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 @@
NEWS.md
-