release

.gitattributes

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+
+PyNucleus/_version.py export-subst

Dockerfile

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

LICENSE

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+Copyright 2021 National Technology & Engineering Solutions of Sandia,
+LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the
+U.S. Government retains certain rights in this software.
+
+MIT License
+
+Copyright (c) 2017-2021 Christian Glusa
+
+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 versioneer.py
+include PyNucleus/_version.py

Makefile

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

PyNucleus/__init__.py

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