Merge pull request #380 from pharmaR/dev

Next release (for shiny conf 2023)

.Rbuildignore

@@ -1,12 +1,22 @@
+^renv$
+^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^data-raw$
 dev_history.R
 ^dev$
 $run_dev.*
-$credentials.*
-$database.*
 ^README\.Rmd$
 ^\.github$
+^LICENSE\.md$
+^.open$
+^docs$
+^loggit.json$
 ^app\.R$
 ^rsconnect$
+^((?!/).)*sqlite$
+^auto_decisions\.json$
+
+_\.new\.png$
+^_pkgdown\.yml$
+^pkgdown$

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

.github/workflows/R-CMD-check-dev.yaml

@@ -0,0 +1,56 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [dev]
+  pull_request:
+    branches: [dev]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          # - {os: macOS-latest,   r: 'release'}
+          # - {os: windows-latest, r: 'release'}
+          # - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          # - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - name: Install Linux system dependencies
+        if: runner.os == 'Linux'
+        shell: bash
+        run: |
+          sudo apt-get install -y libcurl4-openssl-dev
+          sudo apt-get install -y libharfbuzz-dev
+          sudo apt-get install -y libfribidi-dev
+
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-renv@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+          extra-packages: rcmdcheck
+
+      - name: Install riskassessment
+        shell: bash
+        run: R CMD INSTALL --preclean .
+
+      - uses: r-lib/actions/check-r-package@v2

.github/workflows/R-CMD-check.yaml → .github/workflows/R-CMD-check-master.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, dev]
+    branches: [main, master]
   pull_request:
-    branches: [main, master, dev]
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -29,18 +29,28 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - name: Install Linux system dependencies
+        if: runner.os == 'Linux'
+        shell: bash
+        run: |
+          sudo apt-get install -y libcurl4-openssl-dev
+          sudo apt-get install -y libharfbuzz-dev
+          sudo apt-get install -y libfribidi-dev
+          
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-renv@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
           extra-packages: rcmdcheck
 
+      - name: Install riskassessment
+        shell: bash
+        run: R CMD INSTALL --preclean .
+
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/pkgdown.yaml

@@ -28,7 +28,7 @@ jobs:
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: r-lib/actions/setup-renv@v2
         with:
           extra-packages: any::pkgdown, local::.
           needs: website
@@ -37,6 +37,10 @@ jobs:
         run: install.packages("remotes") ; remotes::install_version("pkgdown", version = "2.0.3", repos = "cran.rstudio.com", dependencies = FALSE)
         shell: Rscript {0}
 
+      - name: Install riskassessment
+        shell: bash
+        run: R CMD INSTALL --preclean .
+
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}

.github/workflows/render-readme.yml

@@ -0,0 +1,40 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+
+# this is set to re-render whenever README.Rmd is changed on a given branch
+# the file is rendered and committed to the same branch
+# adapted from: https://github.com/r-lib/actions/tree/v2/examples#render-rmarkdown
+on:
+  push:
+    paths: ['README.Rmd']
+
+name: render-readme
+
+jobs:
+  render-rmarkdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+
+      # install packages needed
+      - name: install required packages
+        run: Rscript -e 'install.packages(c("rmarkdown"))'
+
+      - name: Render Rmarkdown files and Commit Results
+        run: |
+          Rscript -e 'rmarkdown::render("README.Rmd", output_format = "github_document")'
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add README.md || echo "WARN: README.md was not updated"
+          git add man/figures/README-* || echo "No figure updates were found"
+          git commit -m 'Re-build Rmarkdown files' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"

.github/workflows/test-coverage.yaml

@@ -0,0 +1,36 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master, dev]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-renv@v2
+        with:
+          extra-packages: covr
+
+      - name: Install riskassessment
+        shell: bash
+        run: R CMD INSTALL --preclean .
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

.gitignore

@@ -1,8 +1,14 @@
 rsconnect/
-*.sqlite
+/*.sqlite
 .Rproj.user
 .Rhistory
 .RData
 .Ruserdata
 loggit.json
 .DS_Store
+inst/doc
+# {shinytest2}: Ignore new debug snapshots for `$expect_values()`
+*_.new.png
+auto_decisions.json
+^docs$
+docs/

DESCRIPTION

@@ -1,15 +1,21 @@
 Package: riskassessment
 Title: A web app designed to interface with the `riskmetric` package
-Version: 0.0.1
-Authors@R: as.person(c( 
-    "Aaron Clark <[email protected]> [aut, cre]",
-    "Robert Krajcik <[email protected]> [aut]",
-    "Jeff Thompson <[email protected]> [aut]",
-    "Marly Gotti <[email protected]> [aut]",
-    "Maya Gans <[email protected]> [aut]",
-    "Aravind Reddy Kallem [aut]",
-    "Fission Labs India Pvt Ltd [aut]"
-  ))
+Version: 0.1.0
+Authors@R: c( 
+    person("Aaron", "Clark", role = c("aut", "cre"), email = "[email protected]"),
+    person("Robert", "Krajcik", role = "aut", email = "[email protected]"),
+    person("Jeff", "Thompson", role = "aut", email = "[email protected]"),
+    person("Lars", "Andersen", role = "aut", email = "[email protected]"),
+    person("Andrew", "Borgman", role = "aut", email = "[email protected]"),
+    person("Munshi Imran", "Hossain", role = "ctb"),
+    person("Scott", "Schumacker", role = "ctb", email = "[email protected]"),
+    person("Marly", "Gotti", role = "aut", email = "[email protected]"),
+    person("Maya", "Gans", role = "aut", email = "[email protected]"),
+    person("Aravind Reddy", "Kallem", role = "aut"),
+    person(family = "Fission Labs India Pvt Ltd", role = "aut"),
+	  person(family = "PSI special interest group Application and Implementation of Methodologies in Statistics", role = c("cph", "fnd")),
+    person(family = "R Validation Hub", role = c("cph", "fnd"))
+  )
 Description: The `riskassessment` application allows users to define a list of R
     packages to assess against metrics engineered by the `riskmetric` package.
     In general, those metrics evaluate package development best practices, code
@@ -22,33 +28,27 @@ Description: The `riskassessment` application allows users to define a list of R
     authentication wall where roles are assigned to various users and 'final
     decisions' can be made at the package level.
 License: MIT + file LICENSE
-URL: https://github.com/pharmaR/risk_assessment
-BugReports: https://github.com/pharmaR/risk_assessment/issues
+URL: https://github.com/pharmaR/riskassessment
+BugReports: https://github.com/pharmaR/riskassessment/issues
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.0
 Imports: 
     bslib (>= 0.3.0),
     config (>= 0.3.1),
     cranlogs,
-    crayon,
     DBI,
-    desc,
     dplyr,
     DT,
-    forcats,
     formattable,
     glue,
     golem (>= 0.3.2),
-    keyring,
+    jsonlite,
     loggit,
     lubridate,
-    magrittr,
-    pkgload,
     plotly,
     purrr,
-    readr (>= 2.0.1),
     rintrojs,
     riskmetric (>= 0.1.1),
     rlang,
@@ -57,19 +57,21 @@ Imports:
     rvest,
     shiny (>= 1.7.1),
     shinydashboard,
-    shinyhelper,
     shinyjs,
     shinymanager,
     shinyWidgets,
-    stringr,
-    tibble,
-    tidyr,
-    waiter
+    stringr
 Suggests: 
+    fontawesome,
+    knitr,
+    pkgload,
     rstudioapi,
+    shinytest2,
     spelling,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    tinytex
 Config/testthat/edition: 3
 Language: en-US
 Depends: 
     R (>= 2.10)
+VignetteBuilder: knitr

LICENSE

@@ -0,0 +1,4 @@
+YEAR: 2020
+COPYRIGHT HOLDER:
+  - PSI special interest group Application and Implementation of Methodologies in Statistics
+  - R Validation Hub