v23.12.1 testing into staging

.github/workflows/shinyapps_deploy.yml

@@ -27,6 +27,7 @@ jobs:
       SCHEMATIC_URL_PROD: https://schematic.api.sagebionetworks.org
       # This should not be necessary for installing from public repo's however remotes::install_github() fails without it.
       GITHUB_PAT:  ${{ secrets.GITHUB_TOKEN }}
+
 
     steps:
       - name: Install System Dependencies
@@ -39,15 +40,28 @@ jobs:
 
       # this action sets up pandoc
       - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+          r-version: 'renv' 
+
+      # install packages
+      - name: Install rsconnect
+        run: |
+          install.packages("renv")
+          renv::upgrade(version = "0.17.3")
+          renv::install("rsconnect@0.8.29")
+        shell: Rscript {0}
 
       # this action activates renv
       - uses: r-lib/actions/setup-renv@v2
+
         # deploy app using rsconnect
       - name: Authorize and deploy app
         run: |
-          renv::restore()
-          install.packages("rsconnect")
-
+          renv::restore(packages = "renv")
+
           refName <- Sys.getenv("GITHUB_REF_NAME")
           repo <- Sys.getenv("GITHUB_REPOSITORY")
           appName <- strsplit(repo, "/")[[1]][2]
@@ -98,6 +112,7 @@ jobs:
           # get app names. If app exists, configure then deploy. Otherwise
           # deploy then configure.
           apps <- rsconnect::applications()$name
+
           if (appName %in% apps) {
             rsconnect::configureApp(appName = appName, size = "xxxlarge", logLevel = "verbose")
             rsconnect::deployApp(appName = appName)

.pre-commit-config.yaml

@@ -0,0 +1,72 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.3.2.9019
+    hooks:
+    -   id: style-files
+        args: [--style_pkg=styler, --style_fun=tidyverse_style]
+    # codemeta must be above use-tidy-description when both are used
+    # -   id: codemeta-description-updated
+    -   id: use-tidy-description
+    -   id: lintr
+    -   id: readme-rmd-rendered
+    -   id: parsable-R
+    -   id: no-browser-statement
+    -   id: no-debug-statement
+    -   id: deps-in-desc
+    -   id: spell-check
+        exclude: >
+          (?x)^(
+          .*\.[rR]|
+          .*\.feather|
+          .*\.jpeg|
+          .*\.pdf|
+          .*\.png|
+          .*\.py|
+          .*\.RData|
+          .*\.rds|
+          .*\.Rds|
+          .*\.Rproj|
+          .*\.sh|
+          (.*/|)\.gitignore|
+          (.*/|)\.gitlab-ci\.yml|
+          (.*/|)\.lintr|
+          (.*/|)\.pre-commit-.*|
+          (.*/|)\.Rbuildignore|
+          (.*/|)\.Renviron|
+          (.*/|)\.Rprofile|
+          (.*/|)\.travis\.yml|
+          (.*/|)appveyor\.yml|
+          (.*/|)NAMESPACE|
+          (.*/|)renv/settings\.dcf|
+          (.*/|)renv\.lock|
+          (.*/|)WORDLIST|
+          \.github/workflows/.*|
+          data/.*|
+          )$
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks: 
+    -   id: check-added-large-files
+        args: ['--maxkb=200']
+    -   id: file-contents-sorter
+        files: '^\.Rbuildignore$'
+    -   id: end-of-file-fixer
+        exclude: '\.Rd'
+    -   id: check-merge-conflict
+-   repo: https://github.com/pre-commit-ci/pre-commit-ci-config
+    rev: v1.5.1
+    hooks:
+    # Only reuiqred when https://pre-commit.ci is used for config validation
+    -   id: check-pre-commit-ci-config
+-   repo: local
+    hooks:
+    -   id: forbid-to-commit
+        name: Don't commit common R artifacts
+        entry: Cannot commit .Rhistory, .RData, .Rds or .rds.
+        language: fail
+        files: '\.(Rhistory|RData|Rds|rds)$'
+        # `exclude: <regex>` to allow committing specific files
+ci:
+    autoupdate_schedule: monthly

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dataflow
 Title: Data Flow App Demo
-Version: 23.06.1
+Version: 23.10.1
 Authors@R: person('L', 'Wolfe', email = 'loren.wolfe@sagebase.org', role = c('cre', 'aut'))
 Description: A data flow package.
 License: MIT + file LICENSE