automatic import of python-cooler

3 files changed, 530 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..0159a54 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1 @@
+/cooler-0.9.1.tar.gz
diff --git a/python-cooler.spec b/python-cooler.spec
new file mode 100644
index 0000000..a10feef
--- /dev/null
+++ b/python-cooler.spec
@@ -0,0 +1,528 @@
+%global _empty_manifest_terminate_build 0
+Name:		python-cooler
+Version:	0.9.1
+Release:	1
+Summary:	Sparse binary format for genomic interaction matrices.
+License:	BSD-3-Clause
+URL:		https://pypi.org/project/cooler/
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/80/65/96c623d5ee993ebd51d643bd877621161a3e6a0ebbca8029693311833633/cooler-0.9.1.tar.gz
+BuildArch:	noarch
+
+Requires:	python3-numpy
+Requires:	python3-scipy
+Requires:	python3-pandas
+Requires:	python3-h5py
+Requires:	python3-click
+Requires:	python3-cytoolz
+Requires:	python3-multiprocess
+Requires:	python3-pyfaidx
+Requires:	python3-asciitree
+Requires:	python3-pyyaml
+Requires:	python3-simplejson
+Requires:	python3-biopython
+Requires:	python3-dask[array,dataframe]
+Requires:	python3-ipytree
+Requires:	python3-ipywidgets
+Requires:	python3-matplotlib
+Requires:	python3-pypairix
+Requires:	python3-psutil
+Requires:	python3-pysam
+Requires:	python3-Sphinx
+Requires:	python3-sphinx-rtd-theme
+Requires:	python3-m2r
+Requires:	python3-numpydoc
+Requires:	python3-recommonmark
+Requires:	python3-coverage[toml]
+Requires:	python3-flake8
+Requires:	python3-flake8-pyproject
+Requires:	python3-isort
+Requires:	python3-pytest
+Requires:	python3-pytest-cov
+
+%description
+# Cooler
+
+<a href="https://open2c.github.io/cooler"><img width="25%" src="https://github.com/open2c/cooler/raw/master/docs/cooler_logo.png" alt="Cooler"></a>
+
+<table>
+    <tr>
+        <td>Latest Release</td>
+        <td>
+            <a href="https://pypi.org/project/cooler/">
+                <img src="https://img.shields.io/pypi/v/cooler?color=blue&label=PyPI%20package" alt="latest release pypi">
+            </a>
+            <a href="https://bioconda.github.io/recipes/cooler/README.html">
+                <img src="https://img.shields.io/conda/vn/bioconda/cooler?color=blue" alt="latest release bioconda">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>License</td>
+        <td>
+            <a href="https://github.com/open2c/cooler/blob/master/LICENSE">
+                <img src="https://img.shields.io/badge/license-BSD-green" alt="license">
+                <!-- <img src="https://img.shields.io/pypi/l/cooler.svg" alt="license"> -->
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Build Status</td>
+        <td>
+            <a href="https://github.com/open2c/cooler/blob/master/.github/workflows/ci.yml">
+                <img src="https://github.com/open2c/cooler/actions/workflows/ci.yml/badge.svg" alt="build status">
+            </a>
+        </td>
+    </tr>
+    <tr>
+      <td>Pre-commit Status</td>
+      <td>
+        <a href="https://results.pre-commit.ci/repo/github/49553222">
+        <img src="https://results.pre-commit.ci/badge/github/open2c/cooler/master.svg" alt="pre-commit status" />
+        </a>
+      </td>
+    </tr>
+    <tr>
+        <td>Docs Status</td>
+        <td>
+            <a href="http://cooler.readthedocs.org/en/latest/">
+                <img src="https://readthedocs.org/projects/cooler/badge/?version=latest">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Coverage</td>
+        <td>
+            <a href="https://codecov.io/gh/open2c/cooler">
+                <img src="https://codecov.io/gh/open2c/cooler/branch/master/graph/badge.svg" alt="coverage">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Downloads</td>
+        <td>
+            <a href="https://pypi.org/project/cooler">
+                <img src="https://static.pepy.tech/personalized-badge/cooler?period=total&units=international_system&left_color=grey&right_color=blue&left_text=PyPI%20downloads" alt="pypi downloads">
+            </a>
+            <a href="http://bioconda.github.io/recipes/cooler/README.html">
+                <img src="https://img.shields.io/conda/dn/bioconda/cooler.svg?style=flat&label=Bioconda downloads" alt="bioconda downloads">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Citation</td>
+        <td>
+            <a href="https://doi.org/10.1093/bioinformatics/btz540">
+                <img src="https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtz540-blue" alt="paper doi">
+            </a>
+            <a href="https://zenodo.org/badge/latestdoi/49553222">
+                <img src="https://zenodo.org/badge/49553222.svg" alt="zenodo doi">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Community</td>
+        <td>
+            <a href="https://bit.ly/open2c-slack">
+                <img src="https://img.shields.io/badge/chat-slack-%233F0F3F?logo=slack" alt="slack">
+            </a>
+        </td>
+    </tr>
+</table>
+
+## A cool place to store your Hi-C
+
+Cooler is a support library for a **sparse, compressed, binary** persistent storage [format](http://cooler.readthedocs.io/en/latest/schema.html), also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.
+
+The cooler file format is an implementation of a genomic matrix data model using [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) as the container format. The `cooler` package includes a suite of [command line tools](http://cooler.readthedocs.io/en/latest/cli.html) and a [Python API](http://cooler.readthedocs.io/en/latest/api.html) to facilitate creating, querying and manipulating cooler files.
+
+To get started:
+
+- [Install](#Installation) cooler
+- Read the [documentation](http://cooler.readthedocs.org/en/stable/) and see the Jupyter Notebook [walkthrough](https://github.com/open2c/cooler-binder).
+- _cool_ files from published Hi-C data sets are available at `ftp://cooler.csail.mit.edu/coolers`.
+- Many more multires (_mcool_) files are available on the [4DN data portal](https://data.4dnucleome.org/visualization/index).
+
+### Installation
+
+Install from PyPI using pip.
+```sh
+$ pip install cooler
+```
+
+If you are using `conda`, you can alternatively install `cooler` from the [bioconda](https://bioconda.github.io/index.html) channel.
+```sh
+$ conda install -c conda-forge -c bioconda cooler
+```
+
+### Citing
+
+Abdennur, N., and Mirny, L.A. (2020). Cooler: scalable storage for Hi-C data and other genomically labeled arrays. _Bioinformatics_. doi: [10.1093/bioinformatics/btz540](https://doi.org/10.1093/bioinformatics/btz540).
+
+```bibtex
+@article{cooler2020,
+    author = {Abdennur, Nezar and Mirny, Leonid A},
+    title = "{Cooler: scalable storage for Hi-C data and other genomically labeled arrays}",
+    journal={Bioinformatics},
+    volume={36},
+    number={1},
+    pages={311--316},
+    year={2020},
+    doi = {10.1093/bioinformatics/btz540},
+    url = {https://doi.org/10.1093/bioinformatics/btz540},
+}
+```
+
+### Contributing
+
+Interested in contributing to cooler? That's great! To get started, check out the [contributing guide](https://github.com/open2c/cooler/blob/master/CONTRIBUTING.md).
+
+
+### Related projects
+
+- Process Hi-C data with [distiller](https://github.com/open2c/distiller)!
+- Downstream analysis with [cooltools](https://github.com/open2c/cooltools)!
+- Visualize your cooler data with [HiGlass](http://higlass.io)!
+
+
+%package -n python3-cooler
+Summary:	Sparse binary format for genomic interaction matrices.
+Provides:	python-cooler
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-cooler
+# Cooler
+
+<a href="https://open2c.github.io/cooler"><img width="25%" src="https://github.com/open2c/cooler/raw/master/docs/cooler_logo.png" alt="Cooler"></a>
+
+<table>
+    <tr>
+        <td>Latest Release</td>
+        <td>
+            <a href="https://pypi.org/project/cooler/">
+                <img src="https://img.shields.io/pypi/v/cooler?color=blue&label=PyPI%20package" alt="latest release pypi">
+            </a>
+            <a href="https://bioconda.github.io/recipes/cooler/README.html">
+                <img src="https://img.shields.io/conda/vn/bioconda/cooler?color=blue" alt="latest release bioconda">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>License</td>
+        <td>
+            <a href="https://github.com/open2c/cooler/blob/master/LICENSE">
+                <img src="https://img.shields.io/badge/license-BSD-green" alt="license">
+                <!-- <img src="https://img.shields.io/pypi/l/cooler.svg" alt="license"> -->
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Build Status</td>
+        <td>
+            <a href="https://github.com/open2c/cooler/blob/master/.github/workflows/ci.yml">
+                <img src="https://github.com/open2c/cooler/actions/workflows/ci.yml/badge.svg" alt="build status">
+            </a>
+        </td>
+    </tr>
+    <tr>
+      <td>Pre-commit Status</td>
+      <td>
+        <a href="https://results.pre-commit.ci/repo/github/49553222">
+        <img src="https://results.pre-commit.ci/badge/github/open2c/cooler/master.svg" alt="pre-commit status" />
+        </a>
+      </td>
+    </tr>
+    <tr>
+        <td>Docs Status</td>
+        <td>
+            <a href="http://cooler.readthedocs.org/en/latest/">
+                <img src="https://readthedocs.org/projects/cooler/badge/?version=latest">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Coverage</td>
+        <td>
+            <a href="https://codecov.io/gh/open2c/cooler">
+                <img src="https://codecov.io/gh/open2c/cooler/branch/master/graph/badge.svg" alt="coverage">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Downloads</td>
+        <td>
+            <a href="https://pypi.org/project/cooler">
+                <img src="https://static.pepy.tech/personalized-badge/cooler?period=total&units=international_system&left_color=grey&right_color=blue&left_text=PyPI%20downloads" alt="pypi downloads">
+            </a>
+            <a href="http://bioconda.github.io/recipes/cooler/README.html">
+                <img src="https://img.shields.io/conda/dn/bioconda/cooler.svg?style=flat&label=Bioconda downloads" alt="bioconda downloads">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Citation</td>
+        <td>
+            <a href="https://doi.org/10.1093/bioinformatics/btz540">
+                <img src="https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtz540-blue" alt="paper doi">
+            </a>
+            <a href="https://zenodo.org/badge/latestdoi/49553222">
+                <img src="https://zenodo.org/badge/49553222.svg" alt="zenodo doi">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Community</td>
+        <td>
+            <a href="https://bit.ly/open2c-slack">
+                <img src="https://img.shields.io/badge/chat-slack-%233F0F3F?logo=slack" alt="slack">
+            </a>
+        </td>
+    </tr>
+</table>
+
+## A cool place to store your Hi-C
+
+Cooler is a support library for a **sparse, compressed, binary** persistent storage [format](http://cooler.readthedocs.io/en/latest/schema.html), also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.
+
+The cooler file format is an implementation of a genomic matrix data model using [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) as the container format. The `cooler` package includes a suite of [command line tools](http://cooler.readthedocs.io/en/latest/cli.html) and a [Python API](http://cooler.readthedocs.io/en/latest/api.html) to facilitate creating, querying and manipulating cooler files.
+
+To get started:
+
+- [Install](#Installation) cooler
+- Read the [documentation](http://cooler.readthedocs.org/en/stable/) and see the Jupyter Notebook [walkthrough](https://github.com/open2c/cooler-binder).
+- _cool_ files from published Hi-C data sets are available at `ftp://cooler.csail.mit.edu/coolers`.
+- Many more multires (_mcool_) files are available on the [4DN data portal](https://data.4dnucleome.org/visualization/index).
+
+### Installation
+
+Install from PyPI using pip.
+```sh
+$ pip install cooler
+```
+
+If you are using `conda`, you can alternatively install `cooler` from the [bioconda](https://bioconda.github.io/index.html) channel.
+```sh
+$ conda install -c conda-forge -c bioconda cooler
+```
+
+### Citing
+
+Abdennur, N., and Mirny, L.A. (2020). Cooler: scalable storage for Hi-C data and other genomically labeled arrays. _Bioinformatics_. doi: [10.1093/bioinformatics/btz540](https://doi.org/10.1093/bioinformatics/btz540).
+
+```bibtex
+@article{cooler2020,
+    author = {Abdennur, Nezar and Mirny, Leonid A},
+    title = "{Cooler: scalable storage for Hi-C data and other genomically labeled arrays}",
+    journal={Bioinformatics},
+    volume={36},
+    number={1},
+    pages={311--316},
+    year={2020},
+    doi = {10.1093/bioinformatics/btz540},
+    url = {https://doi.org/10.1093/bioinformatics/btz540},
+}
+```
+
+### Contributing
+
+Interested in contributing to cooler? That's great! To get started, check out the [contributing guide](https://github.com/open2c/cooler/blob/master/CONTRIBUTING.md).
+
+
+### Related projects
+
+- Process Hi-C data with [distiller](https://github.com/open2c/distiller)!
+- Downstream analysis with [cooltools](https://github.com/open2c/cooltools)!
+- Visualize your cooler data with [HiGlass](http://higlass.io)!
+
+
+%package help
+Summary:	Development documents and examples for cooler
+Provides:	python3-cooler-doc
+%description help
+# Cooler
+
+<a href="https://open2c.github.io/cooler"><img width="25%" src="https://github.com/open2c/cooler/raw/master/docs/cooler_logo.png" alt="Cooler"></a>
+
+<table>
+    <tr>
+        <td>Latest Release</td>
+        <td>
+            <a href="https://pypi.org/project/cooler/">
+                <img src="https://img.shields.io/pypi/v/cooler?color=blue&label=PyPI%20package" alt="latest release pypi">
+            </a>
+            <a href="https://bioconda.github.io/recipes/cooler/README.html">
+                <img src="https://img.shields.io/conda/vn/bioconda/cooler?color=blue" alt="latest release bioconda">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>License</td>
+        <td>
+            <a href="https://github.com/open2c/cooler/blob/master/LICENSE">
+                <img src="https://img.shields.io/badge/license-BSD-green" alt="license">
+                <!-- <img src="https://img.shields.io/pypi/l/cooler.svg" alt="license"> -->
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Build Status</td>
+        <td>
+            <a href="https://github.com/open2c/cooler/blob/master/.github/workflows/ci.yml">
+                <img src="https://github.com/open2c/cooler/actions/workflows/ci.yml/badge.svg" alt="build status">
+            </a>
+        </td>
+    </tr>
+    <tr>
+      <td>Pre-commit Status</td>
+      <td>
+        <a href="https://results.pre-commit.ci/repo/github/49553222">
+        <img src="https://results.pre-commit.ci/badge/github/open2c/cooler/master.svg" alt="pre-commit status" />
+        </a>
+      </td>
+    </tr>
+    <tr>
+        <td>Docs Status</td>
+        <td>
+            <a href="http://cooler.readthedocs.org/en/latest/">
+                <img src="https://readthedocs.org/projects/cooler/badge/?version=latest">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Coverage</td>
+        <td>
+            <a href="https://codecov.io/gh/open2c/cooler">
+                <img src="https://codecov.io/gh/open2c/cooler/branch/master/graph/badge.svg" alt="coverage">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Downloads</td>
+        <td>
+            <a href="https://pypi.org/project/cooler">
+                <img src="https://static.pepy.tech/personalized-badge/cooler?period=total&units=international_system&left_color=grey&right_color=blue&left_text=PyPI%20downloads" alt="pypi downloads">
+            </a>
+            <a href="http://bioconda.github.io/recipes/cooler/README.html">
+                <img src="https://img.shields.io/conda/dn/bioconda/cooler.svg?style=flat&label=Bioconda downloads" alt="bioconda downloads">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Citation</td>
+        <td>
+            <a href="https://doi.org/10.1093/bioinformatics/btz540">
+                <img src="https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtz540-blue" alt="paper doi">
+            </a>
+            <a href="https://zenodo.org/badge/latestdoi/49553222">
+                <img src="https://zenodo.org/badge/49553222.svg" alt="zenodo doi">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Community</td>
+        <td>
+            <a href="https://bit.ly/open2c-slack">
+                <img src="https://img.shields.io/badge/chat-slack-%233F0F3F?logo=slack" alt="slack">
+            </a>
+        </td>
+    </tr>
+</table>
+
+## A cool place to store your Hi-C
+
+Cooler is a support library for a **sparse, compressed, binary** persistent storage [format](http://cooler.readthedocs.io/en/latest/schema.html), also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.
+
+The cooler file format is an implementation of a genomic matrix data model using [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) as the container format. The `cooler` package includes a suite of [command line tools](http://cooler.readthedocs.io/en/latest/cli.html) and a [Python API](http://cooler.readthedocs.io/en/latest/api.html) to facilitate creating, querying and manipulating cooler files.
+
+To get started:
+
+- [Install](#Installation) cooler
+- Read the [documentation](http://cooler.readthedocs.org/en/stable/) and see the Jupyter Notebook [walkthrough](https://github.com/open2c/cooler-binder).
+- _cool_ files from published Hi-C data sets are available at `ftp://cooler.csail.mit.edu/coolers`.
+- Many more multires (_mcool_) files are available on the [4DN data portal](https://data.4dnucleome.org/visualization/index).
+
+### Installation
+
+Install from PyPI using pip.
+```sh
+$ pip install cooler
+```
+
+If you are using `conda`, you can alternatively install `cooler` from the [bioconda](https://bioconda.github.io/index.html) channel.
+```sh
+$ conda install -c conda-forge -c bioconda cooler
+```
+
+### Citing
+
+Abdennur, N., and Mirny, L.A. (2020). Cooler: scalable storage for Hi-C data and other genomically labeled arrays. _Bioinformatics_. doi: [10.1093/bioinformatics/btz540](https://doi.org/10.1093/bioinformatics/btz540).
+
+```bibtex
+@article{cooler2020,
+    author = {Abdennur, Nezar and Mirny, Leonid A},
+    title = "{Cooler: scalable storage for Hi-C data and other genomically labeled arrays}",
+    journal={Bioinformatics},
+    volume={36},
+    number={1},
+    pages={311--316},
+    year={2020},
+    doi = {10.1093/bioinformatics/btz540},
+    url = {https://doi.org/10.1093/bioinformatics/btz540},
+}
+```
+
+### Contributing
+
+Interested in contributing to cooler? That's great! To get started, check out the [contributing guide](https://github.com/open2c/cooler/blob/master/CONTRIBUTING.md).
+
+
+### Related projects
+
+- Process Hi-C data with [distiller](https://github.com/open2c/distiller)!
+- Downstream analysis with [cooltools](https://github.com/open2c/cooltools)!
+- Visualize your cooler data with [HiGlass](http://higlass.io)!
+
+
+%prep
+%autosetup -n cooler-0.9.1
+
+%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-cooler -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 0.9.1-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..8e999fc
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+eea7594f756d8350b4cd241e9a41e218  cooler-0.9.1.tar.gz