Question 83111 in Docker Question posted in
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Dockerfile struggling to install Python Geopandas module

I have a dockerfile in which I am trying to build a container with my required python modules from.

See my dockerfile below to understand how and what modules I am trying to install:

FROM ubuntu:bionic

ENV ROOTDIR /usr/local/
ENV GDAL_VERSION 2.4.1
ENV OPENJPEG_VERSION 2.3.0
ENV CURL_CA_BUNDLE /etc/ssl/certs/ca-certificates.crt

# Load assets
WORKDIR $ROOTDIR/

ADD http://download.osgeo.org/gdal/${GDAL_VERSION}/gdal-${GDAL_VERSION}.tar.gz $ROOTDIR/src/
ADD https://github.com/uclouvain/openjpeg/archive/v${OPENJPEG_VERSION}.tar.gz $ROOTDIR/src/openjpeg-${OPENJPEG_VERSION}.tar.gz

# Install basic dependencies
RUN apt-get update -y && apt-get install -y 
    software-properties-common 
    build-essential 
    python-dev 
    python3-dev 
    python-numpy 
    python3-numpy 
    python3-pyproj 
    libspatialite-dev 
    sqlite3 
    libpq-dev 
    libcurl4-gnutls-dev 
    libproj-dev 
    libxml2-dev 
    libgeos-dev 
    libnetcdf-dev 
    libpoppler-dev 
    libspatialite-dev 
    libhdf4-alt-dev 
    libhdf5-serial-dev 
    bash-completion 
    cython 
    cmake

# Compile and install OpenJPEG
RUN cd src && tar -xvf openjpeg-${OPENJPEG_VERSION}.tar.gz && cd openjpeg-${OPENJPEG_VERSION}/ 
    && mkdir build && cd build 
    && cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$ROOTDIR 
    && make && make install && make clean 
    && cd $ROOTDIR && rm -Rf src/openjpeg*

# Compile and install GDAL
RUN cd src && tar -xvf gdal-${GDAL_VERSION}.tar.gz && cd gdal-${GDAL_VERSION} 
    && ./configure --with-python --with-spatialite --with-pg --with-curl --with-openjpeg 
    && make -j $(nproc) && make install && ldconfig 
    && apt-get update -y 
    && cd $ROOTDIR && cd src/gdal-${GDAL_VERSION}/swig/python 
    && python3 setup.py build 
    && python3 setup.py install 
    && apt-get remove -y --purge build-essential 
      python-dev 
      python3-dev 
    && cd $ROOTDIR && rm -Rf src/gdal*


# install Vim
RUN apt-get -y install vim

# Install Pip3 and required python modules
RUN apt-get -y install python3-pip

RUN pip3 install rasterio &&
    pip3 install rdp &&
    pip3 install gdal2tiles&&
    pip3 install awscli &&
    pip3 install pandas &&
    pip3 install boto3 &&
    pip3 install requests &&
    pip3 install shapely &&
    pip3 install geopandas &&   
    pip3 install math

However, it seems to get as far as the geopandas module and then I hit this error:

Collecting pyproj>=2.2.0 (from geopandas)
  Downloading https://files.pythonhosted.org/packages/2c/12/7a8cca32506747c05ffd5c6ba556cf8435754af0939906cbcc7fa5802ea3/pyproj-3.0.1.tar.gz (168kB)
    Complete output from command python setup.py egg_info:
    ERROR: Cython.Build.cythonize not found. Cython is required to build pyproj.

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-vtfufrfs/pyproj/

Has anyone any ideas on how to overcome this?

Tags:

2

Answers


  1. 0

    Your Python3 environment is missing the Cython package. Add the line pip3 install cython before the pip3 install geopandas line.

    You will need to upgrade your pip version as well.
    And it is more convenient to use pip directly from the Python3 interpreter rather than the pip3 wrapper. So I will go to refactor your last RUN block like so:

    RUN 
   python3 -m pip install --upgrade pip 
   && python3 -m pip install 
        cython 
        rasterio 
        rdp 
        gdal2tiles 
        awscli 
        pandas 
        boto3 
        requests 
        shapely 
        geopandas
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  2. 0

    Try this way in your dockerfile

    RUN wget http://download.osgeo.org/libspatialindex/spatialindex-src-1.8.5.tar.gz && 
  tar -xvzf spatialindex-src-1.8.5.tar.gz && 
  cd spatialindex-src-1.8.5 && 
  ./configure && 
  make && 
  make install && 
  cd - && 
  rm -rf spatialindex-src-1.8.5* && 
  ldconfig

### Install rtree and geopandas
RUN pip install rtree geopandas
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