new workflow based on docker-blessed GHA

.github/workflows/build-base-extra.yaml

@@ -25,9 +25,12 @@ jobs:
       - uses: actions/checkout@master
       - name: Publish base-extra to Docker Hub
         uses: elgohr/Publish-Docker-Github-Action@master
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
         with:
           name: facilebio/facilebio_base_extra
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
           workdir: facilebio_base_extra
+          buildargs: GITHUB_PAT
 

.github/workflows/build-base.yaml

@@ -25,8 +25,11 @@ jobs:
       - uses: actions/checkout@master
       - name: Publish base to Docker Hub
         uses: elgohr/Publish-Docker-Github-Action@master
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
         with:
           name: facilebio/facilebio_base
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
           workdir: facilebio_base
+          buildargs: GITHUB_PAT

.github/workflows/build-facielbio2.yaml

@@ -0,0 +1,55 @@
+# https://josephrodriguezg.medium.com/build-and-publish-docker-images-with-github-actions-78be3b3fbb9b
+# https://github.com/docker/build-push-action
+name: Build final facilebio image
+on:
+    push:
+      branches:
+        - '*'
+      paths:
+        - 'facilebio/**'
+    schedule:
+      # https://help.github.com/en/actions/reference/workflow-syntax-for-github-actions#onschedule
+      # https://crontab.guru/ to debug cron syntax
+      # run monday's and thursdays (1,4) at 5:00 AM Pacific Time (which is noon UTC)
+      - cron: '0 12 * * 1,4'
+    workflow_dispatch:
+      inputs:
+        dummy:
+          description: 'A dummy variable to enable manual workflow execution'
+          required: false
+          default: 'gitty up'
+jobs:
+    build:
+        name: Build & push docker image
+        runs-on: ubuntu-latest
+        env:
+            IMG_NAME: facilebio/facilebio
+        steps:
+            - name: Checkout
+              uses: actions/checkout@v4
+
+            - name: Debug
+              run: |
+                echo "GITHUB_TOKEN -> {{ secrets.GITHUB_TOKEN }}"
+
+            - name: Docker metadata
+              id: metadata
+              uses: docker/metadata-action@v3
+              with:
+                images: ${{ env.IMG_NAME }}
+                tags: |
+                    type=ref,event=branch
+
+            - name: Log in to Docker Hub
+              uses: docker/login-action@v1
+              with:
+                username: ${{ secrets.DOCKER_USERNAME }}
+                password: ${{ secrets.DOCKER_PASSWORD }}
+
+            - name: Build and push docker image
+              uses: docker/build-push-action@v5
+              with:
+                push: true
+                tags: ${{ env.IMG_NAME }}:latest
+                context: facilebio
+                secret-envs: GITHUB_PAT={{ secrets.GITHUB_TOKEN }}

facilebio_base/base-packages.txt

@@ -47,6 +47,7 @@ crayon
 crosstalk
 curl
 data.table
+datamods
 DBI
 DESeq2
 dbplyr
@@ -169,6 +170,8 @@ qs
 R6
 ragg
 rappdirs
+reactable
+reactR
 RBGL
 RColorBrewer
 RCurl
@@ -195,6 +198,7 @@ S4Vectors
 scales
 shape
 shiny
+shinybusy
 shinycssloaders
 shinydashboard
 shinydashboardPlus
@@ -214,6 +218,7 @@ sva
 sys
 testthat
 tibble
+tictoc
 tidyr
 tidyselect
 tinytex