[PullRequest.com] Project review

AUTHORS.md

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+Jonathan Shimwell
+John Billingsley
+Remi Delaporte-Mathurin
+Declan Morbey
+Matthew Bluteau
+Patrick Shriwise

Dockerfile

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+# This dockerfile can be built in a few different ways.
+# Docker build commands must be run from within the base repository directory
+#
+# There are build args availalbe for specifying the:
+# - cq_version
+#   The version of CadQuery to use master or 2. 
+#   Default is 2.
+#   Options: [master, 2]
+#
+# - include_neutronics
+#   If software dependencies needed for neutronics simulations should be
+#   included true or false.
+#   Default is false.
+#   Options: [true, false]
+#
+# - compile_cores
+#   The number of CPU cores to compile the image with.
+#   Default is 1.
+#   Options: [1, 2, 3, 4, 5, 6...]
+#
+# Example builds:
+# Building using the defaults (cq_version 2, no neutronics and 1 core compile)
+# docker build -t ukaea/paramak .
+#
+# Building to include cadquery master, neutronics dependencies and use 8 cores.
+# Run command from within the base repository directory
+# docker build -t ukaea/paramak --build-arg include_neutronics=true --build-arg compile_cores=8 --build-arg cq_version=master .
+
+# Once build the dockerimage can be run in a few different ways.
+#
+# Run with the following command for a terminal notebook interface
+# docker run -it ukaea/paramak .
+#
+# Run with the following command for a jupyter notebook interface
+# docker run -p 8888:8888 ukaea/paramak /bin/bash -c "jupyter notebook --notebook-dir=/examples --ip='*' --port=8888 --no-browser --allow-root"
+
+
+# Once built, the docker image can be tested with either of the following commands
+# docker run --rm ukaea/paramak pytest /tests
+# docker run --rm ukaea/paramak  /bin/bash -c "cd .. && bash run_tests.sh"
+
+FROM continuumio/miniconda3
+
+# By default this Dockerfile builds with the latest release of CadQuery 2
+ARG cq_version=2
+ARG include_neutronics=false
+ARG compile_cores=1
+
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8 \
+    PATH=/opt/openmc/bin:/opt/NJOY2016/build:$PATH \
+    LD_LIBRARY_PATH=/opt/openmc/lib:$LD_LIBRARY_PATH \
+    CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx \
+    DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update -y && \
+    apt-get upgrade -y
+
+RUN apt-get install -y libgl1-mesa-glx libgl1-mesa-dev libglu1-mesa-dev \
+                       freeglut3-dev libosmesa6 libosmesa6-dev \
+                       libgles2-mesa-dev && \
+                       apt-get clean
+
+# Installing CadQuery
+# jupyter is installed before cadquery to avoid a conflict
+RUN echo installing CadQuery version $cq_version && \
+    conda install jupyter -y --quiet && \
+    conda install -c cadquery -c conda-forge cadquery="$cq_version" && \
+    conda clean -afy
+
+# Install neutronics dependencies from Debian package manager
+RUN if [ "$include_neutronics" = "true" ] ; \
+    then echo installing with include_neutronics=true ; \
+         apt-get install -y \
+            wget git gfortran g++ cmake \
+            mpich libmpich-dev libhdf5-serial-dev libhdf5-mpich-dev \
+            imagemagick ; \
+    fi
+
+# install addition packages required for MOAB
+RUN if [ "$include_neutronics" = "true" ] ; \
+    then echo installing with include_neutronics=true ; \
+    apt-get --yes install libeigen3-dev ; \
+    apt-get --yes install libblas-dev ; \
+    apt-get --yes install liblapack-dev ; \
+    apt-get --yes install libnetcdf-dev ; \
+    apt-get --yes install libtbb-dev ; \
+    apt-get --yes install libglfw3-dev ; \
+    fi
+
+# Clone and install NJOY2016
+RUN if [ "$include_neutronics" = "true" ] ; \
+    then git clone https://github.com/njoy/NJOY2016 /opt/NJOY2016 ; \
+    cd /opt/NJOY2016 ; \
+    mkdir build ; \
+    cd build ; \
+    cmake -Dstatic=on .. ; \
+    make 2>/dev/null ; \
+    make install ; \
+    fi
+
+# Clone and install Embree
+RUN if [ "$include_neutronics" = "true" ] ; \
+    then git clone https://github.com/embree/embree ; \
+    cd embree ; \
+    mkdir build ; \
+    cd build ; \
+    cmake .. -DCMAKE_INSTALL_PREFIX=.. \
+        -DEMBREE_ISPC_SUPPORT=OFF ; \
+    make -j"$compile_cores" ; \
+    make -j"$compile_cores" install ; \
+    fi
+
+# Clone and install MOAB
+RUN if [ "$include_neutronics" = "true" ] ; \
+    then pip install --upgrade numpy cython ; \
+    mkdir MOAB ; \
+    cd MOAB ; \
+    mkdir build ; \
+    git clone  --single-branch --branch develop https://bitbucket.org/fathomteam/moab/ ; \
+    cd build ; \
+    cmake ../moab -DENABLE_HDF5=ON \
+                -DENABLE_NETCDF=ON \
+                -DBUILD_SHARED_LIBS=OFF \
+                -DENABLE_FORTRAN=OFF \
+                -DCMAKE_INSTALL_PREFIX=/MOAB ; \
+    make -j"$compile_cores" ; \
+    make -j"$compile_cores" install ; \
+    rm -rf * ; \
+    cmake ../moab -DBUILD_SHARED_LIBS=ON \
+                -DENABLE_HDF5=ON \
+                -DENABLE_PYMOAB=ON \
+                -DENABLE_BLASLAPACK=OFF \
+                -DENABLE_FORTRAN=OFF \
+                -DCMAKE_INSTALL_PREFIX=/MOAB ; \
+    make -j"$compile_cores" ; \
+    make -j"$compile_cores" install ; \
+    cd pymoab ; \
+    bash install.sh ; \
+    python setup.py install ; \
+    fi
+
+
+# Clone and install Double-Down
+RUN if [ "$include_neutronics" = "true" ] ; \
+    then git clone https://github.com/pshriwise/double-down ; \
+    cd double-down ; \
+    mkdir build ; \
+    cd build ; \
+    cmake .. -DCMAKE_INSTALL_PREFIX=.. \
+        -DMOAB_DIR=/MOAB \
+        -DEMBREE_DIR=/embree/lib/cmake/embree-3.12.1 \
+        -DEMBREE_ROOT=/embree/lib/cmake/embree-3.12.1 ; \
+    make -j"$compile_cores" ; \
+    make -j"$compile_cores" install ; \
+    fi
+
+# Clone and install DAGMC
+RUN if [ "$include_neutronics" = "true" ] ; \
+    then mkdir DAGMC ; \
+    cd DAGMC ; \
+    git clone -b develop https://github.com/svalinn/dagmc ; \
+    mkdir build ; \
+    cd build ; \
+    cmake ../dagmc -DBUILD_TALLY=ON \
+        -DCMAKE_INSTALL_PREFIX=/dagmc/ \
+        -DMOAB_DIR=/MOAB \
+        -DBUILD_STATIC_LIBS=OFF \
+        -DBUILD_STATIC_EXE=OFF ; \
+    make -j"$compile_cores" install ; \
+    rm -rf /DAGMC/dagmc /DAGMC/build ; \
+    fi
+
+# Clone and install OpenMC with DAGMC
+RUN if [ "$include_neutronics" = "true" ] ; \
+    then git clone --recurse-submodules https://github.com/openmc-dev/openmc.git /opt/openmc ; \
+    cd /opt/openmc ; \
+    mkdir build ; \
+    cd build ; \
+    cmake -Doptimize=on -Ddagmc=ON \
+        -DDAGMC_DIR=/DAGMC/ \
+        -DHDF5_PREFER_PARALLEL=on ..  ; \
+    make -j"$compile_cores" ; \
+    make -j"$compile_cores" install ; \
+    cd ..  ; \
+    pip install -e .[test] ; \
+    /opt/openmc/tools/ci/download-xs.sh ; \
+    fi
+
+ENV OPENMC_CROSS_SECTIONS=/root/nndc_hdf5/cross_sections.xml
+
+# Copies over the Paramak code from the local repository
+
+RUN if [ "$include_neutronics" = "true" ] ; \
+    then pip install neutronics_material_maker ; \
+    pip install parametric_plasma_source ; \
+    fi
+
+COPY requirements.txt requirements.txt
+RUN pip install -r requirements.txt
+
+
+# Copy over the source code, examples and tests
+COPY run_tests.sh run_tests.sh
+COPY paramak paramak/
+COPY examples examples/
+COPY setup.py setup.py
+COPY tests tests/
+COPY README.md README.md
+
+# using setup.py instead of pip due to https://github.com/pypa/pip/issues/5816
+RUN python setup.py install
+
+WORKDIR examples

LICENSE.txt

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+MIT License
+
+Copyright (c) 2020 UKAEA
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

MANIFEST.in

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+include README.md
+include requirements.txt
+include LICENSE.txt