update install micromamba shell script

2024-02-24 17:38:00 +08:00
parent e0ff4e6ba6
commit 57ee612b16
5 changed files with 248 additions and 97 deletions
--- a/spawnerdockerfile/Dockerfile.base
+++ b/spawnerdockerfile/Dockerfile.base
@@ -79,6 +79,7 @@ ARG HOME="/home/${CREATE_USER}"
 ARG DEBIAN_FRONTEND="noninteractive"
 ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}

+COPY install.sh /tmp
 RUN <<EOT
 #!/bin/bash
 # 更新软件源
@@ -95,7 +96,9 @@ useradd -m -s /bin/bash ${CREATE_USER}
 echo "${CREATE_USER}:${CREATE_USER_PASSWD}" | chpasswd
 echo "${CREATE_USER} ALL=(ALL:ALL) NOPASSWD:ALL" >> /etc/sudoers
 # 安装micromamba
-echo "1" | bash <(curl -s https://cdn.jsdelivr.net/gh/hotwa/MicroMamba_Installer@main/install.sh)
+echo "1" | bash /tmp/install.sh
+mkdir -p /home/${CREATE_USER}/micromamba
+chown -R ${NB_UID}:${NB_GID} /home/${CREATE_USER}/micromamba
 # 安装 Jupyter 和相关软件
 npm install -g configurable-http-proxy
 python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel>=6.25.0 jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
--- a/spawnerdockerfile/Dockerfile.base-notebook
+++ b/spawnerdockerfile/Dockerfile.base-notebook
@@ -79,6 +79,7 @@ ARG HOME="/home/${CREATE_USER}"
 ARG DEBIAN_FRONTEND="noninteractive"
 ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}

+COPY install.sh /tmp
 RUN <<EOT
 #!/bin/bash
 # 更新软件源
@@ -95,10 +96,12 @@ useradd -m -s /bin/bash ${CREATE_USER}
 echo "${CREATE_USER}:${CREATE_USER_PASSWD}" | chpasswd
 echo "${CREATE_USER} ALL=(ALL:ALL) NOPASSWD:ALL" >> /etc/sudoers
 # 安装micromamba
-echo 1 | bash <(curl -s https://cdn.jsdelivr.net/gh/hotwa/MicroMamba_Installer@main/install.sh)
+echo "1" | bash /tmp/install.sh
+mkdir -p /home/${CREATE_USER}/micromamba
+chown -R ${NB_UID}:${NB_GID} /home/${CREATE_USER}/micromamba
 # 安装 Jupyter 和相关软件
 npm install -g configurable-http-proxy
-python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
+python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel>=6.25.0 jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
 EOT

 RUN <<EOT
@@ -124,14 +127,6 @@ EOT
 # Switch back to jovyan to avoid accidental container runs as root
 USER ${NB_UID}
 ENV MAMBA_ROOT_PREFIX=/home/${CREATE_USER}/micromamba
-RUN <<EOT
-#!/bin/bash
-sudo apt update
-sudo apt install -y texlive-full
-micromamba create -n plot -c conda-forge scienceplots autopep8 python=3 ipykernel pandas numpy matplotlib scipy seaborn orange3 -y
-micromamba run -n plot python -m pip install bamboolib
-micromamba run -n plot python -m ipykernel install --user --name="sciplot" --display-name="SCIPlot Environment"
-EOT

 # install mojo
 ENV PATH="/home/${CREATE_USER}/.local/bin:$PATH"
@@ -152,15 +147,6 @@ modular auth $AUTH_KEY
 modular install mojo
 EOT

-RUN <<EOT
-#!/bin/bash
-micromamba create -n mixtral_env -c conda-forge ipykernel -y
-git clone https://github.com/Lightning-AI/lit-gpt.git
-cd lit-gpt
-micromamba run -n mixtral_env python -m pip install -r requirements.txt
-micromamba run -n mixtral_env python -m ipykernel install --user --name="mixtral" --display-name="mixtral Environment"
-EOT
-
 # Install Rust
 ENV PATH="/home/${CREATE_USER}/.cargo/bin:$PATH"
 RUN <<EOT
@@ -171,11 +157,5 @@ cargo install evcxr_jupyter
 evcxr_jupyter --install
 EOT

-RUN <<EOT
-#!/bin/bash
-micromamba create -n mdgnn -c pytorch -c conda-forge python=3.9 pytorch=1.10.2 torchvision torchaudio cudatoolkit=11.3 pandas matplotlib seaborn scipy numpy=1.24.4 mdanalysis biopandas pymol-open-source ipykernel ipywidgets jupyter einops python-calamine scikit-learn  -y
-micromamba run -n mdgnn python -m ipykernel install --user --name="mdgnn" --display-name="mdgnn Environment"
-EOT
+WORKDIR "${HOME}"

-
-WORKDIR "${HOME}"
--- a/spawnerdockerfile/Dockerfile.mdgnn
+++ b/spawnerdockerfile/Dockerfile.mdgnn
@@ -79,6 +79,7 @@ ARG HOME="/home/${CREATE_USER}"
 ARG DEBIAN_FRONTEND="noninteractive"
 ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}

+COPY install.sh /tmp
 RUN <<EOT
 #!/bin/bash
 # 更新软件源
@@ -95,82 +96,17 @@ useradd -m -s /bin/bash ${CREATE_USER}
 echo "${CREATE_USER}:${CREATE_USER_PASSWD}" | chpasswd
 echo "${CREATE_USER} ALL=(ALL:ALL) NOPASSWD:ALL" >> /etc/sudoers
 # 安装micromamba
-echo "1" | bash <(curl -s https://raw.githubusercontent.com/hotwa/MicroMamba_Installer/main/install.sh)
+echo "1" | bash /tmp/install.sh
+mkdir -p /home/${CREATE_USER}/micromamba
+chown -R ${NB_UID}:${NB_GID} /home/${CREATE_USER}/micromamba
 # 安装 Jupyter 和相关软件
 npm install -g configurable-http-proxy
-python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
-EOT
-
-RUN <<EOT
-#!/bin/bash
-# install rserver
-apt update 
-apt update -qq
-apt install -y --no-install-recommends software-properties-common dirmngr
-wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
-echo | add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
-apt-get update
-apt install -y --no-install-recommends r-base
-wget "https://download2.rstudio.org/server/$(lsb_release -cs)/amd64/rstudio-server-2023.06.1-524-amd64.deb" -O /tmp/rstudio-server.deb
-chmod +x /tmp/rstudio-server.deb 
-gdebi -n /tmp/rstudio-server.deb
-rm -rf /tmp/rstudio-server.deb
-chown -R ${CREATE_USER}:users /home/${CREATE_USER}
-# 清理和减小镜像大小
-apt-get clean 
-rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /usr/share/man/?? /usr/share/man/??_*
+python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel>=6.25.0 jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
 EOT

 # Switch back to jovyan to avoid accidental container runs as root
 USER ${NB_UID}
 ENV MAMBA_ROOT_PREFIX=/home/${CREATE_USER}/micromamba
-RUN <<EOT
-#!/bin/bash
-sudo apt update
-sudo apt install -y texlive-full
-micromamba create -n plot -c conda-forge scienceplots autopep8 python=3 ipykernel pandas numpy matplotlib scipy seaborn orange3 -y
-micromamba run -n plot python -m pip install bamboolib
-micromamba run -n plot python -m ipykernel install --user --name="sciplot" --display-name="SCIPlot Environment"
-EOT
-
-# install mojo
-ENV PATH="/home/${CREATE_USER}/.local/bin:$PATH"
-# A random default token
-ARG AUTH_KEY=5ca1ab1e
-ENV AUTH_KEY=$AUTH_KEY
-
-RUN curl https://get.modular.com | sh - && \
-    modular auth $AUTH_KEY 
-RUN 
-
-ARG MODULAR_HOME="/home/${CREATE_USER}/.modular"
-ENV MODULAR_HOME=$MODULAR_HOME
-ENV PATH="$PATH:$MODULAR_HOME/pkg/packages.modular.com_mojo/bin"
-RUN <<EOT
-#!/bin/bash
-curl https://get.modular.com | sh - && \
-modular auth $AUTH_KEY 
-modular install mojo
-EOT
-
-RUN <<EOT
-#!/bin/bash
-micromamba create -n mixtral_env -c conda-forge ipykernel -y
-git clone https://github.com/Lightning-AI/lit-gpt.git
-cd lit-gpt
-micromamba run -n mixtral_env python -m pip install -r requirements.txt
-micromamba run -n mixtral_env python -m ipykernel install --user --name="mixtral" --display-name="mixtral Environment"
-EOT
-
-# Install Rust
-RUN <<EOT
-#!/bin/bash
-curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
-source $HOME/.cargo/env
-cargo install evcxr_jupyter
-evcxr_jupyter --install
-EOT
-
 RUN <<EOT
 #!/bin/bash
 micromamba create -n mdgnn -c pytorch -c conda-forge python=3.9 pytorch=1.10.2 torchvision torchaudio cudatoolkit=11.3 pandas matplotlib seaborn scipy numpy=1.24.4 mdanalysis biopandas pymol-open-source ipykernel ipywidgets jupyter -y
--- a/spawnerdockerfile/Dockerfile.plot
+++ b/spawnerdockerfile/Dockerfile.plot
@@ -79,6 +79,7 @@ ARG HOME="/home/${CREATE_USER}"
 ARG DEBIAN_FRONTEND="noninteractive"
 ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}

+COPY install.sh /tmp
 RUN <<EOT
 #!/bin/bash
 # 更新软件源
@@ -95,7 +96,9 @@ useradd -m -s /bin/bash ${CREATE_USER}
 echo "${CREATE_USER}:${CREATE_USER_PASSWD}" | chpasswd
 echo "${CREATE_USER} ALL=(ALL:ALL) NOPASSWD:ALL" >> /etc/sudoers
 # 安装micromamba
-echo "1" | bash <(curl -s https://cdn.jsdelivr.net/gh/hotwa/MicroMamba_Installer@main/install.sh)
+echo "1" | bash /tmp/install.sh
+mkdir -p /home/${CREATE_USER}/micromamba
+chown -R ${NB_UID}:${NB_GID} /home/${CREATE_USER}/micromamba
 # 安装 Jupyter 和相关软件
 npm install -g configurable-http-proxy
 python3 -m pip install jupyterhub jupyterlab notebook radian pycurl jupyter-rsession-proxy ipykernel>=6.25.0 jupyterlab-language-pack-zh-CN jupyterlab-git jupyterlab-system-monitor jupyter_nbextensions_configurator jupyter_contrib_nbextensions jupyterlab_widgets jupyterlab-drawio jupyterlab-spreadsheet-editor jupyterlab-cell-flash jedi-language-server jupyterlab_code_formatter jupyterlab-spellchecker jupyterlab_vim nbresuse ipydrawio jedi ipympl black isort theme-darcula ipywidgets tensorboard jupyterlab_latex jupyter_bokeh autopep8 xeus-python jupyterlab-lsp python-lsp-server nglview dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
--- a/spawnerdockerfile/install.sh
+++ b/spawnerdockerfile/install.sh
@@ -0,0 +1,229 @@
+#!/bin/bash
+
+# 安装所需依赖
+install_dependencies() {
+    # 检查并安装 jq, curl, tar, bzip2
+    for dep in jq curl tar bzip2; do
+        if ! command -v $dep >/dev/null 2>&1; then
+            sudo apt-get update && sudo apt-get install -y $dep
+        fi
+    done
+}
+
+# 在脚本开始时调用依赖安装函数
+install_dependencies
+
+# 默认的MAMBA_ROOT_PREFIX路径
+DEFAULT_MAMBA_ROOT_PREFIX="/usr/local/bin"
+
+# 显示用法信息
+usage() {
+    echo "用法: sudo $0 [--silent-install [custom_root_prefix]] [--silent-uninstall] [--silent-update]"
+    echo "  --silent-install      静默模式安装，不进行任何交互"
+    echo "  custom_root_prefix    (可选) 在静默模式下设置 MAMBA_ROOT_PREFIX 的路径"
+    echo "  --silent-uninstall    静默模式卸载，不进行任何交互"
+    echo "  --silent-update       静默模式更新，不进行任何交互"
+    exit 1
+}
+
+# 安装micromamba
+install_micromamba() {
+    local mamba_prefix="$1"
+
+    # 自动检测操作系统和处理器架构
+    OS="$(uname)"
+    ARCH="$(uname -m)"
+
+    # 根据操作系统和架构设置下载链接
+    case "$OS" in
+        "Linux")
+            case "$ARCH" in
+                "x86_64") URL="https://micro.mamba.pm/api/micromamba/linux-64/latest" ;;
+                "aarch64") URL="https://micro.mamba.pm/api/micromamba/linux-aarch64/latest" ;;
+                "ppc64le") URL="https://micro.mamba.pm/api/micromamba/linux-ppc64le/latest" ;;
+                *) echo "不支持的架构: $ARCH"; exit 1 ;;
+            esac
+            ;;
+        "Darwin")
+            case "$ARCH" in
+                "x86_64") URL="https://micro.mamba.pm/api/micromamba/osx-64/latest" ;;
+                "arm64") URL="https://micro.mamba.pm/api/micromamba/osx-arm64/latest" ;;
+                *) echo "不支持的架构: $ARCH"; exit 1 ;;
+            esac
+            ;;
+        *)
+            echo "不支持的操作系统: $OS"; exit 1 ;;
+    esac
+
+    # 下载并解压 micromamba 到指定的路径
+    echo "正在下载 micromamba..."
+    if curl -Ls "$URL" | tar -xvj -C "$mamba_prefix"; then
+        echo "micromamba 下载并解压完成。"
+        ls -l /usr/local/bin/bin/micromamba
+        echo "micromamba 赋予执行权限"
+        chmod +x /usr/local/bin/bin/micromamba
+        echo "micromamba 安装完成"
+        echo "MAMBA_ROOT_PREFIX 路径：$mamba_prefix"
+        # 初始化 shell 环境
+        echo "正在为root初始化 micromamba shell 环境..."
+        "$mamba_prefix/bin/micromamba" shell init -s bash -p "~/micromamba"
+        ln -s /usr/local/bin/bin/micromamba /usr/local/bin/micromamba 
+    else
+        echo "micromamba 下载失败"
+    fi
+}
+
+# 清理 .bashrc 文件
+cleanup_bashrc() {
+    local mamba_bin_path="$1"
+    
+    # 删除 .bashrc 中相关的行
+    sed -i '/MICROMAMBA_BIN_PATH/d' ~/.bashrc
+    sed -i '/MAMBA_ROOT_PREFIX/d' ~/.bashrc
+    sed -i '/alias mba=/d' ~/.bashrc
+}
+
+# 删除micromamba
+uninstall_micromamba() {
+
+    echo "正在卸载 micromamba..."
+    rm -rf /usr/local/bin/micromamba /usr/local/bin/bin /usr/local/bin/info /usr/local/bin/etc
+
+    # 清理 .bashrc 文件
+    cleanup_bashrc "$mamba_prefix"
+
+    echo "micromamba 已卸载。"
+}
+
+
+# 获取当前 micromamba 版本
+get_current_version() {
+    local mamba_path="$1/micromamba"
+    if [ -f "$mamba_path" ]; then
+        local current_version
+        current_version=$("$mamba_path" --version | grep -o 'version [^ ]*' | cut -d ' ' -f2 | cut -d '-' -f1)
+        echo "$current_version"
+    else
+        echo "未安装"
+    fi
+}
+
+# 获取最新的 micromamba 版本
+get_latest_version() {
+    local latest_version
+    latest_version=$(curl -s https://api.github.com/repos/mamba-org/micromamba-releases/releases/latest | jq -r '.tag_name' | cut -d '-' -f1)
+    echo "$latest_version"
+}
+
+# 检查是否有更新并提示用户
+check_for_updates() {
+    local current_version latest_version
+    current_version=$(get_current_version "$1")
+    latest_version=$(get_latest_version)
+
+    if [ "$latest_version" != "$current_version" ]; then
+        echo "有可用的更新：当前版本 $current_version, 最新版本 $latest_version"
+        read -p "是否更新到最新版本? (y/N): " confirm
+        if [[ "$confirm" =~ ^[Yy]$ ]]; then
+            update_micromamba "$1"
+        else
+            echo "更新已取消"
+        fi
+    else
+        echo "当前已是最新版本 ($current_version)"
+    fi
+}
+
+# 更新micromamba
+update_micromamba() {
+    local mamba_prefix="$1"
+    local current_version latest_version
+    current_version=$(get_current_version "$mamba_prefix")
+    latest_version=$(get_latest_version)
+
+    if [ "$latest_version" != "$current_version" ]; then
+        echo "有可用的更新：当前版本 $current_version, 最新版本 $latest_version"
+        read -p "是否更新到最新版本? (y/N): " confirm
+        if [[ "$confirm" =~ ^[Yy]$ ]]; then
+            echo "正在卸载旧版本 micromamba..."
+            uninstall_micromamba "$mamba_prefix"
+            echo "正在安装最新版本 micromamba..."
+            install_micromamba "$mamba_prefix"
+        else
+            echo "更新已取消"
+        fi
+    else
+        echo "当前已是最新版本 ($current_version)"
+    fi
+}
+
+
+# 交互式安装、卸载和更新菜单
+interactive_menu() {
+    local current_version latest_version
+    current_version=$(get_current_version "$DEFAULT_MAMBA_ROOT_PREFIX")
+    latest_version=$(get_latest_version)
+
+    # 检测并显示当前和最新版本
+    echo "当前 micromamba 版本: $current_version"
+    echo "最新 micromamba 版本: $latest_version"
+    if [ "$latest_version" != "$current_version" ]; then
+        echo "有可用的更新。"
+    fi
+
+    echo "选择操作："
+    echo "1) 安装 micromamba"
+    echo "2) 删除 micromamba"
+    echo "3) 更新 micromamba"
+    echo "q) 退出"
+    read -p "请输入选项（1、2、3或q）: " main_choice
+
+    case "$main_choice" in
+        1)
+            echo "MAMBA_ROOT_PREFIX 的路径: $DEFAULT_MAMBA_ROOT_PREFIX: " 
+            install_micromamba "$DEFAULT_MAMBA_ROOT_PREFIX"
+            ;;
+        2)
+            uninstall_micromamba "$DEFAULT_MAMBA_ROOT_PREFIX"
+            ;;
+        3)
+            update_micromamba "$DEFAULT_MAMBA_ROOT_PREFIX"
+            ;;
+        q)
+            echo "退出。"
+            exit 0
+            ;;
+        *)
+            echo "无效的选项。退出。"
+            exit 1
+            ;;
+    esac
+}
+
+# 静默卸载
+silent_uninstall() {
+    # 在卸载之前保留虚拟环境目录
+    local envs_dir="$DEFAULT_MAMBA_ROOT_PREFIX/envs"
+    mkdir -p "$envs_dir"
+    mv "$DEFAULT_MAMBA_ROOT_PREFIX/envs" "$(mktemp -d)"
+    uninstall_micromamba "$DEFAULT_MAMBA_ROOT_PREFIX"
+    mv "$(mktemp -d)/envs" "$envs_dir"
+}
+
+# 静默更新
+silent_update() {
+    update_micromamba "$DEFAULT_MAMBA_ROOT_PREFIX"
+}
+
+# 解析命令行参数
+if [ "$1" = "--silent-install" ]; then
+    silent_install "$2"
+elif [ "$1" = "--silent-uninstall" ]; then
+    silent_uninstall
+elif [ "$1" = "--silent-update" ]; then
+    silent_update
+elif [ "$1" = "--help" ]; then
+    usage
+else
+    interactive_menu
+fi