From a7919d1cedbf901206472a962507ab3e633cbcea Mon Sep 17 00:00:00 2001 From: aravindhebbali Date: Mon, 4 Nov 2024 19:21:13 +0530 Subject: [PATCH] ci: closes #81 --- .github/workflows/R-CMD-check.yaml | 80 +++++++++------------------- .github/workflows/test-coverage.yaml | 71 ++++++++++++++---------- README.Rmd | 4 +- README.md | 45 +++++++--------- 4 files changed, 86 insertions(+), 114 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index b0f3cd6..3cdf68c 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,16 +1,14 @@ -# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. -# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions +# 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: - - master - - develop + branches: [master, develop] pull_request: - branches: - - master - - develop + branches: [master, develop] -name: R-CMD-check +name: R-CMD-check.yaml + +permissions: read-all jobs: R-CMD-check: @@ -22,63 +20,33 @@ jobs: fail-fast: false matrix: config: + - {os: macos-latest, r: 'release'} - {os: windows-latest, r: 'release'} - - {os: macOS-latest, r: 'release'} - - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true - - uses: r-lib/actions/setup-pandoc@v1 - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Cache R packages - if: runner.os != 'Windows' - uses: actions/cache@v2 + - 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' - run: | - while read -r cmd - do - eval sudo $cmd - done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') - - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") - shell: Rscript {0} - - - name: Check - env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") - shell: Rscript {0} + extra-packages: any::rcmdcheck + needs: check - - name: Upload check results - if: failure() - uses: actions/upload-artifact@main + - uses: r-lib/actions/check-r-package@v2 with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 9245d3a..5679b54 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -1,48 +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: - - master - - develop + branches: [master, develop] pull_request: - branches: - - master - - develop + branches: [master, develop] -name: test-coverage +name: test-coverage.yaml + +permissions: read-all jobs: test-coverage: - runs-on: macOS-latest + runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true - - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr, any::xml2 + needs: coverage - - name: Query dependencies + - name: Test coverage run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + 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} - - name: Cache R packages - uses: actions/cache@v2 + - uses: codecov/codecov-action@v4 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 dependencies + fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} + file: ./cobertura.xml + plugin: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + + - name: Show testthat output + if: always() run: | - install.packages(c("remotes")) - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("covr") - shell: Rscript {0} + ## -------------------------------------------------------------------- + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash - - name: Test coverage - run: covr::codecov() - shell: Rscript {0} + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v4 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package diff --git a/README.Rmd b/README.Rmd index 8fb39a6..1bf6a9a 100644 --- a/README.Rmd +++ b/README.Rmd @@ -17,10 +17,8 @@ knitr::opts_chunk$set( > Tools for Statistical Inference -[![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/inferr)](https://cran.r-project.org/package=inferr) [![cran checks](https://cranchecks.info/badges/summary/inferr)](https://cran.r-project.org/web/checks/check_results_inferr.html) -[![R build status](https://github.com/rsquaredacademy/inferr/workflows/R-CMD-check/badge.svg)](https://github.com/rsquaredacademy/inferr/actions) +[![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/inferr)](https://cran.r-project.org/package=inferr) [![R-CMD-check](https://github.com/rsquaredacademy/inferr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rsquaredacademy/inferr/actions/workflows/R-CMD-check.yaml) [![Coverage status](https://codecov.io/gh/rsquaredacademy/inferr/branch/master/graph/badge.svg)](https://codecov.io/github/rsquaredacademy/inferr?branch=master) -[![status](https://tinyverse.netlify.com/badge/inferr)](https://CRAN.R-project.org/package=inferr) [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html) [![](https://cranlogs.r-pkg.org/badges/grand-total/inferr)](https://cran.r-project.org/package=inferr) ## Overview diff --git a/README.md b/README.md index d944f36..7c75792 100644 --- a/README.md +++ b/README.md @@ -7,17 +7,10 @@ -[![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/inferr)](https://cran.r-project.org/package=inferr) -[![cran -checks](https://cranchecks.info/badges/summary/inferr)](https://cran.r-project.org/web/checks/check_results_inferr.html) -[![R build -status](https://github.com/rsquaredacademy/inferr/workflows/R-CMD-check/badge.svg)](https://github.com/rsquaredacademy/inferr/actions) +[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/inferr)](https://cran.r-project.org/package=inferr) +[![R-CMD-check](https://github.com/rsquaredacademy/inferr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rsquaredacademy/inferr/actions/workflows/R-CMD-check.yaml) [![Coverage status](https://codecov.io/gh/rsquaredacademy/inferr/branch/master/graph/badge.svg)](https://codecov.io/github/rsquaredacademy/inferr?branch=master) -[![status](https://tinyverse.netlify.com/badge/inferr)](https://CRAN.R-project.org/package=inferr) -[![Lifecycle: -stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html) -[![](https://cranlogs.r-pkg.org/badges/grand-total/inferr)](https://cran.r-project.org/package=inferr) ## Overview @@ -27,21 +20,21 @@ additional and flexible input options and more detailed and structured test results. As of version 0.3, **inferr** includes a select set of parametric and non-parametric statistical tests which are listed below: -- One Sample t Test -- Paired Sample t Test -- Independent Sample t Test -- One Sample Proportion Test -- Two Sample Proportion Test -- One Sample Variance Test -- Two Sample Variance Test -- Binomial Test -- ANOVA -- Chi Square Goodness of Fit Test -- Chi Square Independence Test -- Levene’s Test -- Cochran’s Q Test -- McNemar Test -- Runs Test for Randomness +- One Sample t Test +- Paired Sample t Test +- Independent Sample t Test +- One Sample Proportion Test +- Two Sample Proportion Test +- One Sample Variance Test +- Two Sample Variance Test +- Binomial Test +- ANOVA +- Chi Square Goodness of Fit Test +- Chi Square Independence Test +- Levene’s Test +- Cochran’s Q Test +- McNemar Test +- Runs Test for Randomness ## Installation @@ -56,8 +49,8 @@ devtools::install_github("rsquaredacademy/inferr") ## Articles -- [Introduction to - inferr](https://inferr.rsquaredacademy.com/articles/intro.html) +- [Introduction to + inferr](https://inferr.rsquaredacademy.com/articles/intro.html) ## Usage