Add note in docs for array slices that output is always centered on the Yee cell #1893
Workflow file for this run
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| name: run tests | |
| on: | |
| pull_request: | |
| push: | |
| schedule: | |
| - cron: 0 2 * * * # run at 2 AM UTC | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| name: "Test Python ${{ matrix.python-version }} with MPI (${{ matrix.enable-mpi }})" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.7, '3.10'] | |
| enable-mpi: [false, true] | |
| steps: | |
| - name: Define common environment variables | |
| run: | | |
| echo "CPPFLAGS=-I${HOME}/local/include" >> $GITHUB_ENV | |
| echo "LDFLAGS=-L${HOME}/local/lib" >> $GITHUB_ENV | |
| echo "HDF5_BASE_CPPFLAGS=-I/usr/include/hdf5" >> $GITHUB_ENV | |
| echo "HDF5_BASE_LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5" >> $GITHUB_ENV | |
| echo "GEN_CTL_IO=${HOME}/local/bin/gen-ctl-io" >> $GITHUB_ENV | |
| - run: | | |
| echo "HDF5_SERIAL_CPPFLAGS=${HDF5_BASE_CPPFLAGS}/serial" >> $GITHUB_ENV | |
| echo "HDF5_PARALLEL_CPPFLAGS=${HDF5_BASE_CPPFLAGS}/openmpi" >> $GITHUB_ENV | |
| echo "HDF5_SERIAL_LDFLAGS=${HDF5_BASE_LDFLAGS}/serial" >> $GITHUB_ENV | |
| echo "HDF5_PARALLEL_LDFLAGS=${HDF5_BASE_LDFLAGS}/openmpi" >> $GITHUB_ENV | |
| - name: Install pre-compiled dependencies | |
| run: | | |
| sudo apt-get -y update | |
| sudo apt-get -y install autoconf automake libfftw3-dev libgsl-dev liblapack-dev guile-3.0-dev libpng-dev libtool swig | |
| - name: Checkout libctl repository | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: NanoComp/libctl | |
| path: libctl-src | |
| - name: Build and install libctl | |
| run: cd libctl-src && sh autogen.sh --prefix=${HOME}/local --enable-shared && make -j $(nproc) && make install | |
| - name: Checkout harminv repository | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: NanoComp/harminv | |
| path: harminv-src | |
| - name: Build and install harminv | |
| run: cd harminv-src && sh autogen.sh --prefix=${HOME}/local --enable-shared && make -j $(nproc) && make install | |
| - name: Checkout MPB repository | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: NanoComp/mpb | |
| path: mpb-src | |
| - name: Build and install MPB | |
| run: cd mpb-src && sh autogen.sh --prefix=${HOME}/local --enable-shared LIBS=-ldl --with-libctl=${HOME}/local/share/libctl --with-hermitian-eps && make -j $(nproc) && make install | |
| - name: Checkout libGDSII repository | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: HomerReid/libGDSII | |
| path: libGDSII-src | |
| - name: Build and install libGDSII | |
| run: cd libGDSII-src && sh autogen.sh --prefix=${HOME}/local && make install | |
| - name: Define environment variables for serial build | |
| if: ${{ matrix.enable-mpi == false }} | |
| run: | | |
| echo "MKCHECKFLAGS=-j $(nproc)" >> $GITHUB_ENV | |
| echo "CPPFLAGS=${HDF5_SERIAL_CPPFLAGS} ${CPPFLAGS}" >> $GITHUB_ENV | |
| echo "LDFLAGS=${HDF5_SERIAL_LDFLAGS} ${LDFLAGS}" >> $GITHUB_ENV | |
| echo "MPICONF=--without-mpi" >> $GITHUB_ENV | |
| - name: Define environment variables for MPI build | |
| if: matrix.enable-mpi | |
| run: | | |
| echo "MKCHECKFLAGS=" >> $GITHUB_ENV | |
| echo "CPPFLAGS=${HDF5_PARALLEL_CPPFLAGS} ${CPPFLAGS}" >> $GITHUB_ENV | |
| echo "LDFLAGS=${HDF5_PARALLEL_LDFLAGS} ${LDFLAGS}" >> $GITHUB_ENV | |
| echo "CC=mpicc" >> $GITHUB_ENV | |
| echo "CXX=mpic++" >> $GITHUB_ENV | |
| echo "HDF5_MPI=ON" >> $GITHUB_ENV | |
| echo "MPICONF=--with-mpi" >> $GITHUB_ENV | |
| - name: Install serial dependencies | |
| if: ${{ matrix.enable-mpi == false }} | |
| run: sudo apt-get -y install libhdf5-serial-dev | |
| - name: Install MPI dependencies | |
| if: matrix.enable-mpi | |
| run: sudo apt-get -y install libopenmpi-dev mpi-default-bin openmpi-bin libhdf5-openmpi-dev libaec-dev | |
| - name: Checkout Meep repository | |
| uses: actions/checkout@v3 | |
| - name: Set up Python (version ${{ matrix.python-version }}) | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Get pip cache dir | |
| id: pip-cache | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT | |
| - name: pip cache | |
| uses: actions/cache@v3 | |
| id: cache | |
| with: | |
| path: ${{ steps.pip-cache.outputs.dir }} | |
| key: ${{ runner.os }}-py${{ matrix.python-version }}-mpi-${{ matrix.enable-mpi }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: ${{ runner.os }}-py${{ matrix.python-version }}-mpi-${{ matrix.enable-mpi }}-pip- | |
| - name: Install Python dependencies | |
| run: pip install -r python/requirements.txt | |
| - name: Install nlopt | |
| run: pip install nlopt | |
| - name: Install coverage | |
| if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.7 }} | |
| run: pip install coverage | |
| - name: Install mpi4py | |
| if: ${{ matrix.enable-mpi && steps.cache.outputs.cache-hit != true }} | |
| run: pip install mpi4py | |
| - name: Run autoreconf | |
| run: | | |
| autoreconf --verbose --install --symlink --force | |
| MEEP_VERSION=$(./configure -V | grep meep | awk '{print $3}') | |
| echo "MEEP_VERSION=${MEEP_VERSION}" >> $GITHUB_ENV | |
| - name: Run configure with OpenMP | |
| if: ${{ !(matrix.enable-mpi == false && matrix.python-version == 3.7) && !(matrix.enable-mpi == true && matrix.python-version == 3.10) }} | |
| run: | | |
| mkdir -p build && | |
| pushd build && | |
| ../configure --enable-maintainer-mode --prefix=${HOME}/local --with-libctl=${HOME}/local/share/libctl ${MPICONF} --with-openmp && | |
| popd | |
| - name: Run configure with coverage | |
| if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.7 }} | |
| run: ./configure --enable-maintainer-mode --with-coverage --prefix=${HOME}/local --with-libctl=${HOME}/local/share/libctl ${MPICONF} | |
| - name: Run configure with single-precision floating point and swig threads | |
| if: ${{ matrix.enable-mpi == true && matrix.python-version == 3.10 }} | |
| run: | | |
| mkdir -p build && | |
| pushd build && | |
| ../configure --enable-maintainer-mode --prefix=${HOME}/local --with-libctl=${HOME}/local/share/libctl ${MPICONF} --enable-single --enable-swig-python-threads && | |
| popd | |
| - name: Run make | |
| if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.7 }} | |
| run: make ${MKCHECKFLAGS} | |
| - name: Run make check | |
| if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.7 }} | |
| run: | | |
| pushd python/ && | |
| { make ${MKCHECKFLAGS} check || cat test-suite.log; } && | |
| popd | |
| - name: Run make distcheck | |
| if: ${{ !(matrix.enable-mpi == false && matrix.python-version == 3.7) }} | |
| run: | | |
| pushd build && | |
| make ${MKCHECKFLAGS} distcheck DISTCHECK_CONFIGURE_FLAGS="--with-libctl=${HOME}/local/share/libctl ${MPICONF}" && | |
| popd | |
| - name: Generate coverage report | |
| if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.7 }} | |
| run: | | |
| pushd python/ && | |
| coverage combine -a && | |
| coverage report -i && | |
| coverage xml -i && | |
| popd | |
| - name: Upload coverage to Codecov | |
| if: ${{ matrix.enable-mpi == false && matrix.python-version == 3.7 }} | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| files: ${{ github.workspace }}/python/coverage.xml | |
| - name: Archive C++ test logs | |
| if: ${{ failure() && !(matrix.enable-mpi == false && matrix.python-version == 3.7) }} | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: cpp-tests-mpi-${{ matrix.enable-mpi }}-log | |
| path: ${{ github.workspace }}/build/meep-${{ env.MEEP_VERSION }}/_build/sub/tests/test-suite.log | |
| - name: Archive Python test logs | |
| if: ${{ failure() && !(matrix.enable-mpi == false && matrix.python-version == 3.7) }} | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: py${{ matrix.python-version }}-tests-mpi-${{ matrix.enable-mpi }}-log | |
| path: ${{ github.workspace }}/build/meep-${{ env.MEEP_VERSION }}/_build/sub/python/test-suite.log |