deploy to azure

.Rbuildignore

@@ -17,3 +17,4 @@ hoad.code-workspace
 ^R/.scoap\.R$
 ^R/.unpaywall_integration\.R$
 .vscode
+.azure

.dockerignore

@@ -6,3 +6,4 @@
 !/NAMESPACE
 !/LICENSE.md
 !/.Rbuildignore
+!/.azure/init.sh

.github/newsletter.md

@@ -1,6 +1,6 @@
 # Newsletter abonnieren
 
-In unserem deutschsprachigen Newsletter informieren wir Sie über neue Entwicklungen und Veranstaltungen rund um das Projekt.
+In unserem deutschsprachigen Newsletter `[email protected]` informieren wir Sie über neue Entwicklungen und Veranstaltungen rund um das Projekt.
 
 <form method="post" action="https://listserv.gwdg.de/mailman/subscribe/hoad">
   <div class="form-group">

.github/workflows/main.yaml

@@ -1,5 +1,4 @@
-on:
-  push:
+on: push
 
 jobs:
   CICD:
@@ -8,8 +7,11 @@ jobs:
       run:
         shell: Rscript {0}
     container:
-      # this needs to be the same as in Dockerfile
-      image: subugoe/muggle-onbuild:f60004c31979947dab53fbf9cfbb0e7f1c4bea55
+      # update muggle here and in Dockerfile
+      image: subugoe/muggle-buildtime-onbuild:9ee02c2d9b32cab07681288de9995dc3d4124e4d
+    env:
+      MUGGLE_PKG_NAME: ${{ github.event.repository.name }}
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
       - name: Cache R Packages
@@ -23,21 +25,23 @@ jobs:
       - name: Install R Dependencies
         env:
           # see builder.Dockerfile for explanation, this resets after this step
-          R_LIBS_SITE: $R_LIBS_APP_GH
+          R_LIBS_SITE: $R_LIBS_RUNTIME_GH
         run: remotes::install_deps(dependencies = TRUE)
       - name: Check
-        run: muggle::rcmdcheck2()
+        # TODO error out on all but note again https://github.com/subugoe/hoad/issues/194
+        run: devtools::check(error_on = "error")
       - name: Test Coverage
         run: covr::codecov()
       - name: Build Package Website
         run: |
           # extra step is necessary to build index.md to integrate readme and landing page
           rmarkdown::render("pkgdown/index.Rmd")
           pkgdown::build_site(override = list(new_process = FALSE))
-      - uses: docker/build-push-action@v1
-        name: Build Dev Image
+      - name: Build Buildtime Image
+        uses: docker/build-push-action@v1
         with:
-          repository: ${{ github.repository }}/hoad-dev
+          repository: ${{ github.repository }}/${{ env.MUGGLE_PKG_NAME }}-buildtime
+          target: buildtime
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
           registry: docker.pkg.github.com
@@ -48,29 +52,37 @@ jobs:
           tags: ${{ github.sha }}
           add_git_labels: true
           push: ${{ github.event_name != 'pull_request' }}
-      - name: Setup GCP Cloud SDK
-        uses: GoogleCloudPlatform/github-actions/setup-gcloud@master
+      - name: Build Runtime Image
+        uses: docker/build-push-action@v1
         with:
-          project_id: ${{ secrets.GCP_PROJECT_ID }}
-          service_account_key: ${{ secrets.GCP_SA_KEY }}
-          export_default_credentials: true
-      - run: gcloud info
-        shell: bash
-      - name: Deploy Shiny Application to shinyapps.io ref
-        env:
-          SHINYAPPS_TOKEN: ${{ secrets.SHINYAPPS_TOKEN }}
-          SHINYAPPS_SECRET: ${{ secrets.SHINYAPPS_SECRET }}
-          GITHUB_REF: ${{ github.ref }}
-        if: github.event_name != 'pull_request'
+          repository: ${{ github.repository }}/${{ env.MUGGLE_PKG_NAME }}-runtime
+          target: runtime
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+          registry: docker.pkg.github.com
+          # this will set "latest" if master as per https://github.com/docker/build-push-action
+          tag_with_ref: true
+          # we're relying on long shas only to keep things easy
+          tag_with_sha: false
+          tags: ${{ github.sha }}
+          add_git_labels: true
+          push: ${{ github.event_name != 'pull_request' }}
+      - name: Log in to Azure
+        uses: azure/[email protected]
+        with:
+          creds: ${{ secrets.AZURE_CREDENTIALS }}
+      - name: Deploy to Azure Webapps
         run: |
-          remotes::install_github(repo = "subugoe/hoad", ref = "master", force = TRUE, dependencies = TRUE)
-          rsconnect::setAccountInfo(name = 'subugoe', token = Sys.getenv('SHINYAPPS_TOKEN'), secret = Sys.getenv('SHINYAPPS_SECRET'))
-          app_name <- paste0("hoad-", gsub("/", "-", Sys.getenv('GITHUB_REF')))
-          rsconnect::deployDoc(doc = "inst/app/dashboard.Rmd", appName = app_name)
-        shell: Rscript {0}
+          muggle::az_webapp_config_muggle(
+            plan = "hoad",
+            resource_group = "hoad",
+            subscription = "f0dd3a37-0a4e-4e7f-9c9b-cb9f60146edc",
+            restart = TRUE
+          )
       - name: Deploy to GitHub Pages
         if: github.ref == 'refs/heads/master'
         uses: maxheld83/ghpages@github-token
         env:
           BUILD_DIR: docs
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Sleep to let GITHUB_TOKEN persist
+        run: Sys.sleep(240)

DESCRIPTION

@@ -62,20 +62,20 @@ Suggests:
     DT,
     writexl,
     echarts4r,
-    metar,
     DBI,
     dbplyr,
     haven,
     lubridate,
     modelr,
     reprex,
-    rsconnect,
     rvest,
     selectr,
     httr,
     purrr,
     covr,
-    testthat
+    testthat,
+    subugoetheme,
+    shinycaas
 URL: https://subugoe.github.io/hoad, https://github.com/subugoe/hoad/
 BugReports: https://github.com/subugoe/hoad/issues
 RoxygenNote: 7.1.1
@@ -88,4 +88,5 @@ Imports:
     ggplot2,
     rlang
 Remotes:
-    subugoe/metar@7ccc2a0
+    subugoe/[email protected],
+    subugoe/shinycaas@31684600b286d5da5639a430a4b83a04de36bd34

Dockerfile

@@ -1 +1,4 @@
-FROM subugoe/muggle-onbuild:f60004c31979947dab53fbf9cfbb0e7f1c4bea55
+ARG MUGGLE_TAG=9ee02c2d9b32cab07681288de9995dc3d4124e4d
+FROM subugoe/muggle-buildtime-onbuild:${MUGGLE_TAG} as buildtime
+FROM subugoe/muggle-runtime-onbuild:${MUGGLE_TAG} as runtime
+CMD shinycaas::az_webapp_shiny_opts(); hoad::runHOAD()

R/plots.R

@@ -1,5 +1,5 @@
 #' Color palettes
-#' Colors used in the hybrid open access dashboard, based on [metar::ugoe_pal()]
+#' Colors used in the hybrid open access dashboard, based on [subugoetheme::ugoe_pal()]
 #' @family visualisation functions
 #' @name colors
 NULL

inst/app/dashboard.Rmd

@@ -4,7 +4,7 @@ output:
   flexdashboard::flex_dashboard:
     orientation: rows
     vertical_layout: fill
-    css: !expr metar::subugoe_template()$assets$css
+    css: !expr subugoetheme::pkgdown_template()$assets$css
 runtime: shiny
 ---
 
@@ -124,7 +124,7 @@ hybrid_sub <- reactive({
 # })
 ```
 
-Notice that only those hybrid open access journals were included where
+Notice we here only include those hybrid open access journals were included where
 academic institutions sponsored the open access publication according to the [Open APC initiative](https://github.com/openapc/openapc-de)
 and where publishers shared license information about immediate open access with [Crossref](https://github.com/CrossRef/rest-api-doc).
 

pkgdown/_pkgdown.yml

@@ -1,3 +1,4 @@
+url: https://subugoe.github.io/hoad/
 authors:
   Najko Jahn:
     href: https://www.sub.uni-goettingen.de/kontakt/personen-a-z/personendetails/person/najko-jahn/
@@ -17,7 +18,7 @@ authors:
     href: https://github.com/openapc
     html: <img src="reference/figures/openAPC_01+.png" height="15">
 template:
-  package: metar
+  package: subugoetheme
   opengraph:
     twitter:
       site: "@subugoe"

vignettes/interactive.Rmd

@@ -2,33 +2,6 @@
 title: "Interactive Dashboard"
 ---
 
-<style>
-.shiny-app-frame {
-  margin-top: 50px;
-  position: fixed;
-  left: 0;
-  top: 0;
-  bottom: 0;
-  right: 0;
-}
-.shiny-app-frame iframe {
-  width: 100%;
-  height: 100%;
-  border: none;
-}
-/* must be hidden otherwise it gets overlaid over the app */
-footer{
-  visibility: hidden
-}
-.page-header{
-  visibility: hidden
-}
-</style>
-
-
-<!-- TODO this needs to be updated manually, until https://github.com/subugoe/hoad/issues/180 -->
-
-<div class="shiny-app-frame">
-<iframe id="2343078" src="https://subugoe.shinyapps.io/hoad-refs-heads-refactor-as-pkg/">
-</iframe>
-</div>
+```{r echo=FALSE}
+shinycaas::include_app2("https://hoad.azurewebsites.net")
+```