Update working yass dockerfile

Author: alejoe91

yass/Dockerfile

@@ -1,48 +1,21 @@
-#docker build -t ibl/yass:base .
 FROM nvidia/cuda:10.0-cudnn7-devel-ubuntu18.04
 
 # link the cuda libraries
 ENV LD_LIBRARY_PATH /usr/local/cuda/extras/CUPTI/lib64:$LD_LIBRARY_PATH
 
-# setup time zone for tz
-ENV TZ=Europe/Paris
-RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
-ENV LANG C.UTF-8
-
+# install ubuntu packages
 RUN apt-get update
 RUN apt-get install -y software-properties-common wget git
 
-# Install conda from: https://towardsdatascience.com/conda-pip-and-docker-ftw-d64fe638dc45
-SHELL [ "/bin/bash", "--login", "-c" ]
-
-# Create a non-root user
-ARG username=si
-ARG uid=1000
-ARG gid=100
-ENV USER $username
-ENV UID $uid
-ENV GID $gid
-ENV HOME /home/$USER
-RUN adduser --disabled-password \
-    --gecos "Non-root user" \
-    --uid $UID \
-    --gid $GID \
-    --home $HOME \
-    $USER
-
-COPY entrypoint.sh /usr/local/bin/
-RUN chown $UID:$GID /usr/local/bin/entrypoint.sh && \
-    chmod u+x /usr/local/bin/entrypoint.sh
+# set shell to /bin/bash for compatibility with conda
+# (hints from: https://towardsdatascience.com/conda-pip-and-docker-ftw-d64fe638dc45)
+SHELL [ "/bin/bash", "--login",  "-c" ]
 
-
-USER $USER
 # install miniconda
 ENV MINICONDA_VERSION 4.8.2
-ENV CONDA_DIR $HOME/miniconda3
-#https://repo.anaconda.com/miniconda/Miniconda3-py39_4.9.2-Linux-x86_64.sh
+ENV CONDA_DIR /home/miniconda3
 ENV LATEST_CONDA_SCRIPT "Miniconda3-py37_$MINICONDA_VERSION-Linux-x86_64.sh"
 
-
 RUN wget --quiet https://repo.anaconda.com/miniconda/$LATEST_CONDA_SCRIPT -O ~/miniconda.sh && \
     chmod +x ~/miniconda.sh && \
     ~/miniconda.sh -b -p $CONDA_DIR && \
@@ -51,26 +24,14 @@ RUN wget --quiet https://repo.anaconda.com/miniconda/$LATEST_CONDA_SCRIPT -O ~/m
 # make non-activate conda commands available
 ENV PATH=$CONDA_DIR/bin:$PATH
 # make conda activate command available from /bin/bash --login shells
-RUN echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> ~/.profile
-# make conda activate command available from /bin/bash --interative shells
+RUN echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> /root/.profile 
+# make conda activate command available from /bin/bash --interactive shells
 RUN conda init bash
 
-# create a project directory inside user home
-ENV PROJECT_DIR $HOME/app
-RUN mkdir $PROJECT_DIR
-WORKDIR $PROJECT_DIR
-
-ENV CONDA_ENV_NAME yass
-RUN conda create -n $CONDA_ENV_NAME
-RUN conda activate $CONDA_ENV_NAME 
-
-
-# install yass
+# install YASS
 RUN conda install pytorch==1.2
-#RUN git clone --depth 1 --branch v2.0 https://github.com/paninski-lab/yass \
 RUN git clone https://github.com/paninski-lab/yass \
    && cd yass \
-   && git checkout d9c9e2c52287afeb3256bdfde749f75f5083fd5d \
    && pip --no-cache-dir install -e . \
    && cd src/gpu_bspline_interp \
    && python setup.py install --force \
@@ -81,5 +42,3 @@ RUN git clone https://github.com/paninski-lab/yass \
    && pip install .
 
 RUN pip install scipy==1.2.0
-
-ENTRYPOINT [ "/usr/local/bin/entrypoint.sh" ]