Loading .circleci/installHDF5.sh +1 −1 Original line number Diff line number Diff line set -x set -e if [ ! -e prefix/lib/libhdf5.so ]; then wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.12/src/hdf5-1.8.12.tar.gz wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.12/src/hdf5-1.8.12.tar.gz tar xzf hdf5-1.8.12.tar.gz mkdir -p prefix PREFIX=$PWD/prefix Loading .gitignore +3 −0 Original line number Diff line number Diff line Loading @@ -5,9 +5,12 @@ doc/_build *.pyc *.egg-info nosetests.xml coverage.xml .coverage .circleci/prefix .circleci/hdf5-1.8.12.tar.gz .circleci/hdf5-1.8.12 .vagrant .DS_Store LICENSES.txt→LICENSE +14 −22 Original line number Diff line number Diff line PacBio "BSD clear" license: =========================== Copyright (c) 2011-2015, Pacific Biosciences of California, Inc. Copyright (c) 2011-2018, Pacific Biosciences of California, Inc. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Pacific Biosciences nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. BioPython license (for pbcore/io/align/_bgzf.py): Loading MANIFEST.in +6 −10 Original line number Diff line number Diff line Loading @@ -3,13 +3,9 @@ include *.org include *.txt include *.yml include Makefile recursive-include bin *.py recursive-include doc *.conf recursive-include doc *.css recursive-include doc *.jpg recursive-include doc *.png recursive-include doc *.py recursive-include doc *.rst recursive-include doc Makefile recursive-include pbcore Makefile recursive-include tests *.py include LICENSE graft bin graft doc graft pbcore graft tests Makefile +8 −2 Original line number Diff line number Diff line Loading @@ -15,7 +15,7 @@ install: @pip install ./ pylint: pylint --errors-only pbcore/ pylint --errors-only --ignore=pyxb pbcore/ clean: doc-clean rm -rf build/;\ Loading @@ -33,7 +33,8 @@ doctest: cd doc && make doctest unit-test: nosetests --with-coverage --cover-xml-file=coverage.xml --cover-package=pbcore --cover-xml --with-xunit -v tests #nosetests --with-coverage --cover-xml-file=coverage.xml --cover-package=pbcore --cover-xml --with-xunit -v tests pytest -v -n auto --dist=loadscope --durations=20 --junitxml=nosetests.xml --cov=./pbcore --cov-report=xml:coverage.xml tests/test_*.py sed -i -e 's@filename="@filename="./@g' coverage.xml test: doctest unit-test Loading Loading @@ -71,3 +72,8 @@ xsd-codegen: validate-metadata: xmllint --schema ../xsd-datamodels/PacBioCollectionMetadata.xsd pbcore/data/datasets/CollectionMetadata.xml wheel: which pip pip wheel --wheel-dir=${WHEELHOUSE} --no-deps . ls -larth ${WHEELHOUSE} Loading
.circleci/installHDF5.sh +1 −1 Original line number Diff line number Diff line set -x set -e if [ ! -e prefix/lib/libhdf5.so ]; then wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.12/src/hdf5-1.8.12.tar.gz wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.12/src/hdf5-1.8.12.tar.gz tar xzf hdf5-1.8.12.tar.gz mkdir -p prefix PREFIX=$PWD/prefix Loading
.gitignore +3 −0 Original line number Diff line number Diff line Loading @@ -5,9 +5,12 @@ doc/_build *.pyc *.egg-info nosetests.xml coverage.xml .coverage .circleci/prefix .circleci/hdf5-1.8.12.tar.gz .circleci/hdf5-1.8.12 .vagrant .DS_Store
LICENSES.txt→LICENSE +14 −22 Original line number Diff line number Diff line PacBio "BSD clear" license: =========================== Copyright (c) 2011-2015, Pacific Biosciences of California, Inc. Copyright (c) 2011-2018, Pacific Biosciences of California, Inc. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Pacific Biosciences nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. BioPython license (for pbcore/io/align/_bgzf.py): Loading
MANIFEST.in +6 −10 Original line number Diff line number Diff line Loading @@ -3,13 +3,9 @@ include *.org include *.txt include *.yml include Makefile recursive-include bin *.py recursive-include doc *.conf recursive-include doc *.css recursive-include doc *.jpg recursive-include doc *.png recursive-include doc *.py recursive-include doc *.rst recursive-include doc Makefile recursive-include pbcore Makefile recursive-include tests *.py include LICENSE graft bin graft doc graft pbcore graft tests
Makefile +8 −2 Original line number Diff line number Diff line Loading @@ -15,7 +15,7 @@ install: @pip install ./ pylint: pylint --errors-only pbcore/ pylint --errors-only --ignore=pyxb pbcore/ clean: doc-clean rm -rf build/;\ Loading @@ -33,7 +33,8 @@ doctest: cd doc && make doctest unit-test: nosetests --with-coverage --cover-xml-file=coverage.xml --cover-package=pbcore --cover-xml --with-xunit -v tests #nosetests --with-coverage --cover-xml-file=coverage.xml --cover-package=pbcore --cover-xml --with-xunit -v tests pytest -v -n auto --dist=loadscope --durations=20 --junitxml=nosetests.xml --cov=./pbcore --cov-report=xml:coverage.xml tests/test_*.py sed -i -e 's@filename="@filename="./@g' coverage.xml test: doctest unit-test Loading Loading @@ -71,3 +72,8 @@ xsd-codegen: validate-metadata: xmllint --schema ../xsd-datamodels/PacBioCollectionMetadata.xsd pbcore/data/datasets/CollectionMetadata.xml wheel: which pip pip wheel --wheel-dir=${WHEELHOUSE} --no-deps . ls -larth ${WHEELHOUSE}
