From 87757748bd473b4ad5bf8d0cd65c94f10e5fa280 Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Tue, 23 Oct 2018 16:49:40 +0200
Subject: [PATCH] switch to gitlab

---
 .Rbuildignore  |  5 +++--
 .gitlab-ci.yml |  6 +++---
 .travis.yml    | 52 --------------------------------------------------
 DESCRIPTION    |  6 +++---
 NEWS.md        |  1 +
 README.md      | 17 ++++++++---------
 appveyor.yml   |  9 ---------
 7 files changed, 18 insertions(+), 78 deletions(-)
 delete mode 100755 .travis.yml

diff --git a/.Rbuildignore b/.Rbuildignore
index fad9f2b1..68f59973 100755
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,7 +1,8 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 .travis.yml
+appveyor.yml
+.gitlab-ci.yml
 .zenodo.json
-^cran-comments\.md$
-^appveyor\.yml$
 _noinclude
+^cran-comments\.md$
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 07aefec6..4440355a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,10 +1,10 @@
 # from https://stackoverflow.com/questions/51866926
 image: rocker/r-base
-test:
+gitlab:
    script:
     - apt-get update
     - apt-get install --yes --no-install-recommends r-cran-testthat r-cran-devtools
-    - R -e "devtools::install_deps()"
+    - R -e "devtools::install_deps(dependencies = TRUE)"
     - R CMD build . --no-build-vignettes --no-manual
     - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
-    - R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual
+    - R CMD check "${PKG_FILE_NAME}" --no-manual --as-cran
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100755
index 187650ed..00000000
--- a/.travis.yml
+++ /dev/null
@@ -1,52 +0,0 @@
-# Setting up R deps
-language: r
-jobs:
-  include:
-  - r: 3.1
-    os: linux
-    warnings_are_errors: false
-  - r: 3.2
-    os: linux
-  - r: 3.2
-    os: osx
-  - r: 3.3
-    os: linux
-  - r: 3.3
-    os: osx
-  - r: 3.4
-    os: linux
-  - r: 3.4
-    os: osx
-  - r: release
-    os: linux
-  - r: release
-    os: osx
-  - r: devel
-    os: linux
-    warnings_are_errors: false
-matrix:
-  allow_failures:
-    - r: 3.2
-      os: osx
-    - r: 3.3
-      os: osx
-    - r: 3.4
-      os: osx
-r_packages: covr
-cache: packages
-cran: https://cran.rstudio.com
-
-install:
-  - Rscript -e "install.packages(c('devtools', 'backports', 'clipr', 'curl', 'data.table', 'dplyr', 'hms', 'knitr', 'readr', 'rlang', 'rvest', 'xml2', 'covr', 'ggplot2', 'rmarkdown', 'testthat', 'tidyr'))"
-  - if [ $TRAVIS_OS_NAME = osx ]; then Rscript -e "devtools::install_github('r-lib/rlang')"; fi
-
-# postrun
-after_success:
-  - Rscript -e 'covr::codecov()'
-notifications:
-  email:
-    recipients:
-      - m.s.berends@umcg.nl
-      # - c.f.luz@umcg.nl
-    on_success: change
-    on_failure: change
diff --git a/DESCRIPTION b/DESCRIPTION
index cd2545ef..d3d844f9 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 0.4.0.9006
+Version: 0.4.0.9007
 Date: 2018-10-23
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
@@ -62,8 +62,8 @@ Suggests:
     rstudioapi,
     testthat (>= 1.0.2)
 VignetteBuilder: knitr
-URL: https://github.com/msberends/AMR
-BugReports: https://github.com/msberends/AMR/issues
+URL: https://gitlab.com/msberends/AMR
+BugReports: https://gitlab.com/msberends/AMR/issues
 License: GPL-2 | file LICENSE
 Encoding: UTF-8
 LazyData: true
diff --git a/NEWS.md b/NEWS.md
index 4b3ff0ac..a4df0567 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,7 @@
 # 0.4.0.90xx (latest development version)
 
 #### New
+* Repository moved to GitLab: https://gitlab.com/msberends/AMR
 * Function `count_all` to get all available isolates (that like all `portion_*` and `count_*` functions also supports `summarise` and `group_by`), the old `n_rsi` is now an alias of `count_all`
 
 #### Changed
diff --git a/README.md b/README.md
index 544d8bb8..c5c788bf 100755
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@ This R package was created for academic research by PhD students of the Faculty
 
 :arrow_forward: Get it with `install.packages("AMR")` or see below for other possibilities.
 
-:arrow_forward: Read the [changelog here](https://github.com/msberends/AMR/blob/master/NEWS.md).
+:arrow_forward: Read the [changelog here](https://gitlab.com/msberends/AMR/blob/master/NEWS.md).
 
 ## Authors
 Matthijs S. Berends <a href="https://orcid.org/0000-0001-7620-1800"><img src="https://cran.r-project.org/web/orcid.svg" height="16px"></a> <sup>1,2,a</sup>,
@@ -32,7 +32,7 @@ Bhanu Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https://cr
 * [How to get it?](#how-to-get-it)
   * [Install from CRAN](#install-from-cran)
   * [Install from Zenodo](#install-from-zenodo)
-  * [Install from GitHub](#install-from-github)
+  * [Install from GitLab](#install-from-gitlab)
 * [How to use it?](#how-to-use-it)
   * [New classes](#new-classes)
   * [Overwrite/force resistance based on EUCAST rules](#overwriteforce-resistance-based-on-eucast-rules)
@@ -134,20 +134,20 @@ All stable versions of this package [are published on CRAN](http://cran.r-projec
 
 This package was also published on Zenodo (stable releases only): https://doi.org/10.5281/zenodo.1305355
 
-### Install from GitHub
+### Install from GitLab
 
 This is the latest **development version**. Although it may contain bugfixes and even new functions compared to the latest released version on CRAN, it is also subject to change and may be unstable or behave unexpectedly. Always consider this a beta version. All below 'badges' should be green:
 
 Development Test | Result | Reference
 --- | :---: | ---
-All functions checked on Linux and macOS | [![Travis_Build](https://travis-ci.org/msberends/AMR.svg?branch=master)](https://travis-ci.org/msberends/AMR) | Travis CI, GmbH [[ref 1]](https://travis-ci.org/msberends/AMR) 
-All functions checked on Windows | [![AppVeyor_Build](https://ci.appveyor.com/api/projects/status/github/msberends/AMR?branch=master&svg=true)](https://ci.appveyor.com/project/msberends/AMR) | Appveyor Systems Inc. [[ref 2]](https://ci.appveyor.com/project/msberends/AMR)
-Percentage of syntax lines checked | [![Code_Coverage](https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gh/msberends/AMR) | Codecov LLC [[ref 3]](https://codecov.io/gh/msberends/AMR)
+All functions checked on Linux and macOS | [(click view)](https://gitlab.com/msberends/AMR/pipelines) | GitLab [[ref 1]](https://gitlab.com/msberends/AMR/pipelines) 
+All functions checked on Windows | [![AppVeyor_Build](https://ci.appveyor.com/api/projects/status/gitlab/msberends/AMR?branch=master&svg=true)](https://ci.appveyor.com/project/msberends/amr-svxon) | Appveyor Systems Inc. [[ref 2]](https://ci.appveyor.com/project/msberends/amr-svxon)
+Percentage of syntax lines checked | [![Code_Coverage](https://codecov.io/gl/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gl/msberends/AMR) | Codecov LLC [[ref 3]](https://codecov.io/gl/msberends/AMR)
 
 If so, try it with:
 ```r
 install.packages("devtools") 
-devtools::install_github("msberends/AMR")
+devtools::install_git("https://gitlab.com/msberends/AMR")
 ```
 
 ## How to use it?
@@ -558,9 +558,8 @@ microbenchmark(A = mo_species("aureus"),
 Of course, when running `mo_phylum("Firmicutes")` the function has zero knowledge about the actual microorganism, namely *S. aureus*. But since the result would be `"Firmicutes"` too, there is no point in calculating the result. And since this package 'knows' all phyla of all known microorganisms (according to ITIS), it can just return the initial value immediately.
 
 ## Copyright
-[![License](https://img.shields.io/github/license/msberends/AMR.svg?colorB=3679BC)](https://github.com/msberends/AMR/blob/master/LICENSE)
 
-This R package is licensed under the [GNU General Public License (GPL) v2.0](https://github.com/msberends/AMR/blob/master/LICENSE). In a nutshell, this means that this package:
+This R package is licensed under the [GNU General Public License (GPL) v2.0](https://gitlab.com/msberends/AMR/blob/master/LICENSE). In a nutshell, this means that this package:
 
 - May be used for commercial purposes
 
diff --git a/appveyor.yml b/appveyor.yml
index 98e6e33f..ee100eaa 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -25,15 +25,6 @@ environment:
   - R_VERSION: release
   - R_VERSION: devel
 
-notifications:
-- provider: Email
-  to: m.s.berends@umcg.nl
-  subject: 'AppVeyor: status changed'
-  message: The status of https://ci.appveyor.com/project/msberends/amr has changed.
-  on_build_success: false
-  on_build_failure: false
-  on_build_status_changed: true
-
 build_script:
   - travis-tool.sh install_deps