From d39d32448bba7f8c39bedce3eba2cd13e5bc940a Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Wed, 8 Jul 2020 20:43:25 +0200 Subject: [PATCH] (v1.2.0.9028) GitHub actions --- .github/workflows/check.yaml | 4 ++-- .github/workflows/codecovr.yaml | 4 ++-- .github/workflows/lintr.yaml | 7 ++++--- .gitlab-ci.yml | 9 ++++++--- DESCRIPTION | 2 +- NEWS.md | 2 +- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 8 ++++---- docs/pkgdown.yml | 2 +- docs/reference/index.html | 2 +- vignettes/SPSS.Rmd | 6 +++--- 15 files changed, 30 insertions(+), 26 deletions(-) diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 750b5deb..9d4cfac8 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -28,10 +28,10 @@ on: branches: - master -name: check +name: R-code-check jobs: - check: + R-code-check: runs-on: ${{ matrix.config.os }} name: ${{ matrix.config.os }} (${{ matrix.config.r }}) diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml index 0d490599..beff5296 100644 --- a/.github/workflows/codecovr.yaml +++ b/.github/workflows/codecovr.yaml @@ -28,10 +28,10 @@ on: branches: - master -name: test-coverage +name: code-tested jobs: - test-coverage: + code-tested: runs-on: macOS-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml index 35be8957..a30b594e 100644 --- a/.github/workflows/lintr.yaml +++ b/.github/workflows/lintr.yaml @@ -26,12 +26,13 @@ on: - master pull_request: branches: + - premaster - master -name: lint +name: lintr jobs: - lint: + lintr: runs-on: macOS-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} @@ -62,5 +63,5 @@ jobs: shell: Rscript {0} - name: Lint - run: lint_package(linters = with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, object_length_linter = object_length_linter(length = 50L)), exclusions = list("R/aa_helper_functions_dplyr.R")) + run: lintr::lint_package(linters = with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, object_length_linter = object_length_linter(length = 50L)), exclusions = list("R/aa_helper_functions_dplyr.R")) shell: Rscript {0} diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 37fcda76..e3077c82 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -3,7 +3,7 @@ # Antimicrobial Resistance (AMR) Analysis # # # # SOURCE # -# https://gitlab.com/msberends/AMR # +# https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2020 Berends MS, Luz CF et al. # @@ -16,12 +16,15 @@ # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitlab.io/AMR. # +# Visit our website for more info: https://msberends.github.io/AMR. # # ==================================================================== # # as long as GitLab used - make sure the website will be updated +stages: + - deploy + pages: - stage: website + stage: deploy allow_failure: true when: always only: diff --git a/DESCRIPTION b/DESCRIPTION index a6a1ec7e..693b3389 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.2.0.9027 +Version: 1.2.0.9028 Date: 2020-07-08 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 0300d65c..7c8176d4 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.2.0.9027 +# AMR 1.2.0.9028 ## Last updated: 08-Jul-2020 ### New diff --git a/docs/404.html b/docs/404.html index 72724511..34c898b5 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9027 + 1.2.0.9028 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 2d308e1d..ea33ab90 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9027 + 1.2.0.9028 diff --git a/docs/articles/index.html b/docs/articles/index.html index 8fb616cb..6ce639a9 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9027 + 1.2.0.9028 diff --git a/docs/authors.html b/docs/authors.html index 713402e0..3dcb347f 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9027 + 1.2.0.9028 diff --git a/docs/index.html b/docs/index.html index 651b8b6a..fb59f0ec 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.2.0.9027 + 1.2.0.9028 diff --git a/docs/news/index.html b/docs/news/index.html index a1318260..2240fed7 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9027 + 1.2.0.9028 @@ -229,9 +229,9 @@ Source: NEWS.md -
-

-AMR 1.2.0.9027 Unreleased +
+

+AMR 1.2.0.9028 Unreleased

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 164a9ac5..ffb098d4 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: WHONET: WHONET.html benchmarks: benchmarks.html resistance_predict: resistance_predict.html -last_built: 2020-07-08T15:02Z +last_built: 2020-07-08T18:41Z urls: reference: https://msberends.github.io/AMR/reference article: https://msberends.github.io/AMR/articles diff --git a/docs/reference/index.html b/docs/reference/index.html index 6e3f7783..13d0d6e2 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9027 + 1.2.0.9028

diff --git a/vignettes/SPSS.Rmd b/vignettes/SPSS.Rmd index 91eb4f4f..8b88242f 100755 --- a/vignettes/SPSS.Rmd +++ b/vignettes/SPSS.Rmd @@ -33,7 +33,7 @@ As said, SPSS is easier to learn than R. But SPSS, SAS and Stata come with major * **R is highly modular.** - The [official R network (CRAN)](https://cran.r-project.org/) features almost 14,000 packages at the time of writing, our `AMR` package being one of them. All these packages were peer-reviewed before publication. Aside from this official channel, there are also developers who choose not to submit to CRAN, but rather keep it on their own public repository, like GitLab or GitHub. So there may even be a lot more than 14,000 packages out there. + The [official R network (CRAN)](https://cran.r-project.org/) features almost 14,000 packages at the time of writing, our `AMR` package being one of them. All these packages were peer-reviewed before publication. Aside from this official channel, there are also developers who choose not to submit to CRAN, but rather keep it on their own public repository, like GitHub. So there may even be a lot more than 14,000 packages out there. Bottom line is, you can really extend it yourself or ask somebody to do this for you. Take for example our `AMR` package. Among other things, it adds reliable reference data to R to help you with the data cleaning and analysis. SPSS, SAS and Stata will never know what a valid MIC value is or what the Gram stain of *E. coli* is. Or that all species of *Klebiella* are resistant to amoxicillin and that Floxapen^®^ is a trade name of flucloxacillin. These facts and properties are often needed to clean existing data, which would be very inconvenient in a software package without reliable reference data. See below for a demonstration. @@ -99,13 +99,13 @@ To work with R, probably the best option is to use [RStudio](https://www.rstudio To import a data file, just click *Import Dataset* in the Environment tab: -![](https://gitlab.com/msberends/AMR/raw/master/docs/import1.png) +![](https://github.com/msberends/AMR/raw/master/docs/import1.png) If additional packages are needed, RStudio will ask you if they should be installed on beforehand. In the the window that opens, you can define all options (parameters) that should be used for import and you're ready to go: -![](https://gitlab.com/msberends/AMR/raw/master/docs/import2.png) +![](https://github.com/msberends/AMR/raw/master/docs/import2.png) If you want named variables to be imported as factors so it resembles SPSS more, use `as_factor()`.