From 5195e0b9daef15309330ee28788f5d26a1f06315 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Wed, 8 Jul 2020 17:48:57 +0200 Subject: [PATCH] (v1.2.0.9027) move to github --- .../{R-CMD-check.yaml => check.yaml} | 10 +-- .github/workflows/codecovr.yaml | 2 +- .github/workflows/lintr.yaml | 2 +- codecov.yml => .gitlab-ci.yml | 37 +++++------ DESCRIPTION | 2 +- NEWS.md | 5 +- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/extra.js | 2 +- docs/index.html | 8 +-- docs/news/index.html | 63 ++++++++++--------- docs/pkgdown.yml | 2 +- docs/reference/index.html | 2 +- index.md | 8 +-- pkgdown/extra.js | 2 +- 17 files changed, 77 insertions(+), 76 deletions(-) rename .github/workflows/{R-CMD-check.yaml => check.yaml} (95%) rename codecov.yml => .gitlab-ci.yml (72%) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/check.yaml similarity index 95% rename from .github/workflows/R-CMD-check.yaml rename to .github/workflows/check.yaml index 8a049769..750b5deb 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/check.yaml @@ -28,10 +28,10 @@ on: branches: - master -name: R-CMD-check +name: check jobs: - R-CMD-check: + check: runs-on: ${{ matrix.config.os }} name: ${{ matrix.config.os }} (${{ matrix.config.r }}) @@ -43,9 +43,9 @@ jobs: - {os: windows-latest, r: 'release'} - {os: macOS-latest, r: 'release'} - {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: windows-latest, r: 'oldrel'} - - {os: macOS-latest, r: 'oldrel'} - - {os: ubuntu-16.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + # - {os: windows-latest, r: 'oldrel'} + # - {os: macOS-latest, r: 'oldrel'} + # - {os: ubuntu-16.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: windows-latest, r: 'devel'} - {os: macOS-latest, r: 'devel'} - {os: ubuntu-16.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml index 425e9086..0d490599 100644 --- a/.github/workflows/codecovr.yaml +++ b/.github/workflows/codecovr.yaml @@ -64,5 +64,5 @@ jobs: shell: Rscript {0} - name: Test coverage - run: covr::codecov() + run: covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/resistance_predict.R", "R/aa_helper_functions_dplyr.R")) shell: Rscript {0} diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml index c16fa476..35be8957 100644 --- a/.github/workflows/lintr.yaml +++ b/.github/workflows/lintr.yaml @@ -62,5 +62,5 @@ jobs: shell: Rscript {0} - name: Lint - run: lintr::lint_package() + 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")) shell: Rscript {0} diff --git a/codecov.yml b/.gitlab-ci.yml similarity index 72% rename from codecov.yml rename to .gitlab-ci.yml index 6859c06e..37fcda76 100644 --- a/codecov.yml +++ b/.gitlab-ci.yml @@ -3,7 +3,7 @@ # Antimicrobial Resistance (AMR) Analysis # # # # SOURCE # -# https://github.com/msberends/AMR # +# https://gitlab.com/msberends/AMR # # # # LICENCE # # (c) 2018-2020 Berends MS, Luz CF et al. # @@ -16,27 +16,18 @@ # 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.github.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # -codecov: - require_ci_to_pass: no # allow fail - ci: - - !appveyor # ignore CI builds by AppVeyor - -comment: no - -coverage: - precision: 1 - round: up - range: "0...100" - status: - project: no - patch: no - changes: no - -ignore: - - "R/atc_online.R" - - "R/mo_history.R" - - "R/mo_source.R" - - "R/resistance_predict.R" # gives a strange error but unit tests work +# as long as GitLab used - make sure the website will be updated +pages: + stage: website + allow_failure: true + when: always + only: + - master + script: + - mv docs public + artifacts: + paths: + - public diff --git a/DESCRIPTION b/DESCRIPTION index 252f8333..a6a1ec7e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.2.0.9026 +Version: 1.2.0.9027 Date: 2020-07-08 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 6e183891..0300d65c 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.2.0.9026 +# AMR 1.2.0.9027 ## Last updated: 08-Jul-2020 ### New @@ -37,6 +37,9 @@ * Improved error handling, giving more useful info when functions return an error * Any progress bar will now only show in interactive mode (i.e. not in R Markdown) +### Other +* Project moved to GitHub + # AMR 1.2.0 ### Breaking diff --git a/docs/404.html b/docs/404.html index e1f668e2..72724511 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9026 + 1.2.0.9027 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index a1b3c299..2d308e1d 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9026 + 1.2.0.9027 diff --git a/docs/articles/index.html b/docs/articles/index.html index 29f5ece2..8fb616cb 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9026 + 1.2.0.9027 diff --git a/docs/authors.html b/docs/authors.html index 3d8f1e1a..713402e0 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9026 + 1.2.0.9027 diff --git a/docs/extra.js b/docs/extra.js index 2a7781fe..68e7f536 100644 --- a/docs/extra.js +++ b/docs/extra.js @@ -41,7 +41,7 @@ $( document ).ready(function() { // redirect to GitLab var url_old = window.location.href; - var url_new = url_old.replace("github", "gitlab"); + var url_new = url_old.replace("gitlab", "github"); if (url_old != url_new) { window.location.replace(url_new); } diff --git a/docs/index.html b/docs/index.html index 14ac1afe..651b8b6a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.2.0.9026 + 1.2.0.9027 @@ -235,7 +235,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/
  • Applying EUCAST expert rules (manual)
  • Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (manual)
  • Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (manual)
    • -
  • Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI (link)
    • +
  • Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI (link)
  • Principal component analysis for AMR (tutorial)
    • @@ -253,9 +253,9 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/

    Latest development version

    -

    The latest and unpublished development version can be installed with (precaution: may be unstable):

    +

    The latest and unpublished development version can be installed from GitHub using:

    install.packages("remotes")
-remotes::install_gitlab("msberends/AMR")
    +remotes::install_github("msberends/AMR")
    diff --git a/docs/news/index.html b/docs/news/index.html index b0a0d215..a1318260 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9026 + 1.2.0.9027
    @@ -229,9 +229,9 @@ Source: NEWS.md -
    -

    -AMR 1.2.0.9026 Unreleased +
    +

    +AMR 1.2.0.9027 Unreleased

    @@ -288,6 +288,13 @@
  • Any progress bar will now only show in interactive mode (i.e. not in R Markdown)

    • +
    +

    +Other

    +
      +
    • Project moved to GitHub
      • +
    +

    @@ -344,9 +351,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
  • Added abbreviation “cfsc” for Cefoxitin and “cfav” for Ceftazidime/avibactam
    • -
    +

    -Other

    +Other
    • Removed previously deprecated function p.symbol() - it was replaced with p_symbol()
      • @@ -386,9 +393,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
    • Added generic CLSI rules for R/SI interpretation using as.rsi() for years 2010-2019 (thanks to Anthony Underwood)
    -
    +

    -Other

    +Other
    • Support for the upcoming dplyr version 1.0.0
    • More robust assigning for classes rsi and mic @@ -484,9 +491,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
    -
    +

    -Other

    +Other
    • Add a CITATION file
    • Full support for the upcoming R 4.0
      • @@ -584,9 +591,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
    -
    +

    -Other

    +Other
    • Rewrote the complete documentation to markdown format, to be able to use the very latest version of the great Roxygen2, released in November 2019. This tremously improved the documentation quality, since the rewrite forced us to go over all texts again and make changes where needed.
    • Change dependency on clean to cleaner, as this package was renamed accordingly upon CRAN request
      • @@ -738,9 +745,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
    • Added more MIC factor levels (as.mic())
    -
    +

    -Other

    +Other
    • Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors
    • Cleaned the coding style of every single syntax line in this package with the help of the lintr package
      • @@ -821,9 +828,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
    -
    +

    -Other

    +Other
    • Fixed a note thrown by CRAN tests
    @@ -917,9 +924,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

  • Fix for mo_shortname() where species would not be determined correctly

    • -
    +

    -Other

    +Other
    • Support for R 3.6.0 and later by providing support for staged install
      • @@ -1164,9 +1171,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
    • if using different lengths of pattern and x in %like%, it will now return the call
    -
    +

    -Other

    +Other
    • Updated licence text to emphasise GPL 2.0 and that this is an R package.
    @@ -1281,9 +1288,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/

  • Percentages will now will rounded more logically (e.g. in freq function)

    • -
    +

    -Other

    +Other
    • New dependency on package crayon, to support formatted text in the console
    • Dependency tidyr is now mandatory (went to Import field) since portion_df and count_df rely on it
      • @@ -1416,9 +1423,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
    -
    +

    -Other

    +Other
    • More unit tests to ensure better integrity of functions
    @@ -1545,9 +1552,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
  • Other small fixes
    • -
    +

    -Other

    +Other
    • Added integration tests (check if everything works as expected) for all releases of R 3.1 and higher
        @@ -1607,9 +1614,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
      • Functions as.rsi and as.mic now add the package name and version as attributes
    -
    +

    -Other

    +Other
    • Expanded README.md with more examples
    • Added ORCID of authors to DESCRIPTION file
      • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 2881a184..164a9ac5 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: 2020-07-08T12:47Z +last_built: 2020-07-08T15:02Z 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 9ff31e9e..6e3f7783 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9026 + 1.2.0.9027
    diff --git a/index.md b/index.md index 24e76d71..7e628f4f 100644 --- a/index.md +++ b/index.md @@ -50,7 +50,7 @@ This package can be used for: * Applying EUCAST expert rules ([manual](./reference/eucast_rules.html)) * Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code ([manual](./reference/mo_property.html)) * Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code ([manual](./reference/ab_property.html)) - * Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI ([link](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt)) + * Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI ([link](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt)) * Principal component analysis for AMR ([tutorial](./articles/PCA.html)) ### Get this package @@ -69,10 +69,10 @@ It will be downloaded and installed automatically. For RStudio, click on the men #### Latest development version -The latest and unpublished development version can be installed with (**precaution: may be unstable**): +The latest and unpublished development version can be installed from GitHub using: ```r -install.packages("remotes") -remotes::install_gitlab("msberends/AMR") +install.packages("remotes") +remotes::install_github("msberends/AMR") ``` ### Get started diff --git a/pkgdown/extra.js b/pkgdown/extra.js index 2a7781fe..68e7f536 100644 --- a/pkgdown/extra.js +++ b/pkgdown/extra.js @@ -41,7 +41,7 @@ $( document ).ready(function() { // redirect to GitLab var url_old = window.location.href; - var url_new = url_old.replace("github", "gitlab"); + var url_new = url_old.replace("gitlab", "github"); if (url_old != url_new) { window.location.replace(url_new); }