Merge pull request #102 from ContextLab/rev-2

Merging revision 2 changes into master branch

Author: jeremymanning

.dockerignore

@@ -0,0 +1 @@
+*

Dockerfile

@@ -0,0 +1,157 @@
+FROM ubuntu:bionic
+
+LABEL maintainer="Contextual Dynamics Lab <contextualdynamics@gmail.com>"
+
+ARG DEBIAN_FRONTEND=noninteractive
+ARG WORKDIR="/mnt"
+ARG NOTEBOOK_IP=0.0.0.0
+ARG PORT=9999
+
+ENV LANG=C.UTF-8 \
+    PATH="/opt/conda/bin:$PATH" \
+    NOTEBOOK_DIR=$WORKDIR \
+    NOTEBOOK_IP=$NOTEBOOK_IP \
+    NOTEBOOK_PORT=$PORT
+
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
+RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc \
+    && apt-get update --fix-missing \
+    && apt-get install -y --no-install-recommends eatmydata \
+    && eatmydata apt-get install -y --no-install-recommends \
+        bzip2 \
+        ca-certificates \
+        curl \
+        gcc \
+        git \
+        libfontconfig1-dev \
+        libgl1-mesa-glx -y \
+        mpich \
+        pkg-config \
+        sudo \
+        swig \
+        vim \
+        wget \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh -O ~/miniconda.sh \
+    && /bin/bash ~/miniconda.sh -b -p /opt/conda \
+    && rm ~/miniconda.sh \
+    && conda config --set auto_update_conda false \
+    && conda config --set notify_outdated_conda false \
+    && conda install -y \
+        _libgcc_mutex=0.1=main \
+        blas=1.0=mkl \
+        ca-certificates=2019.5.15=1 \
+        certifi=2019.6.16=py36_1 \
+        ipykernel=5.3.4 \
+        ipython=7.16.1 \
+        ipywidgets=7.5.1 \
+        jinja2=2.11.2 \
+        libedit=3.1.20181209=hc058e9b_0 \
+        libffi=3.2.1=hd88cf55_4 \
+        libgcc-ng=8.2.0=hdf63c60_1 \
+        libgfortran-ng=7.3.0=hdf63c60_0 \
+        libstdcxx-ng=8.2.0=hdf63c60_1 \
+        mkl-service=2.0.2=py36h7b6447c_0 \
+        mkl_fft=1.0.12=py36ha843d7b_0 \
+        mkl_random=1.0.2=py36hd81dba3_0 \
+        nbconvert=5.6.1 \
+        nbformat=5.0.7 \
+        ncurses=6.1=he6710b0_1 \
+        notebook=6.1.4 \
+        numpy-base=1.16.4=py36hde5b4d6_0 \
+        openssl=1.1.1c=h7b6447c_1 \
+        pandoc=2.10 \
+        pip=19.0.3=py36_0 \
+        prometheus_client=0.8.0 \
+        python=3.6.8=h0371630_0 \
+        pyzmq=19.0.2 \
+        readline=7.0=h7b6447c_5 \
+        setuptools=40.8.0=py36_0 \
+        sqlite=3.27.2=h7b6447c_0 \
+        terminado=0.9.1 \
+        tk=8.6.8=hbc83047_0 \
+        tornado=6.0.4 \
+        traitlets=4.3.3 \
+        wheel=0.33.1=py36_0 \
+        widgetsnbextension=3.5.1 \
+        xz=5.2.4=h14c3975_4 \
+        zlib=1.2.11=h7b6447c_3 \
+    && conda clean -tipsy \
+    && pip install \
+        alabaster==0.7.12 \
+        babel==2.6.0 \
+        biopython==1.74 \
+        chardet==3.0.4 \
+        citeproc-py==0.4.0 \
+        cycler==0.10.0 \
+        deepdish==0.3.6 \
+        docutils==0.14 \
+        duecredit==0.7.0 \
+        future==0.17.1 \
+        hypertools==0.5.1 \
+        idna==2.8 \
+        imagesize==1.1.0 \
+        intel-openmp==2019.0 \
+        jinja2==2.10 \
+        jupyter_contrib_nbextensions==0.5.1 \
+        kiwisolver==1.0.1 \
+        llvmlite==0.28.0 \
+        lxml==4.3.3 \
+        markupsafe==1.1.1 \
+        matplotlib==3.0.3 \
+        mkl==2019.0 \
+        mock==2.0.0 \
+        neurosynth==0.3.8 \
+        nibabel==2.5.0 \
+        nose==1.3.7 \
+        numba==0.43.1 \
+        numexpr==2.6.9 \
+        numpy==1.16.2 \
+        packaging==19.0 \
+        pandas==0.24.2 \
+        pbr==5.1.3 \
+        ply==3.11 \
+        ppca==0.0.4 \
+        pygments==2.3.1 \
+        pyparsing==2.3.1 \
+        python-dateutil==2.8.0 \
+        pytz==2018.9 \
+        requests==2.21.0 \
+        scikit-learn==0.19.2 \
+        scipy==1.2.1 \
+        seaborn==0.9.0 \
+        six==1.12.0 \
+        snowballstemmer==1.2.1 \
+        sphinx==2.0.0 \
+        sphinxcontrib-applehelp==1.0.1 \
+        sphinxcontrib-devhelp==1.0.1 \
+        sphinxcontrib-htmlhelp==1.0.1 \
+        sphinxcontrib-jsmath==1.0.1 \
+        sphinxcontrib-qthelp==1.0.2 \
+        sphinxcontrib-serializinghtml==1.1.3 \
+        tables==3.5.1 \
+        umap-learn==0.3.8 \
+        urllib3==1.24.1 \
+        git+git://github.com/lucywowen/timecorr-1.git@spot_check \
+        git+https://github.com/FIU-Neuro/brainconn.git \
+    && rm -rf ~/.cache/pip \
+    && jupyter nbextension enable --py widgetsnbextension --sys-prefix \
+    && jupyter notebook --generate-config \
+    && ipython profile create \
+    &&  sed -i \
+        -e 's/^# c.Completer.use_jedi = True/c.Completer.use_jedi = False/' \
+        -e 's/^#c.Completer.use_jedi = True/c.Completer.use_jedi = False/' \
+        -e 's/^# c.IPCompleter.use_jedi = True/c.IPCompleter.use_jedi = False/' \
+        ~/.ipython/profile_default/ipython_config.py \
+    && mkdir -p /root/.jupyter \
+    && echo "from os import getenv" > /root/.jupyter/jupyter_notebook_config.py \
+    && echo "c.NotebookApp.ip = getenv(\"NOTEBOOK_IP\")" >> /root/.jupyter/jupyter_notebook_config.py \
+    && echo "c.NotebookApp.port = int(getenv(\"NOTEBOOK_PORT\"))" >> /root/.jupyter/jupyter_notebook_config.py \
+    && echo "c.NotebookApp.notebook_dir = getenv(\"NOTEBOOK_DIR\")" >> /root/.jupyter/jupyter_notebook_config.py \
+    && echo "c.NotebookApp.open_browser = False" >> /root/.jupyter/jupyter_notebook_config.py \
+    && echo "c.NotebookApp.allow_root = True" >> /root/.jupyter/jupyter_notebook_config.py \
+    && echo "c.FileContentsManager.delete_to_trash = False" >> /root/.jupyter/jupyter_notebook_config.py
+
+WORKDIR $WORKDIR

README.md

@@ -16,24 +16,26 @@ root
 ```
 
 Content of the data folder is provided [here](https://drive.google.com/file/d/1CZYe8eyAkZFuLqfwwlKoeijgkjdW6vFs/view?usp=sharing).
-We also include a Dockerfile to reproduce our computational environment. Instruction for use are below (copied and modified from [MIND](https://github.com/Summer-MIND/mind-tools) repo):
+We also include a Dockerfile to reproduce our computational environment. Instruction for use are below:
 
-## One time setup
+
+## Docker setup
 1. Install Docker on your computer using the appropriate guide below:
     - [OSX](https://docs.docker.com/docker-for-mac/install/#download-docker-for-mac)
     - [Windows](https://docs.docker.com/docker-for-windows/install/)
     - [Ubuntu](https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/)
     - [Debian](https://docs.docker.com/engine/installation/linux/docker-ce/debian/)
 2. Launch Docker and adjust the preferences to allocate sufficient resources (e.g. > 4GB RAM)
 3. Build the docker image by opening a terminal in this repo folder and enter `docker build -t timecorr_paper .`  
-4. Use the image to create a new container for the workshop
-    - The command below will create a new container that will map your computer's `Desktop` to `/mnt` within the container, so that location is shared between your host OS and the container. Feel free to change `Desktop` to whatever folder you prefer to share instead, but make sure to provide the full path. The command will also share port `9999` with your host computer so any jupyter notebooks launched from *within* the container will be accessible at `localhost:9999` in your web browser
-    - `docker run -it -p 9999:9999 --name Timecorr_paper -v ~/Desktop:/mnt timecorr_paper `
+4. Use the image to create a new container
+    - The command below will create a new container that will map your local copy of the repository to `/mnt` within the container, so that location is shared between your host OS and the container. The command will also share port `9999` with your host computer so any jupyter notebooks launched from *within* the container will be accessible in your web browser.
+    - `docker run -it -p 9999:9999 --name Timecorr_paper -v $PWD:/mnt timecorr_paper `
     - You should now see the `root@` prefix in your terminal, if so you've successfully created a container and are running a shell from *inside*!
-5. To launch any of the notebooks: `jupyter notebook --port=9999 --no-browser --ip=0.0.0.0 --allow-root`
+5. To launch any of the notebooks: `jupyter notebook`
 
 ## Using the container after setup
 1. You can always fire up the container by typing the following into a terminal
-    - `docker start Timecorr_paper && docker attach Timecorr_paper`
-    - When you see the `root@` prefix, letting you know you're inside the container
-2. Close a running container with `ctrl + d` from the same terminal you used to launch the container, or `docker stop Timecorr_paper` from any other terminal
+    - `docker start --attach Timecorr_paper`
+    - When you see the `root@` prefix, you're inside the container
+2. Stop a running jupyter notebook server with `ctrl + c`
+3. Close a running container with `ctrl + d` or `exit` from the same terminal window you used to launch the container, or `docker stop Timecorr_paper` from any other terminal window