Merge pull request #201 from Sage-Bionetworks/dev

Dev

.Rprofile

@@ -1,10 +1,10 @@
-source("renv/activate.R")
-
 .First <- function() {
   options(
     repos = c(
       CRAN = "https://cran.rstudio.com/",
       SAGE = "http://ran.synapse.org"
     )
   )
-}
+}
+
+source("renv/activate.R")

.github/workflows/shinyapps_deploy.yml

@@ -20,17 +20,16 @@ on:
 jobs:
   shiny-deploy:
     runs-on: ubuntu-latest
-    # This image seems to be based on rocker/r-ver which in turn is based on debian
     container: rocker/rstudio:4.1.2
     env:
       # This should not be necessary for installing from public repo's however remotes::install_github() fails without it.
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      GITHUB_PAT:  ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - name: Install System Dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install -y pip python3.8-venv libcurl4-openssl-dev libpng-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libtiff-dev libxml2-dev
+          sudo apt-get install -y pip libcurl4-openssl-dev libpng-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libtiff-dev libxml2-dev
         # this action checks out the $GITHUB_WORKSPACE repository so that the workflow can access it
       - uses: actions/checkout@v3
         # this action sets up pandoc
@@ -45,7 +44,9 @@ jobs:
         # deploy app using rsconnect
       - name: Authorize and deploy app
         run: |
+          renv::restore()
           install.packages("rsconnect")
+
           refName <- Sys.getenv("GITHUB_REF_NAME")
           repo <- Sys.getenv("GITHUB_REPOSITORY")
           appName <- strsplit(repo, "/")[[1]][2]

DESCRIPTION

@@ -1,34 +1,36 @@
 Package: dataflow
-Title: Data Flow
+Title: Data Flow App Demo
 Version: 0.0.0.9000
 Authors@R: person('L', 'Wolfe', email = '[email protected]', role = c('cre', 'aut'))
 Description: A data flow package.
-License: What license is it under?
+License: MIT + file LICENSE
 Imports: 
     attempt,
-    config (>= 0.3.1),
+    config,
     dcamodules,
+    dfamodules,
     dplyr,
     DT,
-    ggplot2,
     glue,
-    golem (>= 0.3.1),
+    golem,
     htmltools,
-    lubridate,
+    jsonlite,
     magrittr,
     pkgload,
     processx,
-    reticulate,
-    shiny (>= 1.7.1),
-    shinydashboard,
-    shinydashboardPlus,
-    shinyjs,
-    waiter
+    shiny,
+    shinyjs
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.3
 Suggests: 
     spelling,
-    testthat (>= 3.0.0)
+    testthat,
+    devtools,
+    usethis,
+    renv
 Config/testthat/edition: 3
 Language: en-US
+Remotes: 
+    Sage-Bionetworks/dcamodules,
+    Sage-Bionetworks/dfamodules

NAMESPACE

@@ -1,39 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
-export(calculate_items_per_manifest)
-export(convert_column_type)
-export(create_dashboard)
-export(dt_replace_na)
-export(generate_data_flow_manifest_skeleton)
-export(get_all_manifests)
-export(get_colname_by_type)
-export(get_na_replace_colnames)
-export(get_na_replace_defs)
-export(get_renamed_colnames)
-export(list_to_dataframe)
-export(manifest_download)
-export(model_submit)
-export(prep_manifest_dash)
-export(prep_manifest_dfa)
-export(prep_manifest_submit)
-export(rearrange_dataframe)
 export(run_app)
-export(storage_project_datasets)
-export(storage_project_manifests)
-export(storage_projects)
-export(style_dashboard)
-export(true_false_icon)
-export(update_data_flow_manifest)
-export(update_dfs_manifest)
-export(visualize_component)
 import(shiny)
 importFrom(golem,activate_js)
 importFrom(golem,add_resource_path)
 importFrom(golem,bundle_resources)
 importFrom(golem,favicon)
 importFrom(golem,with_golem_options)
 importFrom(magrittr,"%>%")
-importFrom(shiny,NS)
 importFrom(shiny,shinyApp)
-importFrom(shiny,tagList)