Merge branch 'feat/SBG-25314' into 'develop'

Add options for file selection guide customization in file picker module

See merge request r-shiny-apps/sbshinymodules!10

.gitlab-ci.yml

@@ -1,34 +1,10 @@
-image: rocker/r-ver:4.4.0
+image: images.sbgenomics.com/marko_trifunovic/sbshinymodules-ci-docker:latest
 
 stages:
-  - build
-  - document
-  - check
-  - deploy
-
-variables:
-  APT_DEPS: "git libssl-dev libcurl4-openssl-dev libfreetype6-dev libfribidi-dev libharfbuzz-dev libxml2-dev libfontconfig1-dev libgit2-dev pandoc libicu-dev libz-dev libcurl4-openssl-dev libjpeg-dev libpng-dev libtiff-dev make zlib1g-dev libbz2-dev liblzma-dev libattr1-dev"
-  IMAGE: dockerhub.sbgenomics.com/$CI_PROJECT_NAME
-  RENV_PATHS_CACHE: ${CI_PROJECT_DIR}/cache
-  RENV_PATHS_LIBRARY: ${CI_PROJECT_DIR}/renv/library
-  RENV_CONFIG_REPOS_OVERRIDE: http://cran.r-project.org
-  LIBRARY_NAME: sbShinyModules
-
-cache:
-  key: $CI_JOB_NAME
-  paths:
-    - ${RENV_PATHS_CACHE}
-    - ${RENV_PATHS_LIBRARY}
-
-before_script:
-  - mkdir -p ${RENV_PATHS_CACHE} ${RENV_PATHS_LIBRARY}
-  - apt-get -qq update;
-  - apt-get -y install ${APT_DEPS}
-  - apt-get install -y nodejs
-  - apt-get install -y npm
-  - R -e "install.packages(c('remotes', 'devtools', 'golem'), repos='http://cran.us.r-project.org')"
-  - R -e "if (!requireNamespace('renv', quietly = TRUE)) remotes::install_version('renv')"
-  - R -e "renv::restore(lockfile = 'renv.lock')"
+  - build           # Build the R package binaries
+  - document        # Generate package documentation using 'roxygen2'
+  - check           # Run various checks (linting, coverage) on the codebase
+  - deploy          # Deploy the package site using pkgdown
 
 buildbinary:
   stage: build

DESCRIPTION

@@ -31,13 +31,16 @@ Imports:
     reactable.extras,
     reactR,
     rlang,
+    stats,
     shiny,
     shinyalert,
     shinydashboard,
     shinyFeedback,
     shinyjs,
     shinyWidgets,
-    tidyr
+    tidyr,
+    commonmark,
+    xml2
 Suggests:
     knitr,
     rmarkdown,
@@ -50,6 +53,4 @@ Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.2
 Language: en-US
-Remotes: 
-    jeroen/jsonlite
 VignetteBuilder: knitr

NAMESPACE

@@ -18,12 +18,14 @@ importFrom(bslib,input_task_button)
 importFrom(checkmate,assert_character)
 importFrom(checkmate,assert_choice)
 importFrom(checkmate,assert_data_frame)
+importFrom(checkmate,assert_flag)
 importFrom(checkmate,assert_function)
 importFrom(checkmate,assert_list)
 importFrom(checkmate,assert_logical)
 importFrom(checkmate,assert_string)
 importFrom(checkmate,assert_subset)
 importFrom(checkmate,assert_true)
+importFrom(commonmark,markdown_html)
 importFrom(dplyr,join_by)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
@@ -63,4 +65,10 @@ importFrom(shinyWidgets,useShinydashboard)
 importFrom(shinyalert,shinyalert)
 importFrom(shinydashboard,box)
 importFrom(shinyjs,useShinyjs)
+importFrom(stats,na.exclude)
 importFrom(tidyr,pivot_wider)
+importFrom(tools,file_ext)
+importFrom(xml2,read_html)
+importFrom(xml2,xml_attr)
+importFrom(xml2,xml_find_all)
+importFrom(xml2,xml_remove)