automatic import of python-cyvcf2

1 files changed, 105 insertions, 0 deletions

diff --git a/python-cyvcf2.spec b/python-cyvcf2.spec
new file mode 100644
index 0000000..4bcf996
--- /dev/null
+++ b/python-cyvcf2.spec
@@ -0,0 +1,105 @@
+%global _empty_manifest_terminate_build 0
+Name:		python-cyvcf2
+Version:	0.30.18
+Release:	1
+Summary:	fast vcf parsing with cython + htslib
+License:	MIT
+URL:		https://github.com/brentp/cyvcf2/
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/8e/b1/31b20c3453944fda0eb43d519787bcce4178b6f3b29c94a6286a801fbad3/cyvcf2-0.30.18.tar.gz
+BuildArch:	noarch
+
+Requires:	python3-numpy
+Requires:	python3-coloredlogs
+Requires:	python3-click
+
+%description
+Note: cyvcf2 versions < 0.20.0 require htslib < 1.10. cyvcf2 versions >= 0.20.0 require htslib >= 1.10
+<!-- ghp-import -p docs/build/html/ -->
+The latest documentation for cyvcf2 can be found here:
+[![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](http://brentp.github.io/cyvcf2/)
+If you use cyvcf2, please cite the [paper](https://academic.oup.com/bioinformatics/article/2971439/cyvcf2)
+Fast python **(2 and 3)** parsing of VCF and BCF including region-queries.
+[![Build Status](https://github.com/brentp/cyvcf2/workflows/Build/badge.svg)](https://github.com/brentp/cyvcf2/actions?query=workflow%3ABuild)
+cyvcf2 is a cython wrapper around [htslib](https://github.com/samtools/htslib) built for fast parsing of [Variant Call Format](https://en.m.wikipedia.org/wiki/Variant_Call_Format) (VCF) files.
+Attributes like `variant.gt_ref_depths` return a numpy array directly so they are immediately ready for downstream use.
+**note** that the array is backed by the underlying C data, so, once `variant` goes out of scope. The array will contain nonsense.
+To persist a copy, use: `cpy = np.array(variant.gt_ref_depths)` instead of just `arr = variant.gt_ref_depths`.
+
+%package -n python3-cyvcf2
+Summary:	fast vcf parsing with cython + htslib
+Provides:	python-cyvcf2
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-cyvcf2
+Note: cyvcf2 versions < 0.20.0 require htslib < 1.10. cyvcf2 versions >= 0.20.0 require htslib >= 1.10
+<!-- ghp-import -p docs/build/html/ -->
+The latest documentation for cyvcf2 can be found here:
+[![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](http://brentp.github.io/cyvcf2/)
+If you use cyvcf2, please cite the [paper](https://academic.oup.com/bioinformatics/article/2971439/cyvcf2)
+Fast python **(2 and 3)** parsing of VCF and BCF including region-queries.
+[![Build Status](https://github.com/brentp/cyvcf2/workflows/Build/badge.svg)](https://github.com/brentp/cyvcf2/actions?query=workflow%3ABuild)
+cyvcf2 is a cython wrapper around [htslib](https://github.com/samtools/htslib) built for fast parsing of [Variant Call Format](https://en.m.wikipedia.org/wiki/Variant_Call_Format) (VCF) files.
+Attributes like `variant.gt_ref_depths` return a numpy array directly so they are immediately ready for downstream use.
+**note** that the array is backed by the underlying C data, so, once `variant` goes out of scope. The array will contain nonsense.
+To persist a copy, use: `cpy = np.array(variant.gt_ref_depths)` instead of just `arr = variant.gt_ref_depths`.
+
+%package help
+Summary:	Development documents and examples for cyvcf2
+Provides:	python3-cyvcf2-doc
+%description help
+Note: cyvcf2 versions < 0.20.0 require htslib < 1.10. cyvcf2 versions >= 0.20.0 require htslib >= 1.10
+<!-- ghp-import -p docs/build/html/ -->
+The latest documentation for cyvcf2 can be found here:
+[![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](http://brentp.github.io/cyvcf2/)
+If you use cyvcf2, please cite the [paper](https://academic.oup.com/bioinformatics/article/2971439/cyvcf2)
+Fast python **(2 and 3)** parsing of VCF and BCF including region-queries.
+[![Build Status](https://github.com/brentp/cyvcf2/workflows/Build/badge.svg)](https://github.com/brentp/cyvcf2/actions?query=workflow%3ABuild)
+cyvcf2 is a cython wrapper around [htslib](https://github.com/samtools/htslib) built for fast parsing of [Variant Call Format](https://en.m.wikipedia.org/wiki/Variant_Call_Format) (VCF) files.
+Attributes like `variant.gt_ref_depths` return a numpy array directly so they are immediately ready for downstream use.
+**note** that the array is backed by the underlying C data, so, once `variant` goes out of scope. The array will contain nonsense.
+To persist a copy, use: `cpy = np.array(variant.gt_ref_depths)` instead of just `arr = variant.gt_ref_depths`.
+
+%prep
+%autosetup -n cyvcf2-0.30.18
+
+%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-cyvcf2 -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Mon Apr 10 2023 Python_Bot <Python_Bot@openeuler.org> - 0.30.18-1
+- Package Spec generated