Merge pull request #20 from simon-smart88/dev

Merge 0.2.2

.Rbuildignore

@@ -19,4 +19,9 @@ Dockerfile
 runtime.txt
 apt.txt
 install.R
+inst/shiny/rsconnect/
+inst/shiny/debug*
+inst/shiny/install*
+.lintr
 paper/
+renv.lock

.github/workflows/R-CMD-check-no-suggests.yaml

@@ -0,0 +1,61 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# via https://github.com/tidymodels/workflowsets/blob/main/.github/workflows/R-CMD-check-no-suggests.yaml
+#
+# NOTE: This workflow only directly installs "hard" dependencies, i.e. Depends,
+# Imports, and LinkingTo dependencies. Notably, Suggests dependencies are never
+# installed, with the exception of testthat, knitr, and rmarkdown. The cache is
+# never used to avoid accidentally restoring a cache containing a suggested
+# dependency.
+on:
+  push:
+    branches:
+      '**'
+  pull_request:
+    branches: [master]
+
+name: R-CMD-check-no-suggests.yaml
+
+permissions: read-all
+
+jobs:
+  check-no-suggests:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@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:
+          dependencies: '"hard"'
+          cache: false
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
+            any::shinytest2
+            any::knitr
+            any::rmarkdown
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          build_args: 'c("--no-manual")'

DESCRIPTION

@@ -1,54 +1,78 @@
 Package: shinyscholar
-Version: 0.2.1
-Date: 2024-09-26
-Title: A template for creating modular reproducible shiny applications
-Description: The 'shiny' application shinyscholar is a modular platform for 
-    creating reproducible applications to academic standards. 'shinyscholar' is 
-    forked from 'wallace' and provides a template for producing applications 
-    that are interactive, reproducible, adaptable and built to high standards.
+Version: 0.2.2
+Date: 2024-12-10
+Title: A template for creating reproducible 'shiny' applications
+Description: Create a skeleton shiny application with create_template() that is 
+    reproducible, can be saved and meets academic standards for attribution. 
+    Forked from 'wallace'. Code is split into modules that are loaded and linked
+    together automatically and each call one function. Guidance pages explain 
+    modules to users and flexible logging informs them of any errors. Options 
+    enable asynchronous operations, viewing of source code, interactive maps and
+    data tables. Use to create complex analytical applications, following best 
+    practices in open science and software development. Includes functions for
+    automating repetitive development tasks and an example application at 
+    run_shinyscholar() that requires 
+    install.packages("shinyscholar", dependencies = TRUE).
 Authors@R: 
-    c(person("Simon E. H.", "Smart", email = "[email protected]", role = c("aut","cre")))
+    c(person("Simon E. H.", "Smart", email = "[email protected]", role = c("aut", "cre", "cph")),
+      person("Jamie M.", "Kass", email = "[email protected]", role = "ctb"),
+      person("Gonzalo E.", "Pinilla-Buitrago", email = "[email protected]", role = "ctb"),
+      person("Andrea", "Paz", email = "[email protected]", role = "ctb"),
+      person("Bethany A.", "Johnson", email = "[email protected]", role = "ctb"),
+      person("Valentina", "Grisales-Betancur", email = "[email protected]", role = "ctb"),
+      person("Dean", "Attali", email = "[email protected]", role = "ctb"),
+      person("Matthew E.", "Aiello-Lammens", email = "[email protected]", role = "ctb"),
+      person("Cory", "Merow", email = "[email protected]", role = "ctb"),
+      person("Mary E.", "Blair", email = "[email protected]", role = "ctb"),
+      person("Robert P.", "Anderson", email = "[email protected]", role = "ctb"),
+      person("Sarah I.", "Meenan", email = "[email protected]", role = "ctb"),
+      person("Olivier", "Broennimann", email = "[email protected]", role = "ctb"),
+      person("Peter J.", "Galante", email = "[email protected]", role = "ctb"),
+      person("Brian S.", "Maitner", email = "[email protected]", role = "ctb"),
+      person("Hannah L.", "Owens", email = "[email protected]", role = "ctb"),
+      person("Sara", "Varela", email = "[email protected]", role = "ctb"),
+      person("Bruno", "Vilela", email = "[email protected]", role = "ctb"),
+      person("Robert", "Muscarella", email = "[email protected]", role = "ctb"))
 Depends:
     R (>= 3.5.0),
-    shiny (>= 1.8.1),
+    gargoyle,
     leaflet (>= 2.0.2),
-    gargoyle
+    shiny (>= 1.8.1)
 Imports:
-    bslib,
     curl,
     devtools,
-    dplyr (>= 1.0.2),
+    glue,
+    knitr,
+    magrittr,
+    tools,
+    zip
+Suggests:
+    bslib,
     DT (>= 0.5),
+    dplyr (>= 1.0.2),
     future,
-    glue,
     httr2,
     knitcitations,
-    knitr,
-    leafem,
     leaflet.extras (>= 1.0.0),
-    magrittr,
     markdown,
     promises,
     R6,
     RColorBrewer,
     renv,
     rintrojs,
-    rlang,
     rmarkdown,
     shinyAce,
     shinyalert,
     shinybusy,
     shinyjs,
+    shinytest2,
     shinyWidgets (>= 0.6.0),
     terra,
-    tools,
-    xml2,
-    zip
-Suggests: 
-    shinytest2,
-    testthat
+    testthat,
+    xml2
 License: GPL-3
 URL: https://simon-smart88.github.io/shinyscholar/
+BugReports: https://github.com/simon-smart88/shinyscholar/issues
 Encoding: UTF-8
 RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+export(asyncLog)
+export(check_suggests)
 export(check_url)
 export(close_loading_modal)
 export(create_module)
@@ -10,7 +12,6 @@ export(plot_hist)
 export(plot_scatter)
 export(printVecAsis)
 export(register_module)
-export(run_module)
 export(run_shinyscholar)
 export(save_and_load)
 export(select_async)

NEWS.md

@@ -12,7 +12,7 @@ shinyscholar 0.1.0
 2. Due to objects inside `common` not being inherently reactive, event triggers have been added using `{gargoyle}`
 3. A Code tab has been added to the Visualization panel to allow the code for each module and the function that each module calls to be viewed.
 4. Unit tests for each module have been created using `{shinytest2}` in addition to unit tests for the function that the module calls.
-5. Added a new function `run_module()` which can be used to run a single module.
+5. ~~Added a new function `run_module()` which can be used to run a single module.~~ Removed in 0.2.2 use `run_<app name>()` or `load_file`
 6. Added a new function `create_template()` which can be used to create a skeleton app.
 7. Added a Dockerfile which can be used to run the app on a shiny-server.
 8. Added `show_loading_modal()` which uses `{shinybusy}` to display a modal whilst slow functions are running.
@@ -42,3 +42,12 @@ shinyscholar 0.2.0
 shinyscholar 0.2.1
 =============
 - The `select_query` and `select_async` modules in the demonstration have been re-written to use a different API.
+
+shinyscholar 0.2.2
+=============
+- Removed `run_module()` as it was not maintainable.
+- Moved all packages to Suggests unless they are required for development of new applications.
+- Added `asyncLog()` to improve logging from inside async functions.
+- Updated `run_<app name>()` to take a load file as an argument which is loaded automatically.
+- Creating `load_file` containing the path to a save file will attempt to load it on app start up.
+- Made `create_template()`, `metadata()` and `save_and_load()` more robust.

R/check_suggests.R

@@ -0,0 +1,32 @@
+#' @title Check suggests
+#' @description
+#' Checks whether all the packages in Suggests are installed and stops execution
+#' if not.
+#' @author Simon Smart <simon.smart@@cantab.net>
+#' @param testing logical. For use in testing.
+#' @param example logical. For use in examples.
+#' @keywords internal
+#' @export
+check_suggests <- function(testing = FALSE, example = FALSE){
+  desc <- read.dcf(system.file("DESCRIPTION", package = "shinyscholar"))
+  suggests <- trimws(
+    gsub(
+      "\\(.*\\)", "",
+      gsub("\\n", "", unlist(strsplit(desc[,"Suggests"], ",")))
+    )
+  )
+  if (testing){
+    suggests <- c(suggests, "phantompackage")
+  }
+
+  check <- any(!sapply(suggests, requireNamespace, quietly = TRUE))
+
+  if (example){
+    return(!check)
+  } else {
+    if (check){
+      stop('Some packages required to run the application are not installed, please reinstall using:
+       install.packages("shinyscholar", dependencies = TRUE)')
+    }
+  }
+}