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‎.gitattributes

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PyNucleus/_version.py export-subst

‎Dockerfile

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# VERSION: 0.1
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# DESCRIPTION: Dockerized PyNucleus build
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# AUTHOR: Christian Glusa
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# Base docker image
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FROM debian:testing
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LABEL maintainer Christian Glusa
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ENV LANG C.UTF-8
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# based on recommendations from
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# https://docs.nersc.gov/development/shifter/how-to-use/
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# add contrib and non-free debian repos
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RUN sed -i "s#deb http://deb.debian.org/debian testing main#deb http://deb.debian.org/debian testing main contrib non-free#g" /etc/apt/sources.list
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# install packages needed for build
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RUN apt-get update && \
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DEBIAN_FRONTEND=noninteractive apt-get install -y \
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autoconf automake gcc g++ make gfortran wget zlib1g-dev libffi-dev \
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tk-dev \
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libssl-dev ca-certificates cmake \
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git less \
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libboost-dev \
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hdf5-tools \
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libsuitesparse-dev \
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libarpack2-dev \
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libmkl-avx2 libmkl-dev \
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--no-install-recommends \
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&& rm -rf /var/lib/apt/lists/*
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ENV LD_LIBRARY_PATH /usr/local/lib
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RUN echo "alias ls='ls --color=auto -FN'" >> /root/.bashrc
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RUN mkdir /build/
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# install python
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# Consider adding configure flags:
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# --enable-optimizations
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# --with-lto
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# --build="$gnuArch"
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# --enable-shared
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# --with-system-expat
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# --with-system-ffi
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ARG pythonVersion=3.8.2
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RUN cd /build && wget --no-check-certificate https://www.python.org/ftp/python/${pythonVersion}/Python-${pythonVersion}.tgz \
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&& tar xvzf Python-${pythonVersion}.tgz && cd /build/Python-${pythonVersion} \
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&& ./configure --enable-optimizations --with-pymalloc --enable-shared && make -j4 && make install && make clean && rm /build/Python-${pythonVersion}.tgz && rm -rf /build/Python-${pythonVersion}
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# install mpich
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ARG mpichVersion=3.2
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RUN cd /build && wget --no-check-certificate https://www.mpich.org/static/downloads/${mpichVersion}/mpich-${mpichVersion}.tar.gz \
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&& tar xvzf mpich-${mpichVersion}.tar.gz && cd /build/mpich-${mpichVersion} \
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&& ./configure && make -j4 && make install && make clean && rm /build/mpich-${mpichVersion}.tar.gz && rm -rf /build/mpich-${mpichVersion}
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# install mpi4py
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ARG mpi4pyVersion=3.0.3
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RUN cd /build && wget --no-check-certificate https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-${mpi4pyVersion}.tar.gz \
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&& tar xvzf mpi4py-${mpi4pyVersion}.tar.gz && cd /build/mpi4py-${mpi4pyVersion} \
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&& python3 setup.py build && python3 setup.py install && rm -rf /build/mpi4py-${mpi4pyVersion}
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# install parmetis
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ARG parmetisVersion=4.0.3
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RUN cd /build && wget --no-check-certificate http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-${parmetisVersion}.tar.gz \
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&& tar xvzf parmetis-${parmetisVersion}.tar.gz && cd /build/parmetis-${parmetisVersion} \
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&& make config shared=1 && make -j4 && make install && make clean && rm /build/parmetis-${parmetisVersion}.tar.gz && rm -rf /build/parmetis-${parmetisVersion}
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# install metis
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ARG metisVersion=5.1.0
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RUN cd /build && wget --no-check-certificate http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-${metisVersion}.tar.gz \
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&& tar xvzf metis-${metisVersion}.tar.gz && cd /build/metis-${metisVersion} \
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&& make config shared=1 && make -j4 && make install && make clean && rm /build/metis-${metisVersion}.tar.gz && rm -rf /build/metis-${metisVersion}
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# delete build directory
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RUN rm -rf /build/
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RUN /sbin/ldconfig
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# copy code to container and build
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# we copy only the packages over, not any run scripts
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COPY PyNucleus_* /home/pynucleus-build/
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COPY setup.py /home/pynucleus-build/
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COPY Makefile /home/pynucleus-build/
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RUN cd /home/pynucleus-build && python -m pip install .

‎LICENSE

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Copyright 2021 National Technology & Engineering Solutions of Sandia,
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LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the
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U.S. Government retains certain rights in this software.
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MIT License
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Copyright (c) 2017-2021 Christian Glusa
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
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CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
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TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
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SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

‎MANIFEST.in

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include versioneer.py
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include PyNucleus/_version.py

‎Makefile

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PYTHON ?= python3
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VIRTUAL_ENV ?=
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ifeq ($(VIRTUAL_ENV),)
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FLAGS ?= --no-use-pep517 -e
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PIP_FLAGS ?= --user
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else
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PYTHON = python
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FLAGS ?= -e
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PIP_FLAGS ?=
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endif
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TEST_RESULTS ?= index.html
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install :
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$(PYTHON) -m pip install packageTools/. && \
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$(PYTHON) -m pip install base/. && \
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$(PYTHON) -m pip install metisCy/. && \
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$(PYTHON) -m pip install fem/. && \
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$(PYTHON) -m pip install multilevelSolver/. && \
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$(PYTHON) -m pip install nl/. && \
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$(PYTHON) -m pip install .
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clean :
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$(PYTHON) -m pip uninstall PyNucleus_packageTools PyNucleus_base PyNucleus_metisCy PyNucleus_fem PyNucleus_multilevelSolver PyNucleus_nl
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dev : dev_packageTools dev_base dev_metisCy dev_fem dev_multilevelSolver dev_nl dev_package
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dev_packageTools :
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@ echo "Entering directory \`packageTools/'"
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cd packageTools; $(PYTHON) -m pip install $(FLAGS) .
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dev_base_build :
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@ echo "Entering directory \`base'"
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cd base; $(PYTHON) -m pip install $(FLAGS) .
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dev_base :
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make dev_base_build
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$(PYTHON) -c "import PyNucleus_base" || (make clean_base && make dev_base_build)
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dev_metisCy_build :
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@ echo "Entering directory \`metisCy'"
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cd metisCy; $(PYTHON) -m pip install $(FLAGS) .
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dev_metisCy :
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make dev_metisCy_build
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$(PYTHON) -c "import PyNucleus_metisCy" || (make clean_metisCy && make dev_metisCy_build)
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dev_fem_build :
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@ echo "Entering directory \`fem'"
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cd fem; $(PYTHON) -m pip install $(FLAGS) .
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dev_fem :
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make dev_fem_build
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$(PYTHON) -c "import PyNucleus_fem" || (make clean_fem && make dev_fem_build)
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dev_multilevelSolver_build :
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@ echo "Entering directory \`multilevelSolver'"
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cd multilevelSolver; $(PYTHON) -m pip install $(FLAGS) .
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dev_multilevelSolver :
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make dev_multilevelSolver_build
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$(PYTHON) -c "import PyNucleus_multilevelSolver" || (make clean_multilevelSolver && make dev_multilevelSolver_build)
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dev_nl_build :
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@ echo "Entering directory \`nl'"
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cd nl; $(PYTHON) -m pip install $(FLAGS) .
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dev_nl :
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make dev_nl_build
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$(PYTHON) -c "import PyNucleus_nl" || (make clean_nl && make dev_nl_build)
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dev_package :
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$(PYTHON) -m pip install $(FLAGS) .
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clean_dev: clean_package clean_packageTools clean_base clean_metisCy clean_fem clean_multilevelSolver clean_nl
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clean_packageTools :
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$(PYTHON) -m pip uninstall PyNucleus_packageTools -y
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clean_base :
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$(PYTHON) -m pip uninstall PyNucleus_base -y
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cd base/PyNucleus_base && \
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rm -f *.so *.c *.pyc && \
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rm -rf __pycache__
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cd base && rm -rf build __pycache__ *.egg-info
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clean_metisCy :
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$(PYTHON) -m pip uninstall PyNucleus_metisCy -y
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cd metisCy/PyNucleus_metisCy && \
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rm -f *.so *.c *.pyc && \
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rm -rf __pycache__
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cd metisCy && rm -rf build __pycache__ *.egg-info
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clean_fem :
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$(PYTHON) -m pip uninstall PyNucleus_fem -y
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cd fem/PyNucleus_fem && \
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rm -f *.so *.c *.pyc && \
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rm -rf __pycache__
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cd fem && rm -rf build __pycache__ *.egg-info
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clean_multilevelSolver :
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$(PYTHON) -m pip uninstall PyNucleus_multilevelSolver -y
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cd multilevelSolver/PyNucleus_multilevelSolver && \
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rm -f *.so *.c *.pyc && \
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rm -rf __pycache__
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cd multilevelSolver && rm -rf build __pycache__ *.egg-info
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clean_nl :
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$(PYTHON) -m pip uninstall PyNucleus_nl -y
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cd nl/PyNucleus_nl && \
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rm -rf *.so *.c *.pyc *.html __pycache__ kernelsCy.cpp adaptiveQuad.cpp
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cd nl && rm -rf build __pycache__ *.egg-info
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clean_package :
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$(PYTHON) -m pip uninstall PyNucleus -y
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.PHONY: docs
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docs :
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cd docs && make
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sphinx-build -b html docs docs/build
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clean_docs :
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cd docs; rm -rf build
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createVirtualEnv:
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$(PYTHON) -m virtualenv --python=$(PYTHON) venv --system-site-packages
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list-tests:
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$(PYTHON) -m pytest --collect-only tests/ tests/test.py
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.PHONY: tests
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tests:
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$(PYTHON) -m pytest -rA --html=$(TEST_RESULTS) --self-contained-html tests/ tests/test.py
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docker:
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./build-docker.sh
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docker-linux:
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./run-docker-linux.sh
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docker-mac:
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./run-docker-mac.sh
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prereq:
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$(PYTHON) -m pip install $(PIP_FLAGS) Cython cython numpy scipy matplotlib pyyaml h5py pybind11 MeshPy tabulate modepy mpi4py scikit-sparse pyamg
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prereq-extra:
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$(PYTHON) -m pip install $(PIP_FLAGS) pytest pytest-html pytest-xdist Sphinx sphinxcontrib-programoutput

‎PyNucleus/__init__.py

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###################################################################################
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# Copyright 2021 National Technology & Engineering Solutions of Sandia, #
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# LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the #
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# U.S. Government retains certain rights in this software. #
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# If you want to use this code, please refer to the README.rst and LICENSE files. #
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###################################################################################
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import importlib
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import pkgutil
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import sys
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subpackages = {}
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for finder, name, ispkg in pkgutil.iter_modules():
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if ispkg and name.find('PyNucleus_') == 0:
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importName = name[len('PyNucleus_'):]
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module = importlib.import_module(name, 'PyNucleus')
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sys.modules['PyNucleus.'+importName] = module
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subpackages[importName] = module
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if "__all__" in module.__dict__:
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names = module.__dict__["__all__"]
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else:
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names = [name for name in module.__dict__ if not name.startswith('_')]
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locals().update({name: getattr(module, name) for name in names})
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from . import _version
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__version__ = _version.get_versions()['version']

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