Add R - Jupyter - R Markdown - Data Science - Machine Learning DevConatiner

containers/r-jupyter-rmd-datascience-machinelearning/.devcontainer/Dockerfile

@@ -0,0 +1,87 @@
+# R version: 4, 4.1, 4.0
+ARG VARIANT="4"
+FROM rocker/r-ver:${VARIANT}
+
+# Use the [Option] comment to specify true/false arguments that should appear in VS Code UX
+#
+# [Option] Install zsh
+ARG INSTALL_ZSH="true"
+# [Option] Upgrade OS packages to their latest versions
+ARG UPGRADE_PACKAGES="false"
+
+# Install needed packages and setup non-root user. Use a separate RUN statement to add your own dependencies.
+ARG USERNAME=vscode
+ARG USER_UID=1000
+ARG USER_GID=$USER_UID
+COPY library-scripts/*.sh /tmp/library-scripts/
+RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+ && /bin/bash /tmp/library-scripts/common-debian.sh "${INSTALL_ZSH}" "${USERNAME}" "${USER_UID}" "${USER_GID}" "${UPGRADE_PACKAGES}" "true" "true" \
+ && usermod -a -G staff ${USERNAME} \
+ && apt-get -y install \
+ python3-pip \
+ libgit2-dev \
+ libxml2-dev \
+ pandoc \
+ libxt-dev \
+ # Set up R Kernel for Jupyter Notebooks.
+ # See more details: https://irkernel.github.io/installation/#source-panel
+ libzmq3-dev \
+ libcurl4-openssl-dev \
+ libssl-dev \
+ jupyter-core \
+ jupyter-client \
+ && apt-get autoremove -y && apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/library-scripts \
+ && python3 -m pip --no-cache-dir install radian \
+ && install2.r --error --skipinstalled --ncpus -1 \
+ devtools \
+ languageserver \
+ httpgd \
+ tidyverse \
+ tidymodels \
+ statip \
+ patchwork \
+ paletteer \
+ glmnet \
+ randomForest \
+ xgboost \
+ here \
+ doParallel \
+ janitor \
+ vip \
+ ranger \
+ palmerpenguins \
+ skimr \
+ nnet \
+ kernlab \
+ plotly \
+ factoextra \
+ cluster \
+ ottr \
+ && rm -rf /tmp/downloaded_packages 
+
+# Install summarytools and load some R package off the bat
+RUN R -e "devtools::install_github('https://github.com/dcomtois/summarytools/tree/0-8-9')"
+RUN R -e "library(ottr)"
+RUN R -e "library(here)"
+RUN R -e "library(languageserver)"
+# RUN installGithub.r ucbds-infra/ottr@stable
+
+# Set up R and Python Kernels for Jupyter Notebooks.
+# See more details: https://irkernel.github.io/installation/#source-panel
+RUN R -e "install.packages(c('repr', 'IRdisplay', 'IRkernel'), type = 'source')"
+RUN R -e "IRkernel::installspec()"
+RUN python3 -m pip install -U ipykernel
+
+# VSCode R Debugger dependency. Install the latest release version from GitHub without using GitHub API.
+# See https://github.com/microsoft/vscode-dev-containers/issues/1032
+RUN export TAG=$(git ls-remote --tags --refs --sort='version:refname' https://github.com/ManuelHentschel/vscDebugger v\* | tail -n 1 | cut --delimiter='/' --fields=3) \
+ && Rscript -e "remotes::install_git('https://github.com/ManuelHentschel/vscDebugger.git', ref = '"${TAG}"', dependencies = FALSE)"
+
+# R Session watcher settings.
+# See more details: https://github.com/REditorSupport/vscode-R/wiki/R-Session-watcher
+RUN echo 'source(file.path(Sys.getenv("HOME"), ".vscode-R", "init.R"))' >> ${R_HOME}/etc/Rprofile.site
+
+# [Optional] Uncomment this section to install additional OS packages.
+# RUN apt-get update \
+# && export DEBIAN_FRONTEND=noninteractive \
+# && apt-get -y install --no-install-recommends <your-package-list-here>

containers/r-jupyter-rmd-datascience-machinelearning/.devcontainer/devcontainer.json

@@ -0,0 +1,54 @@
+{
+ "name": "R Data Science Environment",
+ "build": {
+ "dockerfile": "Dockerfile",
+ // Update VARIANT to pick a specific R version: 4, 4.1, 4.0
+ "args": { "VARIANT": "4" }
+ },
+
+ // Set *default* container specific settings.json values on container create.
+ "settings": {
+ "r.rpath.linux": "/usr/local/lib/R/bin/R",
+ "r.rterm.linux": "/usr/local/bin/radian",
+ "r.bracketedPaste": true,
+ "r.plot.useHttpgd": true,
+ "r.lsp.enabled": true,
+ "[r]": {
+ "editor.wordSeparators": "`~!@#%$^&*()-=+[{]}\\|;:'\",<>/?"
+ }
+ },
+
+ // Add the IDs of extensions you want installed when the container is created.
+ "extensions": [
+ // Add Jupyter, R and Python vscode extensions
+ "ikuyadeu.r",
+ "rdebugger.r-debugger",
+ "ms-toolsai.jupyter",
+ "ms-python.python",
+
+ // Other extensions that make life a little bit easier right off the bat
+ "ionutvmi.path-autocomplete",
+ "usernamehw.errorlens",
+ "mhutchie.git-graph",
+ "tomoki1207.pdf",
+ "DavidAnson.vscode-markdownlint",
+ "Rubymaniac.vscode-paste-and-indent",
+ "GrapeCity.gc-excelviewer",
+ "IBM.output-colorizer",
+ "Mohamed-El-Fodil-Ihaddaden.shinysnip",
+ "hediet.vscode-drawio",
+ "MS-vsliveshare.vsliveshare-pack",
+ "eamodio.gitlens",
+ "GitHub.vscode-pull-request-github"
+ ],
+
+ // Use 'forwardPorts' to make a list of ports inside the container available locally.
+ // "forwardPorts": [],
+
+ // Use 'postCreateCommand' to run commands after the container is created.
+ // "postCreateCommand": "R --version",
+
+ // Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+ // Jupyter seems to detect the R kernel out of the box when user is root
+ //"remoteUser": "vscode"
+}

containers/r-jupyter-rmd-datascience-machinelearning/.devcontainer/library-scripts/README.md

@@ -0,0 +1,5 @@
+# Warning: Folder contents may be replaced
+
+The contents of this folder will be automatically replaced with a file of the same name in the [vscode-dev-containers](https://github.com/microsoft/vscode-dev-containers) repository's [script-library folder](https://github.com/microsoft/vscode-dev-containers/tree/main/script-library) whenever the repository is packaged.
+
+To retain your edits, move the file to a different location. You may also delete the files if they are not needed.