Merge pull request #48 from brucehoff/develop

ShinyApps deployment

.github/workflows/deploy.yml

@@ -2,15 +2,11 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 
 name: shiny-deploy
-
-env:
-  RENV_PATHS_ROOT: ~/.local/share/renv
 
 on:
   push:
     branches:
       - develop
-      - IT-828
       - release*
 
 jobs:
@@ -26,24 +22,28 @@ jobs:
           sudo apt-get install -y libcurl4-openssl-dev gdal-bin libgdal-dev default-jdk
  
       - uses: actions/checkout@v2
-
-      - name: Cache packages
-        uses: actions/cache@v1
-        with:
-          path: ${{ env.RENV_PATHS_ROOT }}
-          key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-renv-
+
+      - name: disable renv
+        run: rm .Rprofile
 
-      - name: Restore packages
+      - name: Install packages
         shell: sudo Rscript {0} # running this step as 'sudo' is necessary to be able to install packages in default library
         run: |
-          if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
-          options(repos = c(RSPM = "https://packagemanager.rstudio.com/all/latest"))
-          renv::restore()
-        
+          options(repos = 'http://cran.fhcrc.org')
+          install.packages('BiocManager', dependencies=TRUE)
+          options(repos = c(BiocManager::repositories(),  getOption("repos")))
+ 
+          install.packages(c("shiny","golem","processx","attempt","DT","glue","htmltools",
+             "ggplot2","plotly","shinydashboard","readr","shinycssloaders","wrapr","forcats",
+             "scales","ggridges","maftools","pkgload","waiter","dr4pl","rsconnect", "brio", "callr", 
+             "diffobj", "praise", "rematch2", "markdown", "rmarkdown", "testthat", "tinytex", "waldo",
+             "TSP", "anytime", "ca", "egg", "gclus", "heatmaply", "qap", "seriation", "shinyWidgets"), 
+             dependencies=TRUE)
+
       - name: Deploy app
         run: |
+          options(repos = c(BiocManager::repositories(), 'http://cran.fhcrc.org', getOption("repos")))
+          
           branch<-Sys.getenv("GITHUB_REF_NAME")
           repo<-Sys.getenv("GITHUB_REPOSITORY")
           appName<-strsplit(repo, "/")[[1]][2]
@@ -54,9 +54,7 @@ jobs:
           rsConnectToken <- "${{ secrets.RSCONNECT_TOKEN }}"
           rsConnectSecret <- "${{ secrets.RSCONNECT_SECRET }}" 
           rsconnect::setAccountInfo(rsConnectUser, rsConnectToken, rsConnectSecret)
-          # omit archive/ folder from the collection to be deployed
-          # (Tried using .rcsignore file but it did not work as documented.)
-          appFiles<-dir()[which(dir()!="archive")]
+          appFiles<-dir()[which(dir()!="renv")]
           rsconnect::deployApp(appName = appName, appFiles=appFiles)
           # important NOT to run this step as sudo, otherwise env var's will be missing
         shell: Rscript {0}

.gitignore

@@ -3,3 +3,4 @@
 .RData
 .Ruserdata
 .DS_Store
+.project

DESCRIPTION

@@ -29,12 +29,141 @@ Imports:
     pkgload,
     waiter,
     dr4pl,
-    rsconnect
+    rsconnect,
+    MASS,
+    Matrix,
+    R6,
+    RColorBrewer,
+    Rcpp,Rdpack,
+    Rhtslib,
+    TSP,
+    askpass,
+    assertthat,
+    base64enc,
+    bit,
+    bit64,
+    brew,
+    brio,
+    bslib,
+    cachem,
+    callr,
+    cli,
+    clipr,
+    cluster,
+    codetools,
+    colorspace,
+    commonmark,
+    config,
+    cpp11,
+    crayon,
+    credentials,
+    crosstalk,
+    curl,
+    data.table,
+    dendextend,
+    desc,
+    diffobj,
+    digest,
+    dockerfiler,
+    dplyr,
+    egg,
+    ellipsis,
+    evaluate,
+    fansi,
+    farver,
+    fastmap,
+    fontawesome,
+    foreach,fs,
+    gclus,
+    generics,
+    gert,
+    gh,
+    gitcreds,
+    gridExtra,
+    gtable,
+    heatmaply,
+    here,
+    highr,
+    hms,
+    htmlwidgets,
+    httpuv,
+    httr,
+    ini,
+    isoband,
+    iterators,
+    jquerylib,
+    jsonlite,
+    knitr,
+    labeling,
+    later,
+    lattice,
+    lazyeval,
+    lifecycle,
+    magrittr,
+    markdown,
+    mgcv,
+    mime,
+    munsell,
+    nlme,
+    openssl,
+    packrat,
+    pillar,
+    pkgbuild,
+    pkgconfig,
+    plyr,
+    praise,
+    prettyunits,
+    progress,
+    promises,
+    ps,
+    purrr,
+    qap,
+    rappdirs,
+    rbibutils,
+    registry,
+    rematch2,
+    remotes,
+    renv,
+    reshape2,
+    rlang,
+    rmarkdown,
+    roxygen2,
+    rprojroot,
+    rstudioapi,
+    sass,
+    seriation,
+    shinyWidgets,
+    sourcetools,
+    stringr,
+    survival,
+    sys,
+    tensor,
+    testthat,
+    tibble,
+    tidyr,
+    tidyselect,
+    tinytex,
+    tzdb,
+    usethis,
+    utf8,
+    vctrs,
+    viridis,
+    viridisLite,
+    vroom,
+    waldo,
+    webshot,
+    whisker,
+    withr,
+    xfun,
+    xml2,
+    xtable,
+    yaml,
+    zip,
+    zlibbioc
 RoxygenNote: 7.1.2
 Suggests: 
     testthat (>= 2.1.0),
-    knitr,
-    rmarkdown
+    knitr
 VignetteBuilder: knitr
 URL: https://github.com/allaway/kairos
 BugReports: https://github.com/allaway/kairos/issues

README.Rmd

@@ -30,3 +30,13 @@ You can install the latest version of kairos from with:
 devtools::install_github("nf-osi/kairos")
 ```
 
+## Deployment to ShinyApps
+
+- Enable workflows in the GitHub repository
+- Under [secrets](https://github.com/nf-osi/kairos/settings/secrets/actions) click 'New repository secret'
+- Enter secrets for `RSCONNECT_USER`, `RSCONNECT_TOKEN`, and `RSCONNECT_SECRET`, the values for which are saved in Sage's LastPass.
+- Trigger the GitHub action.
+- Check out the app here: https://sagebio.shinyapps.io/kairos-staging.
+- After verifying correctness, create a Git branch named release*, e.g., `release-1.0`.
+- The application will become available at https://sagebio.shinyapps.io/kairos
+