Add quarto

.github/workflows/merge.yml

@@ -86,3 +86,17 @@ jobs:
       GH_PAT: ${{ secrets.GH_PAT }}
       DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
       DOCKERHUB_TOKEN: ${{ secrets.DOCKERHUB_TOKEN }}
+
+  build-quarto:
+    name: Build quarto 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
+      dockerhubpush: true
+    secrets:
+      GH_PAT: ${{ secrets.GH_PAT }}
+      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+      DOCKERHUB_TOKEN: ${{ secrets.DOCKERHUB_TOKEN }}

.github/workflows/pull_request.yml

@@ -1,4 +1,4 @@
-# Candace Savonen May 2022
+# Candace Savonen March 2024
 
 name: Pull Request
 
@@ -41,17 +41,25 @@ 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.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}}
       python_changed: ${{steps.python.outputs.any_changed}}
+      quarto_changed: ${{steps.quarto.outputs.any_changed}}
 
   build-base:
     name: Build base ottr image
@@ -96,3 +104,14 @@ 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 }}

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/')"
 

base_ottr/git_token.txt

@@ -0,0 +1,67 @@
+AnVIL
+Audiographer
+Audiography
+automagic
+BIPOC
+Bloomberg
+Bookdown
+chapt
+Coursera
+creativecommons
+css
+Datatrail
+DataTrail
+DISCOVERABLE
+Dockerfile
+Dockerhub
+dropdown
+enforceability
+faq
+favicon
+FirstName
+Funder
+fyi
+GDSCN
+Generis
+GH
+Github
+GitHub
+https
+ies
+iframe
+immunities
+impactful
+ITCR
+itcrtraining
+ITN
+LastName
+Leanpub
+Licensor
+LICENSOR
+Markua
+mentorship
+MERCHANTABILITY
+Muschelli
+NCI
+NHGRI
+OTTR
+ottrpal
+ottrproject
+Pandoc
+png
+pre
+reproducibility
+rmarkdown
+RMarkdown
+Savonen
+sexualized
+socio
+synched
+tada
+UE
+UE5
+underserved
+Videographer
+Videography
+WIPO	
+www

ottr_quarto/Dockerfile

@@ -0,0 +1,84 @@
+FROM rocker/tidyverse:4.0.2
+LABEL maintainer="[email protected]"
+WORKDIR /rocker-build/
+
+COPY install_github.R .
+
+# Install apt-getable packages to start
+RUN apt-get update && apt-get install -y --no-install-recommends apt-utils dialog
+RUN apt-get install -y --no-install-recommends \
+    libxt6 \
+    libpoppler-cpp-dev \
+    vim \
+    libglpk40 \
+    curl \
+    gpg
+
+# Install gh
+RUN curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | gpg --dearmor -o /usr/share/keyrings/githubcli-archive-keyring.gpg;
+RUN echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | tee /etc/apt/sources.list.d/github-cli.list > /dev/null;
+RUN apt update && apt install -y gh;
+
+# Remove old symlinks to old pandoc
+RUN unlink /usr/lib/rstudio-server/bin/pandoc/pandoc
+
+# Uninstall old version of pandoc
+RUN sudo apt-get purge pandoc pandoc-citeproc pandoc-data \
+  && sudo apt-get autoremove --purge
+
+# Install pandoc
+RUN wget https://github.com/jgm/pandoc/releases/download/2.14.1/pandoc-2.14.1-1-amd64.deb \
+  && sudo apt-get install ./pandoc-2.14.1-1-amd64.deb
+
+# Create new symlinks
+RUN ln -s /usr/bin/pandoc /usr/lib/rstudio-server/bin/pandoc/pandoc
+
+# Add curl, bzip2
+RUN apt-get update -qq && apt-get -y --no-install-recommends install \
+    bzip2 \
+    curl
+
+# Install pip3 and installation tools
+RUN apt-get -y --no-install-recommends install \
+    python3-pip  python3-dev
+
+RUN Rscript -e "remove.packages('rlang')"
+
+# Commonly used R packages
+RUN Rscript -e  "options(warn = 2);install.packages( \
+    c('rlang', \
+      'bookdown', \
+      'emojifont', \
+      'here', \
+      'leanpubr', \
+      'optparse', \
+      'oro.nifti', \
+      'qpdf', \
+      'R.utils', \
+      'rprojroot', \
+      'rgoogleslides', \
+      'servr', \
+      'spelling', \
+      'styler', \
+      'reticulate', \
+      'gh', \
+      'tibble'), \
+      repos = 'https://cloud.r-project.org/')"
+
+# cow needs this dependency:
+RUN Rscript -e  "devtools::install_version('gitcreds', version = '0.1.1', repos = 'http://cran.us.r-project.org')"
+
+# Copy over git token and package list
+COPY git_token.txt .
+COPY github_package_list.tsv .
+
+# Install packages from github
+RUN Rscript install_github.R \
+  --packages github_package_list.tsv \
+  --token git_token.txt
+
+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/git_token.txt

@@ -0,0 +1,67 @@
+AnVIL
+Audiographer
+Audiography
+automagic
+BIPOC
+Bloomberg
+Bookdown
+chapt
+Coursera
+creativecommons
+css
+Datatrail
+DataTrail
+DISCOVERABLE
+Dockerfile
+Dockerhub
+dropdown
+enforceability
+faq
+favicon
+FirstName
+Funder
+fyi
+GDSCN
+Generis
+GH
+Github
+GitHub
+https
+ies
+iframe
+immunities
+impactful
+ITCR
+itcrtraining
+ITN
+LastName
+Leanpub
+Licensor
+LICENSOR
+Markua
+mentorship
+MERCHANTABILITY
+Muschelli
+NCI
+NHGRI
+OTTR
+ottrpal
+ottrproject
+Pandoc
+png
+pre
+reproducibility
+rmarkdown
+RMarkdown
+Savonen
+sexualized
+socio
+synched
+tada
+UE
+UE5
+underserved
+Videographer
+Videography
+WIPO	
+www

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)