Merge pull request #16 from inbo/checklist

Checklist

.Rbuildignore

@@ -1,10 +1,19 @@
+.travis.yml
 ^.*\.Rproj$
+^CITATION\.cff$
+^LICENSE.md$
+^README\.Rmd$
 ^\.Rproj\.user$
-^man-roxygen$
-.travis.yml
-appveyor.yml
-tic.R
+^\.github$
+^\.httr-oauth$
+^\.zenodo\.json$
+^_pkgdown.yml$
 ^_pkgdown\.yml$
+^checklist.yml$
+^codecov\.yml$
+^data-raw$
 ^docs$
+^man-roxygen$
 ^pkgdown$
-^data-raw$
+appveyor.yml
+tic.R

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,25 @@
+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who 
+contribute through reporting issues, posting feature requests, updating documentation,
+submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for
+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 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.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments,
+commits, code, wiki edits, issues, and other contributions that are not aligned to this 
+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 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 
+(http://contributor-covenant.org), version 1.0.0, available at 
+http://contributor-covenant.org/version/1/0/0/

.github/CONTRIBUTING.md

@@ -0,0 +1,39 @@
+# CONTRIBUTING #
+
+### 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 `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 [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). 
+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).
+
+### Code of Conduct
+
+Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). 
+By contributing to this project you agree to abide by its terms.
+
+### Prefer to Email? 
+
+Email the person listed as maintainer in the `DESCRIPTION` file of this repo.
+
+Though note that private discussions over email don't help others - of course
+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 

.github/workflows/check_on_branch.yml

@@ -0,0 +1,20 @@
+on:
+  push:
+    branches-ignore:
+      - main
+      - master
+      - ghpages
+
+name: "check package with checklist"
+
+jobs:
+  check-package:
+    runs-on: ubuntu-latest
+    name: "check package"
+    env:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: read
+    steps:
+      - uses: inbo/actions/check_pkg@checklist-0.3.6

.github/workflows/check_on_different_r_os.yml

@@ -0,0 +1,51 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: R-CMD-check-OS
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {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 }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          error-on: '"error"'

.github/workflows/check_on_main.yml

@@ -0,0 +1,19 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+permissions:
+  contents: write
+
+name: "check package on main with checklist"
+
+jobs:
+  check-package:
+    runs-on: ubuntu-latest
+    name: "check package"
+    env:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: inbo/actions/check_pkg@checklist-0.3.6

.github/workflows/release.yml

@@ -0,0 +1,30 @@
+name: Releases
+
+on:
+  push:
+    tags:
+      - v*
+  workflow_run:
+    workflows: ["check package on main with checklist"]
+    types:
+      - completed
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+      - name: Get tag
+        run: |
+          git fetch --tags --force
+          TAG=$(git tag --contains $(git rev-parse HEAD))
+          TAG_BODY=$(git tag --contains $(git rev-parse HEAD) --format='%(contents)')
+          echo "tag=$TAG" >> $GITHUB_ENV
+          echo "$TAG_BODY" > body.md
+      - uses: ncipollo/release-action@v1
+        with:
+          name: Release ${{ env.tag }}
+          tag: ${{ env.tag }}
+          bodyFile: body.md

.gitignore

@@ -1,6 +1,23 @@
-.Rproj.user
-.Rhistory
+*.dbf
+*.doc*
+*.gddoc
+*.gdsheet
+*.gpkg
+*.html
+*.mdb
+*.shp*
+*.shx
+*.xls*
+*_files
+.DS_Store
 .RData
+.Renviron
+.Rhistory
+.Rproj.user
 .Ruserdata
-inst/doc
+.httr-oauth
 docs
+inst/doc
+libs
+output
+renv/library

.zenodo.json

@@ -0,0 +1,39 @@
+{
+  "title": "effectclass: Classification and Visualisation of Effects",
+  "version": "0.1.4",
+  "license": "GPL-3.0",
+  "upload_type": "software",
+  "description": "<p>Classify effects by comparing the confidence intervals with\nthresholds.<\/p>",
+  "keywords": [
+    "classification",
+    "effect size",
+    "uncertainty",
+    "visualisation"
+  ],
+  "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",
+      "affiliation": "Research Institute for Nature and Forest (INBO)",
+      "orcid": "0000-0001-8804-4216"
+    }
+  ],
+  "communities": [
+    {
+      "identifier": "inbo"
+    }
+  ]
+}

CITATION.cff

@@ -0,0 +1,27 @@
+cff-version: 1.2.0
+message: If you use this software, please cite it using these metadata.
+title: "effectclass: Classification and Visualisation of Effects"
+authors:
+- given-names: Thierry
+  family-names: Onkelinx
+  affiliation: Research Institute for Nature and Forest (INBO)
+  orcid: 0000-0001-8804-4216
+keywords:
+- classification
+- effect size
+- uncertainty
+- visualisation
+contact:
+- given-names: Thierry
+  family-names: Onkelinx
+  affiliation: Research Institute for Nature and Forest (INBO)
+  orcid: 0000-0001-8804-4216
+doi: ~
+license: GPL-3.0
+repository-code: https://github.com/inbo/effectclass/
+type: software
+abstract: "Classify effects by comparing the confidence intervals with thresholds."
+identifiers:
+- type: url
+  value: https://inbo.github.io/effectclass/
+version: 0.1.4