Merge pull request #78 from inbo/0.4.10

0.4.10

.Rbuildignore

@@ -1,12 +1,20 @@
+^_pkgdown.yml$
 ^.*\.Rproj$
+^\.github$
+^\.httr-oauth$
 ^\.Rproj\.user$
-^wercker\.yml$
 ^\.zenodo\.json$
+^checklist.yml$
+^codecov\.yml$
+^data-raw$
+^docs$
+^LICENSE.md$
+^man-roxygen$
+^pkgdown$
+^README\.Rmd$
 CODE_OF_CONDUCT.md
 CONTRIBUTING.md
-appveyor.yml
+create_docker.sh
 Dockerfile
-_pkgdown.yml
-pkgdown
+docker
 docs
-^data-raw$

CODE_OF_CONDUCT.md → .github/CODE_OF_CONDUCT.md

@@ -1,6 +1,6 @@
 # Contributor Code of Conduct
 
-As contributors and maintainers of this project, we pledge to respect all people who
+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.
 
@@ -13,13 +13,13 @@ imagery, derogatory comments or personal attacks, trolling, public or private ha
 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
+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 behavior may be reported by
+Instances of abusive, harassing, or otherwise unacceptable behavior 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
-(https://contributor-covenant.org), version 1.0.0, available at
-https://contributor-covenant.org/version/1/0/0/
+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 roxygen 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).
+
+### 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"
+
+jobs:
+  check-package:
+    runs-on: ubuntu-latest
+    name: "check package"
+    steps:
+      - uses: inbo/actions/check_pkg@master
+        with:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
+          token: ${{ secrets.pat }}
+          aptget: libpoppler-cpp-dev

.github/workflows/check_on_different_r_os.yml

@@ -0,0 +1,97 @@
+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-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"}
+
+    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: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        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"
+
+      - 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
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/check_on_main.yml

@@ -0,0 +1,21 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+  schedule:
+    - cron: '6 0 15 * *'
+
+name: "check package on main"
+
+jobs:
+  check-package:
+    runs-on: ubuntu-latest
+    name: "check package"
+    steps:
+      - uses: inbo/actions/check_pkg@master
+        with:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          ORCID_TOKEN: ${{ secrets.ORCID_TOKEN }}
+          token: ${{ secrets.pat }}
+          aptget: libpoppler-cpp-dev

.github/workflows/examples.yml

@@ -0,0 +1,31 @@
+on:
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: test-inbomd-examples
+jobs:
+  test-examples:
+    runs-on: ubuntu-latest
+    name: "test Rmd"
+    steps:
+      - name: checkout
+        uses: actions/checkout@v2
+      - name: build examples
+        uses: inbo/actions/render_inbomd@master
+      - name: push gh-pages
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          ls
+          git config --global user.email "info@inbo.be"
+          git config --global user.name "INBO"
+          git status
+          git checkout gh-pages
+          git status
+          git rm -r .
+          ls
+          cp -R $GITHUB_WORKSPACE/docs/. $GITHUB_WORKSPACE/.
+          git add --all
+          git commit --amend --message="Voorbeelden voor INBOmd"
+          git push -f

.github/workflows/release.yml

@@ -0,0 +1,30 @@
+on:
+  push:
+    tags:
+      - 'v*'
+
+name: Create Release
+
+jobs:
+  build:
+    name: Create Release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+      - name: Get tag message
+        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 }}
+        with:
+          tag_name: ${{ github.ref }}
+          release_name: Release ${{ github.ref }}
+          body: ${{ steps.tag-body.outputs.TAG_BODY }}
+          draft: false
+          prerelease: false

.github/workflows/remove_old_artifacts.yml

@@ -0,0 +1,18 @@
+name: Remove old artifacts
+
+on:
+  schedule:
+    # Every day at 1am
+    - cron: '0 1 * * *'
+
+jobs:
+  remove-old-artifacts:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+    - name: Remove old artifacts
+      uses: c-hive/gha-remove-artifacts@v1
+      with:
+        age: '1 days'
+        skip-recent: 4

.gitignore

@@ -1,8 +1,11 @@
-.Rproj.user
-.Rhistory
+.httr-oauth
 .RData
+.Rhistory
+.Rproj.user
+.Ruserdata
+*.html
 *.log
-*.toc
 *.synctex.gz
-inst/doc
+*.toc
 docs
+inst/doc