change nodejs to 18 and all install nglview

Dockerfile.jupyterhub

@@ -8,6 +8,8 @@ ARG ROOT_PASSWD="password"
 ARG HOME="/home/${CREATE_USER}"
 ARG DEBIAN_FRONTEND="noninteractive"
 ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
+ARG NODEJS_VERSION='18'
+ENV NODEJS_VERSION=${NODEJS_VERSION}
 
 USER root
 RUN <<EOT
@@ -19,6 +21,8 @@ apt-get install -y tzdata
 ln -sf /usr/share/zoneinfo/Asia/Shanghai /etc/localtime
 echo 'Asia/Shanghai' > /etc/timezone
 dpkg-reconfigure -f noninteractive tzdata
+sudo apt-get remove --purge libnode72:amd64 -y
+curl -fsSL https://deb.nodesource.com/setup_${NODEJS_VERSION}.x | sudo -E bash - 
 # 安装所需的软件包
 apt-get install -y python3 python3-pip gcc g++ build-essential nodejs npm gdebi-core curl wget openssh-server vim lrzsz net-tools sudo git
 # 创建新用户
@@ -30,8 +34,20 @@ EOT
 RUN <<EOT
 #!/bin/bash
 # 安装 Jupyter 和相关软件
-npm install -g configurable-http-proxy
+npm install -g configurable-http-proxy yarn --registry=https://registry.npmmirror.com
-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-unfold 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
+python3 -m pip install ipython jupyter_packaging 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-unfold 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
+git clone https://ghproxy.dockless.eu.org/https://github.com/arose/nglview
+cd nglview
+python3 setup.py install
+cd js
+rm -rf node_modules package-lock.json
+npm install typescript@latest --registry=https://registry.npmmirror.com
+npm install --registry=https://registry.npmmirror.com
+cd ../..
+python -m ipykernel install --sys-prefix
+jupyter nbextension enable --py --sys-prefix widgetsnbextension
+jupyter nbextension enable --py --sys-prefix nglview
+jupyter-nbextension enable nglview --py --sys-prefix
 # 创建 JupyterHub 配置目录
 mkdir -p /root/.jupyterhub
 EOT
@@ -52,22 +68,9 @@ sudo wget "https://download2.rstudio.org/server/$(lsb_release -cs)/amd64/rstudio
 sudo chmod +x /tmp/rstudio-server.deb 
 sudo gdebi -n /tmp/rstudio-server.deb
 sudo rm -rf /tmp/rstudio-server.deb
-EOT
-
-RUN <<EOT
-#!/bin/bash
-# 安装micromamba
-echo "1" | bash <(curl -s https://raw.githubusercontent.com/hotwa/MicroMamba_Installer/main/install.sh)
-mkdir -p /root/workspace/personal /root/workspace/project
-EOT
-
-RUN <<EOT
-#!/bin/bash
 # 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/??_*
 EOT
 
-
-
 CMD ["jupyterhub", "-f", "/srv/jupyterhub/jupyterhub_config.py"]

jupyterhub_config.py

@@ -10,6 +10,19 @@ c = get_config()  # noqa: F821
 # avoid having to rebuild the JupyterHub container every time we change a
 # configuration parameter.
 
+# from dockerspawner import DockerSpawner
+
+# class MyDockerSpawner(DockerSpawner):
+#     def start(self):
+#         # 启动父类的start方法
+#         self.user_options['environment']['JUPYTER_ENABLE_NBEXTENSIONS'] = 'true'
+#         self.user_options['cmd'] = [
+#             'bash',
+#             '-c',
+#             'pip install nglview jupyter_packaging -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com && jupyter nbextension enable nglview --py --sys-prefix && jupyter labextension install nglview-js-widgets && jupyter labextension install @jupyter-widgets/jupyterlab-manager && start-singleuser.sh'
+#         ]
+#         return super().start()
+        
 # Spawn single-user servers as Docker containers
 c.JupyterHub.spawner_class = "dockerspawner.DockerSpawner"
 

spawnerdockerfile/Dockerfile.base-notebook

@@ -78,6 +78,8 @@ ARG ROOT_PASSWD="password"
 ARG HOME="/home/${CREATE_USER}"
 ARG DEBIAN_FRONTEND="noninteractive"
 ENV DEBIAN_FRONTEND=${DEBIAN_FRONTEND}
+ARG NODEJS_VERSION='18'
+ENV NODEJS_VERSION=${NODEJS_VERSION}
 
 COPY install.sh /tmp
 RUN <<EOT
@@ -90,7 +92,10 @@ ln -sf /usr/share/zoneinfo/Asia/Shanghai /etc/localtime
 echo 'Asia/Shanghai' > /etc/timezone
 dpkg-reconfigure -f noninteractive tzdata
 # 安装所需的软件包
+sudo apt-get remove --purge libnode72:amd64 -y
+curl -fsSL https://deb.nodesource.com/setup_${NODEJS_VERSION}.x | sudo -E bash - 
 apt-get install -y python3 python3-pip gcc g++ build-essential nodejs npm gdebi-core curl wget openssh-server vim lrzsz net-tools sudo git nodejs
+npm install -g configurable-http-proxy yarn --registry=https://registry.npmmirror.com
 # 创建新用户
 useradd -m -s /bin/bash ${CREATE_USER}
 echo "${CREATE_USER}:${CREATE_USER_PASSWD}" | chpasswd
@@ -100,11 +105,7 @@ EOT
 # 安装 Jupyter 和相关软件
 RUN <<EOT
 #!/bin/bash
-npm install -g configurable-http-proxy
+python3 -m pip install ipython jupyterhub jupyterlab notebook jupyter_packaging -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
-git clone https://github.com/arose/nglview
-cd nglview
-python setup.py install
-cd ..
 python3 -m pip install aiohttp -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
 python3 -m pip install jupyterhub jupyterlab notebook radian pycurl aiohttp 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 dockerspawner jupyterhub-nativeauthenticator lckr_jupyterlab_variableinspector -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com
 EOT
@@ -178,8 +179,16 @@ RUN <<EOT
 #!/bin/bash
 sudo apt update
 sudo apt install -y texlive-full
-mamba create -n torch pytorch torchvision torchaudio python=3 ipython nglview requests scienceplots autopep8 ipykernel\
+mamba create -n torch jupyter_packaging pytorch biopython biopandas pymol-open-source mdtraj torchvision torchaudio python=3 ipython requests scienceplots autopep8 ipykernel\
  pandas numpy matplotlib scipy seaborn orange3 -c pytorch -c nvidia -c conda-forge -y 
+git clone https://ghproxy.dockless.eu.org/https://github.com/arose/nglview
+cd nglview
+mamba run -n torch python3 setup.py install
+cd js
+rm -rf node_modules package-lock.json
+npm install typescript@latest --registry=https://registry.npmmirror.com
+npm install --registry=https://registry.npmmirror.com
+cd ../..
 mamba run -n torch python -m ipykernel install --user --name="torch" --display-name="torch_env"
 EOT