remove unnecessary packages; non-root user version (currently has permission denied bugs)

Author: xiu-cs

Dockerfile

@@ -1,54 +1,44 @@
+# Base image with PyTorch and CUDA support
 FROM pytorch/pytorch:2.3.1-cuda11.8-cudnn8-runtime
+
+# User arguments for container setup
 ARG user_name
 ARG uid
 ARG gid
-ENV HOME=/root 
-WORKDIR ${HOME}
 
+# Install system dependencies
 ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get update -y && apt-get install -y --no-install-recommends \
-    vim zsh tmux wget curl htop jupyter python3 python3-pip libgl1-mesa-glx git sudo ssh libglib2.0-0 \
-    tree \
+    libgl1-mesa-glx libglib2.0-0 \
     && apt-get -y autoclean \
     && apt-get -y autoremove \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
-    && apt-get clean \
-    && apt-get update 
-
-# Install conda packages as root
-SHELL ["/bin/bash", "-lc"]
-RUN conda install -y python=3.10 pytables=3.8.0 hdf5 jupyter
-
-# Install DeepLabCut and other pip packages as root
-RUN pip install --no-cache-dir --upgrade pip setuptools && \
-    pip install --no-cache-dir gpustat nvitop pytest PySide6==6.3.1 streamlit networkx isort black && \
-    pip install --no-cache-dir amadeusgpt && \
-    pip install --no-cache-dir git+https://github.com/DeepLabCut/DeepLabCut.git
-
-# Initialize conda for zsh shell
-RUN /opt/conda/bin/conda init zsh
+    && apt-get clean
 
 # Create a non-root user
-RUN mkdir /app /logs /data
+RUN mkdir -p /app /home/${user_name}
 RUN groupadd -g ${gid} ${user_name} \
     && useradd -m -u ${uid} -g ${gid} ${user_name} \
-    && chown -R ${uid}:${gid} /home
+    && chown -R ${uid}:${gid} /home/${user_name}
 
 # Switch to the new user and set home directory as working directory
 USER ${user_name}
 ENV HOME=/home/${user_name}
 WORKDIR ${HOME}
 
-# Install Oh My Zsh and plugins
-RUN sh -c "$(curl -fsSL https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master/tools/install.sh)" --unattended \
-    && git clone https://github.com/zsh-users/zsh-autosuggestions ~/.oh-my-zsh/custom/plugins/zsh-autosuggestions \
-    && git clone https://github.com/zsh-users/zsh-syntax-highlighting ~/.oh-my-zsh/custom/plugins/zsh-syntax-highlighting \
-    && sed -i 's/^plugins=(.*)$/plugins=(git zsh-autosuggestions zsh-syntax-highlighting)/' ~/.zshrc
+# Create a user conda environment to avoid permission issues
+SHELL ["/bin/bash", "-c"]
+RUN conda create -y --name amadeusGPT python=3.10
+ENV PATH=/opt/conda/envs/amadeusGPT/bin:$PATH
+RUN conda install -y -n amadeusGPT hdf5 pytables=3.8.0
 
-RUN echo "export PATH=$PATH:/home/${user_name}/.local/bin" >> /home/${user_name}/.zshrc
+# Install pip packages in the user environment
+RUN pip install --no-cache-dir notebook amadeusgpt
+RUN pip install -U --pre deeplabcut
 
-USER root
-WORKDIR /app
+# Initialize conda for the user's bash
+RUN conda init bash
+RUN echo 'conda activate amadeusGPT' >> ${HOME}/.bashrc
 
-CMD ["zsh"]
-SHELL ["/bin/zsh", "-c"]
+# Default command when container starts (activating the conda env)
+CMD ["bash", "-l"]