diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 865d8be9..31258517 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -23,6 +23,7 @@ # chck <- rhub::check(devtools::build(), platform = rhub::platforms()[!is.na(rhub::platforms()$`cran-name`), 'name']) stages: + - test - check - lint - website @@ -53,9 +54,25 @@ before_script: - echo 'LANG="en_US.utf8"' >> .Renviron - echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron +R-release-test-only: + stage: test + when: always + allow_failure: false + script: + - Rscript -e 'sessionInfo()' + # install missing and outdated packages + - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)' + - Rscript -e 'devtools::test(stop_on_failure = FALSE)' + cache: + key: release_4_0 + paths: + - installed_deps/ + policy: pull # no uploading after run + R-release: stage: check - allow_failure: false + when: on_success + allow_failure: true script: - Rscript -e 'sessionInfo()' # install missing and outdated packages @@ -80,6 +97,7 @@ R-release: R-devel: stage: check + when: on_success image: rocker/r-devel allow_failure: true script: @@ -107,7 +125,7 @@ R-devel: lintr: stage: lint allow_failure: true - when: on_success + when: always cache: key: release_4_0 paths: @@ -122,6 +140,7 @@ lintr: pages: stage: website + allow_failure: true when: always only: - master @@ -134,7 +153,7 @@ pages: codecovr: stage: coverage allow_failure: true - when: on_success + when: always cache: key: release_4_0 paths: diff --git a/DESCRIPTION b/DESCRIPTION index ab32382b..5ec4f71f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.1.0.9000 +Version: 1.1.0.9002 Date: 2020-04-30 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 208fbcae..7e426054 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.1.0.9000 +# AMR 1.1.0.9002 ## Last updated: 30-Apr-2020 ### Changed diff --git a/appveyor.yml b/appveyor.yml index f7100c88..04de586a 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -51,7 +51,7 @@ matrix: - R_VERSION: "devel" build_script: - - travis_tool.sh clean_library # turn off for caching, turn on for release of new R versions + # - travis_tool.sh clean_library # turn off for caching, turn on for release of new R versions - travis_tool.sh install_deps test_script: diff --git a/docs/404.html b/docs/404.html index 97a8f6b7..0e9338be 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9000 + 1.1.0.9002 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 380088a9..17bd49df 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9000 + 1.1.0.9002 diff --git a/docs/articles/index.html b/docs/articles/index.html index b04168bc..9b8fee54 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9000 + 1.1.0.9002 diff --git a/docs/authors.html b/docs/authors.html index a0400fcc..e8f16353 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9000 + 1.1.0.9002 diff --git a/docs/index.html b/docs/index.html index 03064061..530bb727 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.1.0.9000 + 1.1.0.9002 diff --git a/docs/news/index.html b/docs/news/index.html index 85060cb6..b3cb1c6b 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9000 + 1.1.0.9002 @@ -229,9 +229,9 @@ Source: NEWS.md -
-

-AMR 1.1.0.9000 Unreleased +
+

+AMR 1.1.0.9002 Unreleased

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 6450ee97..80a4b612 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: 2020-04-30T07:04Z +last_built: 2020-04-30T16:46Z urls: reference: https://msberends.gitlab.io/AMR/reference article: https://msberends.gitlab.io/AMR/articles diff --git a/docs/reference/index.html b/docs/reference/index.html index bdc6fc95..e237a3ad 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9000 + 1.1.0.9002

diff --git a/git_premaster.sh b/git_premaster.sh index c2ac3e6d..f5d9e7e6 100755 --- a/git_premaster.sh +++ b/git_premaster.sh @@ -63,21 +63,20 @@ if [ -z "$3" ]; then # no version number set, so get latest tags to create it git pull --tags --quiet current_tag=`git describe --tags --abbrev=0 | sed 's/v//'` - -# current_commit=`git describe --tags | sed 's/.*-\(.*\)-.*/\1/'` if [ -z "current_tag" ]; then echo "FATAL - could not determine current tag" exit 1 fi - current_tag_dots=`echo $current_tag | grep -o "[.]" | wc -l` - if (( "$current_tag_dots" < 3 )); then - # contains two dots, so version number is like "1.0.0", commit nr is 0 + current_tag_full=`git describe --tags | sed 's/v//'` + current_tag_dashes=`echo $current_tag_full | grep -o "[-]" | wc -l` + if (( "$current_tag_dashes" < 1 )); then + # so version number is like "1.0.0", commit nr is 0 current_commit=0 echo "---------------" echo "Mind NEWS.md! Assuming sequence number 9000." echo "---------------" else - current_commit=`git describe --tags | sed 's/.*[.]//'` + current_commit=`git describe --tags | sed 's/.*-\(.*\)-.*/\1/'` fi if [ -z "current_commit" ]; then echo "FATAL - could not determine last commit index number"