Merge branch 'master' into feature/qfeature

.github/workflows/build.yml

@@ -66,6 +66,7 @@ jobs:
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          extra-repositories: https://janmarvin.r-universe.dev
 
       # Step 4: Setup pandoc from r-lib
       - name: Setup pandoc from r-lib

DESCRIPTION

@@ -4,7 +4,7 @@ Title: MetFamily: Discovering Regulated Metabolite Families in Untargeted Metabo
 Version: 0.99.4
 Date: 2024-08-22
 Author: c( person("Hendrik", "Treutler, role = c("aut"), email = "[email protected]"),
-           person("Khabat", "Vahabi, role = c("aut"), email = "[email protected]"),
+           person("Khabat", "Vahabi", role = c("aut"), email = "[email protected]"),
            person("Norman", "Storz", 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")) )
@@ -41,14 +41,16 @@ Imports:
     QFeatures,
     stats,
     utils
-Remotes: decisionpatterns/searchable
+Remotes: 
+    decisionpatterns/searchable
 Suggests:
     knitr,
     BiocStyle,
-    testthat
+    testthat,
+    shinytest2
 VignetteBuilder: knitr
-Maintainer: Hendrik Treutler<hendrik.treutler@ipb-halle.de>
-Description: We present a novel approach for the untargeted discovery 
+Maintainer: Steffen Neumann <sneumann@ipb-halle.de>
+Description: 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 

Dockerfile

@@ -1,10 +1,10 @@
 #FROM sneumann/metfamily-base:latest
-FROM sneumann/metfamily-base:4.3.2
+FROM sneumann/metfamily-base:4.4
+#FROM sneumann/metfamily-base:4.3.2
 #FROM sneumann/metfamily-base:4.0.5
 #FROM sneumann/metfamily-base:3.6.3
 
-MAINTAINER Steffen Neumann <[email protected]>
-
+LABEL maintainer="Steffen Neumann <[email protected]>"
 LABEL Description="MetFamily helps identifying metabolites and groups them into metabolite clusters (a.k.a. families)."
 
 ADD . /tmp/MetFamily

Dockerfile-base

@@ -1,8 +1,7 @@
 # syntax=docker/dockerfile:1.3-labs
-FROM rocker/shiny:4.3.2
-
-MAINTAINER Steffen Neumann <[email protected]>
+FROM rocker/shiny:4.4
 
+LABEL maintainer="Steffen Neumann <[email protected]>"
 LABEL Description="MetFamily Base Image with dependencies."
 
 ## Older base images might need libigraph0-dev instead of libigraph-dev 
@@ -16,6 +15,7 @@ RUN echo 'sanitize_errors off;disable_protocols xdr-streaming xhr-streaming ifra
 ## The following Rprofile allows to use CRAN snapshots
 ## (The HERE document COPY <<EOF requires syntax=docker/dockerfile:1.3-labs)
 ## We have tested the following combinations of FROM and CRAN:
+## rocker/shiny:4.3.2
 ## rocker/shiny:3.6.3	https://packagemanager.posit.co/cran/2020-04-23/
 ## rocker/shiny:4.0.5	https://packagemanager.posit.co/cran/2021-03-01/
 ## rocker/shiny:4.3.2	https://packagemanager.posit.co/cran/2023-12-01/

NEWS

@@ -1,3 +1,12 @@
+CHANGES IN VERSION 0.99.4
+-------------------------
+NEW FEATURES
+
+    o Reading and parsing of intensity matrix now via QFeatures package
+    o First parallelisation (and speedup) in distance matrix calculation
+    o Adding of new contributor, change of maintainer
+
+
 CHANGES IN VERSION 0.99.2
 -------------------------
 

R/DataProcessing.R

@@ -196,6 +196,8 @@ readProjectData <- function(fileLines, progress = FALSE)
   listMatrixRows <- NULL
   listMatrixCols <- NULL
 
+  ## Disable command line reading of answer
+  if (FALSE) {
   ################################################################################
   #Start of importing  annotation part1 from two
   # Display the message and give the user the option to choose whether to upload the annotation file or not. 
@@ -257,6 +259,7 @@ readProjectData <- function(fileLines, progress = FALSE)
 
   #####################################################################################################################################
   #end of importing  annotation part1 from two
+  }
 
   listMatrixVals <- NULL
 
@@ -315,6 +318,8 @@ readProjectData <- function(fileLines, progress = FALSE)
     dataFrameHeader[3, target + 1] <- annotationColumnName
   }
 
+  ## STN: Disabled. 
+  if (FALSE) {
   #Start of importing annotation part2 from two
   ################################################################################
    #adding HEX color codes from external annotations to the annotationColorsMapInitValue of dataFrameHeader
@@ -336,6 +341,7 @@ readProjectData <- function(fileLines, progress = FALSE)
   }
 ################################################################################
 #End of importing  annotation part2 from two
+  }
 
   annotationColumnIndex <- which(metaboliteProfileColumnNames == annotationColumnName)
   annotationColorsValue <- dataFrameHeader[2, annotationColumnIndex]