Merge pull request #18 from jimbrig/main

Enhancement: Added Docker Container Support

.Rbuildignore

@@ -29,3 +29,5 @@ testdata/
 ^R/rsconnect$
 ^app\.R$
 ^dev$
+^\.dockerignore$
+^Dockerfile$

.dockerignore

@@ -0,0 +1,7 @@
+.RData
+.Rhistory
+.git
+.gitignore
+manifest.json
+rsconnect/
+.Rproj.user

.github/workflows/docker.yml

@@ -0,0 +1,23 @@
+name: Publish-Docker
+on: 
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+      - develop
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3.5.2
+    - name: Publish to Registry
+      uses: elgohr/Publish-Docker-Github-Action@v5
+      with:
+        name: ${{ github.repository }}
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+        registry: ghcr.io
+        default_branch: main
+        workdir: .
+        tags: ${{ github.ref_name }}
+        tag_semver: true

DESCRIPTION

@@ -1,41 +1,42 @@
 Package: shinymde
-Title: A Shiny Interface to mde, the missing data explorer 
-Version: 0.1.2.9000
-Authors@R: 
-    person(given = "Nelson",
-           family = "Gonzabato",
-           role = c("aut", "cre"),
-           email = "gonzabato@hotmail.com")
-Description: Shiny applications provide an easy way for users to perform simple
-             or complex analyses. The package (app), "shinymde" provides a graphical user 
-             interface to "mde", the missing data explorer R package. 
+Title: A Shiny Interface to mde, the missing data explorer
+Version: 0.1.3
+Authors@R: c(
+    person("Nelson", "Gonzabato", , "gonzabato@hotmail.com", role = c("aut", "cre")),
+    person("Jimmy", "Briggs", , "jimmy.briggs@jimbrig.com", role = "ctb")
+  )
+Description: Shiny applications provide an easy way for users to perform
+    simple or complex analyses. The package (app), "shinymde" provides a
+    graphical user interface to "mde", the missing data explorer R
+    package.
 License: MIT + file LICENSE
-Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
 URL: https://github.com/Nelson-Gon/shinymde
 BugReports: https://github.com/Nelson-Gon/shinymde/issues
+Depends:
+    shiny (>= 1.6.0),
+    shinydashboard (>= 0.7.1)
 Imports: 
+    config (>= 0.3.1),
     dplyr (>= 1.0.7),
     forcats (>= 0.5.1),
     ggplot2 (>= 3.3.4),
+    golem (>= 0.3.1),
+    grDevices,
+    magrittr (>= 2.0.1),
+    mde,
+    methods,
     readxl (>= 1.3.1),
-    shinyjs (>= 2.0.0),
-    vroom (>= 1.5.3),
+    shinycssloaders (>= 1.0.0),
     shinyFeedback (>= 0.3.0),
-    magrittr (>= 2.0.1),
-    golem (>= 0.3.1),
-    config (>= 0.3.1),
-    mde (>= 0.3.1),
+    shinyjs (>= 2.0.0),
     shinyWidgets (>= 0.6.2),
-    shinycssloaders (>= 1.0.0)
-Depends:
-    shiny (>= 1.6.0),
-    shinydashboard (>= 0.7.1)
-Remotes:
-    Nelson-Gon/mde
+    utils,
+    vroom (>= 1.5.3)
 Suggests:
     knitr,
-    rmarkdown,
-    markdown
-VignetteBuilder: knitr
+    rmarkdown
+VignetteBuilder: 
+    knitr
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3

Dockerfile

@@ -0,0 +1,29 @@
+FROM rocker/verse:4.3.0
+RUN apt-get update && apt-get install -y  libicu-dev make pandoc zlib1g-dev && rm -rf /var/lib/apt/lists/*
+RUN mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/
+RUN echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" | tee /usr/local/lib/R/etc/Rprofile.site | tee /usr/lib/R/etc/Rprofile.site
+RUN R -e 'install.packages("remotes")'
+RUN Rscript -e 'remotes::install_version("magrittr",upgrade="never", version = "2.0.3")'
+RUN Rscript -e 'remotes::install_version("dplyr",upgrade="never", version = "1.1.2")'
+RUN Rscript -e 'remotes::install_version("knitr",upgrade="never", version = "1.42")'
+RUN Rscript -e 'remotes::install_version("shiny",upgrade="never", version = "1.7.4")'
+RUN Rscript -e 'remotes::install_version("config",upgrade="never", version = "0.3.1")'
+RUN Rscript -e 'remotes::install_version("rmarkdown",upgrade="never", version = "2.21")'
+RUN Rscript -e 'remotes::install_version("vroom",upgrade="never", version = "1.6.3")'
+RUN Rscript -e 'remotes::install_version("shinyWidgets",upgrade="never", version = "0.7.6")'
+RUN Rscript -e 'remotes::install_version("shinyjs",upgrade="never", version = "2.1.0")'
+RUN Rscript -e 'remotes::install_version("shinyFeedback",upgrade="never", version = "0.4.0")'
+RUN Rscript -e 'remotes::install_version("shinycssloaders",upgrade="never", version = "1.0.0")'
+RUN Rscript -e 'remotes::install_version("readxl",upgrade="never", version = "1.4.2")'
+RUN Rscript -e 'remotes::install_version("golem",upgrade="never", version = "0.4.0")'
+RUN Rscript -e 'remotes::install_version("ggplot2",upgrade="never", version = "3.4.2")'
+RUN Rscript -e 'remotes::install_version("forcats",upgrade="never", version = "1.0.0")'
+RUN Rscript -e 'remotes::install_version("shinydashboard",upgrade="never", version = "0.7.2")'
+RUN Rscript -e 'remotes::install_cran("mde")'
+RUN mkdir /build_zone
+ADD . /build_zone
+WORKDIR /build_zone
+RUN R -e 'remotes::install_local(upgrade="never")'
+RUN rm -rf /build_zone
+EXPOSE 80
+CMD R -e "options('shiny.port'=80,shiny.host='0.0.0.0');library(shinymde);shinymde::run_app()"

NEWS.md

@@ -1,10 +1,23 @@
 ---
-date: "1/1/2022"
+date: "5/16/2023"
 author: "Nelson Gonzabato"
 title: "Changes to shinymde"
 ---
 
-**shinymde 0.1.2**
+# shinymde 0.1.3
+
+Contributed by [@jimbrig](https://github.com/jimbrig):
+
+* Added Docker support to package
+
+* Fixed `mde` package dependency in DESCRIPTION
+
+* Added dependencies.R script
+
+* Added dev/docker.sh Shell script
+
+
+# shinymde 0.1.2
 
 * Plots now fill the entire page. 
 
@@ -18,7 +31,8 @@ easier to build repetitive UIs. See [#15](https://github.com/Nelson-Gon/shinymde
 * There is now an option to customize plot designs for examples themes.
 See https://github.com/Nelson-Gon/shinymde/issues/14
 
-**shinymde 0.1.1**
+
+# shinymde 0.1.1
 
 * UI overhaul to ensure a much better user experience. Specifically, inputs were decluttered to make it easier to do analyses with minimal interference. 
 
@@ -48,9 +62,9 @@ See https://github.com/Nelson-Gon/shinymde/issues/14
 
 * Non-needed directories for build were removed from the shipped package/app. 
 
----
+# shinymde 0.1.0
 
-**shinymde 0.1.0**
+* Added a `NEWS.md` file to track changes to the package.
 
 * shinymde can now be browsed at https://nelson-gon.shinyapps.io/shinymde.
 
@@ -107,7 +121,6 @@ documentation, and author homepage.
 
 * User feedback is now provided via `shinyFeedback` which is a more helpful way for users to view feedback directly within the application. 
 
-
 * A reset button now exists to enable a user to restore default values for plot save preferences. 
 
 * Grouped summaries now support exclusion following a fix in [mde](https://nelson-gon.github.io/mde). 
@@ -120,20 +133,18 @@ documentation, and author homepage.
 
 * Visual summaries are now shown in a sidebar layout. 
 
-
 * It is now possible to download a summary of missingness, a data set with values recoded as requested, or one where values have been dropped. 
 
 * Initially supported operations
 
-- Data input supports either user data, an inbuilt data set, or a remote data set provided as a web link. For user data, only ".csv", ".xlsx", and ".tsv" are supported. 
-
-- A tabular missingness summary is provided that can be downloaded by the user. The file format to write to is guessed from the user's input. 
+* Data input supports either user data, an inbuilt data set, or a remote data set provided as a web link. For user data, only ".csv", ".xlsx", and ".tsv" are supported. 
 
+* A tabular missingness summary is provided that can be downloaded by the user. The file format to write to is guessed from the user's input. 
 
-- Recoding values supports `recode_as_na`, `recode_na_as`, `recode_na_if`, `recode_as_na_for` and other recode functions from package `mde`.
+* Recoding values supports `recode_as_na`, `recode_na_as`, `recode_na_if`, `recode_as_na_for` and other recode functions from package `mde`.
 
-- Dropping values using `drop_` from `mde`. 
+* Dropping values using `drop_` from `mde`. 
 
-- A visual summary of missingness is also available. This is currently "just" a visual alternative to the tabular summary of missingness.  
+* A visual summary of missingness is also available. This is currently "just" a visual alternative to the tabular summary of missingness.  
 
 * Added a `NEWS.md` file to track changes to the package.

R/app_server.R

@@ -568,7 +568,7 @@ get_all_themes <- eventReactive(input$pkg,
 })
 get_theme <- reactive(
   # akrun credit:https://stackoverflow.com/q/70414757/10323798
-  getFunction(get_all_themes()[grep(req(input$theme), get_all_themes())])()
+  methods::getFunction(get_all_themes()[grep(req(input$theme), get_all_themes())])()
 )
 # Update available themes based on the above
 observe(

README.md

@@ -1,6 +1,6 @@
 shinymde: A shiny interface to mde, the missing data explorer
 ================
-2021-12-18
+2023-05-16
 
 [![R-CMD-check](https://github.com/Nelson-Gon/shinymde/actions/workflows/rcheck.yaml/badge.svg)](https://github.com/Nelson-Gon/shinymde/actions/workflows/rcheck.yaml)
 [![license](https://img.shields.io/badge/license-MIT-blue.svg)](https://opensource.org/licenses/MIT)
@@ -51,39 +51,43 @@ Thank you!
 
 # Currently Implemented features
 
--   [x] Summary of missingness
+- [x] Summary of missingness
 
 This uses [mde](https://nelson-gon.github.io/mde)’s `na_summary`
 function to generate a simple missingness report. The user can also
 download this report for use in other purposes.
 
--   [x] Recoding as NA and recoding NA as
+- [x] Recoding as NA and recoding NA as
 
 This allows a user to recode a given value as `NA`, R’s handler of
 missing values or convert `NA`s to some other value. It uses `mde`’s
 `recode_*` functions.
 
--   [x] Conditional recoding
+- [x] Conditional recoding
 
 This allows one to recode values conditionally. This supports
 `recode_as_na_for`, `recode_as_na_if`, and other conditional recoding
 functions.
 
--   [x] Drop based on missingness
+- [x] Drop based on missingness
 
 This uses `mde`’s `drop_na_*` functions.
 
--   [x] Missingness plots
+- [x] Missingness plots
 
--   [ ] Gear icon that allows users to customize plot options e.g. plot
-    themes, axis labels, legends, etc.
+- [ ] Gear icon that allows users to customize plot options e.g. plot
+  themes, axis labels, legends, etc.
 
 # `shinymde` in action
 
 Below is a screenshot showing current functionality.
 
-![shinymde in
-action](https://github.com/Nelson-Gon/shinymde/blob/main/images/sample_ui.png?raw=true)
+<figure>
+<img
+src="https://github.com/Nelson-Gon/shinymde/blob/main/images/sample_ui.png?raw=true"
+alt="shinymde in action" />
+<figcaption aria-hidden="true">shinymde in action</figcaption>
+</figure>
 
 View the full app at <https://nelson-gon.shinyapps.io/shinymde/>.
 
@@ -92,35 +96,34 @@ View the full app at <https://nelson-gon.shinyapps.io/shinymde/>.
 If you would like to work on this project, here is a features list that
 could be a good place to start.
 
--   [x] Add user guides in the form of tooltips wherever possible.
+- [x] Add user guides in the form of tooltips wherever possible.
 
--   [ ] Add unit tests.
+- [ ] Add unit tests.
 
--   [x] Add hovers to user input
+- [x] Add hovers to user input
 
--   [ ] Switchable dark mode
+- [ ] Switchable dark mode
 
--   [x] Control `pattern_type`/`subset_cols` choice in `na_summary`.
+- [x] Control `pattern_type`/`subset_cols` choice in `na_summary`.
 
--   [ ] Use cached filename in input filename if a user quits the
-    program.
+- [ ] Use cached filename in input filename if a user quits the program.
 
--   [ ] Add user help pages that link to `mde` documentation on click or
-    as an independent tab.
+- [ ] Add user help pages that link to `mde` documentation on click or
+  as an independent tab.
 
--   [x] Allow user to choose plot type.
+- [x] Allow user to choose plot type.
 
--   [x] Support dates in [mde](https://nelson-gon.github.io/mde)
+- [x] Support dates in [mde](https://nelson-gon.github.io/mde)
 
--   [x] Allow control over visible text on visual summaries.
+- [x] Allow control over visible text on visual summaries.
 
 ------------------------------------------------------------------------
 
 Thank you and keep building,
 
 Nelson
 
-2021-12-18
+2023-05-16
 
 Please note that the ‘shinymde’ project is released with a [Contributor
 Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project,

dev/config_attachment.yaml

@@ -0,0 +1,12 @@
+path.n: NAMESPACE
+path.d: DESCRIPTION
+dir.r: R
+dir.v: vignettes
+dir.t: tests
+extra.suggests: ~
+pkg_ignore: ~
+document: yes
+normalize: yes
+inside_rmd: no
+must.exist: yes
+check_if_suggests_is_installed: yes

dev/docker.ps1

@@ -0,0 +1,29 @@
+#!/usr/bin/env pwsh
+# -*- coding: utf-8 -*-
+
+# Set Variables
+$GH_USER="jimbrig"
+$GH_REPO="shinymde"
+$DOCKER_TAG="latest"
+$DOCKER_DESCRIPTION="ShinyMDE Container Image"
+$GH_PAT=$Env:GITHUB_API_TOKEN
+
+$IMAGE_SOURCE="https://github.com/" + $GH_USER + "/" + $GH_REPO
+$IMAGE_REF="ghcr.io/$GH_USER/$GH_REPO" + ':' + $DOCKER_TAG
+
+# Create Container
+RScript -e "golem::add_dockerfile()"
+
+# Login
+echo $GH_PAT | docker login ghcr.io -u $GH_USER --password-stdin
+
+# Build
+docker build `
+ --label "org.opencontainers.image.source=https://github.com/$GH_USER/$GH_REPO" `
+ --label "org.opencontainers.image.description=$DOCKER_DESCRIPTION" `
+ --label "org.opencontainers.image.licenses=MIT" `
+ -t $IMAGE_REF `
+ .
+
+# Push
+docker push $IMAGE_REF