*.html
*.mdb
*.shp*
*.shx
*.xls*
*_cache
*_files
.DS_Store
.RData
.Renviron
.Rhistory
.Rproj.user
.Ruserdata
*_cache
*.html
.httr-oauth
_builds
_projects
_steps
docs
inst/doc
libs
output
renv/library
48 changes: 27 additions & 21 deletions .zenodo.json
Original file line number Diff line number Diff line change
@@ -1,39 +1,45 @@
{
"title": "multimput: Using Multiple Imputation to Address Missing Data",
"version": "0.2.11",
"description": "Accompanying package for the paper: \"Working with population totals in the presence of with missing data\".",
"version": "0.2.12",
"license": "GPL-3.0",
"upload_type": "software",
"description": "<p>Accompanying package for the paper: Working with population totals in\nthe presence of missing data comparing imputation methods in terms of\nbias and precision. Published in 2017 in the Journal of Ornithology\nvolume 158 page 603–615 (doi:10.1007/s10336-016-1404-9).<\/p>",
"keywords": [
"missing data, multiple imputation, Rubin"
],
"access_right": "open",
"language": "eng",
"contributors": [
{
"name": "Onkelinx, Thierry",
"affiliation": "Research Institute for Nature and Forest (INBO)",
"orcid": "0000-0001-8804-4216",
"type": "ContactPerson"
},
{
"name": "Research Institute for Nature and Forest (INBO)",
"type": "RightsHolder"
}
],
"creators": [
{
"name": "Onkelinx, Thierry",
"orcid": "https://orcid.org/0000-0001-8804-4216"
"affiliation": "Research Institute for Nature and Forest (INBO)",
"orcid": "0000-0001-8804-4216"
},
{
"name": "Devos, Koen",
"orcid": "https://orcid.org/0000-0001-7265-6349"
"affiliation": "Research Institute for Nature and Forest (INBO)",
"orcid": "0000-0001-7265-6349"
},
{
"name": "Quataert, Paul",
"orcid": "https://orcid.org/0000-0002-6894-9402"
"orcid": "0000-0002-6894-9402"
}
],
"upload_type": "software",
"access_right": "open",
"license": "GPL-3.0",
"communities": [
{
"identifier": "inbo"
}
],
"contributors": [
{
"name": "Research Institute for Nature and Forest",
"type": "RightsHolder"
},
{
"name": "Onkelinx, Thierry",
"type": "ContactPerson",
"orcid": "https://orcid.org/0000-0001-8804-4216"
}
],
"language": "eng"
]
}
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