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topepomarlycormar‘topepo’
authored
2023 spring cleaning (#35)
* pkgdown and GHA updates * usethis::use_tidy_style() * usethis::use_tidy_description() * regenerate snapshots with newer rlang * rstudio -> posit, fix urls * re-regenerate snapshots * move imports to package docs * udpate testthat and other pkg version * update imports * retrigger checks * update GHA --------- Co-authored-by: Marly Gotti <marlygotti@gmail.com> Co-authored-by: ‘topepo’ <‘mxkuhn@gmail.com’>
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‎.Rbuildignore‎

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^CODE_OF_CONDUCT\.md$
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^\.github$
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^codecov\.yml$
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^README\.Rmd$

‎.github/workflows/R-CMD-check.yaml‎

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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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- {os: ubuntu-latest, r: 'oldrel-2'}
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- {os: ubuntu-latest, r: 'oldrel-3'}
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- {os: ubuntu-latest, r: 'oldrel-4'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/pkgdown.yaml‎

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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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release:
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types: [published]
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workflow_dispatch:
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name: pkgdown
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name: pkgdown.yaml
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permissions: read-all
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jobs:
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pkgdown:
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group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- name: Deploy to GitHub pages 🚀
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if: github.event_name != 'pull_request'
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uses: JamesIves/github-pages-deploy-action@v4.4.1
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uses: JamesIves/github-pages-deploy-action@v4.5.0
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with:
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clean: false
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branch: gh-pages

‎.github/workflows/pr-commands.yaml‎

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issue_comment:
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types: [created]
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name: Commands
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name: pr-commands.yaml
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permissions: read-all
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jobs:
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document:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- uses: r-lib/actions/pr-fetch@v2
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with:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- uses: r-lib/actions/pr-fetch@v2
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with:

‎.github/workflows/test-coverage.yaml‎

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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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name: test-coverage
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name: test-coverage.yaml
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permissions: read-all
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jobs:
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test-coverage:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::covr
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extra-packages: any::covr, any::xml2
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needs: coverage
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- name: Test coverage
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run: |
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covr::codecov(
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cov <- covr::package_coverage(
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quiet = FALSE,
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clean = FALSE,
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install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
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install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
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)
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print(cov)
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covr::to_cobertura(cov)
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shell: Rscript {0}
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- uses: codecov/codecov-action@v5
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with:
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# Fail if error if not on PR, or if on PR and token is given
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fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
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files: ./cobertura.xml
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plugins: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
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run: |
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## --------------------------------------------------------------------
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find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

‎.gitignore‎

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.Rproj.user
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.DS_Store
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inst/doc
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docs

‎DESCRIPTION‎

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Authors@R: c(
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person("Marly", "Gotti", , "marlygotti@gmail.com", role = c("aut", "cre")),
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person("Max", "Kuhn", , "max@posit.co", role = "aut"),
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person(given = "Posit Software, PBC", role = c("cph", "fnd"))
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person("Posit Software, PBC", role = c("cph", "fnd"))
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)
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Description: A modeling package compiling applicability domain methods in
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R. It combines different methods to measure the amount of
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BugReports: https://github.com/tidymodels/applicable/issues
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Depends:
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ggplot2,
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R (>= 3.4)
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R (>= 3.6)
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Imports:
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dplyr,
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glue,
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hardhat (>= 0.1.2),
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hardhat (>= 1.3.0),
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Matrix,
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proxyC,
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purrr,
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rlang,
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rlang (>= 1.1.1),
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stats,
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tibble,
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tidyr,
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covr,
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knitr,
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modeldata,
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recipes (>= 0.1.7),
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recipes (>= 1.0.8),
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rmarkdown,
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spelling,
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testthat (>= 3.0.0),
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testthat (>= 3.2.0),
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xml2
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VignetteBuilder:
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knitr
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Config/Needs/website: tidyverse/tidytemplate
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Config/testthat/edition: 3
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Encoding: UTF-8
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Language: en-US
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LazyData: true
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.2.3
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Config/Needs/website: tidyverse/tidytemplate
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Config/testthat/edition: 3

‎NAMESPACE‎

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export(autoplot.apd_similarity)
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export(score)
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export(score.default)
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import(rlang)
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importFrom(Matrix,Matrix)
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importFrom(Matrix,colSums)
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importFrom(dplyr,"%>%")
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importFrom(proxyC,simil)
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importFrom(purrr,map2_dfc)
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importFrom(purrr,map_dfc)
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importFrom(rlang,abort)
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importFrom(rlang,arg_match)
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importFrom(rlang,enquos)
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importFrom(stats,approx)
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importFrom(stats,ecdf)
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importFrom(stats,prcomp)

‎R/0.R‎

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‎R/applicable-package.R‎

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#' @keywords internal
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"_PACKAGE"
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# The following block is used by usethis to automatically manage
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# roxygen namespace tags. Modify with care!
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## usethis namespace: start
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#' @import rlang
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#' @importFrom dplyr %>%
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#' @importFrom dplyr count
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#' @importFrom dplyr group_by
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#' @importFrom dplyr matches
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#' @importFrom dplyr mutate
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#' @importFrom dplyr mutate_all
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#' @importFrom dplyr rename_all
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#' @importFrom dplyr sample_n
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#' @importFrom dplyr select
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#' @importFrom dplyr slice
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#' @importFrom dplyr starts_with
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#' @importFrom dplyr ungroup
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#' @importFrom ggplot2 ggplot geom_step xlab ylab aes autoplot
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#' @importFrom glue glue
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#' @importFrom hardhat forge
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#' @importFrom hardhat mold
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#' @importFrom hardhat new_model
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#' @importFrom hardhat validate_prediction_size
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#' @importFrom Matrix Matrix colSums
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#' @importFrom proxyC simil
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#' @importFrom purrr map_dfc
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#' @importFrom purrr map2_dfc
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#' @importFrom stats approx
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#' @importFrom stats ecdf
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#' @importFrom stats prcomp
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#' @importFrom stats predict
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#' @importFrom stats quantile
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#' @importFrom stats setNames
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#' @importFrom tibble as_tibble
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#' @importFrom tibble tibble
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#' @importFrom tidyr gather
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#' @importFrom tidyselect vars_select
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#' @importFrom utils globalVariables
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## usethis namespace: end
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# ------------------------------------------------------------------------------
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# global variable" check
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# nocov
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# nocov end
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# Reduce false positives when R CMD check runs its "no visible binding for
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utils::globalVariables(
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c("cumulative", "n", "sim", "percentile", "component", "value")
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)
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