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author | CoprDistGit <infra@openeuler.org> | 2023-05-29 12:54:55 +0000 |
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committer | CoprDistGit <infra@openeuler.org> | 2023-05-29 12:54:55 +0000 |
commit | a7e769ed0d599c004b413b4149626abd72a69986 (patch) | |
tree | c81d8b9dc89f483326d868fd7db53fe768218228 | |
parent | f1da1a84715817eb4e74ace746b5c956d0aca530 (diff) |
automatic import of python-glimix-core
-rw-r--r-- | .gitignore | 1 | ||||
-rw-r--r-- | python-glimix-core.spec | 289 | ||||
-rw-r--r-- | sources | 1 |
3 files changed, 291 insertions, 0 deletions
@@ -0,0 +1 @@ +/glimix-core-3.1.13.tar.gz diff --git a/python-glimix-core.spec b/python-glimix-core.spec new file mode 100644 index 0000000..1f40707 --- /dev/null +++ b/python-glimix-core.spec @@ -0,0 +1,289 @@ +%global _empty_manifest_terminate_build 0 +Name: python-glimix-core +Version: 3.1.13 +Release: 1 +Summary: Fast inference over mean and covariance parameters for Generalised Linear Mixed Models +License: MIT +URL: https://github.com/limix/glimix-core +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/b6/2a/c77df3eff97040fdd82bde3dac78c8130823230e56fce7d3ef86b09a17a9/glimix-core-3.1.13.tar.gz +BuildArch: noarch + +Requires: python3-brent-search +Requires: python3-liknorm +Requires: python3-ndarray-listener +Requires: python3-numpy +Requires: python3-numpy-sugar +Requires: python3-optimix +Requires: python3-pytest +Requires: python3-pytest-doctestplus +Requires: python3-scipy +Requires: python3-tqdm + +%description +# glimix-core + +[](https://glimix-core.readthedocs.io/en/latest/?badge=latest) + +Fast inference over mean and covariance parameters for Generalised Linear Mixed +Models. + +It implements the mathematical tricks of +[FaST-LMM](https://github.com/MicrosoftGenomics/FaST-LMM) for the special case +of Linear Mixed Models with a linear covariance matrix and provides an +interface to perform inference over millions of covariates in seconds. +The Generalised Linear Mixed Model inference is implemented via Expectation +Propagation and also makes use of several mathematical tricks to handle large +data sets with thousands of samples and millions of covariates. + +## Install + +There are two main ways of installing it. +Via [pip](https://pypi.python.org/pypi/pip): + +```bash +pip install glimix-core +``` + +Or via [conda](http://conda.pydata.org/docs/index.html): + +```bash +conda install -c conda-forge glimix-core +``` + +## Running the tests + +After installation, you can test it + +```bash +python -c "import glimix_core; glimix_core.test()" +``` + +as long as you have [pytest](https://docs.pytest.org/en/latest/). + +## Usage + +Here it is a very simple example to get you started: + +```python +>>> from numpy import array, ones +>>> from numpy_sugar.linalg import economic_qs_linear +>>> from glimix_core.lmm import LMM +>>> +>>> X = array([[1, 2], [3, -1], [1.1, 0.5], [0.5, -0.4]], float) +>>> QS = economic_qs_linear(X, False) +>>> X = ones((4, 1)) +>>> y = array([-1, 2, 0.3, 0.5]) +>>> lmm = LMM(y, X, QS) +>>> lmm.fit(verbose=False) +>>> lmm.lml() +-2.2726234086180557 +``` + +We also provide an extensive [documentation](http://glimix-core.readthedocs.org/) about the library. + +## Authors + +* [Danilo Horta](https://github.com/horta) + +## License + +This project is licensed under the [MIT License](https://raw.githubusercontent.com/limix/glimix-core/master/LICENSE.md). + + + +%package -n python3-glimix-core +Summary: Fast inference over mean and covariance parameters for Generalised Linear Mixed Models +Provides: python-glimix-core +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-glimix-core +# glimix-core + +[](https://glimix-core.readthedocs.io/en/latest/?badge=latest) + +Fast inference over mean and covariance parameters for Generalised Linear Mixed +Models. + +It implements the mathematical tricks of +[FaST-LMM](https://github.com/MicrosoftGenomics/FaST-LMM) for the special case +of Linear Mixed Models with a linear covariance matrix and provides an +interface to perform inference over millions of covariates in seconds. +The Generalised Linear Mixed Model inference is implemented via Expectation +Propagation and also makes use of several mathematical tricks to handle large +data sets with thousands of samples and millions of covariates. + +## Install + +There are two main ways of installing it. +Via [pip](https://pypi.python.org/pypi/pip): + +```bash +pip install glimix-core +``` + +Or via [conda](http://conda.pydata.org/docs/index.html): + +```bash +conda install -c conda-forge glimix-core +``` + +## Running the tests + +After installation, you can test it + +```bash +python -c "import glimix_core; glimix_core.test()" +``` + +as long as you have [pytest](https://docs.pytest.org/en/latest/). + +## Usage + +Here it is a very simple example to get you started: + +```python +>>> from numpy import array, ones +>>> from numpy_sugar.linalg import economic_qs_linear +>>> from glimix_core.lmm import LMM +>>> +>>> X = array([[1, 2], [3, -1], [1.1, 0.5], [0.5, -0.4]], float) +>>> QS = economic_qs_linear(X, False) +>>> X = ones((4, 1)) +>>> y = array([-1, 2, 0.3, 0.5]) +>>> lmm = LMM(y, X, QS) +>>> lmm.fit(verbose=False) +>>> lmm.lml() +-2.2726234086180557 +``` + +We also provide an extensive [documentation](http://glimix-core.readthedocs.org/) about the library. + +## Authors + +* [Danilo Horta](https://github.com/horta) + +## License + +This project is licensed under the [MIT License](https://raw.githubusercontent.com/limix/glimix-core/master/LICENSE.md). + + + +%package help +Summary: Development documents and examples for glimix-core +Provides: python3-glimix-core-doc +%description help +# glimix-core + +[](https://glimix-core.readthedocs.io/en/latest/?badge=latest) + +Fast inference over mean and covariance parameters for Generalised Linear Mixed +Models. + +It implements the mathematical tricks of +[FaST-LMM](https://github.com/MicrosoftGenomics/FaST-LMM) for the special case +of Linear Mixed Models with a linear covariance matrix and provides an +interface to perform inference over millions of covariates in seconds. +The Generalised Linear Mixed Model inference is implemented via Expectation +Propagation and also makes use of several mathematical tricks to handle large +data sets with thousands of samples and millions of covariates. + +## Install + +There are two main ways of installing it. +Via [pip](https://pypi.python.org/pypi/pip): + +```bash +pip install glimix-core +``` + +Or via [conda](http://conda.pydata.org/docs/index.html): + +```bash +conda install -c conda-forge glimix-core +``` + +## Running the tests + +After installation, you can test it + +```bash +python -c "import glimix_core; glimix_core.test()" +``` + +as long as you have [pytest](https://docs.pytest.org/en/latest/). + +## Usage + +Here it is a very simple example to get you started: + +```python +>>> from numpy import array, ones +>>> from numpy_sugar.linalg import economic_qs_linear +>>> from glimix_core.lmm import LMM +>>> +>>> X = array([[1, 2], [3, -1], [1.1, 0.5], [0.5, -0.4]], float) +>>> QS = economic_qs_linear(X, False) +>>> X = ones((4, 1)) +>>> y = array([-1, 2, 0.3, 0.5]) +>>> lmm = LMM(y, X, QS) +>>> lmm.fit(verbose=False) +>>> lmm.lml() +-2.2726234086180557 +``` + +We also provide an extensive [documentation](http://glimix-core.readthedocs.org/) about the library. + +## Authors + +* [Danilo Horta](https://github.com/horta) + +## License + +This project is licensed under the [MIT License](https://raw.githubusercontent.com/limix/glimix-core/master/LICENSE.md). + + + +%prep +%autosetup -n glimix-core-3.1.13 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-glimix-core -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 29 2023 Python_Bot <Python_Bot@openeuler.org> - 3.1.13-1 +- Package Spec generated @@ -0,0 +1 @@ +ac6696edb4abb6c30810987493fc8c20 glimix-core-3.1.13.tar.gz |