added github action support

Author: tscheypidi

.buildlibrary

@@ -1,6 +1,7 @@
-ValidationKey: '1303260'
+ValidationKey: '1489520'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'
 AcceptedNotes: unable to verify current time
 AutocreateReadme: yes
+UseGithubActions: yes

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "lucode2: Code Manipulation and Analysis Tools",
-  "version": "0.7.0",
+  "version": "0.8.0",
   "description": "<p>A collection of tools which allow to manipulate and analyze code.<\/p>",
   "creators": [
     {

DESCRIPTION

@@ -1,21 +1,34 @@
 Package: lucode2
 Type: Package
 Title: Code Manipulation and Analysis Tools
-Version: 0.7.0
-Date: 2020-12-22
+Version: 0.8.0
+Date: 2020-12-23
 Authors@R: c(person("Jan Philipp", "Dietrich", email = "[email protected]", role = c("aut","cre")),
              person("David", "Klein", role = "aut"),
              person("Anastasis", "Giannousakis", role = "aut"),
              person("Markus", "Bonsch", role = "aut"),
              person("Benjamin Leon", "Bodirsky", role = "aut"),
              person("Lavinia", "Baumstark", role = "aut"))
 Description: A collection of tools which allow to manipulate and analyze code.
-Imports: citation, data.table, desc, dplyr, rlang, yaml
-Suggests: devtools, ggplot2, gtools, lusweave, magclass, testthat
+Imports: 
+    citation, 
+    data.table, 
+    desc, 
+    dplyr, 
+    rlang,
+    usethis,
+    yaml
+Suggests: 
+    devtools,
+    ggplot2,
+    gtools,
+    lusweave,
+    magclass,
+    testthat,
+    covr
 URL: https://github.com/pik-piam/lucode2
 BugReports: https://github.com/pik-piam/lucode2/issues
 License: BSD_2_clause + file LICENSE
 LazyData: no
 Encoding: UTF-8
 RoxygenNote: 7.1.1
-

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(SystemCommandAvailable)
 export(addEOF)
+export(addGitHubActions)
 export(buildLibrary)
 export(findCoupledruns)
 export(findIterations)
@@ -42,6 +43,8 @@ importFrom(dplyr,mutate)
 importFrom(dplyr,rename)
 importFrom(dplyr,summarize)
 importFrom(rlang,.data)
+importFrom(usethis,use_coverage)
+importFrom(usethis,use_github_action)
 importFrom(utils,available.packages)
 importFrom(utils,capture.output)
 importFrom(utils,citation)

R/addGitHubActions.R

@@ -0,0 +1,29 @@
+#' addGitHubActions
+#' 
+#' adds GitHubActions with a standard workflow including codecov to the package. It will add a standard
+#' Github action "test-buildlibrary.yml" to the project which performs standard tests as well as
+#' creates a coverage report. This file is overwritten automatically each time this function is run and
+#' should not be edited by hand. But additional Github actions can be added as separate files.
+#' 
+#' In addition, this function adds a codecov.yml to the repository, if not already existing. This file
+#' is only created, if missing and can be edited manually.
+#' 
+#' @param lib Path to the package
+#' 
+#' @author Jan Philipp Dietrich
+#' @seealso \code{\link{buildLibrary}}
+#' @importFrom usethis use_github_action use_coverage
+#' @examples
+#' \dontrun{addGitHubActions()}
+#' @export 
+addGitHubActions <- function(lib="."){
+  standardactionfile <- paste0(lib,"/.github/workflows/test-buildlibrary.yaml")
+  if(file.exists(standardactionfile)) file.remove(standardactionfile)
+  usethis::use_github_action(url=system.file("extdata/test-buildlibrary.yaml",package="lucode2"), 
+                             save_as="test-buildlibrary.yaml")
+  if(!file.exists(paste0(lib,"/codecov.yml"))) {
+    usethis::use_coverage("codecov")
+    file.copy(system.file("extdata/codecov.yml", package="lucode2"),paste0(lib,"/codecov.yml"), overwrite = TRUE)
+  }
+}
+  

R/buildLibrary.R

@@ -46,14 +46,20 @@ buildLibrary<-function(lib=".",cran=TRUE, update_type=NULL){
     return(s);
   }  
 
-  didYouPull <- function() {
-    cat("Is your repository up-to-date? Did you pull immediately before running this check? (yes/no)") 
+  askYesNo <- function(question) {
+    cat(paste(question,"(yes/no)"))
     s <- get_line()
-    if(!(tolower(s) %in% c("y","yes"))) stop("Please update your repository first, before you proceed!")
+    if(!(tolower(s) %in% c("y","yes"))) return(FALSE)
+    return(TRUE)
+  }  
+    
+  didYouPull <- function() {
+    if(!askYesNo("Is your repository up-to-date? Did you pull immediately before running this check?")){
+      stop("Please update your repository first, before you proceed!")  
+    }
   }
   didYouPull()
 
-  OS<-Sys.info()["sysname"]
   thisdir<-getwd()
   if(lib!=".") setwd(lib)
   on.exit(setwd(thisdir))
@@ -78,7 +84,6 @@ buildLibrary<-function(lib=".",cran=TRUE, update_type=NULL){
   ############################################################
   #check the library
   ############################################################
-  ck <- devtools::check(".",cran=cran)
 
   if(!file.exists(".buildlibrary")) {
     # if not yet available, add .buildlibrary and add to .Rbuildignore
@@ -99,11 +104,30 @@ buildLibrary<-function(lib=".",cran=TRUE, update_type=NULL){
   }
 
   cfg <- read_yaml(".buildlibrary")
+  
   if(is.null(cfg$AutocreateReadme)) cfg$AutocreateReadme <- TRUE
+  if(is.null(cfg$UseGithubActions) && 
+     askYesNo("Do you want to use GitHub Actions for package testing?")) cfg$UseGithubActions <- TRUE
+  
+  if(isTRUE(cfg$UseGithubActions)) {
+    addGitHubActions(lib)
+    # remove travis related parts
+    travisfile <- paste0(lib,"/.travis.yml")
+    if(file.exists(travisfile)) {
+      file.remove(travisfile)
+      rbuildignore <- paste0(lib,"/.Rbuildignore")
+      if(file.exists(rbuildignore)) {
+        a <- readLines(rbuildignore)
+        writeLines(grep("travis",a,value=TRUE,invert=TRUE), rbuildignore)
+      }
+      travistest <- paste0(lib,"/tests/testthat/test-travisCI.R")
+      if(file.exists(travistest)) file.remove(travistest)
+    }
+  }
+  
+  ck <- devtools::check(".",cran=cran)
 
   #Filter warnings and notes which are accepted
-  accepted_warnings <- c("Warning: package '.*' was built under R version",
-                         "Warning: namespace '.*' is not available and has been replaced")
   for(aw in cfg$AcceptedWarnings) {
     ck$warnings <- grep(aw, ck$warnings, value=TRUE,invert=TRUE)
   }

README.md

@@ -1,6 +1,6 @@
 # Code Manipulation and Analysis Tools
 
-R package **lucode2**, version **0.7.0**
+R package **lucode2**, version **0.8.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/lucode2)](https://cran.r-project.org/package=lucode2)   [![R build status](https://github.com/pik-piam/lucode2/workflows/check/badge.svg)](https://github.com/pik-piam/lucode2/actions) [![codecov](https://codecov.io/gh/pik-piam/lucode2/branch/master/graph/badge.svg)](https://codecov.io/gh/pik-piam/lucode2)
 
@@ -39,7 +39,7 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 To cite package **lucode2** in publications use:
 
 Dietrich J, Klein D, Giannousakis A, Bonsch M, Bodirsky B, Baumstark L (2020). _lucode2: Code Manipulation and
-Analysis Tools_. R package version 0.7.0.
+Analysis Tools_. R package version 0.8.0.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,7 +48,7 @@ A BibTeX entry for LaTeX users is
   title = {lucode2: Code Manipulation and Analysis Tools},
   author = {Jan Philipp Dietrich and David Klein and Anastasis Giannousakis and Markus Bonsch and Benjamin Leon Bodirsky and Lavinia Baumstark},
   year = {2020},
-  note = {R package version 0.7.0},
+  note = {R package version 0.8.0},
 }
 ```
 

inst/extdata/codecov.yml

@@ -0,0 +1,16 @@
+
+coverage:
+  precision: 2
+  round: down
+  range: "0...95"
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true

inst/extdata/test-buildlibrary.yaml

@@ -21,6 +21,10 @@ jobs:
       - uses: r-lib/actions/setup-r@v1
 
       - uses: r-lib/actions/setup-pandoc@v1
+      
+      - name: Install dependencies
+        run: |
+          sudo apt-get install libcurl4-openssl-dev libgit2-dev
 
       - name: Query dependencies
         run: |
@@ -36,12 +40,12 @@ jobs:
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
           restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
-      - name: Install dependencies
+      - name: Install R dependencies
         run: |
           repos <- c("https://cloud.r-project.org","https://rse.pik-potsdam.de/r/packages/")
-          install.packages(c("remotes","lucode2"), repos=repos)
+          install.packages(c("remotes"), repos=repos)
           remotes::install_deps(dependencies = TRUE, repos=repos)
-          remotes::install_cran("covr")
+          remotes::install_cran(c("covr","lucode2"), repos=repos)
         shell: Rscript {0}
 
       - name: Test coverage
@@ -51,4 +55,4 @@ jobs:
       - name: Validation key 
         run: if(!lucode2:::validkey()$valid) stop("Invalid build key!")
         shell: Rscript {0}
-        
+