diff options
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-bioutils.spec | 231 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 233 insertions, 0 deletions
@@ -0,0 +1 @@ +/bioutils-0.5.7.tar.gz diff --git a/python-bioutils.spec b/python-bioutils.spec new file mode 100644 index 0000000..f0aa5e4 --- /dev/null +++ b/python-bioutils.spec @@ -0,0 +1,231 @@ +%global _empty_manifest_terminate_build 0 +Name: python-bioutils +Version: 0.5.7 +Release: 1 +Summary: miscellaneous simple bioinformatics utilities and lookup tables +License: Apache Software License +URL: https://github.com/biocommons/bioutils +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/16/d1/e73a3c707f39bf42019c11835a03650698229527bc4b8b77aa399e0c35d0/bioutils-0.5.7.tar.gz +BuildArch: noarch + +Requires: python3-attrs +Requires: python3-requests +Requires: python3-ipython +Requires: python3-jupyter +Requires: python3-restview +Requires: python3-sphinx +Requires: python3-black +Requires: python3-flake8 +Requires: python3-isort +Requires: python3-pytest +Requires: python3-pytest-cov +Requires: python3-pytest-optional-tests +Requires: python3-tox +Requires: python3-vcrpy +Requires: python3-yapf + +%description +bioutils -- bioinformatics utilities and lookup tables +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +|pypi_badge| |build_status| |cov_badge| |cc_badge| |issues_badge| |contributors| |license| |changelog| + + +bioutils provides some common utilities and lookup tables for bioinformatics. + +* bioutils.accessions -- parse accessions, infer namespaces +* bioutils.assemblies -- Human assembly information (from NCBI/GRCh) +* bioutils.cytobands -- map cytobands to coordinates (from UCSC cytoband tables) +* bioutils.digests -- implementations of various digests +* bioutils.normalize -- allele normalization (left shuffle, right shuffle, expanded, vcf) + + +To use an E-Utilities API key run add it to an environment variable +called `ncbi_api_key` and it will be used in the E-Utilities request. + + +.. |build_status| image:: https://travis-ci.org/biocommons/bioutils.svg?branch=master + :target: https://travis-ci.org/biocommons/bioutils + +.. |changelog| image:: https://img.shields.io/badge/docs-changelog-green.svg + :target: https://bioutils.readthedocs.io + +.. |contributors| image:: https://img.shields.io/github/contributors/biocommons/bioutils.svg + :target: https://github.com/biocommons/bioutils + +.. |docs| image:: https://img.shields.io/badge/docs-readthedocs-green.svg + :target: http://bioutils.readthedocs.io/ + +.. |issues_badge| image:: https://img.shields.io/github/issues/biocommons/bioutils.png + :target: https://github.com/biocommons/bioutils/issues + +.. |license| image:: https://img.shields.io/github/license/biocommons/bioutils.svg + :target: https://github.com/biocommons/bioutils/blob/master/LICENSE + +.. |pypi_badge| image:: https://img.shields.io/pypi/v/bioutils.svg + :target: https://pypi.org/project/bioutils/ + + +.. |cc_badge| image:: https://api.codeclimate.com/v1/badges/3a99e06ad0a842174b0a/maintainability + :target: https://codeclimate.com/github/biocommons/bioutils/maintainability + :alt: Maintainability + +.. |cov_badge| image:: https://coveralls.io/repos/github/biocommons/bioutils/badge.svg?branch=master + :target: https://coveralls.io/github/biocommons/bioutils?branch=master + + + +%package -n python3-bioutils +Summary: miscellaneous simple bioinformatics utilities and lookup tables +Provides: python-bioutils +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-bioutils +bioutils -- bioinformatics utilities and lookup tables +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +|pypi_badge| |build_status| |cov_badge| |cc_badge| |issues_badge| |contributors| |license| |changelog| + + +bioutils provides some common utilities and lookup tables for bioinformatics. + +* bioutils.accessions -- parse accessions, infer namespaces +* bioutils.assemblies -- Human assembly information (from NCBI/GRCh) +* bioutils.cytobands -- map cytobands to coordinates (from UCSC cytoband tables) +* bioutils.digests -- implementations of various digests +* bioutils.normalize -- allele normalization (left shuffle, right shuffle, expanded, vcf) + + +To use an E-Utilities API key run add it to an environment variable +called `ncbi_api_key` and it will be used in the E-Utilities request. + + +.. |build_status| image:: https://travis-ci.org/biocommons/bioutils.svg?branch=master + :target: https://travis-ci.org/biocommons/bioutils + +.. |changelog| image:: https://img.shields.io/badge/docs-changelog-green.svg + :target: https://bioutils.readthedocs.io + +.. |contributors| image:: https://img.shields.io/github/contributors/biocommons/bioutils.svg + :target: https://github.com/biocommons/bioutils + +.. |docs| image:: https://img.shields.io/badge/docs-readthedocs-green.svg + :target: http://bioutils.readthedocs.io/ + +.. |issues_badge| image:: https://img.shields.io/github/issues/biocommons/bioutils.png + :target: https://github.com/biocommons/bioutils/issues + +.. |license| image:: https://img.shields.io/github/license/biocommons/bioutils.svg + :target: https://github.com/biocommons/bioutils/blob/master/LICENSE + +.. |pypi_badge| image:: https://img.shields.io/pypi/v/bioutils.svg + :target: https://pypi.org/project/bioutils/ + + +.. |cc_badge| image:: https://api.codeclimate.com/v1/badges/3a99e06ad0a842174b0a/maintainability + :target: https://codeclimate.com/github/biocommons/bioutils/maintainability + :alt: Maintainability + +.. |cov_badge| image:: https://coveralls.io/repos/github/biocommons/bioutils/badge.svg?branch=master + :target: https://coveralls.io/github/biocommons/bioutils?branch=master + + + +%package help +Summary: Development documents and examples for bioutils +Provides: python3-bioutils-doc +%description help +bioutils -- bioinformatics utilities and lookup tables +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +|pypi_badge| |build_status| |cov_badge| |cc_badge| |issues_badge| |contributors| |license| |changelog| + + +bioutils provides some common utilities and lookup tables for bioinformatics. + +* bioutils.accessions -- parse accessions, infer namespaces +* bioutils.assemblies -- Human assembly information (from NCBI/GRCh) +* bioutils.cytobands -- map cytobands to coordinates (from UCSC cytoband tables) +* bioutils.digests -- implementations of various digests +* bioutils.normalize -- allele normalization (left shuffle, right shuffle, expanded, vcf) + + +To use an E-Utilities API key run add it to an environment variable +called `ncbi_api_key` and it will be used in the E-Utilities request. + + +.. |build_status| image:: https://travis-ci.org/biocommons/bioutils.svg?branch=master + :target: https://travis-ci.org/biocommons/bioutils + +.. |changelog| image:: https://img.shields.io/badge/docs-changelog-green.svg + :target: https://bioutils.readthedocs.io + +.. |contributors| image:: https://img.shields.io/github/contributors/biocommons/bioutils.svg + :target: https://github.com/biocommons/bioutils + +.. |docs| image:: https://img.shields.io/badge/docs-readthedocs-green.svg + :target: http://bioutils.readthedocs.io/ + +.. |issues_badge| image:: https://img.shields.io/github/issues/biocommons/bioutils.png + :target: https://github.com/biocommons/bioutils/issues + +.. |license| image:: https://img.shields.io/github/license/biocommons/bioutils.svg + :target: https://github.com/biocommons/bioutils/blob/master/LICENSE + +.. |pypi_badge| image:: https://img.shields.io/pypi/v/bioutils.svg + :target: https://pypi.org/project/bioutils/ + + +.. |cc_badge| image:: https://api.codeclimate.com/v1/badges/3a99e06ad0a842174b0a/maintainability + :target: https://codeclimate.com/github/biocommons/bioutils/maintainability + :alt: Maintainability + +.. |cov_badge| image:: https://coveralls.io/repos/github/biocommons/bioutils/badge.svg?branch=master + :target: https://coveralls.io/github/biocommons/bioutils?branch=master + + + +%prep +%autosetup -n bioutils-0.5.7 + +%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-bioutils -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Tue Apr 11 2023 Python_Bot <Python_Bot@openeuler.org> - 0.5.7-1 +- Package Spec generated @@ -0,0 +1 @@ +0271cd1798c6a58b6698cc004b990df1 bioutils-0.5.7.tar.gz |