automatic import of python-nextstrain-augur

3 files changed, 246 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..29b3d20 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1 @@
+/nextstrain-augur-22.0.0.tar.gz
diff --git a/python-nextstrain-augur.spec b/python-nextstrain-augur.spec
new file mode 100644
index 0000000..c540388
--- /dev/null
+++ b/python-nextstrain-augur.spec
@@ -0,0 +1,244 @@
+%global _empty_manifest_terminate_build 0
+Name:		python-nextstrain-augur
+Version:	22.0.0
+Release:	1
+Summary:	A bioinformatics toolkit for phylogenetic analysis
+License:	GNU Affero General Public License v3
+URL:		https://github.com/nextstrain/augur
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/3c/b2/86b50f68dcc8bb281fdf1c413f6a9ba098c7ee3f0f921f45be008887418c/nextstrain-augur-22.0.0.tar.gz
+BuildArch:	noarch
+
+Requires:	python3-bcbio-gff
+Requires:	python3-biopython
+Requires:	python3-cvxopt
+Requires:	python3-isodate
+Requires:	python3-jsonschema
+Requires:	python3-networkx
+Requires:	python3-numpy
+Requires:	python3-packaging
+Requires:	python3-pandas
+Requires:	python3-phylo-treetime
+Requires:	python3-pyfastx
+Requires:	python3-scipy
+Requires:	python3-xopen[zstd]
+Requires:	python3-cram
+Requires:	python3-deepdiff
+Requires:	python3-freezegun
+Requires:	python3-nextstrain-sphinx-theme
+Requires:	python3-pylint
+Requires:	python3-pytest
+Requires:	python3-pytest-cov
+Requires:	python3-pytest-mock
+Requires:	python3-recommonmark
+Requires:	python3-snakemake
+Requires:	python3-Sphinx
+Requires:	python3-sphinx-autobuild
+Requires:	python3-sphinx-argparse
+Requires:	python3-sphinx-markdown-tables
+Requires:	python3-sphinx-rtd-theme
+Requires:	python3-sphinx-autodoc-typehints
+Requires:	python3-wheel
+Requires:	python3-ipdb
+
+%description
+[![Build Status](https://github.com/nextstrain/augur/actions/workflows/ci.yaml/badge.svg?branch=master)](https://github.com/nextstrain/augur/actions/workflows/ci.yaml)
+[![PyPI version](https://badge.fury.io/py/nextstrain-augur.svg)](https://pypi.org/project/nextstrain-augur/)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/augur/README.html)
+[![Documentation Status](https://readthedocs.org/projects/nextstrain-augur/badge/?version=latest)](https://docs.nextstrain.org/projects/augur/en/stable/)
+[![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.02906/status.svg)](https://doi.org/10.21105/joss.02906)
+
+## About Nextstrain
+
+Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data.
+We provide a continually-updated view of publicly available data with powerful analytics and visualizations showing pathogen evolution and epidemic spread.
+Our goal is to aid epidemiological understanding and improve outbreak response.
+
+Resulting data and inferences are available live at the website [nextstrain.org](https://nextstrain.org).
+
+## About Augur
+
+*Definition: One held to foretell events by omens.*
+
+Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data.
+It provides a collection of commands which are designed to be composable into larger processing pipelines.
+
+The output of augur is a series of JSONs that can be used to visualize your results using [Auspice](https://github.com/nextstrain/auspice).
+
+## Quickstart
+
+[Follow instructions to install Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html).
+Try out an analysis of real virus data by [completing the Zika tutorial](https://nextstrain.org/docs/tutorials/zika).
+
+## Documentation
+
+* [Overview of how Augur fits together with other Nextstrain tools](https://docs.nextstrain.org/en/latest/learn/parts.html)
+* [Overview of Augur usage](https://docs.nextstrain.org/projects/augur/en/stable/usage/usage.html)
+* [Technical documentation for Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html)
+* [Contributor guide](https://github.com/nextstrain/.github/blob/master/CONTRIBUTING.md)
+* [Developer docs for Augur](./docs/contribute/DEV_DOCS.md)
+* [Changelog](./CHANGES.md)
+
+## Citation
+
+Huddleston J, Hadfield J, Sibley TR, Lee J, Fay K, Ilcisin M, Harkins E, Bedford T, Neher RA, Hodcroft EB, (2021). Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. Journal of Open Source Software, 6(57), 2906, https://doi.org/10.21105/joss.02906
+
+## License and copyright
+
+Copyright 2014-2022 Trevor Bedford and Richard Neher.
+
+Source code to Nextstrain is made available under the terms of the [GNU Affero General Public License](LICENSE.txt) (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Affero General Public License for more details.
+
+
+%package -n python3-nextstrain-augur
+Summary:	A bioinformatics toolkit for phylogenetic analysis
+Provides:	python-nextstrain-augur
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-nextstrain-augur
+[![Build Status](https://github.com/nextstrain/augur/actions/workflows/ci.yaml/badge.svg?branch=master)](https://github.com/nextstrain/augur/actions/workflows/ci.yaml)
+[![PyPI version](https://badge.fury.io/py/nextstrain-augur.svg)](https://pypi.org/project/nextstrain-augur/)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/augur/README.html)
+[![Documentation Status](https://readthedocs.org/projects/nextstrain-augur/badge/?version=latest)](https://docs.nextstrain.org/projects/augur/en/stable/)
+[![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.02906/status.svg)](https://doi.org/10.21105/joss.02906)
+
+## About Nextstrain
+
+Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data.
+We provide a continually-updated view of publicly available data with powerful analytics and visualizations showing pathogen evolution and epidemic spread.
+Our goal is to aid epidemiological understanding and improve outbreak response.
+
+Resulting data and inferences are available live at the website [nextstrain.org](https://nextstrain.org).
+
+## About Augur
+
+*Definition: One held to foretell events by omens.*
+
+Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data.
+It provides a collection of commands which are designed to be composable into larger processing pipelines.
+
+The output of augur is a series of JSONs that can be used to visualize your results using [Auspice](https://github.com/nextstrain/auspice).
+
+## Quickstart
+
+[Follow instructions to install Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html).
+Try out an analysis of real virus data by [completing the Zika tutorial](https://nextstrain.org/docs/tutorials/zika).
+
+## Documentation
+
+* [Overview of how Augur fits together with other Nextstrain tools](https://docs.nextstrain.org/en/latest/learn/parts.html)
+* [Overview of Augur usage](https://docs.nextstrain.org/projects/augur/en/stable/usage/usage.html)
+* [Technical documentation for Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html)
+* [Contributor guide](https://github.com/nextstrain/.github/blob/master/CONTRIBUTING.md)
+* [Developer docs for Augur](./docs/contribute/DEV_DOCS.md)
+* [Changelog](./CHANGES.md)
+
+## Citation
+
+Huddleston J, Hadfield J, Sibley TR, Lee J, Fay K, Ilcisin M, Harkins E, Bedford T, Neher RA, Hodcroft EB, (2021). Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. Journal of Open Source Software, 6(57), 2906, https://doi.org/10.21105/joss.02906
+
+## License and copyright
+
+Copyright 2014-2022 Trevor Bedford and Richard Neher.
+
+Source code to Nextstrain is made available under the terms of the [GNU Affero General Public License](LICENSE.txt) (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Affero General Public License for more details.
+
+
+%package help
+Summary:	Development documents and examples for nextstrain-augur
+Provides:	python3-nextstrain-augur-doc
+%description help
+[![Build Status](https://github.com/nextstrain/augur/actions/workflows/ci.yaml/badge.svg?branch=master)](https://github.com/nextstrain/augur/actions/workflows/ci.yaml)
+[![PyPI version](https://badge.fury.io/py/nextstrain-augur.svg)](https://pypi.org/project/nextstrain-augur/)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/augur/README.html)
+[![Documentation Status](https://readthedocs.org/projects/nextstrain-augur/badge/?version=latest)](https://docs.nextstrain.org/projects/augur/en/stable/)
+[![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.02906/status.svg)](https://doi.org/10.21105/joss.02906)
+
+## About Nextstrain
+
+Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data.
+We provide a continually-updated view of publicly available data with powerful analytics and visualizations showing pathogen evolution and epidemic spread.
+Our goal is to aid epidemiological understanding and improve outbreak response.
+
+Resulting data and inferences are available live at the website [nextstrain.org](https://nextstrain.org).
+
+## About Augur
+
+*Definition: One held to foretell events by omens.*
+
+Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data.
+It provides a collection of commands which are designed to be composable into larger processing pipelines.
+
+The output of augur is a series of JSONs that can be used to visualize your results using [Auspice](https://github.com/nextstrain/auspice).
+
+## Quickstart
+
+[Follow instructions to install Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html).
+Try out an analysis of real virus data by [completing the Zika tutorial](https://nextstrain.org/docs/tutorials/zika).
+
+## Documentation
+
+* [Overview of how Augur fits together with other Nextstrain tools](https://docs.nextstrain.org/en/latest/learn/parts.html)
+* [Overview of Augur usage](https://docs.nextstrain.org/projects/augur/en/stable/usage/usage.html)
+* [Technical documentation for Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html)
+* [Contributor guide](https://github.com/nextstrain/.github/blob/master/CONTRIBUTING.md)
+* [Developer docs for Augur](./docs/contribute/DEV_DOCS.md)
+* [Changelog](./CHANGES.md)
+
+## Citation
+
+Huddleston J, Hadfield J, Sibley TR, Lee J, Fay K, Ilcisin M, Harkins E, Bedford T, Neher RA, Hodcroft EB, (2021). Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. Journal of Open Source Software, 6(57), 2906, https://doi.org/10.21105/joss.02906
+
+## License and copyright
+
+Copyright 2014-2022 Trevor Bedford and Richard Neher.
+
+Source code to Nextstrain is made available under the terms of the [GNU Affero General Public License](LICENSE.txt) (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Affero General Public License for more details.
+
+
+%prep
+%autosetup -n nextstrain-augur-22.0.0
+
+%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-nextstrain-augur -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 22.0.0-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..7a55cbc
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+8fad3cffd4dfd49e092c2701b7c8af6f  nextstrain-augur-22.0.0.tar.gz