Adding the container building logic

.github/workflows/build_docker_image.yml

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+name: build-docker-image
+
+on:
+  push:
+    branches:
+      - 'main'
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      -
+        name: Login to DockerHub
+        uses: docker/login-action@v1 
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: kaybenleroll/btydbayes_investigation:latest

Dockerfile

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+FROM rocker/verse:4.2.1
+
+RUN apt-get update \
+  && apt-get upgrade -y \
+  && apt-get install -y --no-install-recommends \
+    byobu \
+    clang \
+    ditaa \
+    graphviz \
+    htop \
+    less \
+    libclang-dev \
+    libglpk-dev \
+    libgsl-dev \
+    libnlopt-dev \
+    p7zip-full \
+    pbzip2 \
+  && apt-get clean \
+  && rm -rf /var/lib/apt/lists/* \
+  && mkdir -p $HOME/.R \
+  && echo "" > $HOME/.R/Makevars \
+  && echo "CXX=clang++"                                            >> $HOME/.R/Makevars \
+  && echo "CXXFLAGS=-Os"                                           >> $HOME/.R/Makevars \
+  && echo "CXXFLAGS+= -Wno-unused-variable -Wno-unused-function"   >> $HOME/.R/Makevars \
+  && echo "CXXFLAGS+= -Wno-unknown-pragmas -Wno-macro-redefined"   >> $HOME/.R/Makevars \
+  && echo ""                                                       >> $HOME/.R/Makevars \
+  && echo "CXX14=clang++"                                          >> $HOME/.R/Makevars \
+  && echo "CXX14FLAGS=-Os"                                         >> $HOME/.R/Makevars \
+  && echo "CXX14FLAGS+= -Wno-unused-variable -Wno-unused-function" >> $HOME/.R/Makevars \
+  && echo "CXX14FLAGS+= -Wno-unknown-pragmas -Wno-macro-redefined" >> $HOME/.R/Makevars \
+  && echo ""                                                       >> $HOME/.R/Makevars \
+  && install2.r --error \
+    anytime \
+    bayesplot \
+    brms \
+    BTYD \
+    BTYDplus \
+    CLVTools \
+    conflicted \
+    cowplot \
+    DataExplorer \
+    directlabels \
+    evir \
+    fitdistrplus \
+    fs \
+    furrr \
+    loo \
+    modeltime \
+    posterior \
+    projpred \
+    prophet \
+    pryr \
+    quarto \
+    rfm \
+    rstan \
+    rstanarm \
+    sessioninfo \
+    shinybrms \
+    shinystan \
+    snakecase \
+    tictoc \
+    tidybayes \
+    tidyquant \
+    timetk
+
+
+WORKDIR /tmp
+
+COPY build/docker_install_sys_rpkgs.R /tmp
+RUN Rscript /tmp/docker_install_sys_rpkgs.R
+
+COPY build/test_report.qmd /tmp
+RUN quarto render test_report.qmd --to pdf \
+  && rm -fv /tmp/test_report.pdf
+
+
+RUN git clone https://github.com/lindenb/makefile2graph.git \
+  && cd makefile2graph \
+  && make \
+  && make install
+
+RUN cp -r $HOME/.R /home/rstudio \
+  && chown -R rstudio:rstudio /home/rstudio/.R
+
+
+WORKDIR /home/rstudio
+USER rstudio
+
+COPY build/conffiles.7z /tmp
+RUN 7z x /tmp/conffiles.7z       \
+  && cp conffiles/.bash*     .   \
+  && cp conffiles/.gitconfig .   \
+  && cp conffiles/.Renviron  .   \
+  && cp conffiles/.Rprofile  .   \
+  && mkdir -p .config/rstudio    \
+  && cp conffiles/rstudio-prefs.json .config/rstudio/  \
+  && rm -rfv conffiles/ \
+  && touch /home/rstudio/.bash_eternal_history
+
+COPY build/docker_install_user_rpkgs.R /tmp
+RUN Rscript /tmp/docker_install_user_rpkgs.R
+
+
+USER root
+
+RUN chown -R rstudio:rstudio /home/rstudio
+

Makefile

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+### repo variables
+PROJECT_USER=kaybenleroll
+PROJECT_NAME=btydbayes-investigation
+PROJECT_TAG=latest
+
+IMAGE_TAG=${PROJECT_USER}/${PROJECT_NAME}:${PROJECT_TAG}
+
+DOCKER_USER=rstudio
+DOCKER_PASS=CHANGEME
+DOCKER_UID=$(shell id -u)
+DOCKER_GID=$(shell id -g)
+
+RSTUDIO_PORT=8787
+
+PROJECT_FOLDER=btydwork
+
+
+### Set GITHUB_USER with 'gh config set gh_user <<user>>'
+GITHUB_USER=$(shell gh config get gh_user)
+
+CONTAINER_NAME=btyd-work
+
+### Project build targets
+.SUFFIXES: .qmd .html .dot .png
+
+QMD_FILES  := $(wildcard *.qmd)
+HTML_FILES := $(patsubst %.qmd,%.html,$(QMD_FILES))
+
+all-html: $(HTML_FILES)
+
+.qmd.html:
+	echo "TIMESTAMP:" `date` "- Rendering script $<"  >> output.log 2>&1
+	Rscript -e 'quarto::quarto_render("$<")'          >> output.log 2>&1
+	echo "TIMESTAMP:" `date` "- Finished $*.html"     >> output.log 2>&1
+
+
+.dot.png:
+	dot -Tpng -o$*.png $<
+
+full_deps.dot:
+	makefile2graph all-html > full_deps.dot
+
+depgraph: full_deps.png
+
+
+
+
+mrproper: clean-cache clean-data clean-html clean-models
+	rm -fv data/*.xlsx
+	rm -fv *.dot
+	rm -fv output.log
+
+clean-data:
+	rm -fv data/*.rds
+	rm -fv data/*.csv
+
+clean-html:
+	rm -fv *.html
+
+clean-cache:
+	rm -rfv *_cache
+	rm -rfv *_files
+
+clean-models:
+	rm -fv stan_models/*
+
+
+### Docker targets
+docker-build-image: Dockerfile
+	docker build -t ${IMAGE_TAG} -f Dockerfile .
+
+docker-run:
+	docker run --rm -d \
+	  -p ${RSTUDIO_PORT}:8787 \
+	  -e USER=${DOCKER_USER} \
+	  -e PASSWORD=${DOCKER_PASS} \
+	  -e USERID=${DOCKER_UID} \
+	  -e GROUPID=${DOCKER_GID} \
+	  -v "${PWD}":"/home/${DOCKER_USER}/${PROJECT_FOLDER}":rw \
+	  --name ${CONTAINER_NAME} \
+	  ${IMAGE_TAG}
+
+docker-bash:
+	docker exec -it -u ${DOCKER_USER} ${CONTAINER_NAME} bash
+
+docker-stop:
+	docker stop ${CONTAINER_NAME}
+
+docker-rm:
+	docker rm ${CONTAINER_NAME}
+
+docker-start:
+	docker start ${CONTAINER_NAME}
+
+docker-clean: docker-stop-all
+	docker rm $(shell docker ps -q -a)
+
+docker-pull:
+	docker pull ${IMAGE_TAG}

btydwork.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Makefile

build/docker_install_sys_rpkgs.R

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+remotes::install_github(
+  "mjskay/tidybayes",
+  ref = "1efbdef9c1c59c5fa9dc20fdd78e41c9a99113e5"
+  )
+

build/docker_install_user_rpkgs.R

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+remotes::install_github(
+  "paul-buerkner/brms",
+  ref     = "v2.18.0",
+  upgrade = "always"
+)
+
+remotes::install_github(
+  "stan-dev/cmdstanr",
+  ref     = "v0.5.3",
+  upgrade = "never"
+)
+
+
+remotes::install_github(
+  "rmcelreath/rethinking",
+  ref     = "v2.2.1",
+  upgrade = "never"
+)
+
+
+library(cmdstanr)
+
+cmdstan_flags <- list(
+  "CXX"        = "clang++",
+  "CXXFLAGS"   = "-Os -Wno-unused-variable -Wno-unused-function  -Wno-unknown-pragmas -Wno-macro-redefined",
+  "CXX14"      = "clang++",
+  "CXX14FLAGS" = "-Os -Wno-unused-variable -Wno-unused-function  -Wno-unknown-pragmas -Wno-macro-redefined"
+)
+
+install_cmdstan(
+  cores       = parallel::detectCores(),
+  cpp_options = cmdstan_flags,
+  quiet       = FALSE,
+  overwrite   = FALSE,
+  version     = "2.31.0"
+)

build/test_report.qmd

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+---
+title: "Temporary Quarto Document"
+author: "Mick Cooney <[email protected]>"
+date: "`r Sys.Date()`"
+---
+
+
+```{r knit_opts, include = FALSE}
+library(conflicted)
+library(tidyverse)
+library(magrittr)
+library(rlang)
+library(scales)
+library(cowplot)
+
+resolve_conflicts <- function(pkg_priority) {
+  get_index <- function(pkg_name) {
+    idx <- str_which(pkg_priority, pkg_name)
+
+    if(length(idx) == 0) {
+      idx <- 0L
+    }
+
+    return(idx)
+  }
+
+  conflict_lst <- conflict_scout()
+
+  for(func_name in names(conflict_lst)) {
+    pkg_index <- map_int(conflict_lst[[func_name]], get_index)
+
+    pkg_index <- pkg_index[pkg_index > 0]
+
+    if(length(pkg_index) == 0) {
+      pkg_use <- conflict_lst[[func_name]][1]
+    } else {
+      pkg_use <- pkg_index %>%
+        min() %>%
+        pkg_priority[.]
+    }
+
+    conflict_prefer(func_name, pkg_use)
+  }
+
+  return(conflict_lst)
+}
+
+conflict_lst <- resolve_conflicts(
+  c("xml2", "magrittr", "rlang", "dplyr", "readr", "purrr", "ggplot2")
+  )
+
+
+knitr::opts_chunk$set(
+  tidy       = FALSE,
+  cache      = FALSE,
+  warning    = FALSE,
+  message    = FALSE,
+  fig.height =     8,
+  fig.width  =    11
+  )
+
+options(
+  width = 80L,
+  warn  = 1,
+  mc.cores = parallel::detectCores()
+  )
+
+set.seed(42)
+
+theme_set(theme_cowplot())
+```

data/.gitignore

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+*.txt
+*.zip
+*.xlsx
+*.rds