diff --git a/.Rbuildignore b/.Rbuildignore index c25f109..b73796d 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -6,7 +6,10 @@ ^revdep$ ^README\.Rmd$ ^README-.*\.png$ -^\Mitsubishi ^codecov\.yml$ ^docs$ ^CONDUCT\.md$ +^\.github$ +^codemeta\.json$ +^_pkgdown\.yml$ +^pkgdown$ diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..0f2fe08 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,52 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + +name: R-CMD-check + +permissions: read-all + +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-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml new file mode 100644 index 0000000..c9f0165 --- /dev/null +++ b/.github/workflows/pkgdown.yaml @@ -0,0 +1,50 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + release: + types: [published] + workflow_dispatch: + +name: pkgdown + +permissions: read-all + +jobs: + pkgdown: + runs-on: ubuntu-latest + # Only restrict concurrency for non-PR jobs + concurrency: + group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::pkgdown, local::. + needs: website + + - name: Build site + run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) + shell: Rscript {0} + + - name: Deploy to GitHub pages 🚀 + if: github.event_name != 'pull_request' + uses: JamesIves/github-pages-deploy-action@v4.5.0 + with: + clean: false + branch: gh-pages + folder: docs diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml new file mode 100644 index 0000000..d1f7650 --- /dev/null +++ b/.github/workflows/pr-commands.yaml @@ -0,0 +1,81 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + issue_comment: + types: [created] + +name: Commands + +permissions: read-all + +jobs: + document: + if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }} + name: document + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/pr-fetch@v2 + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::roxygen2 + needs: pr-document + + - name: Document + run: roxygen2::roxygenise() + shell: Rscript {0} + + - name: commit + run: | + git config --local user.name "$GITHUB_ACTOR" + git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" + git add man/\* NAMESPACE + git commit -m 'Document' + + - uses: r-lib/actions/pr-push@v2 + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} + + style: + if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }} + name: style + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/pr-fetch@v2 + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} + + - uses: r-lib/actions/setup-r@v2 + + - name: Install dependencies + run: install.packages("styler") + shell: Rscript {0} + + - name: Style + run: styler::style_pkg() + shell: Rscript {0} + + - name: commit + run: | + git config --local user.name "$GITHUB_ACTOR" + git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" + git add \*.R + git commit -m 'Style' + + - uses: r-lib/actions/pr-push@v2 + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml new file mode 100644 index 0000000..fefc52e --- /dev/null +++ b/.github/workflows/test-coverage.yaml @@ -0,0 +1,61 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + +name: test-coverage + +permissions: read-all + +jobs: + test-coverage: + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr, any::xml2 + needs: coverage + + - name: Test coverage + run: | + cov <- covr::package_coverage( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") + ) + covr::to_cobertura(cov) + shell: Rscript {0} + + - uses: codecov/codecov-action@v4 + with: + fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} + file: ./cobertura.xml + plugin: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + + - name: Show testthat output + if: always() + run: | + ## -------------------------------------------------------------------- + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v4 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package diff --git a/.gitignore b/.gitignore index dc59eb0..780068b 100644 --- a/.gitignore +++ b/.gitignore @@ -2,11 +2,10 @@ .Rhistory .RData .Ruserdata -data-raw/BoM_ETA_20150501-20160430 -data-raw/QSC_Extracted_Data_20160729_201837356000-19064 - +data-raw/ inst/doc GADM_2.8_AUS_adm1.rds *.rds +docs diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 756ad0f..0000000 --- a/.travis.yml +++ /dev/null @@ -1,8 +0,0 @@ -# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r - -language: R -sudo: false -cache: packages - -after_success: - - Rscript -e 'covr::codecov()' diff --git a/DESCRIPTION b/DESCRIPTION index c0cb818..44bcc0e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,23 +1,23 @@ -Package: WINS Type: Package +Package: WINS Title: Crop Stress Weather Information Delivery System Version: 0.0.1.9000 -Authors@R: c(person("Adam", "Sparks", role = c("aut", "cre"), - email = "adamhsparks@gmail.com", - comment = c(ORCID = "0000-0002-0061-8359")), - person("Keith", "Pembleton", role = "aut", - email = "keith.pembleton@usq.edu.au", - comment = c(ORCID = "0000-0002-1896-4516")), - person("Gordon", "Grundy", role = "ctb", - email = "gordongrundy@gmail.com")) -URL: https://github.com/ToowoombaTrio/WINS +Authors@R: c( + person("Adam", "Sparks", , "adamhsparks@gmail.com", role = c("aut", "cre"), + comment = c(ORCID = "0000-0002-0061-8359")), + person("Keith", "Pembleton", , "keith.pembleton@usq.edu.au", role = "aut", + comment = c(ORCID = "0000-0002-1896-4516")), + person("Gordon", "Grundy", , "gordongrundy@gmail.com", role = "ctb") + ) +Description: Identifies likely heat or cold stress events in crops and + send an alert via e-mail to subscribers. The chillR package is used to + generate hourly weather data from Australia Bureau of Meteorology + (BOM). +License: MIT + file LICENSE +URL: https://github.com/ToowoombaTrio/WINS, https://toowoombatrio.github.io/WINS/ BugReports: https://github.com/ToowoombaTrio/WINS/issues -Description: Identifies likely heat or cold stress events in crops and send an - alert via e-mail to subscribers. The chillR package is used to generate - hourly weather data from Australia Bureau of Meteorology (BOM). Depends: R (>= 3.2.0) -License: MIT + file LICENSE Imports: chillR, data.table, @@ -27,8 +27,8 @@ Imports: foreach, foreign, ggplot2, - lubridate, iterators, + lubridate, mailR, parallel, plyr, @@ -41,14 +41,15 @@ Imports: tibble, tidyr, xml2 -RoxygenNote: 6.0.1 -Encoding: UTF-8 -NeedsCompilation: no -LazyData: TRUE -ByteCompile: TRUE Suggests: + covr, knitr, rmarkdown, - testthat, - covr -VignetteBuilder: knitr + testthat +VignetteBuilder: + knitr +ByteCompile: TRUE +Encoding: UTF-8 +LazyData: TRUE +NeedsCompilation: no +RoxygenNote: 7.3.1 diff --git a/R/WINS-package.R b/R/WINS-package.R new file mode 100644 index 0000000..a65cf64 --- /dev/null +++ b/R/WINS-package.R @@ -0,0 +1,6 @@ +#' @keywords internal +"_PACKAGE" + +## usethis namespace: start +## usethis namespace: end +NULL diff --git a/_pkgdown.yml b/_pkgdown.yml new file mode 100644 index 0000000..689fd60 --- /dev/null +++ b/_pkgdown.yml @@ -0,0 +1,4 @@ +url: https://toowoombatrio.github.io/WINS/ +template: + bootstrap: 5 + diff --git a/appveyor.yml b/appveyor.yml deleted file mode 100644 index e32d316..0000000 --- a/appveyor.yml +++ /dev/null @@ -1,42 +0,0 @@ -# DO NOT CHANGE the "init" and "install" sections below - -# Download script file from GitHub -init: - ps: | - $ErrorActionPreference = "Stop" - Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" - Import-Module '..\appveyor-tool.ps1' - -install: - ps: Bootstrap - -# Adapt as necessary starting from here - -build_script: - - travis-tool.sh install_deps - -test_script: - - travis-tool.sh run_tests - -on_failure: - - 7z a failure.zip *.Rcheck\* - - appveyor PushArtifact failure.zip - -artifacts: - - path: '*.Rcheck\**\*.log' - name: Logs - - - path: '*.Rcheck\**\*.out' - name: Logs - - - path: '*.Rcheck\**\*.fail' - name: Logs - - - path: '*.Rcheck\**\*.Rout' - name: Logs - - - path: '\*_*.tar.gz' - name: Bits - - - path: '\*_*.zip' - name: Bits diff --git a/codecov.yml b/codecov.yml deleted file mode 100644 index 69cb760..0000000 --- a/codecov.yml +++ /dev/null @@ -1 +0,0 @@ -comment: false diff --git a/codemeta.json b/codemeta.json new file mode 100644 index 0000000..e01f689 --- /dev/null +++ b/codemeta.json @@ -0,0 +1,402 @@ +{ + "@context": "https://doi.org/10.5063/schema/codemeta-2.0", + "@type": "SoftwareSourceCode", + "identifier": "WINS", + "description": "Identifies likely heat or cold stress events in crops and send an alert via e-mail to subscribers. The chillR package is used to generate hourly weather data from Australia Bureau of Meteorology (BOM).", + "name": "WINS: Crop Stress Weather Information Delivery System", + "codeRepository": "https://github.com/ToowoombaTrio/WINS", + "issueTracker": "https://github.com/ToowoombaTrio/WINS/issues", + "license": "https://spdx.org/licenses/MIT", + "version": "0.0.1.9000", + "programmingLanguage": { + "@type": "ComputerLanguage", + "name": "R", + "url": "https://r-project.org" + }, + "runtimePlatform": "R version 4.4.0 (2024-04-24)", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "author": [ + { + "@type": "Person", + "givenName": "Adam", + "familyName": "Sparks", + "email": "adamhsparks@gmail.com", + "@id": "https://orcid.org/0000-0002-0061-8359" + }, + { + "@type": "Person", + "givenName": "Keith", + "familyName": "Pembleton", + "email": "keith.pembleton@usq.edu.au", + "@id": "https://orcid.org/0000-0002-1896-4516" + } + ], + "contributor": [ + { + "@type": "Person", + "givenName": "Gordon", + "familyName": "Grundy", + "email": "gordongrundy@gmail.com" + } + ], + "maintainer": [ + { + "@type": "Person", + "givenName": "Adam", + "familyName": "Sparks", + "email": "adamhsparks@gmail.com", + "@id": "https://orcid.org/0000-0002-0061-8359" + } + ], + "softwareSuggestions": [ + { + "@type": "SoftwareApplication", + "identifier": "covr", + "name": "covr", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=covr" + }, + { + "@type": "SoftwareApplication", + "identifier": "knitr", + "name": "knitr", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=knitr" + }, + { + "@type": "SoftwareApplication", + "identifier": "rmarkdown", + "name": "rmarkdown", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=rmarkdown" + }, + { + "@type": "SoftwareApplication", + "identifier": "testthat", + "name": "testthat", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=testthat" + } + ], + "softwareRequirements": { + "1": { + "@type": "SoftwareApplication", + "identifier": "R", + "name": "R", + "version": ">= 3.2.0" + }, + "2": { + "@type": "SoftwareApplication", + "identifier": "chillR", + "name": "chillR", + "provider": { + 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"identifier": "tibble", + "name": "tibble", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=tibble" + }, + "22": { + "@type": "SoftwareApplication", + "identifier": "tidyr", + "name": "tidyr", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=tidyr" + }, + "23": { + "@type": "SoftwareApplication", + "identifier": "xml2", + "name": "xml2", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=xml2" + }, + "SystemRequirements": null + }, + "fileSize": "126.489KB", + "citation": [ + { + "@type": "SoftwareSourceCode", + "author": [ + { + "@type": "Person", + "givenName": "Adam", + "familyName": "Sparks" + }, + { + "@type": "Person", + "givenName": "Keith", + "familyName": "Pembleton" + }, + { + "@type": "Person", + "givenName": "Gordon", + "familyName": "Grundy" + } + ], + "name": "{WINS}: Crop Stress Weather Information Delivery System in R", + "url": "https://github.com/ToowoombaTrio/WINS", + "description": "R package version 0.0.1.9000" + } + ], + "releaseNotes": "https://github.com/ToowoombaTrio/WINS/blob/master/NEWS.md", + "readme": "https://github.com/ToowoombaTrio/WINS/blob/master/README.md", + "contIntegration": ["https://travis-ci.org/ToowoombaTrio/WINS", "https://ci.appveyor.com/project/adamhsparks/WINS/branch/master", "https://codecov.io/github/NA/NA?branch=master"], + "keywords": ["temperature", "weather", "weather-information", "information-delivery", "crop-stress"] +} diff --git a/man/WINS-package.Rd b/man/WINS-package.Rd new file mode 100644 index 0000000..8ef114f --- /dev/null +++ b/man/WINS-package.Rd @@ -0,0 +1,34 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/WINS-package.R +\docType{package} +\name{WINS-package} +\alias{WINS} +\alias{WINS-package} +\title{WINS: Crop Stress Weather Information Delivery System} +\description{ +Identifies likely heat or cold stress events in crops and send an alert via e-mail to subscribers. The chillR package is used to generate hourly weather data from Australia Bureau of Meteorology (BOM). +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://github.com/ToowoombaTrio/WINS} + \item \url{https://toowoombatrio.github.io/WINS/} + \item Report bugs at \url{https://github.com/ToowoombaTrio/WINS/issues} +} + +} +\author{ +\strong{Maintainer}: Adam Sparks \email{adamhsparks@gmail.com} (\href{https://orcid.org/0000-0002-0061-8359}{ORCID}) + +Authors: +\itemize{ + \item Keith Pembleton \email{keith.pembleton@usq.edu.au} (\href{https://orcid.org/0000-0002-1896-4516}{ORCID}) +} + +Other contributors: +\itemize{ + \item Gordon Grundy \email{gordongrundy@gmail.com} [contributor] +} + +} +\keyword{internal} diff --git a/man/subscribers.Rd b/man/subscribers.Rd index e7fe8c9..3035d8f 100644 --- a/man/subscribers.Rd +++ b/man/subscribers.Rd @@ -4,13 +4,15 @@ \name{subscribers} \alias{subscribers} \title{subscribers} -\format{A table of example e-mail addresses subscribed to the e-mail service +\format{ +A table of example e-mail addresses subscribed to the e-mail service \describe{ \item{email}{User e-mail address} \item{my_location_name}{Users' location} \item{mylat}{Latitude} \item{mylon}{Longitude} -}} +} +} \usage{ subscribers }