From 7085a10a873dd600d95ed8c5c1967bbe9e0cd84b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Franti=C5=A1ek=20Barto=C5=A1?= <38475991+FBartos@users.noreply.github.com> Date: Tue, 28 May 2024 14:01:45 +0200 Subject: [PATCH] Fix input check (#24) * fix: https://github.com/FBartos/zcurve/issues/22 * try fixing CMD check * Update R-CMD-check.yaml * update * update unit tests * Update test-zcurve.R * Update R-CMD-tests.yaml --- .github/workflows/R-CMD-check.yaml | 94 ++++--------------- .github/workflows/R-CMD-tests.yaml | 54 ++++------- .github/workflows/test-coverage.yaml | 61 ++++++++++++ DESCRIPTION | 2 +- NEWS.md | 3 + R/main.R | 10 +- .../_snaps/zcurve/z-curve-kd2-ggplot.svg | 4 +- tests/testthat/_snaps/zcurve/z-curve-kd2.svg | 4 +- tests/testthat/test-zcurve.R | 34 +++---- 9 files changed, 132 insertions(+), 134 deletions(-) create mode 100644 .github/workflows/test-coverage.yaml diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 237cc7b..f4a4f91 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,19 +1,15 @@ -# 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: - - main - - master - - pre-release + branches: [main, master] pull_request: - branches: - - main - - master - - pre-release + branches: [main, master] name: R-CMD-check +permissions: read-all + jobs: R-CMD-check: runs-on: ${{ matrix.config.os }} @@ -24,82 +20,32 @@ jobs: fail-fast: false matrix: config: + - {os: macos-latest, r: 'release'} - {os: windows-latest, r: 'release'} - - {os: macOS-latest, r: 'release'} - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} 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@v3 + - 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: ${{ matrix.config.http-user-agent }} + use-public-rspm: true - - uses: r-lib/actions/setup-pandoc@v2 - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Restore R package cache - 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 - sudo apt-get install libcurl4-openssl-dev - - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") - shell: Rscript {0} - - - name: Check - if: runner.os != 'Windows' - env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: | - options(crayon.enabled = TRUE) - rcmdcheck::rcmdcheck( - args = c("--no-manual", "--as-cran", "--ignore-vignettes"), - build_args = c("--no-build-vignettes"), - error_on = "warning", - check_dir = "check") - shell: Rscript {0}" - - - name: Check - if: runner.os == 'Windows' - env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: | - options(crayon.enabled = TRUE) - rcmdcheck::rcmdcheck( - args = c("--no-manual", "--as-cran", "--ignore-vignettes"), - build_args = c("--no-build-vignettes"), - 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/R-CMD-tests.yaml b/.github/workflows/R-CMD-tests.yaml index d2682c1..0ccf338 100644 --- a/.github/workflows/R-CMD-tests.yaml +++ b/.github/workflows/R-CMD-tests.yaml @@ -1,19 +1,15 @@ -# 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: - - main - - master - - pre-release + branches: [main, master] pull_request: - branches: - - main - - master - - pre-release + branches: [main, master] name: R-CMD-tests +permissions: read-all + jobs: R-CMD-check: runs-on: ${{ matrix.config.os }} @@ -24,50 +20,36 @@ jobs: fail-fast: false matrix: config: + - {os: macos-latest, r: 'release'} - {os: windows-latest, r: 'release'} - - {os: macOS-latest, r: 'release'} - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} 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@v3 + - 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: ${{ matrix.config.http-user-agent }} + use-public-rspm: true - - uses: r-lib/actions/setup-pandoc@v2 - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Restore R package cache - 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 - + extra-packages: any::rcmdcheck + needs: check - name: Install and test z-curve (non-Windows) env: _R_CHECK_CRAN_INCOMING_REMOTE_: false run: | + install.packages("remotes") remotes::install_deps(dependencies = TRUE) remotes::install_cran("rcmdcheck") install.packages("devtools") 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/DESCRIPTION b/DESCRIPTION index 21800d2..88afdce 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: zcurve Title: An Implementation of Z-Curves -Version: 2.4.1 +Version: 2.4.2 Authors@R: c( person("František", "Bartoš", email = "f.bartos96@gmail.com", role = c("aut", "cre")), person("Ulrich", "Schimmack", email = "ulrich.schimmack@utoronto.ca", role = c("aut"))) diff --git a/NEWS.md b/NEWS.md index d86cc07..cd8d3d9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,6 @@ +## version 2.4.2 +- Fixes https://github.com/FBartos/zcurve/issues/22 + ## version 2.4.1 - Fixes ODR computation with censored data diff --git a/R/main.R b/R/main.R index 8ec6603..bc05dca 100644 --- a/R/main.R +++ b/R/main.R @@ -92,19 +92,23 @@ zcurve <- function(z, z.lb, z.ub, p, p.lb, p.ub, data, method = "EM", boot if(missing(z) & missing(p) & missing(z.lb) & missing(p.lb)) stop("No data input") if(!missing(z)){ + if(length(z) == 0) + stop("An empty input was passed as z-scores.") if(!is.numeric(z)) stop("Wrong z-scores input: Data are not nummeric.") if(!is.vector(z)) - stop("Wrong z-scores input: Data are not a vector") + stop("Wrong z-scores input: Data are not a vector.") if(all(z <= 1 & z >= 0)) - stop("It looks like you are entering p-values rather than z-scores. To use p-values, explicitly name your argument 'zcurve(p = [vector of p-values])'") + stop("It looks like you are entering p-values rather than z-scores. To use p-values, explicitly name your argument 'zcurve(p = [vector of p-values])'.") input_type <- c(input_type, "z") } if(!missing(p)){ + if(length(p) == 0) + stop("An empty input was passed as p-values.") if(!is.numeric(p)) stop("Wrong p-values input: Data are not nummeric.") if(!is.vector(p)) - stop("Wrong p-values input: Data are not a vector") + stop("Wrong p-values input: Data are not a vector.") input_type <- c(input_type, "p") } }else if(inherits(data, "zcurve_data")){ diff --git a/tests/testthat/_snaps/zcurve/z-curve-kd2-ggplot.svg b/tests/testthat/_snaps/zcurve/z-curve-kd2-ggplot.svg index 83ea8dc..32ca38d 100644 --- a/tests/testthat/_snaps/zcurve/z-curve-kd2-ggplot.svg +++ b/tests/testthat/_snaps/zcurve/z-curve-kd2-ggplot.svg @@ -56,10 +56,10 @@ - + - + diff --git a/tests/testthat/_snaps/zcurve/z-curve-kd2.svg b/tests/testthat/_snaps/zcurve/z-curve-kd2.svg index 50e38d5..b129144 100644 --- a/tests/testthat/_snaps/zcurve/z-curve-kd2.svg +++ b/tests/testthat/_snaps/zcurve/z-curve-kd2.svg @@ -87,9 +87,9 @@ - + - + diff --git a/tests/testthat/test-zcurve.R b/tests/testthat/test-zcurve.R index 2d94d89..49c8ca7 100644 --- a/tests/testthat/test-zcurve.R +++ b/tests/testthat/test-zcurve.R @@ -59,14 +59,16 @@ test_that("z-curve EM can be fitted and reproduces OSC results", { )) # plot - expect_doppelganger("z-curve EM", function()plot(fit.EM, main = "OSC (with EM)", annotation = TRUE, CI = TRUE)) - expect_doppelganger("z-curve EM (ggplot)", suppressWarnings(plot(fit.EM, main = "OSC (with EM)", annotation = TRUE, CI = TRUE, plot_type = "ggplot"))) + skip_on_os("mac") + vdiffr::expect_doppelganger("z-curve EM", function()plot(fit.EM, main = "OSC (with EM)", annotation = TRUE, CI = TRUE)) + vdiffr::expect_doppelganger("z-curve EM (ggplot)", suppressWarnings(plot(fit.EM, main = "OSC (with EM)", annotation = TRUE, CI = TRUE, plot_type = "ggplot"))) }) test_that("z-curve KD2 can be fitted and reproduces OSC results", { - + # set seed for reproducibility set.seed(666) + skip_on_os("mac") # fit the EM method fit.KD2 <- zcurve(OSC.z, method = "density", bootstrap = 10) @@ -79,7 +81,7 @@ test_that("z-curve KD2 can be fitted and reproduces OSC results", { "" , "Estimates:" , " ERR EDR " , - "0.6133950 0.5064392 " + "0.6133975 0.5064694 " )) # basic summary @@ -94,14 +96,14 @@ test_that("z-curve KD2 can be fitted and reproduces OSC results", { "ERR 0.613 0.496 0.745" , "EDR 0.506 0.141 0.714" , "" , - "Model converged in 47 iterations" , + "Model converged in 46 iterations" , "Fitted using 73 z-values. 90 supplied, 85 significant (ODR = 0.94, 95% CI [0.87, 0.98]).", "RMSE = 0.11, 95% CI[0.09, 0.19]" )) # plot - expect_doppelganger("z-curve KD2", function()plot(fit.KD2)) - expect_doppelganger("z-curve KD2 (ggplot)", plot(fit.KD2, plot_type = "ggplot")) + vdiffr::expect_doppelganger("z-curve KD2", function()plot(fit.KD2)) + vdiffr::expect_doppelganger("z-curve KD2 (ggplot)", plot(fit.KD2, plot_type = "ggplot")) }) test_that("z-curve EM censoring works", { @@ -132,8 +134,8 @@ test_that("z-curve EM censoring works", { )) # plot - expect_doppelganger("z-curve mixed EM", function()plot(fit.mixed, CI = TRUE)) - expect_doppelganger("z-curve mixed EM (ggplot)", plot(fit.mixed, CI = TRUE, plot_type = "ggplot")) + vdiffr::expect_doppelganger("z-curve mixed EM", function()plot(fit.mixed, CI = TRUE)) + vdiffr::expect_doppelganger("z-curve mixed EM (ggplot)", plot(fit.mixed, CI = TRUE, plot_type = "ggplot")) # censoring only @@ -157,8 +159,8 @@ test_that("z-curve EM censoring works", { )) # plot - expect_doppelganger("z-curve cens EM", function()plot(fit.cens, CI = TRUE)) - expect_doppelganger("z-curve cens EM (ggplot)", plot(fit.cens, CI = TRUE, plot_type = "ggplot")) + vdiffr::expect_doppelganger("z-curve cens EM", function()plot(fit.cens, CI = TRUE)) + vdiffr::expect_doppelganger("z-curve cens EM (ggplot)", plot(fit.cens, CI = TRUE, plot_type = "ggplot")) }) test_that("z-curve clustered works", { @@ -204,7 +206,7 @@ test_that("z-curve clustered works", { "Q = -238.11, 95% CI[-269.95, -219.12]" )) - expect_doppelganger("z-curve clustered rounded", function(){ + vdiffr::expect_doppelganger("z-curve clustered rounded", function(){ oldpar <- graphics::par(no.readonly = TRUE) on.exit(graphics::par(mfrow = oldpar[["mfrow"]])) par(mfrow = c(1, 2)) @@ -251,7 +253,7 @@ test_that("z-curve clustered works", { "Q = -201.69, 95% CI[-219.18, -185.82]" )) - expect_doppelganger("z-curve clustered precise", function(){ + vdiffr::expect_doppelganger("z-curve clustered precise", function(){ oldpar <- graphics::par(no.readonly = TRUE) on.exit(graphics::par(mfrow = oldpar[["mfrow"]])) par(mfrow = c(1, 2)) @@ -298,7 +300,7 @@ test_that("z-curve clustered works", { "Q = -321.39, 95% CI[-361.78, -298.20]" )) - expect_doppelganger("z-curve clustered mixed", function(){ + vdiffr::expect_doppelganger("z-curve clustered mixed", function(){ oldpar <- graphics::par(no.readonly = TRUE) on.exit(graphics::par(mfrow = oldpar[["mfrow"]])) par(mfrow = c(1, 2)) @@ -306,6 +308,6 @@ test_that("z-curve clustered works", { plot(fitw) }) - expect_doppelganger("z-curve clustered mixed (ggplot-1)", plot(fitb, plot_type = "ggplot")) - expect_doppelganger("z-curve clustered mixed (ggplot-2)", plot(fitw, plot_type = "ggplot")) + vdiffr::expect_doppelganger("z-curve clustered mixed (ggplot-1)", plot(fitb, plot_type = "ggplot")) + vdiffr::expect_doppelganger("z-curve clustered mixed (ggplot-2)", plot(fitw, plot_type = "ggplot")) }) \ No newline at end of file