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 @@
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 @@ 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 @@ 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 @@ 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 @@ @@ -235,7 +235,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/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")
NEWS.md
-
p.symbol()
- it was replaced with p_symbol()
as.rsi()
for years 2010-2019 (thanks to Anthony Underwood)dplyr
version 1.0.0rsi
and mic
@@ -484,9 +491,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
CITATION
fileclean
to cleaner
, as this package was renamed accordingly upon CRAN requestas.mic()
)lintr
packageFix for mo_shortname()
where species would not be determined correctly
%like%
, it will now return the callPercentages will now will rounded more logically (e.g. in freq
function)
crayon
, to support formatted text in the consoletidyr
is now mandatory (went to Import
field) since portion_df
and count_df
rely on itas.rsi
and as.mic
now add the package name and version as attributesREADME.md
with more examples