Fix typo in usage comment #169
Workflow file for this run
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| name: unifrac-binaries CI | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| build-and-test: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, linux-gpu-cuda] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| - name: Install | |
| shell: bash -l {0} | |
| run: | | |
| df -h . | |
| if [[ "$(uname -s)" == "Linux" ]]; | |
| then | |
| conda create -q --yes --strict-channel-priority -n unifrac -c conda-forge -c bioconda gxx_linux-64 gfortran_linux-64 hdf5 mkl-include lz4 zlib hdf5-static libcblas liblapacke make curl | |
| else | |
| conda create -q --yes --strict-channel-priority -n unifrac -c conda-forge -c bioconda clangxx_osx-64 hdf5 mkl-include lz4 hdf5-static libcblas liblapacke make curl | |
| fi | |
| conda clean --yes -t | |
| df -h . | |
| conda activate unifrac | |
| echo "$(uname -s)" | |
| if [[ "$(uname -s)" == "Linux" ]]; | |
| then | |
| which x86_64-conda-linux-gnu-gcc | |
| x86_64-conda-linux-gnu-gcc -v | |
| x86_64-conda-linux-gnu-g++ -v | |
| else | |
| which clang | |
| clang -v | |
| fi | |
| which h5c++ | |
| if [[ "$(uname -s)" == "Linux" ]]; | |
| then | |
| # install PGI but do not source it | |
| # the makefile will do it automatically | |
| ./scripts/install_hpc_sdk.sh </dev/null | |
| fi | |
| df -h . | |
| export PERFORMING_CONDA_BUILD=True | |
| echo "======= begin env =====" | |
| env | |
| echo "======= end env =====" | |
| # all == build (shlib,bins,tests) and install | |
| make all | |
| df -h . | |
| pushd src | |
| if [[ "$(uname -s)" == "Linux" ]]; | |
| then | |
| rm -f ~/.R/Makevars | |
| conda install -q --yes --strict-channel-priority -c conda-forge r-base | |
| unset CXXFLAGS | |
| unset CFLAGS | |
| unset DEBUG_CXXFLAGS | |
| unset DEBUG_CFLAGS | |
| # the r-base package has a broken dependency | |
| ln -s $CONDA_PREFIX/lib/libreadline.so $CONDA_PREFIX/lib/libreadline.so.6 | |
| R -e 'install.packages("Rcpp", repos="http://lib.stat.cmu.edu/R/CRAN/")' | |
| make rapi_test | |
| fi | |
| popd | |
| - name: Tests | |
| shell: bash -l {0} | |
| run: | | |
| conda activate unifrac | |
| # keep it low for runs in containers | |
| # and a weird number to potentially catch potential bugs | |
| export OMP_NUM_THREADS=3 | |
| # diagnostic messages for debugging, if needed | |
| export UNIFRAC_GPU_INFO=Y | |
| pushd src | |
| ./test_su | |
| ./test_api | |
| ./test_ska | |
| popd | |
| pushd test | |
| ./capi_test 1 | |
| # explicitly check that we do not have hdf5 dependencies | |
| if [[ "$(uname -s)" == "Linux" ]]; | |
| then | |
| ldd ./capi_test |awk 'BEGIN{a=0}/hdf/{a=a+1;print $0}END{if (a==0) {print "No dynamic hdf5 found"} else {exit 2}}' | |
| else | |
| otool -L ./capi_test|awk 'BEGIN{a=0}/hdf/{a=a+1;print $0}END{if (a==0) {print "No dynamic hdf5 found"} else {exit 2}}' | |
| fi | |
| popd | |
| pushd src/testdata | |
| conda install --yes -c conda-forge h5py | |
| # weighted_unnormalized | |
| time ssu -m weighted_unnormalized_fp32 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 -o t1.h5 | |
| ./compare_unifrac_matrix.py test500.weighted_unnormalized_fp32.h5 t1.h5 1.e-5 | |
| ./compare_unifrac_pcoa.py test500.weighted_unnormalized_fp32.h5 t1.h5 3 0.1 | |
| rm -f t1.h5 | |
| # retry with default precision handling | |
| time ssu -m weighted_unnormalized -i test500.biom -t test500.tre --pcoa 4 -r hdf5 -o t1.h5 | |
| ./compare_unifrac_matrix.py test500.weighted_unnormalized_fp32.h5 t1.h5 1.e-5 | |
| ./compare_unifrac_pcoa.py test500.weighted_unnormalized_fp32.h5 t1.h5 3 0.1 | |
| rm -f t1.h5 | |
| time ssu -f -m weighted_unnormalized_fp32 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 -o t1.h5 | |
| # matrrix will be different, but PCOA similar | |
| ./compare_unifrac_pcoa.py test500.weighted_unnormalized_fp32.h5 t1.h5 3 0.1 | |
| rm -f t1.h5 | |
| time ssu -m weighted_unnormalized_fp64 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp64 -o t1.h5 | |
| # minimal precision loss between fp32 and fp64 | |
| ./compare_unifrac_matrix.py test500.weighted_unnormalized_fp32.h5 t1.h5 1.e-5 | |
| ./compare_unifrac_pcoa.py test500.weighted_unnormalized_fp32.h5 t1.h5 3 0.1 | |
| rm -f t1.h5 | |
| # weighted_normalized | |
| time ssu -f -m weighted_normalized -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 -o t1.h5 | |
| ./compare_unifrac_matrix.py test500.weighted_normalized_fp32.f.h5 t1.h5 1.e-5 | |
| ./compare_unifrac_pcoa.py test500.weighted_normalized_fp32.f.h5 t1.h5 3 0.1 | |
| rm -f t1.h5 | |
| time ssu -f -m weighted_normalized_fp64 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp64 -o t1.h5 | |
| ./compare_unifrac_matrix.py test500.weighted_normalized_fp32.f.h5 t1.h5 1.e-5 | |
| ./compare_unifrac_pcoa.py test500.weighted_normalized_fp32.f.h5 t1.h5 3 0.1 | |
| rm -f t1.h5 | |
| # unweighted | |
| time ssu -f -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 -o t1.h5 | |
| ./compare_unifrac_matrix.py test500.unweighted_fp32.f.h5 t1.h5 1.e-5 | |
| ./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1 | |
| rm -f t1.h5 | |
| time ssu -f -m unweighted_fp64 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp64 -o t1.h5 | |
| ./compare_unifrac_matrix.py test500.unweighted_fp32.f.h5 t1.h5 1.e-5 | |
| ./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1 | |
| ls -l t1.h5 | |
| rm -f t1.h5 | |
| # hdf5 without distance matrix, just PCoA | |
| echo "hdf5_nodist" | |
| time ssu -f -m unweighted_fp64 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_nodist -o t1.h5 | |
| ./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1 | |
| ls -l t1.h5 | |
| rm -f t1.h5 | |
| time ssu -f -m unweighted_fp32 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_nodist -o t1.h5 | |
| ./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1 | |
| ls -l t1.h5 | |
| rm -f t1.h5 | |
| # permanova | |
| echo "permanova" | |
| time ssu -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5 --permanova 999 -g test500.tsv -c empo_2 -o t1.h5 | |
| # compare to values given by skbio.stats.distance.permanova | |
| python compare_unifrac_stats.py t1.h5 5 999 1.001112 0.456 0.001 0.1 | |
| ls -l t1.h5 | |
| rm -f t1.h5 | |
| time ssu -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5 --permanova 99 -g test500.tsv -c empo_2 -o t1.h5 | |
| python compare_unifrac_stats.py t1.h5 5 99 1.001112 0.456 0.001 0.2 | |
| ls -l t1.h5 | |
| rm -f t1.h5 | |
| time ssu -m weighted_unnormalized_fp32 -i test500.biom -t test500.tre --pcoa 4 -r hdf5_nodist -g test500.tsv -c empo_3 -o t1.h5 | |
| # compare to values given by skbio.stats.distance.permanova | |
| python compare_unifrac_stats.py t1.h5 17 999 0.890697 0.865 0.001 0.1 | |
| ls -l t1.h5 | |
| rm -f t1.h5 | |
| # partials | |
| echo "partials" | |
| ssu -f -m unweighted_fp32 -i test500.biom -t test500.tre --mode partial-report --n-partials 2 | |
| time ssu -f -m unweighted_fp32 -i test500.biom -t test500.tre --mode partial --start 0 --stop 125 -o t1.partial.1 | |
| time ssu -f -m unweighted_fp32 -i test500.biom -t test500.tre --mode partial --start 125 --stop 250 -o t1.partial.2 | |
| ls -l t1.partial* | |
| ssu -f -m unweighted_fp32 -i test500.biom -t test500.tre --mode check-partial --partial-pattern 't1.partial.*' | |
| time ssu -f -m unweighted_fp64 -i test500.biom -t test500.tre --pcoa 4 --mode merge-partial --partial-pattern 't1.partial.*' -r hdf5_fp64 -o t1.h5 | |
| ./compare_unifrac_matrix.py test500.unweighted_fp32.f.h5 t1.h5 1.e-5 | |
| ./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1 | |
| ls -l t1.h5 | |
| rm -f t1.h5 | |
| time ssu -f -m unweighted_fp32 -i test500.biom -t test500.tre --pcoa 4 --mode merge-partial --partial-pattern 't1.partial.*' -r hdf5_fp32 -o t1.h5 | |
| ./compare_unifrac_matrix.py test500.unweighted_fp32.f.h5 t1.h5 1.e-5 | |
| ./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1 | |
| ls -l t1.h5 | |
| rm -f t1.h5 | |
| time ssu -f -m unweighted_fp32 -i test500.biom -t test500.tre --pcoa 4 --mode merge-partial --partial-pattern 't1.partial.*' -r hdf5_nodist -o t1.h5 | |
| ./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.1 | |
| ls -l t1.h5 | |
| rm -f t1.h5 | |
| rm -f t1.partial.* | |
| # subsample | |
| echo "subsample" | |
| time ssu -f -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 --subsample-depth 100 -o t1.h5 | |
| ./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.3 | |
| rm -f t1.h5 | |
| time ssu -f -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 --subsample-depth 100 --subsample-replacement with -o t1.h5 | |
| ./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.3 | |
| rm -f t1.h5 | |
| time ssu -f -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5_fp32 --subsample-depth 100 --subsample-replacement without -o t1.h5 | |
| ./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.3 | |
| rm -f t1.h5 | |
| time ssu -m unweighted -i test500.biom -t test500.tre --pcoa 4 -r hdf5_nodist --permanova 99 -g test500.tsv -c empo_2 --subsample-depth 100 -o t1.h5 | |
| python compare_unifrac_stats.py t1.h5 5 99 1.001112 0.456 0.05 0.6 | |
| ls -l t1.h5 | |
| rm -f t1.h5 | |
| # multi | |
| echo "multi" | |
| time ssu -f -m unweighted -i test500.biom -t test500.tre --pcoa 4 --mode multi --subsample-depth 100 --n-subsamples 10 -o t1.h5 | |
| ./compare_unifrac_pcoa_multi.py test500.unweighted_fp32.f.h5 t1.h5 10 3 0.3 | |
| ls -l t1.h5 | |
| rm -f t1.h5 | |
| time ssu -m unweighted -i test500.biom -t test500.tre --pcoa 4 --mode multi --n-subsamples 10 --permanova 99 -g test500.tsv -c empo_2 --subsample-depth 100 -o t1.h5 | |
| python compare_unifrac_stats_multi.py t1.h5 10 5 99 1.001112 0.456 0.08 0.6 | |
| ls -l t1.h5 | |
| rm -f t1.h5 | |
| time ssu -m unweighted -i test500.biom -t test500.tre --pcoa 4 --mode multi --n-subsamples 10 --permanova 99 -g test500.tsv -c empo_2 --subsample-depth 100 --subsample-replacement without -o t1.h5 | |
| python compare_unifrac_stats_multi.py t1.h5 10 5 99 1.001112 0.456 0.08 0.6 | |
| ls -l t1.h5 | |
| rm -f t1.h5 | |
| popd | |
| - name: Sanity checks | |
| shell: bash -l {0} | |
| run: | | |
| conda activate unifrac | |
| pushd ci | |
| ./crawford_test.sh | |
| popd |