Merge branch 'main' into cansavvy/jekyll

.github/workflows/merge.yml

@@ -103,28 +103,42 @@ jobs:
       DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
       DOCKERHUB_TOKEN: ${{ secrets.DOCKERHUB_TOKEN }}
 
+  build-jekyll:
+    name: Build jekyll image
+    needs: dockerfiles-changed
+    if: ${{needs.dockerfiles-changed.outputs.jekyll_changed == 'true'}}
+    uses: ./.github/workflows/docker-test.yml
+    with:
+      directory: ottr_jekyll
+      tag: jhudsl/ottr_jekyll
+      dockerhubpush: true
+    secrets:
+      GH_PAT: ${{ secrets.GH_PAT }}
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_TOKEN: ${{ secrets.DOCKERHUB_TOKEN }}
+
   build-python:
     name: Build python image
     needs: dockerfiles-changed
     if: ${{needs.dockerfiles-changed.outputs.python_changed == 'true'}}
     uses: ./.github/workflows/docker-test.yml
     with:
-      directory: python
+      directory: ottr_python
       tag: jhudsl/ottr_python
       dockerhubpush: true
     secrets:
       GH_PAT: ${{ secrets.GH_PAT }}
       DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
       DOCKERHUB_TOKEN: ${{ secrets.DOCKERHUB_TOKEN }}
 
-  build-jekyll:
-    name: Build jekyll image
+  build-quarto:
+    name: Build quarto image
     needs: dockerfiles-changed
-    if: ${{needs.dockerfiles-changed.outputs.jekyll_changed == 'true'}}
+    if: ${{needs.dockerfiles-changed.outputs.quarto_changed == 'true'}}
     uses: ./.github/workflows/docker-test.yml
     with:
-      directory: jekyll
-      tag: jhudsl/ottr_jekyll
+      directory: ottr_quarto
+      tag: jhudsl/ottr_quarto
       dockerhubpush: true
     secrets:
       GH_PAT: ${{ secrets.GH_PAT }}

.github/workflows/pull_request.yml

@@ -1,4 +1,4 @@
-# Candace Savonen May 2022
+# Candace Savonen March 2024
 
 name: Pull Request
 
@@ -47,19 +47,27 @@ jobs:
         with:
           files: ottr_python/*
 
+      - name: Get specific changed files
+        id: quarto
+        uses: tj-actions/[email protected]
+        with:
+          files: ottr_quarto/*
+
       - run: |
           echo ${{steps.base_ottr.outputs.any_changed}}
           echo ${{steps.ottrpal.outputs.any_changed}}
           echo ${{steps.bioconductor.outputs.any_changed}}
           echo ${{steps.jekyll.outputs.any_changed}}
           echo ${{steps.python.outputs.any_changed}}
+          echo ${{steps.quarto.outputs.any_changed}}
 
     outputs:
       base_ottr_changed: ${{steps.base_ottr.outputs.any_changed}}
       ottrpal_changed: ${{steps.ottrpal.outputs.any_changed}}
       bioconductor_changed: ${{steps.bioconductor.outputs.any_changed}}
       jekyll_changed: ${{steps.jekyll.outputs.any_changed}}
       python_changed: ${{steps.python.outputs.any_changed}}
+      quarto_changed: ${{steps.quarto.outputs.any_changed}}
 
   build-base:
     name: Build base ottr image
@@ -115,3 +123,14 @@ jobs:
       tag: jhudsl/ottr_python
     secrets:
       GH_PAT: ${{ secrets.GH_PAT }}
+
+  build-quarto:
+    name: Build quarto ottr image
+    needs: dockerfiles-changed
+    if: ${{needs.dockerfiles-changed.outputs.quarto_changed == 'true'}}
+    uses: ./.github/workflows/docker-test.yml
+    with:
+      directory: ottr_quarto
+      tag: jhudsl/ottr_quarto
+    secrets:
+      GH_PAT: ${{ secrets.GH_PAT }}

.gitignore

@@ -8,3 +8,4 @@ spell_check_results.tsv
 .RData
 .httr-oauth
 docker/git_token.txt
+git_token.txt

base_ottr/Dockerfile

@@ -61,6 +61,7 @@ RUN Rscript -e  "options(warn = 2);install.packages( \
       'spelling', \
       'styler', \
       'reticulate', \
+      'gh', \
       'tibble'), \
       repos = 'https://cloud.r-project.org/')"
 

ottr_quarto/Dockerfile

@@ -0,0 +1,15 @@
+FROM jhudsl/base_ottr:main
+LABEL maintainer="[email protected]"
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    pandoc \
+    pandoc-citeproc \
+    curl \
+    gdebi-core \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN curl -LO https://quarto.org/download/latest/quarto-linux-amd64.deb
+RUN gdebi --non-interactive quarto-linux-amd64.deb
+
+# Set final workdir for commands
+WORKDIR /home/rstudio

ottr_quarto/github_package_list.tsv

@@ -0,0 +1,8 @@
+rstudio/rmarkdown	02d3c2512686fda9c14c2a0e300aa02525f16ca5
+yihui/xfun	74c2a6605d8f0fb19314da542baeead6dc8697d9
+yihui/knitr	a1052d12e0ff8f4ead365b4c85ef5835faa1c492
+jhudsl/ottrpal	HEAD
+tidyverse/rvest	4fe39fb5089512d77b6a9cc026e5c895258ff6ce
+R-lib/testthat	e99155af85261e065192feb946dcfa6679cffae4
+rstudio/bookdown	88bc4ead8562ea281838041c795b38fc4a6a7165
+jhudsl/cow	HEAD

ottr_quarto/install_github.R

@@ -0,0 +1,52 @@
+#!/usr/bin/env Rscript
+
+if (!"optparse" %in% installed.packages()) {
+  install.packages("optparse")
+}
+
+library(optparse)
+
+################################ Set up options ################################
+# Set up optparse options
+option_list <- list(
+  make_option(
+    opt_str = c("-p", "--packages"), type = "character",
+    default = "github_package_list.tsv" ,
+    help = "Path to a TSV with a list of packages to be installed through Github, 
+    where file where the first column is the github package name e.g. 
+    jhudsl/ottrpal and the second column is the commit ID to be installed 
+    (to be supplied to the ref argument).
+    ",
+    metavar = "character"
+  ),
+  make_option(
+    opt_str = c("--token"), type = "character",
+    default = NULL,
+    help = "GITHUB PAT file",
+    metavar = "character"
+  )
+)
+
+# Parse options
+opt <- parse_args(OptionParser(option_list = option_list))
+
+# Read in the token
+token <- as.character(readLines(opt$token)[1])
+
+# Reset GITHUB PAT to be token
+Sys.unsetenv("GITHUB_PAT")
+Sys.setenv(GITHUB_PAT = token)
+
+# set up list of packages to install
+packages <- readr::read_tsv(opt$packages, 
+                                col_names = c("package_name", "ref"))
+
+purrr::pmap(
+  packages,
+  ~remotes::install_github(..1,
+                           auth_token = token,
+                           ref = ..2)
+                )
+
+# Remove the file after we are done
+file.remove(opt$token)