├── .flake8 ├── .github └── workflows │ └── tests.yml ├── .gitignore ├── .readthedocs.yaml ├── .travis.yml ├── LICENSE.txt ├── MANIFEST.in ├── Makefile ├── README.md ├── bin ├── generate_build.sh └── test_mpi.sh ├── codecov.yaml ├── compat └── win32 │ └── stdint.h ├── docs ├── Makefile └── source │ ├── api.rst │ ├── art │ ├── pyuoi.pdf │ └── pyuoi.png │ ├── conf.py │ ├── contributing.rst │ ├── index.rst │ ├── installation.rst │ ├── introduction.rst │ ├── mpi.rst │ └── pyuoi │ ├── datasets │ └── datasets.rst │ ├── decomposition │ └── decomposition.rst │ ├── linear_model │ └── linear_model.rst │ ├── mpi_utils.rst │ └── utils.rst ├── examples ├── README.rst ├── plot_swimmer.py └── plot_uoi_lasso.py ├── liblbfgs ├── COPYING ├── README ├── arithmetic_ansi.h ├── arithmetic_sse_double.h ├── arithmetic_sse_float.h ├── lbfgs.c └── lbfgs.h ├── paper ├── paper.bib └── paper.md ├── pyproject.toml ├── pytest.ini ├── requirements-dev.txt ├── requirements.txt ├── setup.py ├── src └── pyuoi │ ├── __init__.py │ ├── data │ └── Swimmer.h5 │ ├── datasets │ └── __init__.py │ ├── decomposition │ ├── CUR.py │ ├── NMF.py │ ├── __init__.py │ ├── base.py │ └── utils.py │ ├── lbfgs │ ├── LICENSE │ ├── __init__.py │ └── _lowlevel.pyx │ ├── linear_model │ ├── __init__.py │ ├── base.py │ ├── elasticnet.py │ ├── lasso.py │ ├── logistic.py │ ├── poisson.py │ ├── scikit-learn_license │ └── utils.py │ ├── mpi_utils.py │ └── utils.py └── tests ├── test_cur.py ├── test_elasticnet.py ├── test_lbfgs.py ├── test_mpi ├── __init__.py ├── test_mpi_uoi_linear_model.py └── test_mpi_utils.py ├── test_nmf.py ├── test_poisson.py ├── test_scores.py ├── test_uoi_l1logistic.py ├── test_uoi_lasso.py └── test_utils.py /.flake8: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/.flake8 -------------------------------------------------------------------------------- /.github/workflows/tests.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/.github/workflows/tests.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/.travis.yml -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/README.md -------------------------------------------------------------------------------- /bin/generate_build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/bin/generate_build.sh -------------------------------------------------------------------------------- /bin/test_mpi.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/bin/test_mpi.sh -------------------------------------------------------------------------------- /codecov.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/codecov.yaml -------------------------------------------------------------------------------- /compat/win32/stdint.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/compat/win32/stdint.h -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/source/api.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/docs/source/api.rst -------------------------------------------------------------------------------- /docs/source/art/pyuoi.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/docs/source/art/pyuoi.pdf -------------------------------------------------------------------------------- /docs/source/art/pyuoi.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/docs/source/art/pyuoi.png -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/docs/source/conf.py -------------------------------------------------------------------------------- /docs/source/contributing.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/docs/source/contributing.rst -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/docs/source/index.rst -------------------------------------------------------------------------------- /docs/source/installation.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/docs/source/installation.rst -------------------------------------------------------------------------------- /docs/source/introduction.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/docs/source/introduction.rst -------------------------------------------------------------------------------- /docs/source/mpi.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/docs/source/mpi.rst -------------------------------------------------------------------------------- /docs/source/pyuoi/datasets/datasets.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/docs/source/pyuoi/datasets/datasets.rst -------------------------------------------------------------------------------- /docs/source/pyuoi/decomposition/decomposition.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/docs/source/pyuoi/decomposition/decomposition.rst -------------------------------------------------------------------------------- /docs/source/pyuoi/linear_model/linear_model.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/docs/source/pyuoi/linear_model/linear_model.rst -------------------------------------------------------------------------------- /docs/source/pyuoi/mpi_utils.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/docs/source/pyuoi/mpi_utils.rst -------------------------------------------------------------------------------- /docs/source/pyuoi/utils.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/docs/source/pyuoi/utils.rst -------------------------------------------------------------------------------- /examples/README.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/examples/README.rst -------------------------------------------------------------------------------- /examples/plot_swimmer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/examples/plot_swimmer.py -------------------------------------------------------------------------------- /examples/plot_uoi_lasso.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/examples/plot_uoi_lasso.py -------------------------------------------------------------------------------- /liblbfgs/COPYING: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/liblbfgs/COPYING -------------------------------------------------------------------------------- /liblbfgs/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/liblbfgs/README -------------------------------------------------------------------------------- /liblbfgs/arithmetic_ansi.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/liblbfgs/arithmetic_ansi.h -------------------------------------------------------------------------------- /liblbfgs/arithmetic_sse_double.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/liblbfgs/arithmetic_sse_double.h -------------------------------------------------------------------------------- /liblbfgs/arithmetic_sse_float.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/liblbfgs/arithmetic_sse_float.h -------------------------------------------------------------------------------- /liblbfgs/lbfgs.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/liblbfgs/lbfgs.c -------------------------------------------------------------------------------- /liblbfgs/lbfgs.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/liblbfgs/lbfgs.h -------------------------------------------------------------------------------- /paper/paper.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/paper/paper.bib -------------------------------------------------------------------------------- /paper/paper.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/paper/paper.md -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/pyproject.toml -------------------------------------------------------------------------------- /pytest.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/pytest.ini -------------------------------------------------------------------------------- /requirements-dev.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/requirements-dev.txt -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/requirements.txt -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/setup.py -------------------------------------------------------------------------------- /src/pyuoi/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/__init__.py -------------------------------------------------------------------------------- /src/pyuoi/data/Swimmer.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/data/Swimmer.h5 -------------------------------------------------------------------------------- /src/pyuoi/datasets/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/datasets/__init__.py -------------------------------------------------------------------------------- /src/pyuoi/decomposition/CUR.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/decomposition/CUR.py -------------------------------------------------------------------------------- /src/pyuoi/decomposition/NMF.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/decomposition/NMF.py -------------------------------------------------------------------------------- /src/pyuoi/decomposition/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/decomposition/__init__.py -------------------------------------------------------------------------------- /src/pyuoi/decomposition/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/decomposition/base.py -------------------------------------------------------------------------------- /src/pyuoi/decomposition/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/decomposition/utils.py -------------------------------------------------------------------------------- /src/pyuoi/lbfgs/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/lbfgs/LICENSE -------------------------------------------------------------------------------- /src/pyuoi/lbfgs/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/lbfgs/__init__.py -------------------------------------------------------------------------------- /src/pyuoi/lbfgs/_lowlevel.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/lbfgs/_lowlevel.pyx -------------------------------------------------------------------------------- /src/pyuoi/linear_model/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/linear_model/__init__.py -------------------------------------------------------------------------------- /src/pyuoi/linear_model/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/linear_model/base.py -------------------------------------------------------------------------------- /src/pyuoi/linear_model/elasticnet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/linear_model/elasticnet.py -------------------------------------------------------------------------------- /src/pyuoi/linear_model/lasso.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/linear_model/lasso.py -------------------------------------------------------------------------------- /src/pyuoi/linear_model/logistic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/linear_model/logistic.py -------------------------------------------------------------------------------- /src/pyuoi/linear_model/poisson.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/linear_model/poisson.py -------------------------------------------------------------------------------- /src/pyuoi/linear_model/scikit-learn_license: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/linear_model/scikit-learn_license -------------------------------------------------------------------------------- /src/pyuoi/linear_model/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/linear_model/utils.py -------------------------------------------------------------------------------- /src/pyuoi/mpi_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/mpi_utils.py -------------------------------------------------------------------------------- /src/pyuoi/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/src/pyuoi/utils.py -------------------------------------------------------------------------------- /tests/test_cur.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/tests/test_cur.py -------------------------------------------------------------------------------- /tests/test_elasticnet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/tests/test_elasticnet.py -------------------------------------------------------------------------------- /tests/test_lbfgs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/tests/test_lbfgs.py -------------------------------------------------------------------------------- /tests/test_mpi/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/test_mpi/test_mpi_uoi_linear_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/tests/test_mpi/test_mpi_uoi_linear_model.py -------------------------------------------------------------------------------- /tests/test_mpi/test_mpi_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/tests/test_mpi/test_mpi_utils.py -------------------------------------------------------------------------------- /tests/test_nmf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/tests/test_nmf.py -------------------------------------------------------------------------------- /tests/test_poisson.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/tests/test_poisson.py -------------------------------------------------------------------------------- /tests/test_scores.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/tests/test_scores.py -------------------------------------------------------------------------------- /tests/test_uoi_l1logistic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/tests/test_uoi_l1logistic.py -------------------------------------------------------------------------------- /tests/test_uoi_lasso.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/tests/test_uoi_lasso.py -------------------------------------------------------------------------------- /tests/test_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BouchardLab/pyuoi/HEAD/tests/test_utils.py --------------------------------------------------------------------------------