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@@ -0,0 +1 @@ +/klusta-3.0.16.tar.gz diff --git a/python-klusta.spec b/python-klusta.spec new file mode 100644 index 0000000..f8c3061 --- /dev/null +++ b/python-klusta.spec @@ -0,0 +1,315 @@ +%global _empty_manifest_terminate_build 0 +Name: python-klusta +Version: 3.0.16 +Release: 1 +Summary: Spike detection and automatic clustering for spike sorting +License: BSD +URL: https://klusta.cortexlab.net +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/46/d7/52ef7083c56d1bf1bf9d65c709f43c8802c45d7f5373182ddea367df2c4b/klusta-3.0.16.tar.gz +BuildArch: noarch + + +%description +# Klusta: automatic spike sorting up to 64 channels + +[](https://travis-ci.org/kwikteam/klusta) +[](http://codecov.io/github/kwikteam/klusta?branch=master) +[](http://klusta.readthedocs.org/en/latest/) +[](https://pypi.python.org/pypi/klusta) +[](https://github.com/kwikteam/klusta/releases/latest) + +[**klusta**](https://github.com/kwikteam/klusta) is an open source package for automatic spike sorting of multielectrode neurophysiological recordings made with probes containing up to a few dozens of sites. + +We are also working actively on more sophisticated algorithms that will scale to hundreds/thousands of channels. This work is being done within the [phy project](https://github.com/kwikteam/phy), which is still experimental at this point. + +## Overview + +**klusta** implements the following features: + +* **Kwik**: An HDF5-based file format that stores the results of a spike sorting session. +* **Spike detection** (also known as SpikeDetekt): an algorithm designed for probes containing tens of channels, based on a flood-fill algorithm in the adjacency graph formed by the recording sites in the probe. +* **Automatic clustering** (also known as Masked KlustaKwik): an automatic clustering algorithm designed for high-dimensional structured datasets. + + +## GUI + +You will need a GUI to visualize the spike sorting results. + +We have developed two GUI programs with the same features: + +* **phy KwikGUI**: newer project, scales to hundreds/thousands of channels, still relatively experimental. **It will be automatically installed if you follow the install instructions below.** +* **[KlustaViewa](https://github.com/klusta-team/klustaviewa)**: widely used, but older and a bit hard to install since it relies on very old dependencies. + +Both GUIs work with the same **Kwik** format. + + +## Quick install guide + +The following instructions will install both **klusta** and the **phy KwikGUI**. + +1. Make sure that you have [**miniconda**](http://conda.pydata.org/miniconda.html) installed. You can choose the Python 3.5 64-bit version for your operating system (Linux, Windows, or OS X). +2. [Download the environment file.](https://raw.githubusercontent.com/kwikteam/klusta/master/installer/environment.yml) +3. Open a terminal (on Windows, `cmd`, not Powershell) in the directory where you saved the file and type: + + ```bash + conda env create -n klusta -f environment.yml + ``` + +4. **Done**! Now, to use klusta and the phy KwikGUI, enter the directory that contains your files and type: + + ```bash + source activate klusta # omit the `source` on Windows + klusta yourfile.prm # spikesort your data with a PRM file + phy kwik-gui yourfile.kwik # open the GUI + ``` + + See the documentation for more details. + + +### Updating the software + +To get the latest version of the software, open a terminal and type: + +``` +source activate klusta # omit the `source` on Windows +pip install klusta phy phycontrib --upgrade +``` + + +## Technical details + +**klusta** is written in pure Python. The clustering code, written in Python and Cython, currently lives in [another repository](https://github.com/kwikteam/klustakwik2/). + + +## Links + +* [Documentation](http://klusta.readthedocs.org/en/latest/) (work in progress) +* [Paper in Nature Neuroscience (April 2016)](http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4268.html) +* [Mailing list](https://groups.google.com/forum/#!forum/klustaviewas) +* [Sample data repository](http://phy.cortexlab.net/data/) (work in progress) + + +## Credits + +**klusta** is developed by [Cyrille Rossant](http://cyrille.rossant.net), [Shabnam Kadir](https://iris.ucl.ac.uk/iris/browse/profile?upi=SKADI56), [Dan Goodman](http://thesamovar.net/), [Max Hunter](https://iris.ucl.ac.uk/iris/browse/profile?upi=MLDHU99), and [Kenneth Harris](https://iris.ucl.ac.uk/iris/browse/profile?upi=KDHAR02), in the [Cortexlab](https://www.ucl.ac.uk/cortexlab), University College London. + +%package -n python3-klusta +Summary: Spike detection and automatic clustering for spike sorting +Provides: python-klusta +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-klusta +# Klusta: automatic spike sorting up to 64 channels + +[](https://travis-ci.org/kwikteam/klusta) +[](http://codecov.io/github/kwikteam/klusta?branch=master) +[](http://klusta.readthedocs.org/en/latest/) +[](https://pypi.python.org/pypi/klusta) +[](https://github.com/kwikteam/klusta/releases/latest) + +[**klusta**](https://github.com/kwikteam/klusta) is an open source package for automatic spike sorting of multielectrode neurophysiological recordings made with probes containing up to a few dozens of sites. + +We are also working actively on more sophisticated algorithms that will scale to hundreds/thousands of channels. This work is being done within the [phy project](https://github.com/kwikteam/phy), which is still experimental at this point. + +## Overview + +**klusta** implements the following features: + +* **Kwik**: An HDF5-based file format that stores the results of a spike sorting session. +* **Spike detection** (also known as SpikeDetekt): an algorithm designed for probes containing tens of channels, based on a flood-fill algorithm in the adjacency graph formed by the recording sites in the probe. +* **Automatic clustering** (also known as Masked KlustaKwik): an automatic clustering algorithm designed for high-dimensional structured datasets. + + +## GUI + +You will need a GUI to visualize the spike sorting results. + +We have developed two GUI programs with the same features: + +* **phy KwikGUI**: newer project, scales to hundreds/thousands of channels, still relatively experimental. **It will be automatically installed if you follow the install instructions below.** +* **[KlustaViewa](https://github.com/klusta-team/klustaviewa)**: widely used, but older and a bit hard to install since it relies on very old dependencies. + +Both GUIs work with the same **Kwik** format. + + +## Quick install guide + +The following instructions will install both **klusta** and the **phy KwikGUI**. + +1. Make sure that you have [**miniconda**](http://conda.pydata.org/miniconda.html) installed. You can choose the Python 3.5 64-bit version for your operating system (Linux, Windows, or OS X). +2. [Download the environment file.](https://raw.githubusercontent.com/kwikteam/klusta/master/installer/environment.yml) +3. Open a terminal (on Windows, `cmd`, not Powershell) in the directory where you saved the file and type: + + ```bash + conda env create -n klusta -f environment.yml + ``` + +4. **Done**! Now, to use klusta and the phy KwikGUI, enter the directory that contains your files and type: + + ```bash + source activate klusta # omit the `source` on Windows + klusta yourfile.prm # spikesort your data with a PRM file + phy kwik-gui yourfile.kwik # open the GUI + ``` + + See the documentation for more details. + + +### Updating the software + +To get the latest version of the software, open a terminal and type: + +``` +source activate klusta # omit the `source` on Windows +pip install klusta phy phycontrib --upgrade +``` + + +## Technical details + +**klusta** is written in pure Python. The clustering code, written in Python and Cython, currently lives in [another repository](https://github.com/kwikteam/klustakwik2/). + + +## Links + +* [Documentation](http://klusta.readthedocs.org/en/latest/) (work in progress) +* [Paper in Nature Neuroscience (April 2016)](http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4268.html) +* [Mailing list](https://groups.google.com/forum/#!forum/klustaviewas) +* [Sample data repository](http://phy.cortexlab.net/data/) (work in progress) + + +## Credits + +**klusta** is developed by [Cyrille Rossant](http://cyrille.rossant.net), [Shabnam Kadir](https://iris.ucl.ac.uk/iris/browse/profile?upi=SKADI56), [Dan Goodman](http://thesamovar.net/), [Max Hunter](https://iris.ucl.ac.uk/iris/browse/profile?upi=MLDHU99), and [Kenneth Harris](https://iris.ucl.ac.uk/iris/browse/profile?upi=KDHAR02), in the [Cortexlab](https://www.ucl.ac.uk/cortexlab), University College London. + +%package help +Summary: Development documents and examples for klusta +Provides: python3-klusta-doc +%description help +# Klusta: automatic spike sorting up to 64 channels + +[](https://travis-ci.org/kwikteam/klusta) +[](http://codecov.io/github/kwikteam/klusta?branch=master) +[](http://klusta.readthedocs.org/en/latest/) +[](https://pypi.python.org/pypi/klusta) +[](https://github.com/kwikteam/klusta/releases/latest) + +[**klusta**](https://github.com/kwikteam/klusta) is an open source package for automatic spike sorting of multielectrode neurophysiological recordings made with probes containing up to a few dozens of sites. + +We are also working actively on more sophisticated algorithms that will scale to hundreds/thousands of channels. This work is being done within the [phy project](https://github.com/kwikteam/phy), which is still experimental at this point. + +## Overview + +**klusta** implements the following features: + +* **Kwik**: An HDF5-based file format that stores the results of a spike sorting session. +* **Spike detection** (also known as SpikeDetekt): an algorithm designed for probes containing tens of channels, based on a flood-fill algorithm in the adjacency graph formed by the recording sites in the probe. +* **Automatic clustering** (also known as Masked KlustaKwik): an automatic clustering algorithm designed for high-dimensional structured datasets. + + +## GUI + +You will need a GUI to visualize the spike sorting results. + +We have developed two GUI programs with the same features: + +* **phy KwikGUI**: newer project, scales to hundreds/thousands of channels, still relatively experimental. **It will be automatically installed if you follow the install instructions below.** +* **[KlustaViewa](https://github.com/klusta-team/klustaviewa)**: widely used, but older and a bit hard to install since it relies on very old dependencies. + +Both GUIs work with the same **Kwik** format. + + +## Quick install guide + +The following instructions will install both **klusta** and the **phy KwikGUI**. + +1. Make sure that you have [**miniconda**](http://conda.pydata.org/miniconda.html) installed. You can choose the Python 3.5 64-bit version for your operating system (Linux, Windows, or OS X). +2. [Download the environment file.](https://raw.githubusercontent.com/kwikteam/klusta/master/installer/environment.yml) +3. Open a terminal (on Windows, `cmd`, not Powershell) in the directory where you saved the file and type: + + ```bash + conda env create -n klusta -f environment.yml + ``` + +4. **Done**! Now, to use klusta and the phy KwikGUI, enter the directory that contains your files and type: + + ```bash + source activate klusta # omit the `source` on Windows + klusta yourfile.prm # spikesort your data with a PRM file + phy kwik-gui yourfile.kwik # open the GUI + ``` + + See the documentation for more details. + + +### Updating the software + +To get the latest version of the software, open a terminal and type: + +``` +source activate klusta # omit the `source` on Windows +pip install klusta phy phycontrib --upgrade +``` + + +## Technical details + +**klusta** is written in pure Python. The clustering code, written in Python and Cython, currently lives in [another repository](https://github.com/kwikteam/klustakwik2/). + + +## Links + +* [Documentation](http://klusta.readthedocs.org/en/latest/) (work in progress) +* [Paper in Nature Neuroscience (April 2016)](http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4268.html) +* [Mailing list](https://groups.google.com/forum/#!forum/klustaviewas) +* [Sample data repository](http://phy.cortexlab.net/data/) (work in progress) + + +## Credits + +**klusta** is developed by [Cyrille Rossant](http://cyrille.rossant.net), [Shabnam Kadir](https://iris.ucl.ac.uk/iris/browse/profile?upi=SKADI56), [Dan Goodman](http://thesamovar.net/), [Max Hunter](https://iris.ucl.ac.uk/iris/browse/profile?upi=MLDHU99), and [Kenneth Harris](https://iris.ucl.ac.uk/iris/browse/profile?upi=KDHAR02), in the [Cortexlab](https://www.ucl.ac.uk/cortexlab), University College London. + +%prep +%autosetup -n klusta-3.0.16 + +%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-klusta -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Thu Mar 09 2023 Python_Bot <Python_Bot@openeuler.org> - 3.0.16-1 +- Package Spec generated @@ -0,0 +1 @@ +592641723844a40719ce7d987deaff74 klusta-3.0.16.tar.gz |