Docker file for TM5 installation

pycif-ubuntu.Dockerfile

@@ -23,11 +23,6 @@ RUN apt update \
     && cd netcdf-fortran-4.5.3 \
     && ./configure --prefix=${NCDIR} --disable-netcdf-4 \
     && make install \
-# Install utilities for TM5 default-jre
-    && apt-get install -y  tcsh bison flex openjdk-8-jdk\
-    && mkdir -p /usr/local/gfortran;
-# Install HDF4
-#    && apt-get install -y libhdf4-dev;
 
 RUN apt update \
     && apt-get install -y python3-yaml \

pycif-ubuntu.TM5.Dockerfile

+# Build a Docker image that contains all requirements to run the PyCIF CI.
+FROM ubuntu:20.10
+
+RUN apt update \
+    && DEBIAN_FRONTEND=noninteractive apt install -y software-properties-common rsync git \
+    && apt update \
+# Install Python
+    && DEBIAN_FRONTEND=noninteractive apt install -y python3.9 python3-pip \
+# Install GDAL
+    && apt-get install -y gdal-bin libgdal-dev \
+    && pip install numpy GDAL \
+# Install important packages
+	&& DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential xmlstarlet gfortran libeccodes0 graphviz \
+	&& pip install scipy tox sphinx sphinxcontrib-plantuml graphviz \
+	               pyproj cython numpy pandas bottleneck \
+# Install MPI
+    && apt-get install -y libopenmpi-dev openmpi-bin libhdf5-openmpi-dev \
+# Install NetCDF
+    && cd /tmp \
+    && apt install -y wget \
+    && wget https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.5.3.tar.gz \
+    && tar -xf netcdf-fortran-4.5.3.tar.gz \
+    && cd netcdf-fortran-4.5.3 \
+    && ./configure --prefix=${NCDIR} --disable-netcdf-4 \
+    && make install;
+
+
+# Install utilities for TM5
+RUN apt-get install -y  tcsh bison flex openjdk-8-jdk\
+    && mkdir -p /usr/local/gfortran;
+
+# Copy libraries and compile them
+COPY ./TM5_libs /tmp/TM5_libs
+
+WORKDIR /tmp/TM5_libs
+
+RUN ./INSTALL_ALL.sh
+
+# Install python packages to install pycif locally
+RUN apt update \
+    && apt-get install -y python3-yaml \
+    && pip install pytest pytest-html pyyaml;
+
+# Install pycif on the container
+COPY ./ /tmp/CIF
+
+WORKDIR /tmp/CIF/
+
+RUN python3 setup.py develop
+
+# Command to run at execution
+COPY ./bin/docker_entrypoint.sh /bin/
+
+# Create directories
+RUN mkdir /workdir/ \
+    && mkdir /config/;
+
+ENTRYPOINT ["docker_entrypoint.sh"]