Merge branch 'master' into fix/issue74

DESCRIPTION

@@ -1,11 +1,14 @@
 Package: MetFamily
 Type: Package
 Title: MetFamily: Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies
-Version: 0.99.1
-Date: 2016-07-24
-Author: c( person("Hendrik", "Treutler, role = c("aut", "cre"), email = "[email protected]") )
+Version: 0.99.2
+Date: 2024-03-02
+Author: c( person("Hendrik", "Treutler, role = c("aut"), email = "[email protected]"),
+           person("Khabat", "Vahabi, role = c("aut"), email = "[email protected]"),
+           person(given = "Steffen", family = "Neumann", email = "[email protected]",
+           role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7899-7192")) )
 Depends:
-    R (>= 3.2.2),
+    R (>= 3.5.0),
     htmltools,
     shiny,
     shinyBS,
@@ -33,8 +36,7 @@ Depends:
 Remotes: decisionpatterns/searchable
 Suggests:
     knitr,
-    testthat,
-    shinytest2
+    testthat
 VignetteBuilder: knitr
 Maintainer: Hendrik Treutler<[email protected]>
 Description: We present a novel approach for the untargeted discovery of metabolite families offering a bird's eye view of metabolic regulation in comparative metabolomics. We implemented the presented methodology in the easy-to-use web application MetFamily to enable the analysis of comprehensive metabolomics studies for all researchers worldwide.

Dockerfile

@@ -1,7 +1,7 @@
 #FROM sneumann/metfamily-base:latest
-FROM sneumann/metfamily-base:4.3.2
+#FROM sneumann/metfamily-base:4.3.2
 #FROM sneumann/metfamily-base:4.0.5
-#FROM sneumann/metfamily-base:3.6.3
+FROM sneumann/metfamily-base:3.6.3
 
 MAINTAINER Steffen Neumann <[email protected]>
 

NEWS

@@ -0,0 +1,10 @@
+CHANGES IN VERSION 0.99.2
+-------------------------
+
+NEW FEATURES
+
+    o More and better colors available for plotting (thanks @khabatv)
+    o improving package and app source organisation
+    o runMetFamily() function to launch the Shiny app
+    o Started testing infrastructure
+

R/runMetFamily.R

@@ -1,12 +1,16 @@
 
-##' Start the web app in browser
+##' Run the web app in browser
 ##'
 ##' @title Start the web app in browser
 ##' @export
-##' @author Hendrik Treutler
+##' @author Hendrik Treutler, Steffen Neumann
 ##' @examples
-##' startMetFamily()
-startMetFamily <- function(){
+##' \dontrun{
+##' runMetFamily()
+##' }
+runMetFamily <- function(){
   shiny::runApp(appDir = system.file("MetFamily", package = "MetFamily"), 
   launch.browser = TRUE)
-}
+}
+
+startMetFamily <- runMetFamily

inst/MetFamily/server.R

@@ -443,16 +443,12 @@ shinyServer(
     ## about page
     output$rInfo <- renderText({
       print(paste("init rInfo"))
-      #paste(R.Version()$version.string, "\nwd: ", getwd(), sep = "")
       paste(
         R.Version()$version.string, 
-        "\nMetFamily build: ", metFamilyBuilt, "-", system(command = "hostname", intern = TRUE),
+        "\nMetFamily build: ", metFamilyAppVersion, "-", system(command = "hostname", intern = TRUE),
         "\nMetFamily package: ", packageVersion,
-        #"\n", getwd(),
-        #"\n", paste(list.files(path = getwd(), all.files = F, full.names = F, recursive = T, include.dirs = F), collapse = "\n"),
         sep = ""
       )
-      #R.Version()$version.string
     })
     output$ipbImage <- renderImage({
       file <- getFile("logo_ipb_en.png")

inst/MetFamily/version.R

@@ -1,13 +1,10 @@
 ## MetFamily properties
+
 toolName       <- "MetFamily"
 toolVersion    <- "1.0"    
-metFamilyBuilt <- "1.3.2"
+metFamilyAppVersion <- "1.3.3"
 
-if ("MetFamily" %in% rownames(installed.packages())) {
-  packageVersion <- package.version("MetFamily")
-} else {
-  packageVersion <- "not packaged"
-}
+packageVersion <- package.version("MetFamily")
 
 
 

inst/MetFamily/www/ipbfooter.html

@@ -35,7 +35,7 @@
       <div id="sitemap-header">
         <div class="wrapper">
           <ul id="left-nav">
-            <li><a class href="#" rel="nofollow"><img style="height:85px" src="img/2020_Logo_schrift_weiß_Trans_EN.png" alt="IPB-Halle" /></a></li>
+            <li><a class href="#" rel="nofollow"><img style="height:85px" src="img/2020_Logo_schrift_weiss_Trans_EN.png" alt="IPB-Halle" /></a></li>
             <li><span class="border"></span></li>
             <li><a class href="#" rel="nofollow"><img style="height:85px" src="img/Leibniz__Logo_EN_Negative_100mm.svg" alt="Die Leibniz-Gemeinschaft" /></a></li>
             <li><span class="border"></span></li>