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pmorispmoris
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Update devcontainers
- Incorporate non-root user changes from devcontainers-update branch. - Incorporate and fix mixed r/miniforge environment from same branch. - Attempt to fix error when launching github codespaces: "Oh no, it looks like you are offline!" Possibly due to blocked network request, or an outdated extension?
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‎.devcontainer/Dockerfile‎

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Original file line numberDiff line numberDiff line change
@@ -1,28 +1,25 @@
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# FROM mcr.microsoft.com/devcontainers/miniconda:0-3
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FROM quay.io/condaforge/miniforge3:23.3.1-1
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FROM quay.io/condaforge/miniforge3:23.11.0-0
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# Or your actual UID, GID on Linux if not the default 1000
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ARG USERNAME=vscode
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ARG USER_UID=1000
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ARG USER_GID="${USER_UID}"
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# add conda-forge and bioconda channels to the top of the priority list and enable mamba solver
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RUN /opt/conda/bin/conda config --add channels defaults && \
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/opt/conda/bin/conda config --add channels bioconda && \
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/opt/conda/bin/conda config --add channels conda-forge
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# channel priority strict seems to mess up package resolution
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# /opt/conda/bin/conda config --set channel_priority strict
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RUN /opt/conda/bin/conda config --add channels bioconda \
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&& /opt/conda/bin/conda config --add channels conda-forge
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# channel priority strict seems to mess up package resolution
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# /opt/conda/bin/conda config --set channel_priority strict
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# Copy environment.yml (if found) to a temp location so we update the environment. Also
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# copy "noop.txt" so the COPY instruction does not fail if no environment.yml exists.
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# This updates the base environment instead of creating a new named virtual environment (mamba env create -f env.yml)
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COPY environment.yml* .devcontainer/noop.txt /tmp/conda-tmp/
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RUN if [ -f "/tmp/conda-tmp/environment.yml" ]; then umask 0002 && /opt/conda/bin/mamba env update -n base -f /tmp/conda-tmp/environment.yml; fi \
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RUN if [ -f "/tmp/conda-tmp/environment.yml" ]; then umask 0002 \
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&& /opt/conda/bin/mamba env update -n base -f /tmp/conda-tmp/environment.yml; fi \
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&& rm -rf /tmp/conda-tmp
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# RUN if [ -f "/tmp/conda-tmp/environment.yml" ]; then umask 0002 && /opt/conda/bin/mamba env create -f /tmp/conda-tmp/environment.yml; fi \
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# && rm -rf /tmp/conda-tmp
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# [Optional] Uncomment to install a different version of Python than the default
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# RUN conda install -y python=3.6 \
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# && pip install --no-cache-dir pipx \
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# && pipx reinstall-all
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# [Optional] Uncomment this section to install additional OS packages.
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# Install additional packages.
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RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
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&& apt-get -y install --no-install-recommends \
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nano \
@@ -37,3 +34,19 @@ RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
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htop \
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tree \
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graphviz
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# Create a non-root user - see https://aka.ms/vscode-remote/containers/non-root-user,
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# https://github.com/microsoft/vscode-dev-containers/issues/108,
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# and https://github.com/mamba-org/micromamba-docker/blob/521003c092aca4be4800220a883ebebf5bacbd6d/Dockerfile#L44
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RUN groupadd --gid 1000 "${USERNAME}" \
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&& useradd -s /bin/bash --uid "${USER_UID}" --gid "${USER_GID}" -m "${USERNAME}" \
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# Add sudo support
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&& apt-get install -y sudo \
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&& echo "${USERNAME}" ALL=\(root\) NOPASSWD:ALL > "/etc/sudoers.d/${USERNAME}" \
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&& chmod 0440 "/etc/sudoers.d/${USERNAME}" \
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# Transfer mamba ownership to user
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&& chmod -R a+rwx /opt/conda \
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# Clean up
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&& apt-get autoremove -y \
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&& apt-get clean -y \
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&& rm -rf /var/lib/apt/lists/*

‎.devcontainer/devcontainer.json‎

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Original file line numberDiff line numberDiff line change
@@ -1,11 +1,12 @@
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// For format details, see https://aka.ms/devcontainer.json. For config options, see the
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// README at: https://github.com/devcontainers/templates/tree/main/src/miniconda
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{
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"name": "Bioinformatics training environment",
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"name": "Unix tools and (bio)conda (miniforge)",
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"build": {
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"context": "..",
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"dockerfile": "Dockerfile"
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},
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"containerUser": "vscode",
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// {
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// "runArgs": [
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// "--log-driver=none"
@@ -48,38 +49,37 @@
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"customizations": {
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"vscode": {
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"settings": {
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"workbench.colorTheme": "Sonokai Maia",
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"workbench.editor.highlightModifiedTabs": true,
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"workbench.tree.renderIndentGuides": "always",
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"indentRainbow.lightIndicatorStyleLineWidth": 5,
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"indentRainbow.indicatorStyle": "light",
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"workbench.editor.wrapTabs": true,
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"explorer.compactFolders": false,
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"files.eol": "\n",
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"editor.wordWrap": "on",
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"editor.renderWhitespace": "trailing",
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"editor.bracketPairColorization.enabled": true,
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"indentRainbow.lightIndicatorStyleLineWidth": 5,
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"indentRainbow.indicatorStyle": "light",
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// "terminal.integrated.scrollback": 10000,
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"editor.renderWhitespace": "trailing",
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"files.trimFinalNewlines": true,
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"files.trimTrailingWhitespace": true,
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"editor.formatOnType": true,
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"editor.formatOnSave": true,
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},
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"extensions": [
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// bash extensions
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"mads-hartmann.bash-ide-vscode",
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"foxundermoon.shell-format",
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"mads-hartmann.bash-ide-vscode",
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"timonwong.shellcheck",
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// QoL
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"streetsidesoftware.code-spell-checker",
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"oderwat.indent-rainbow",
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"mechatroner.rainbow-csv",
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"ionutvmi.path-autocomplete",
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"fabiospampinato.vscode-diff",
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// R
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"REditorSupport.r",
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// // // R
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// // "REditorSupport.r",
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// // "REditorSupport.r-syntax",
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// general formatting
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"esbenp.prettier-vscode",

‎.devcontainer/mix/Dockerfile‎

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This file was deleted.

‎.devcontainer/mix/devcontainer.docker.json‎

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This file was deleted.

‎.devcontainer/mix/devcontainer.json‎

Lines changed: 28 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -1,27 +1,44 @@
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{
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"name": "Unix tools, bioconda and RStudio",
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"name": "Unix tools, (bio)conda (miniforge) and R(Studio)",
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// https://rocker-project.org/images/devcontainer/images.html
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"image": "ghcr.io/rocker-org/devcontainer/tidyverse:4",
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// Base image could be modified to allow non-root user to start rstudio server
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// See https://github.com/rocker-org/rocker-versioned2/issues/592
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// "build": {
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// "context": "../..",
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// "dockerfile": "Dockerfile"
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// },
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// "remoteUser": "rstudio",
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// but this seems to fail.
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// Fortunately, the rocker environments seem to launch
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// a regular user bash session: https://github.com/rocker-org/rocker/wiki/managing-users-in-docker
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"features": {
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// https://github.com/rocker-org/devcontainer-features/blob/main/src/rstudio-server/README.md
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// already pre-installed in tidyverse container - https://rocker-project.org/images/devcontainer/images.html#rstudio-server
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// RStudio is already pre-installed in tidyverse container - https://rocker-project.org/images/devcontainer/images.html#rstudio-server
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"ghcr.io/rocker-org/devcontainer-features/rstudio-server:latest": {},
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// https://github.com/rocker-org/devcontainer-features/tree/main/src/apt-packages
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"ghcr.io/rocker-org/devcontainer-features/apt-packages:1": {
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"packages": "libglpk-dev,nano,vim,less,git,screen,tmux,wget,curl,colordiff,htop,tree,graphviz" // "libglpk-dev" is required for igraph
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},
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// https://github.com/rocker-org/devcontainer-features/blob/main/src/r-packages/README.md
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"ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
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"packages": "tidyverse,rmarkdown,BiocManager,shiny,shinythemes,markdown",
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"packages": "devtools,languageserver,tidyverse,rmarkdown,markdown,shiny,shinythemes,BiocManager,github::bahlolab/isoRelate,sjmisc,networkD3,igraph,RColorBrewer,viridis,vcfR,poppr,ggfortify",
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"installSystemRequirements": true
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},
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// https://github.com/rocker-org/devcontainer-features/blob/main/src/miniforge/README.md
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"ghcr.io/rocker-org/devcontainer-features/miniforge:1": {
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"ghcr.io/rocker-org/devcontainer-features/miniforge:2": {
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"version": "latest",
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"variant": "Mambaforge"
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"variant": "Miniforge3"
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}
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// https://github.com/mamba-org/devcontainer-features/tree/main/src/micromamba
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// "ghcr.io/mamba-org/devcontainer-features/micromamba:1": {}
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},
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// Use 'postCreateCommand' to run commands after the container is created.
2337
// "postStartCommand": "if [ -f environment.yml ]; then umask 0002 && /opt/conda/bin/mamba env update -n base -f environment.yml; fi",
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"postCreateCommand": "/opt/conda/bin/mamba env update -n base -f environment.yml",
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// "postCreateCommand": "/opt/conda/bin/mamba env update -y -n base -f environment.yml",
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// Disabled because the postCreateCommand seems to interfer with the internal commands run
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// by the rocker image which set the R package repositories, and it becomes impossible
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// to use install.packages() afterwards, even when specifying a repository url.
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"postAttachCommand": {
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"rstudio-start": "rserver"
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},
@@ -36,38 +53,37 @@
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"customizations": {
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"vscode": {
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"settings": {
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"workbench.colorTheme": "Sonokai Maia",
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"workbench.editor.highlightModifiedTabs": true,
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"workbench.tree.renderIndentGuides": "always",
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"indentRainbow.lightIndicatorStyleLineWidth": 5,
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"indentRainbow.indicatorStyle": "light",
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"workbench.editor.wrapTabs": true,
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"explorer.compactFolders": false,
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"files.eol": "\n",
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"editor.wordWrap": "on",
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"editor.renderWhitespace": "trailing",
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"editor.bracketPairColorization.enabled": true,
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"indentRainbow.lightIndicatorStyleLineWidth": 5,
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"indentRainbow.indicatorStyle": "light",
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// "terminal.integrated.scrollback": 10000,
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"editor.renderWhitespace": "trailing",
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"files.trimFinalNewlines": true,
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"files.trimTrailingWhitespace": true,
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"editor.formatOnType": true,
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"editor.formatOnSave": true,
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},
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"extensions": [
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// bash extensions
58-
"mads-hartmann.bash-ide-vscode",
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"foxundermoon.shell-format",
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"mads-hartmann.bash-ide-vscode",
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"timonwong.shellcheck",
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// QoL
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"streetsidesoftware.code-spell-checker",
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"oderwat.indent-rainbow",
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"mechatroner.rainbow-csv",
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"ionutvmi.path-autocomplete",
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"fabiospampinato.vscode-diff",
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// R
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"REditorSupport.r",
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"REditorSupport.r-syntax",
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// general formatting
7389
"esbenp.prettier-vscode",

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