Remove extraneous str casts #212
Workflow file for this run
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| name: UniFrac CI | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: flake8 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: 3.9 | |
| - name: install dependencies | |
| run: python -m pip install --upgrade pip | |
| - name: lint | |
| run: | | |
| pip install -q flake8 | |
| flake8 unifrac setup.py | |
| build-and-test: | |
| needs: lint | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.9', '3.10', '3.11'] | |
| os: [ubuntu-latest, macos-latest, linux-gpu-cuda] | |
| exclude: | |
| - os: macos-latest | |
| python-version: '3.9' | |
| - os: macos-latest | |
| python-version: '3.10' | |
| - os: linux-gpu-cuda | |
| python-version: '3.8' | |
| - os: linux-gpu-cuda | |
| python-version: '3.9' | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install | |
| shell: bash -l {0} | |
| run: | | |
| conda create --yes -n unifrac -c conda-forge -c bioconda python=${{ matrix.python-version }} | |
| conda activate unifrac | |
| conda config --add channels conda-forge | |
| conda config --add channels bioconda | |
| if [[ "$(uname -s)" == "Linux" ]]; | |
| then | |
| conda install --yes -c conda-forge -c bioconda gxx_linux-64 | |
| else | |
| conda install --yes -c conda-forge -c bioconda clangxx_osx-64 | |
| fi | |
| conda install --yes -c conda-forge -c bioconda "unifrac-binaries>=1.2" | |
| conda install --yes -c conda-forge -c bioconda cython biom-format numpy "h5py>3.3.0" "scikit-bio>=0.5.8" nose | |
| echo "$(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++ | |
| pip install iow | |
| pip install -e . | |
| - 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 | |
| ls -lrt $CONDA_PREFIX/lib/libhdf5_cpp* | |
| nosetests | |
| - name: Sanity checks | |
| 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 | |
| set -e | |
| ssu -i unifrac/tests/data/crawford.biom -t unifrac/tests/data/crawford.tre -o ci/test.dm -m unweighted | |
| python -c "import skbio; dm = skbio.DistanceMatrix.read('ci/test.dm')" | |
| pushd unifrac/tests | |
| export UNIFRAC_TIMING_INFO=Y | |
| python -c "import unifrac; unifrac.unweighted_to_file('data/crawford.biom','data/crawford.tre','../../ci/test.dm.h5')" | |
| python -c "import unifrac,skbio; dm_u=unifrac.unweighted('data/crawford.biom','data/crawford.tre'); dm = skbio.DistanceMatrix.read('../../ci/test.dm'); t=abs(dm_u.data-dm.data).max(); print(t); assert t < 0.1" | |
| python -c "import unifrac; unifrac.unweighted_to_file('data/crawford.biom','data/crawford.tre','../../ci/test2.dm.h5',permanova_perms=99,grouping_filename='data/crawford.group.tsv',grouping_columns='Treatment')" | |
| python -c "import unifrac; unifrac.weighted_normalized_to_file('data/crawford.biom','data/crawford.tre','../../ci/test3.dm.h5',subsample_depth=2,pcoa_dims=2)" | |
| export UNIFRAC_TIMING_INFO=N | |
| popd | |
| python -c "import h5py,skbio; f_u=h5py.File('ci/test.dm.h5','r'); dm_u=skbio.stats.distance.DistanceMatrix(f_u['matrix'][:,:],f_u['order'][:])" | |
| python -c "import h5py,skbio; dm = skbio.DistanceMatrix.read('ci/test.dm'); f_u=h5py.File('ci/test.dm.h5','r'); dm_u=skbio.stats.distance.DistanceMatrix(f_u['matrix'][:,:],f_u['order'][:]); t=abs(dm_u.data-dm.data).max(); print(t); assert t < 0.1" | |
| python -c "import h5py,skbio; dm = skbio.DistanceMatrix.read('ci/test.dm'); f_u=h5py.File('ci/test2.dm.h5','r'); dm_u=skbio.stats.distance.DistanceMatrix(f_u['matrix'][:,:],f_u['order'][:]); t=abs(dm_u.data-dm.data).max(); print(t); assert t < 0.1" | |
| python -c "import h5py; f_u=h5py.File('ci/test2.dm.h5','r'); print(f_u.keys()); assert len(f_u['stat_methods'][:]) == 1" | |
| python -c "import h5py; f_u=h5py.File('ci/test3.dm.h5','r'); print(f_u.keys()); assert len(f_u['pcoa_eigvals'][:]) == 2" | |
| # repeat using unifrac's h5 interfaces | |
| python -c "import unifrac; dm_u=unifrac.h5unifrac('ci/test.dm.h5'); dm_l=unifrac.h5unifrac_all('ci/test.dm.h5')" | |
| python -c "import unifrac,skbio; dm = skbio.DistanceMatrix.read('ci/test.dm'); dm_u=unifrac.h5unifrac('ci/test.dm.h5'); t=abs(dm_u.data-dm.data).max(); print(t); assert t < 0.1" | |
| python -c "import unifrac,skbio; dm = skbio.DistanceMatrix.read('ci/test.dm'); dm_u=unifrac.h5unifrac_all('ci/test.dm.h5')[0]; t=abs(dm_u.data-dm.data).max(); print(t); assert t < 0.1" | |
| python -c "import unifrac,skbio; dm = skbio.DistanceMatrix.read('ci/test.dm'); dm_u=unifrac.h5unifrac('ci/test2.dm.h5'); t=abs(dm_u.data-dm.data).max(); print(t); assert t < 0.1" | |
| python -c "import unifrac; st_l=unifrac.h5permanova_dict('ci/test2.dm.h5'); assert len(st_l) == 1" | |
| python -c "import unifrac; pc=unifrac.h5pcoa('ci/test3.dm.h5'); print(pc); assert len(pc.eigvals) == 2" | |
| ssu -i unifrac/tests/data/crawford.biom -t unifrac/tests/data/crawford.tre --pcoa 3 --mode multi --subsample-depth 2 --n-subsamples 10 -r hdf5 -o ci/test4.dm.h5 -m unweighted | |
| python -c "import unifrac; dm_u=unifrac.h5unifrac_all('ci/test4.dm.h5'); assert len(dm_u) == 10; print(dm_u[0]); print(dm_u[4]); print(dm_u[9]); dm_u.close(); assert len(dm_u) == 0" | |
| if [[ "$(uname -s)" == "Linux" ]]; | |
| then | |
| MD5=md5sum | |
| else | |
| MD5='md5 -r' | |
| fi | |
| ssu -i unifrac/tests/data/crawford.biom -t unifrac/tests/data/crawford.tre -o ci/test.dm.start0.stop3 -m unweighted --mode partial --start 0 --stop 3 | |
| ssu -i unifrac/tests/data/crawford.biom -t unifrac/tests/data/crawford.tre -o ci/test.dm.start3.stop5 -m unweighted --mode partial --start 3 --stop 5 | |
| ssu -i unifrac/tests/data/crawford.biom -t unifrac/tests/data/crawford.tre -o ci/test.dm.partial --mode merge-partial --partial-pattern "ci/test.dm.start*" | |
| exp=$($MD5 ci/test.dm | awk '{ print $1 }') | |
| obs=$($MD5 ci/test.dm.partial | awk '{ print $1 }') | |
| python -c "assert '${obs}' == '${exp}'" | |
| faithpd -i unifrac/tests/data/crawford.biom -t unifrac/tests/data/crawford.tre -o ci/test.faith.obs | |
| tail -n +2 ci/test.faith.obs > ci/test.faith.header-removed.obs | |
| exp1=$($MD5 unifrac/tests/data/test.faith.exp | awk '{ print $1 }') | |
| obs1=$($MD5 ci/test.faith.header-removed.obs | awk '{ print $1 }') | |
| python -c "assert '${obs1}' == '${exp1}'" | |