diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
index c856fb5..cf5178e 100644
--- a/.github/workflows/main.yaml
+++ b/.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
@@ -23,10 +25,11 @@ 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
@@ -34,10 +37,11 @@ jobs:
# 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/login@v1.1
+ 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: ${{ secrets.GITHUB_TOKEN }}
+ - name: Sleep to let GITHUB_TOKEN persist
+ run: Sys.sleep(240)
diff --git a/DESCRIPTION b/DESCRIPTION
index c8dfe49..178fa86 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -62,20 +62,20 @@ Suggests:
DT,
writexl,
echarts4r,
- metar,
DBI,
dbplyr,
haven,
lubridate,
modelr,
reprex,
- rsconnect,
rvest,
selectr,
httr,
purrr,
covr,
- testthat
+ testthat,
+ subugoetheme,
+ shinycaas
URL: https://subugoe.github.io/hoad, https://github.com/subugoe/hoad/
BugReports: https://github.com/subugoe/hoad/issues
RoxygenNote: 7.1.1
@@ -88,4 +88,5 @@ Imports:
ggplot2,
rlang
Remotes:
- subugoe/metar@7ccc2a0
+ subugoe/subugoetheme@1.0.0,
+ subugoe/shinycaas@31684600b286d5da5639a430a4b83a04de36bd34
diff --git a/Dockerfile b/Dockerfile
index 5ea4d89..bbceab6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1 +1,4 @@
-FROM subugoe/muggle-onbuild:f60004c31979947dab53fbf9cfbb0e7f1c4bea55
+ARG MUGGLE_TAG=9ee02c2d9b32cab07681288de9995dc3d4124e4d
+FROM subugoe/muggle-buildtime-onbuild:${MUGGLE_TAG} as buildtime
+FROM subugoe/muggle-runtime-onbuild:${MUGGLE_TAG} as runtime
+CMD shinycaas::az_webapp_shiny_opts(); hoad::runHOAD()
diff --git a/R/plots.R b/R/plots.R
index b8d9f84..cae5241 100644
--- a/R/plots.R
+++ b/R/plots.R
@@ -1,5 +1,5 @@
#' Color palettes
-#' Colors used in the hybrid open access dashboard, based on [metar::ugoe_pal()]
+#' Colors used in the hybrid open access dashboard, based on [subugoetheme::ugoe_pal()]
#' @family visualisation functions
#' @name colors
NULL
diff --git a/hoad.code-workspace b/hoad.code-workspace
deleted file mode 100644
index 5709732..0000000
--- a/hoad.code-workspace
+++ /dev/null
@@ -1,8 +0,0 @@
-{
- "folders": [
- {
- "path": "."
- }
- ],
- "settings": {}
-}
diff --git a/inst/app/dashboard.Rmd b/inst/app/dashboard.Rmd
index 9017d63..f9be5e0 100644
--- a/inst/app/dashboard.Rmd
+++ b/inst/app/dashboard.Rmd
@@ -4,7 +4,7 @@ output:
flexdashboard::flex_dashboard:
orientation: rows
vertical_layout: fill
- css: !expr metar::subugoe_template()$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).
diff --git a/man/colors.Rd b/man/colors.Rd
index c84793a..809110c 100644
--- a/man/colors.Rd
+++ b/man/colors.Rd
@@ -7,7 +7,7 @@
\alias{colors_license_unpaywall}
\alias{colors_source_disclosure}
\title{Color palettes
-Colors used in the hybrid open access dashboard, based on \code{\link[metar:ugoe_pal]{metar::ugoe_pal()}}}
+Colors used in the hybrid open access dashboard, based on \code{\link[subugoetheme:ugoe_pal]{subugoetheme::ugoe_pal()}}}
\format{
An object of class \code{character} of length 6.
@@ -24,7 +24,7 @@ colors_source_disclosure
}
\description{
Color palettes
-Colors used in the hybrid open access dashboard, based on \code{\link[metar:ugoe_pal]{metar::ugoe_pal()}}
+Colors used in the hybrid open access dashboard, based on \code{\link[subugoetheme:ugoe_pal]{subugoetheme::ugoe_pal()}}
}
\section{Functions}{
\itemize{
diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
index 0acde19..c8f472c 100644
--- a/pkgdown/_pkgdown.yml
+++ b/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:
template:
- package: metar
+ package: subugoetheme
opengraph:
twitter:
site: "@subugoe"
diff --git a/vignettes/interactive.Rmd b/vignettes/interactive.Rmd
index 57a2213..f32617f 100644
--- a/vignettes/interactive.Rmd
+++ b/vignettes/interactive.Rmd
@@ -2,33 +2,6 @@
title: "Interactive Dashboard"
---
-
-
-
-
-
-
-
-
+```{r echo=FALSE}
+shinycaas::include_app2("https://hoad.azurewebsites.net")
+```