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Add a working Gitpod set-up #17

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MiguelRodo opened this issue May 2, 2023 · 6 comments
Closed

Add a working Gitpod set-up #17

MiguelRodo opened this issue May 2, 2023 · 6 comments

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@MiguelRodo
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.gitpod.yml in root directory:

# List the start up tasks. Learn more: https://www.gitpod.io/docs/configure/workspaces/tasks
image:
  file: .gitpod.Dockerfile

tasks:
  - name: Script Task
    init: echo 'init script' # runs during prebuild => https://www.gitpod.io/docs/configure/projects/prebuilds
    command: echo 'start script'

# List the ports to expose. Learn more: https://www.gitpod.io/docs/configure/workspaces/ports
ports:
  - name: Frontend
    description: Port 3000 for the frontend
    port: 3000
    onOpen: open-preview

# Learn more from ready-to-use templates: https://www.gitpod.io/docs/introduction/getting-started/quickstart

.gitpod.Dockerfile in root directory:

FROM rocker/verse:4.2.3

RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
    && apt-get upgrade -y \
    && apt-get install -y apt-utils \
        gdebi-core \
        openssh-client \
        gnupg2 \
        dirmngr \
        iproute2 \
        procps \
        lsof \
        htop \
        net-tools \
        psmisc \
        curl \
        wget \
        rsync \
        ca-certificates \
        unzip \
        zip \
        nano \
        vim-tiny \
        less \
        jq \
        lsb-release \
        apt-transport-https \
        dialog \
        libc6 \
        libgcc1 \
        libkrb5-3 \
        libgssapi-krb5-2 \
        libicu[0-9][0-9] \
        libicu-dev \
        libstdc++6 \
        zlib1g \
        locales \
        sudo \
        ncdu \
        man-db \
        strace \
        manpages \
        manpages-dev \
        librdf0-dev \
        init-system-helpers

RUN apt-get -y install libsecret-1-0 \
    && apt-get -y install \
        python3-pip \
        libgit2-dev \
        libcurl4-openssl-dev \
        libssl-dev \
        libxml2-dev \
        libxt-dev \
        libfontconfig1-dev \
        libcairo2-dev

RUN apt-get -y install \
      libgeos-dev \
      libgdal-dev \
      libproj-dev \
      libudunits2-dev \
      libsodium-dev \
      pandoc \
      openjdk-8-jdk \
      openjdk-8-jre \
      cargo \
      libfreetype6-dev \
      libclang-dev \
      fonts-roboto \
        && apt-get autoremove -y && apt-get clean -y && rm -rf /var/lib/apt/lists/*

RUN python3 -m pip --no-cache-dir install radian \ 
    && echo "options(radian.editing_mode = 'vi')" > ~/.radian_profile \
    && echo "options(radian.auto_match = FALSE)" >> ~/.radian_profile

RUN curl -LO https://quarto.org/download/latest/quarto-linux-amd64.deb \
    && gdebi -n quarto-linux-amd64.deb

RUN curl -LO https://quarto.org/download/latest/quarto-linux-amd64.deb \
    && gdebi -n quarto-linux-amd64.deb \
    && wget -qO \
    "/usr/local/bin/code-server" \
    "https://aka.ms/vscode-server-launcher/x86_64-unknown-linux-gnu" \
    && chmod a+x "/usr/local/bin/code-server"

ENV RENV_VERSION 0.17.3

RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"

WORKDIR /project
COPY renv.lock renv.lock

ENV RENV_PATHS_LIBRARY renv/library

COPY scripts/R/dev.R scripts/R/dev.R
COPY scripts/R/hpc_renv_setup.R scripts/R/hpc_renv_setup.R

RUN R -e "renv::install('pak')"
RUN R -e "options(renv.config.pak.enabled = TRUE); renv::restore(); options(renv.config.pak.enabled = FALSE)"
@MiguelRodo
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Trying to use my HPC settings for renv as it seems to not be restoring properly:

FROM rocker/verse:4.2.3

RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
    && apt-get upgrade -y \
    && apt-get install -y apt-utils \
        gdebi-core \
        openssh-client \
        gnupg2 \
        dirmngr \
        iproute2 \
        procps \
        lsof \
        htop \
        net-tools \
        psmisc \
        curl \
        wget \
        rsync \
        ca-certificates \
        unzip \
        zip \
        nano \
        vim-tiny \
        less \
        jq \
        lsb-release \
        apt-transport-https \
        dialog \
        libc6 \
        libgcc1 \
        libkrb5-3 \
        libgssapi-krb5-2 \
        libicu[0-9][0-9] \
        libicu-dev \
        libstdc++6 \
        zlib1g \
        locales \
        sudo \
        ncdu \
        man-db \
        strace \
        manpages \
        manpages-dev \
        librdf0-dev \
        init-system-helpers

RUN apt-get -y install libsecret-1-0 \
    && apt-get -y install \
        python3-pip \
        libgit2-dev \
        libcurl4-openssl-dev \
        libssl-dev \
        libxml2-dev \
        libxt-dev \
        libfontconfig1-dev \
        libcairo2-dev

RUN apt-get -y install \
      libgeos-dev \
      libgdal-dev \
      libproj-dev \
      libudunits2-dev \
      libsodium-dev \
      pandoc \
      openjdk-8-jdk \
      openjdk-8-jre \
      cargo \
      libfreetype6-dev \
      libclang-dev \
      fonts-roboto \
        && apt-get autoremove -y && apt-get clean -y && rm -rf /var/lib/apt/lists/*

RUN python3 -m pip --no-cache-dir install radian \ 
    && echo "options(radian.editing_mode = 'vi')" > ~/.radian_profile \
    && echo "options(radian.auto_match = FALSE)" >> ~/.radian_profile

RUN curl -LO https://quarto.org/download/latest/quarto-linux-amd64.deb \
    && gdebi -n quarto-linux-amd64.deb

RUN curl -LO https://quarto.org/download/latest/quarto-linux-amd64.deb \
    && gdebi -n quarto-linux-amd64.deb \
    && wget -qO \
    "/usr/local/bin/code-server" \
    "https://aka.ms/vscode-server-launcher/x86_64-unknown-linux-gnu" \
    && chmod a+x "/usr/local/bin/code-server"

ENV RENV_VERSION 0.17.3

RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"

WORKDIR /project
COPY renv.lock renv.lock

ENV RENV_PATHS_CACHE .local/R/lib/renv
ENV RENV_PATHS_ROOT .cache/R/renv
ENV RENV_PATHS_LIBRARY_ROOT .cache/R/renv
ENV RENV_PATHS_LIBRARY .cache/R/renv
ENV RENV_PATHS_PREFIX_AUTO TRUE

COPY scripts/R/dev.R scripts/R/dev.R
COPY scripts/R/hpc_renv_setup.R scripts/R/hpc_renv_setup.R

RUN R -e "renv::install('pak')"
RUN R -e "options(renv.config.pak.enabled = TRUE); renv::restore(); options(renv.config.pak.enabled = FALSE)"

@MiguelRodo
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I could try use an updated code cli as well:
https://code.visualstudio.com/docs/remote/tunnels#_getting-started

@MiguelRodo
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So, renv works with the following library locations:
image
RENV_PATHS_CACHE is "/home/gitpod/renv;/renv" and .libPaths() is " "/home/gitpod/.cache/R/renv/library/Prac23RodoHonsMultFAMemo-addf8176/R-4.2/x86_64-pc-linux-gnu" "/home/gitpod/.cache/R/renv/sandbox/R-4.2/x86_64-pc-linux-gnu/25ebdc09"

@MiguelRodo
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MiguelRodo commented May 3, 2023 •
edited
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Helpful links for renv and docker:

@MiguelRodo
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MiguelRodo commented Jun 7, 2023 •
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Okay, so I can do this as follows:

  • Open a GitPod template that has apptainer
    • Can just use this repo as a template
      • But for tidiness, really should do another one
  • Download the relevant sif container
  • Either run apptainer exec <path/to/sif> code-server tunnel --accept-server-license-terms OR
  • Run apptainer exec </path/to/sif> Rscript -e "projr::projr_restore(); projr::projr_build_dev()

I totally think we should avoid the whole building R thing. It takes a while and it's not even always the same container.

@MiguelRodo
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Deprecated in favour of #24

@MiguelRodo MiguelRodo closed this as not planned Won't fix, can't repro, duplicate, stale Jun 7, 2023
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@MiguelRodo