Merge pull request #172 from Biogen-Inc/devel

Next release: `v0.2.1`

Author: AARON-CLARK

.Rbuildignore

@@ -19,6 +19,7 @@ $run_dev.*
 ^cran-comments\.md$
 ^revdep$
 vignettes/announcing-tidycdisc-0-0-1-1.Rmd
+vignettes/announcing-tidycdisc-0-2-1.Rmd
 vignettes/Blog.Rmd
 vignettes/figures$
 vignettes/tidyCDISC.Rmd
@@ -28,3 +29,4 @@ vignettes/x0*
 ^Meta$
 ^CRAN-SUBMISSION$
 ^scripts$
+\.sass$

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

@@ -0,0 +1,75 @@
+# 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: [devel]
+  pull_request:
+    branches: [devel]
+
+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 update
+          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@v2
+
+      - 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
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: rcmdcheck
+      
+      # likely not needed since 'r-lib/actions/check-r-package@v2' will build
+      # the pkg, but including it for consistency with other workflows
+      - name: Install tidyCDISC
+        shell: bash
+        run: R CMD INSTALL --preclean .
+
+      - uses: r-lib/actions/check-r-package@v2
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/R-CMD-check.yaml .github/workflows/R-CMD-check-master.yaml.github/workflows/R-CMD-check.yaml renamed to .github/workflows/R-CMD-check-master.yaml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master, devel]
+    branches: [main, master]
 
 name: R-CMD-check
 

.github/workflows/pkgdown.yaml

@@ -28,14 +28,18 @@ 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
 
       - name: Install specific pkgdown version
         run: install.packages("remotes") ; remotes::install_version("pkgdown", version = "2.0.3", repos = "cran.rstudio.com", dependencies = FALSE)
         shell: Rscript {0}
+        
+      - name: Install tidyCDISC
+        shell: bash
+        run: R CMD INSTALL --preclean .
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)

.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, devel]
+
+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 tidyCDISC
+        shell: bash
+        run: R CMD INSTALL --preclean .
+          
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

CRAN-SUBMISSION

@@ -1,6 +1,6 @@
 Package: tidyCDISC
 Title: Quick Table Generation & Exploratory Analyses on ADaM-Ish Datasets
-Version: 0.2.0
+Version: 0.2.1
 Authors@R: c(
     person("Aaron", "Clark", , "clark.aaronchris@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-0123-0970")),
@@ -33,7 +33,7 @@ Description: Provides users a quick exploratory dive into common
     modules allow for concise filtering & downloading bulk outputs into
     html or pdf formats to save for later.
 License: AGPL (>= 3)
-URL: https://Biogen-Inc.github.io/tidyCDISC/
+URL: https://github.com/Biogen-Inc/tidyCDISC/, https://Biogen-Inc.github.io/tidyCDISC/
 BugReports: https://github.com/Biogen-Inc/tidyCDISC/issues
 Depends: 
     R (>= 2.10)
@@ -72,4 +72,4 @@ VignetteBuilder:
 Encoding: UTF-8
 Language: en-US
 LazyData: true
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3

DESCRIPTION

@@ -1,3 +1,31 @@
+# tidyCDISC (development version)
+- Allowed for one-element lists in heatmap axis dropdowns.
+
+# tidyCDISC 0.2.1 (CRAN Release)
+
+### General
+* Fixed bug accessing files in `app/www/` (#166)
+* Improved documentation
+    * Added vignette announcing release of `v0.2.1`
+    * Added highly visible links to Blog, YouTube, and NEWS file
+
+### Table Generator
+* Made the html output in the app look slightly more "CSR-like" using minor formatting tricks (#181)
+* Arranged visits in chronological order for dropdown list found in Stat blocks  (#154)
+* Fixed bug where wrong options were being passed on some lab tables (#169)
+* Fixed bug where draggable blocks were not working without inclusion of datasets with ATPT (#173)
+
+### Population Explorer
+* Fixed bug where selected filters were not being applied when 'Apply Filters' was toggled on (#175)
+* Fixed bug where plots' visual appeal was destroyed when faceting variable labels were too long (#200)
+* Fixed bug where scatter plot wouldn't display by categorical variable with `NA` values (#192)
+
+### Individual Explorer
+* Updated the look of the time visualization (#194)
+    * Moved the event description to a tooltip instead of a label
+    * Incorporated end dates (where applicable) to display ranges
+    * Removed the auto-zoom when multiple groups were selected
+
 
 # tidyCDISC 0.2.0 (CRAN Release)
 

NEWS.md

@@ -123,8 +123,10 @@ utils::globalVariables(c(
   "id_stat", "inner_sort",
   "lab", "n_subgroups", "n_tot", "orig_id_rn", "orig_var_rn", "param_x",
   "param_y", "pt", "pval",
-  "pval_hover", "sort_n", "v", "var", "var_rn", "where", "y"
-  ,":="
+  "pval_hover", "sort_n", "v", "var", "var_rn", "where", "y",
+  "type", "title"
+  ,":=",
+  "DATE", "EVENT_TIME", "DATE_ST", "DECODE_ST", "DATE_EN", "DECODE_EN"
 ))
 
 

R/global.R

@@ -277,7 +277,8 @@ gather_reqs <- function(input, output, session,
       gt::text_transform(
         locations = list(gt::cells_body(columns = c(not_exist_disp), rows = not_exist_disp == "X"),
                          gt::cells_body(columns = c(missing_disp), rows = missing_disp == "X")),
-        fn = function(X) gt::local_image(filename = "inst/app/www/red_x.png", height = 15)
+        fn = function(X) gt::local_image(filename =
+          app_sys('app/www', 'red_x.png'), height = 15)
       ) %>%
       gt::tab_header(
         title = paste(ifelse(disp_type == "error", "Required:", "Optional:"),"reconcile variables below"),