From bdbc112f998ada53a4c681bab90081d37536067c Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Sun, 21 Aug 2022 17:22:34 +0200 Subject: [PATCH] website update --- .github/workflows/check.yaml | 41 ++++++++++---------------------- DESCRIPTION | 2 +- NEWS.md | 2 +- R/plot.R | 1 + _pkgdown.yml | 1 + man/plot.Rd | 1 + pkgdown/extra.js | 9 +++---- vignettes/resistance_predict.Rmd | 4 ++-- 8 files changed, 25 insertions(+), 36 deletions(-) diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 48529b67..26380847 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -25,12 +25,8 @@ on: push: - branches: - - development - - main - pull_request: - branches: - - main + # run after a git push on any branch in this repo + branches: '**' schedule: # run a schedule everyday at 1 AM. # this is to check that all dependencies are still available (see R/zzz.R) @@ -55,32 +51,21 @@ jobs: - {os: macOS-latest, r: '4.1', allowfail: false} - {os: macOS-latest, r: '4.0', allowfail: false} - {os: macOS-latest, r: '3.6', allowfail: false} - - {os: macOS-latest, r: '3.5', allowfail: false} - - {os: macOS-latest, r: '3.4', allowfail: false} - # - {os: macOS-latest, r: '3.3', allowfail: false} - # - {os: macOS-latest, r: '3.2', allowfail: false} - # - {os: macOS-latest, r: '3.1', allowfail: true} - # - {os: macOS-latest, r: '3.0', allowfail: true} - - {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-22.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} + - {os: ubuntu-22.04, r: '4.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} + - {os: ubuntu-22.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} + - {os: ubuntu-22.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} + - {os: ubuntu-22.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} + - {os: ubuntu-22.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} + - {os: ubuntu-22.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} + - {os: ubuntu-22.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} + - {os: ubuntu-22.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} + - {os: ubuntu-22.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} + - {os: ubuntu-22.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - {os: windows-latest, r: 'devel', allowfail: true} - {os: windows-latest, r: '4.1', allowfail: false} - {os: windows-latest, r: '4.0', allowfail: false} - {os: windows-latest, r: '3.6', allowfail: false} - - {os: windows-latest, r: '3.5', allowfail: false} - - {os: windows-latest, r: '3.4', allowfail: false} - # - {os: windows-latest, r: '3.3', allowfail: false} - # - {os: windows-latest, r: '3.2', allowfail: true} - # - {os: windows-latest, r: '3.1', allowfail: true} - # - {os: windows-latest, r: '3.0', allowfail: true} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} diff --git a/DESCRIPTION b/DESCRIPTION index 846d10f5..fbc00f8f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.1.9020 +Version: 1.8.1.9021 Date: 2022-08-21 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index a7a12d6b..16e17a4f 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.1.9020 +# AMR 1.8.1.9021 ### New * EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations. diff --git a/R/plot.R b/R/plot.R index 68ec4351..43920a0e 100644 --- a/R/plot.R +++ b/R/plot.R @@ -60,6 +60,7 @@ #' # when providing the microorganism and antibiotic, colours will show interpretations: #' plot(some_mic_values, mo = "S. aureus", ab = "ampicillin") #' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro") +#' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "uk") #' #' \donttest{ #' if (require("ggplot2")) { diff --git a/_pkgdown.yml b/_pkgdown.yml index 4a7892a5..c5f87d34 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -33,6 +33,7 @@ template: bslib: code_font: {google: "Fira Code"} body-text-align: "justify" + line-height-base: 1.75 # the green "success" colour of this bootstrap theme should be the same as the green in our logo success: "#128f76" link-color: "#128f76" diff --git a/man/plot.Rd b/man/plot.Rd index 3d6c4753..20ee1d24 100644 --- a/man/plot.Rd +++ b/man/plot.Rd @@ -142,6 +142,7 @@ plot(some_rsi_values) # when providing the microorganism and antibiotic, colours will show interpretations: plot(some_mic_values, mo = "S. aureus", ab = "ampicillin") plot(some_disk_values, mo = "Escherichia coli", ab = "cipro") +plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "uk") \donttest{ if (require("ggplot2")) { diff --git a/pkgdown/extra.js b/pkgdown/extra.js index c7e099b7..9b247271 100644 --- a/pkgdown/extra.js +++ b/pkgdown/extra.js @@ -28,15 +28,16 @@ $(document).ready(function() { // replace \donttest and \dontrun texts in Examples - if ($(".ref-examples pre").length > 0) { - $(".ref-examples pre").html($(".ref-examples pre").html().replaceAll("# \\donttest{", "")); - $(".ref-examples pre").html($(".ref-examples pre").html().replaceAll("# \\dontrun{", "")); - $(".ref-examples pre").html($(".ref-examples pre").html().replaceAll("# }", "")); + if ($("#ref-examples ~ div pre").length > 0) { + $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\donttest{", "")); + $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\dontrun{", "")); + $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# }", "")); } // remove leading newline in code examples on changelog if ($("body .template-news").length > 0) { $("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n\n% resistance_predict(col_ab = "TZP", model = "binomial") ```