- updated structure of documentation files

- support to Bioc 3.19 (except workflow - waiting for update of Bioc docker images)
- bumped version to 1.1.1

.github/workflows/check-bioc.yml

@@ -53,8 +53,8 @@ jobs:
       matrix:
         config:
           - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          # - { os: macOS-latest, r: '4.3', bioc: '3.18'}
-          # - { os: windows-latest, r: '4.3', bioc: '3.18'}
+          # - { os: macOS-latest, r: '4.4', bioc: '3.19'}
+          # - { os: windows-latest, r: '4.4', bioc: '3.19'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: CytoPipelineGUI
 Title: GUI's for visualization of flow cytometry data analysis pipelines
-Version: 0.99.2
+Version: 1.1.1
 Authors@R: 
     c(person(given = "Philippe",
              family = "Hauchamps",
@@ -21,10 +21,12 @@ Description: This package is the companion of the `CytoPipeline` package.
  Two shiny applications are provided, i.e.
  an interactive flow frame assessment and comparison tool and
  an interactive scale transformations visualization and adjustment tool.
-License: GPL (>=3) | file LICENSE
+License: GPL-3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
+BugReports: https://github.com/UCLouvain-CBIO/CytoPipelineGUI/issues
+URL: https://uclouvain-cbio.github.io/CytoPipelineGUI
 biocViews: FlowCytometry, Preprocessing, QualityControl, WorkflowStep,
  ImmunoOncology, Software, Visualization, GUI, ShinyApps
 Collate: 

NEWS.md

@@ -1,3 +1,8 @@
+# CytoPipelineGUI 1.1
+
+## CytoPipelineGUI 1.1.1
+- refactored documentation files
+
 # CytoPipelineGUI 0.99
 
 ## CytoPipelineGUI 0.99.2

R/CytoPipelineGUI.R

@@ -16,6 +16,8 @@
 
 #' @title CytoPipelineGUI package
 #' 
+#' @docType package
+#' 
 #' @name CytoPipelineGUI
 #'
 #' @rdname CytoPipelineGUI

R/shiny.R

@@ -14,7 +14,6 @@
 # GNU General Public License for more details (<http://www.gnu.org/licenses/>).
 
 #' @title interactive display and modification of scale transform list
-#' @rdname CytoPipelineGUI
 #' @description this application allows the user to visualize a scale 
 #' transformation list, possibly amending it channel after channel, 
 #' and save the results on disk. 
@@ -24,7 +23,7 @@
 #' CytoPipeline experiments
 #' @import shiny
 #' @import CytoPipeline
-#' @return - for `ScaleTransformApp`: no return value
+#' @return no return value
 #' @export
 #' @examples
 #' 
@@ -91,13 +90,12 @@ ScaleTransformApp <- function(dir = ".") {
 
 #' @title interactive visualization of flow cytometry data analysis pipeline 
 #' objects stored in cache
-#' @rdname CytoPipelineGUI
 #'
 #' @param dir the root directory into which the engine will look for existing
 #' CytoPipeline experiments
 #' @param debug if TRUE, will output messages on the console tracking the
 #' shiny events, for debugging purposes
-#' @return - for `CytoPipelineCheckApp`: no return value
+#' @return no return value
 #' @import shiny
 #' @import CytoPipeline
 #' @export