Simplify the Docker image building, and make it run Jupyter notebook as an entry point

.github/workflows/test_docker_build.yaml

@@ -27,6 +27,6 @@ jobs:
         run: |
           docker build -t stdpipe/stdpipe . && docker push stdpipe/stdpipe
 
-      - name: Start containers
-        run: |
-          docker-compose up -d
+      # - name: Start containers
+      #   run: |
+      #     docker-compose up -d

Dockerfile

-ARG SCAMP_version=v2.6.7
-ARG SWARP_version=2.38.0
-ARG Sextractor_version=2.25.0
-ARG PSFEX_version=3.21.1
-
-# Building image from
+# Building image from
 FROM ubuntu:20.04
 
-LABEL maintainer="Michael Coughlin <cough052@umn.edu>"
+LABEL maintainer="Sergey Karpov <karpov.sv@gmail.com>"
 
 # Create a variable corresponding to the name of the new user that will be created inside the Docker.
-ENV USR newuser
+ENV USERNAME newuser
+
+# Create new user
+RUN useradd -ms /bin/bash ${USERNAME}
 
-# Set up working directory
+# Set the working directory
 WORKDIR /home
 
-# Create new user
-RUN useradd -ms /bin/bash ${USR}
+# Fix for tzdata which is pulled by some dependencies
+ARG DEBIAN_FRONTEND=noninteractive
+ENV TZ=Europe/Prague
 
-ARG SCAMP_version
-ARG SWARP_version
-ARG Sextractor_version
-ARG PSFEX_version
 # Install updates to base image, install packages, and remove from cache
-# Create astromatic folder, and install all needed astromatic software and hotpants
-# First download and build cfitsio and the cdsclient used by SCAMP
-# Install all python packages. numpy 1.19.0 is the latest dependency compatible with tensorflow 2.3.1
+# Install hotpants
+# Install Jupyter
+# Install some Python packages
 # All done in one line to limit docker size
 RUN  \
-   apt-get update \
-   && apt-get install software-properties-common -y \ 
-   && add-apt-repository ppa:deadsnakes/ppa -y \ 
-   && apt-get update \
-   && apt-get install -y --no-install-recommends wget curl vim build-essential ca-certificates libtool libatlas3-base libatlas-base-dev libplplot-dev libfftw3-dev libcurl4-openssl-dev autoconf automake git unzip gfortran python3.9 python3.9-dev python3-pip \
-   && apt-get install -y --no-install-recommends libcfitsio-dev sextractor scamp psfex swarp \
-   && rm -rf /var/lib/apt/lists/* \
-   && git clone https://github.com/acbecker/hotpants.git \
-   && cd hotpants \
-   && make \
-   && cp hotpants /usr/local/bin/ \
-   && cd .. \
-   && rm -fr astromatic hotpants cfitsio-* cdsclient-* \
-   && python3.9 -m pip install --upgrade pip \
-   && python3.9 -m pip install setuptools cmake \
-   && python3.9 -m pip install scikit-build  \
-   && python3.9 -m pip install numpy scipy matplotlib astropy pandas shapely requests h5py scikit-image lacosmic hjson voevent-parse xmltodict astroML photutils keras keras-vis cython regions  opencv-python-headless astroscrappy astroquery tqdm 
-RUN  \
-   git clone https://github.com/karpov-sv/stdpipe.git \
-   && cd stdpipe \
-   && python3.9 setup.py install \
-   && rm -fr /home/newuser/.cache/pip \
-   && rm -fr /root/.cache/pip \
-   && rm -fr /root/.cache/* \
-   && rm -fr /tmp/* \
-   && apt-get autoremove --purge -y
-   #&& apt-get purge -y gfortran gfortran-7 git-man libgfortran-7-dev libgfortran4 
+    apt-get update \
+    && apt-get install -y --no-install-recommends build-essential ca-certificates libtool libcfitsio-dev autoconf automake git unzip python3-pip \
+    sextractor scamp psfex swarp \
+    jupyter jupyter-notebook jupyter-nbextension-jupyter-js-widgets python3-ipywidgets \
+    && rm -rf /var/lib/apt/lists/* \
+    && git clone https://github.com/acbecker/hotpants.git \
+    && cd hotpants \
+    && make \
+    && cp hotpants /usr/local/bin/ \
+    && cd .. \
+    && rm -fr hotpants \
+    && python3 -m pip install --upgrade pip \
+    && python3 -m pip install setuptools
 
+# Install STDPipe
+RUN  \
+    git clone https://github.com/karpov-sv/stdpipe.git \
+    && cd stdpipe \
+    && python3 -m pip install -e . \
+    && rm -fr /home/newuser/.cache/pip \
+    && rm -fr /root/.cache/pip \
+    && rm -fr /root/.cache/* \
+    && rm -fr /tmp/* \
+    && apt-get autoremove --purge -y
 
 # switch ownership
 # (all commands are root until a USER command changes that)
-USER ${USR}
-
-# Set the working directory
-WORKDIR /home/${USR}
+USER ${USERNAME}
 
 # change ownership from root to USR:
-# Create directory to link on volume with host machine
-RUN chown -R ${USR}:${USR}  /home/${USR} \
-   && mkdir /home/${USR}/stdpipe/
+# Create `stdpipe` directory to link on volume with host machine
+RUN chown -R ${USERNAME}:${USERNAME}  /home/${USERNAME} \
+    && mkdir /home/${USERNAME}/stdpipe/
 
 # Add local bin to PATH
-ENV PATH="/home/${USR}/.local/bin:$PATH"
+ENV PATH="/home/${USERNAME}/.local/bin:$PATH"
 
 # Change working directory to stdpipe
-WORKDIR /home/${USR}/stdpipe
+WORKDIR /home/${USERNAME}/stdpipe
 
 # define entrypoint which is the default executable at launch
-ENTRYPOINT ["bash"]
+ENTRYPOINT ["jupyter", "notebook", "--no-browser", "--ip=0.0.0.0", "--NotebookApp.token=''"]
+
+EXPOSE 8888

docker-compose.yaml

@@ -4,5 +4,4 @@ services:
   stdpipe:
     image: stdpipe/stdpipe
     ports:
-      - "9000:5000"
-      - "9001:5001"
+      - "9000:8888"

setup.py

@@ -6,12 +6,10 @@ from setuptools import setup, find_packages
 __version__ = '0.1'
 
 requirements = [
-    'configargparse',
     'numpy',
     'scipy',
     'astropy>=4.1',
     'matplotlib',
-    'pandas',
     'astroquery>0.4.1',
     'sep',
     'photutils',
@@ -28,14 +26,14 @@ setup(
     description='Simple Transient Detection Pipeline',
     author='Sergey Karpov',
     author_email='karpov.sv@gmail.com',
-    url='',
+    url='https://github.com/karpov-sv/stdpipe',
     install_requires=requirements,
     packages=['stdpipe'],
     package_data={'stdpipe':['data/*']},
     include_package_data=True,
     extras_require={
-        "example": [
-            'astroscrappy',
-        ],
+	"example": [
+	    'astroscrappy',
+	],
     },
 )