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|
%global _empty_manifest_terminate_build 0
Name: python-navis
Version: 1.4.0
Release: 1
Summary: Neuron Analysis and Visualization library
License: GNU GPL V3
URL: http://navis.readthedocs.io
Source0: https://mirrors.nju.edu.cn/pypi/web/packages/95/89/d4ee8572448ac944b3e3b145928bb998cad0c0fc8f9783ff7236558f6d03/navis-1.4.0.tar.gz
BuildArch: noarch
Requires: python3-h5py
Requires: python3-matplotlib
Requires: python3-morphops
Requires: python3-ncollpyde
Requires: python3-networkx
Requires: python3-numpy
Requires: python3-pandas
Requires: python3-pint
Requires: python3-plotly
Requires: python3-pynrrd
Requires: python3-pypng
Requires: python3-requests
Requires: python3-seaborn
Requires: python3-setuptools
Requires: python3-scipy
Requires: python3-six
Requires: python3-tqdm
Requires: python3-typing-extensions
Requires: python3-trimesh
Requires: python3-fuzzywuzzy
Requires: python3-molesq
Requires: python3-rdata
Requires: python3-igraph
Requires: python3-skeletor
Requires: python3-pathos
Requires: python3-Shapely
Requires: python3-pykdtree
Requires: python3-xxhash
Requires: python3-flybrains
Requires: python3-cloud-volume
Requires: python3-vispy[pyside6]
Requires: python3-open3d
Requires: python3-pyfqmr
Requires: python3-pathos
Requires: python3-Shapely
Requires: python3-pykdtree
Requires: python3-xxhash
Requires: python3-flybrains
Requires: python3-cloud-volume
Requires: python3-vispy[pyside6]
Requires: python3-open3d
Requires: python3-pyfqmr
Requires: python3-jupyter
Requires: python3-neuprint-python
Requires: python3-flake8
Requires: python3-wheel
Requires: python3-mypy
Requires: python3-pytest
Requires: python3-pytest-env
Requires: python3-pytest-xvfb
Requires: python3-gitpython
Requires: python3-cloud-volume
Requires: python3-flake8
Requires: python3-wheel
Requires: python3-mypy
Requires: python3-pytest
Requires: python3-pytest-env
Requires: python3-pytest-xvfb
Requires: python3-gitpython
Requires: python3-flybrains
Requires: python3-xxhash
Requires: python3-pykdtree
Requires: python3-open3d
Requires: python3-pyfqmr
Requires: python3-pathos
Requires: python3-rpy2
Requires: python3-Shapely
Requires: python3-jupyter
Requires: python3-neuprint-python
Requires: python3-Shapely
Requires: python3-vispy[pyside6]
Requires: python3-vispy[glfw]
Requires: python3-vispy[pyglet]
Requires: python3-vispy[pyqt5]
Requires: python3-vispy[pyqt6]
Requires: python3-vispy[pyside]
Requires: python3-vispy[pyside2]
Requires: python3-vispy[pyside6]
Requires: python3-vispy[sdl2]
Requires: python3-vispy[tk]
Requires: python3-vispy[wx]
%description
[](http://navis.readthedocs.io/en/latest/?badge=latest) [](https://github.com/navis-org/navis/actions/workflows/test-package.yml) [](https://github.com/navis-org/navis/actions/workflows/notebooktest-package.yml) [](https://coveralls.io/github/navis-org/navis?branch=master) [](https://colab.research.google.com/github/navis-org/navis/blob/master/examples/colab.ipynb) [](https://zenodo.org/badge/latestdoi/168142416) [](https://pepy.tech/project/navis)
<img src="https://github.com/navis-org/navis/raw/master/docs/_static/favicon.png" height="60">
NAVis is a Python 3 (3.7 or later) library for **N**euron **A**nalysis and **Vis**ualization.
## Documentation
NAVis is on [ReadTheDocs](http://navis.readthedocs.io/ "NAVis ReadTheDocs").
## Features
* works as Jupyter notebook, script or from terminal
* support for various neuron types: **skeletons**, **meshes**, **dotprops**, **voxels**
* 2D (matplotlib) and 3D (vispy, plotly or k3d) **plotting**
* neuron **surgery**: cutting, stitching, pruning, rerooting, intersections, ...
* **morphometrics**: Strahler analysis, cable length, volume, tortuosity, ...
* compare & cluster by morphology (e.g. **NBLAST**, persistence, form factor) and connectivity
* **transform** data between template brains (support for e.g. HDF5, CMTK, Elastix and thin plate spline transforms)
* load neurons directly from [neuPrint](https://neuprint.janelia.org), [neuromorpho.org](http://neuromorpho.org) and others
* simulate neurons and networks using the **NEURON** simulator
* interface with **Blender 3D** for high quality [renderings](https://youtu.be/wl3sFG7WQJc)
* interface with **R** neuron libraries (e.g. [nat](https://github.com/jefferis/nat), [rcatmaid](https://github.com/jefferis/rcatmaid), [elmr](https://github.com/jefferis/elmr))
* import-export from/to **SWC**, neuroglancer's ["**precomputed**"](https://github.com/google/neuroglancer/tree/master/src/neuroglancer/datasource/precomputed) format and more
* scalable thanks to out-of-the-box support for multiprocessing
* designed to be **extensible** - see for example [pymaid](https://pymaid.readthedocs.io/en/latest/)
## Getting started
See the [documentation](http://navis.readthedocs.io/ "NAVis ReadTheDocs") for detailed installation instructions, tutorials and examples. For the impatient:
```sh
pip3 install 'navis[all]'
```
which includes all optional extras providing features and/or performance improvements.
Currently, this is
`igraph`,
`pathos`,
`shapely`,
`kdtree`,
`hash`,
`flybrains`,
`cloudvolume`,
`meshes`,
and `vispy-default`.
3D plotting from a python REPL is provided by `vispy`, which has a choice of backends.
Different backends work best on different combinations of hardware, OS, python distribution, and REPL, so there may be some trial and error involved.
`vispy`'s backends are [listed here](https://vispy.org/installation.html#backend-requirements), and each can be installed as a navis extra, e.g. `pip3 install 'navis[vispy-pyqt6]'`.
## Changelog
A summary of changes can be found
[here](https://navis.readthedocs.io/en/latest/source/whats_new.html).
## NAVis & friends
<p align="center">
<img src="https://github.com/navis-org/navis/blob/master/docs/_static/navis_ecosystem.png?raw=true" width="700">
</p>
NAVis comes with batteries included but is also highly extensible. Some
libraries built on top of NAVis:
* [flybrains](https://github.com/navis-org/navis-flybrains) provides templates and transforms to use with navis
* [pymaid](https://pymaid.readthedocs.io/en/latest/) pulls and pushes data from/to CATMAID servers
* [fafbseg](https://fafbseg-py.readthedocs.io/en/latest/index.html) contains tools to work with autosegmented data for the FAFB EM dataset
## License
This code is under GNU GPL V3
## Acknowledgments
NAVis is inspired by and inherits much of its design from the excellent
[natverse](http://natverse.org) R packages by
[Greg Jefferis](https://github.com/jefferis), [Alex Bates](https://github.com/alexanderbates),
[James Manton](https://github.com/ajdm) and others.
## References
NAVis implements or provides interfaces with algorithms described in:
1. **Comparison of neurons based on morphology**: Neuron. 2016 doi: 10.1016/j.neuron.2016.06.012
*NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases.*
Costa M, Manton JD, Ostrovsky AD, Prohaska S, Jefferis GSXE.
[link](https://www.cell.com/neuron/fulltext/S0896-6273(16)30265-3?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0896627316302653%3Fshowall%3Dtrue)
2. **Comparison of neurons based on connectivity**: Science. 2012 Jul 27;337(6093):437-44. doi: 10.1126/science.1221762.
*The connectome of a decision-making neural network.*
Jarrell TA, Wang Y, Bloniarz AE, Brittin CA, Xu M, Thomson JN, Albertson DG, Hall DH, Emmons SW.
[link](http://science.sciencemag.org/content/337/6093/437.long)
3. **Comparison of neurons based on synapse distribution**: eLife. doi: 10.7554/eLife.16799
*Synaptic transmission parallels neuromodulation in a central food-intake circuit.*
Schlegel P, Texada MJ, Miroschnikow A, Schoofs A, Hückesfeld S, Peters M, … Pankratz MJ.
[link](https://elifesciences.org/content/5/e16799)
4. **Synapse flow centrality and segregation index**: eLife. doi: 10.7554/eLife.12059
*Quantitative neuroanatomy for connectomics in Drosophila.*
Schneider-Mizell CM, Gerhard S, Longair M, Kazimiers T, Li, Feng L, Zwart M … Cardona A.
[link](https://elifesciences.org/articles/12059)
## Contributing
1. Fork this repository
2. `git clone` it to your local machine
3. Install the full development dependencies with `pip install -r requirements.txt`
4. Install the package in editable mode with `pip install -e ".[all]"`
5. Create, `git add`, `git commit`, `git push`, and pull request your changes.
Run the tests locally with `pytest -v`.
Docstrings should use the [numpydoc](https://numpydoc.readthedocs.io/en/latest/format.html) format,
and make sure you include any relevant links and citations.
Unit tests should be [doctests](https://docs.python.org/3/library/doctest.html)
and/or use [pytest](https://docs.pytest.org/en/stable/) in the `./tests` directory.
Doctests have access to the `tmp_dir: pathlib.Path` variable,
which should be used if any files need to be written.
%package -n python3-navis
Summary: Neuron Analysis and Visualization library
Provides: python-navis
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-navis
[](http://navis.readthedocs.io/en/latest/?badge=latest) [](https://github.com/navis-org/navis/actions/workflows/test-package.yml) [](https://github.com/navis-org/navis/actions/workflows/notebooktest-package.yml) [](https://coveralls.io/github/navis-org/navis?branch=master) [](https://colab.research.google.com/github/navis-org/navis/blob/master/examples/colab.ipynb) [](https://zenodo.org/badge/latestdoi/168142416) [](https://pepy.tech/project/navis)
<img src="https://github.com/navis-org/navis/raw/master/docs/_static/favicon.png" height="60">
NAVis is a Python 3 (3.7 or later) library for **N**euron **A**nalysis and **Vis**ualization.
## Documentation
NAVis is on [ReadTheDocs](http://navis.readthedocs.io/ "NAVis ReadTheDocs").
## Features
* works as Jupyter notebook, script or from terminal
* support for various neuron types: **skeletons**, **meshes**, **dotprops**, **voxels**
* 2D (matplotlib) and 3D (vispy, plotly or k3d) **plotting**
* neuron **surgery**: cutting, stitching, pruning, rerooting, intersections, ...
* **morphometrics**: Strahler analysis, cable length, volume, tortuosity, ...
* compare & cluster by morphology (e.g. **NBLAST**, persistence, form factor) and connectivity
* **transform** data between template brains (support for e.g. HDF5, CMTK, Elastix and thin plate spline transforms)
* load neurons directly from [neuPrint](https://neuprint.janelia.org), [neuromorpho.org](http://neuromorpho.org) and others
* simulate neurons and networks using the **NEURON** simulator
* interface with **Blender 3D** for high quality [renderings](https://youtu.be/wl3sFG7WQJc)
* interface with **R** neuron libraries (e.g. [nat](https://github.com/jefferis/nat), [rcatmaid](https://github.com/jefferis/rcatmaid), [elmr](https://github.com/jefferis/elmr))
* import-export from/to **SWC**, neuroglancer's ["**precomputed**"](https://github.com/google/neuroglancer/tree/master/src/neuroglancer/datasource/precomputed) format and more
* scalable thanks to out-of-the-box support for multiprocessing
* designed to be **extensible** - see for example [pymaid](https://pymaid.readthedocs.io/en/latest/)
## Getting started
See the [documentation](http://navis.readthedocs.io/ "NAVis ReadTheDocs") for detailed installation instructions, tutorials and examples. For the impatient:
```sh
pip3 install 'navis[all]'
```
which includes all optional extras providing features and/or performance improvements.
Currently, this is
`igraph`,
`pathos`,
`shapely`,
`kdtree`,
`hash`,
`flybrains`,
`cloudvolume`,
`meshes`,
and `vispy-default`.
3D plotting from a python REPL is provided by `vispy`, which has a choice of backends.
Different backends work best on different combinations of hardware, OS, python distribution, and REPL, so there may be some trial and error involved.
`vispy`'s backends are [listed here](https://vispy.org/installation.html#backend-requirements), and each can be installed as a navis extra, e.g. `pip3 install 'navis[vispy-pyqt6]'`.
## Changelog
A summary of changes can be found
[here](https://navis.readthedocs.io/en/latest/source/whats_new.html).
## NAVis & friends
<p align="center">
<img src="https://github.com/navis-org/navis/blob/master/docs/_static/navis_ecosystem.png?raw=true" width="700">
</p>
NAVis comes with batteries included but is also highly extensible. Some
libraries built on top of NAVis:
* [flybrains](https://github.com/navis-org/navis-flybrains) provides templates and transforms to use with navis
* [pymaid](https://pymaid.readthedocs.io/en/latest/) pulls and pushes data from/to CATMAID servers
* [fafbseg](https://fafbseg-py.readthedocs.io/en/latest/index.html) contains tools to work with autosegmented data for the FAFB EM dataset
## License
This code is under GNU GPL V3
## Acknowledgments
NAVis is inspired by and inherits much of its design from the excellent
[natverse](http://natverse.org) R packages by
[Greg Jefferis](https://github.com/jefferis), [Alex Bates](https://github.com/alexanderbates),
[James Manton](https://github.com/ajdm) and others.
## References
NAVis implements or provides interfaces with algorithms described in:
1. **Comparison of neurons based on morphology**: Neuron. 2016 doi: 10.1016/j.neuron.2016.06.012
*NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases.*
Costa M, Manton JD, Ostrovsky AD, Prohaska S, Jefferis GSXE.
[link](https://www.cell.com/neuron/fulltext/S0896-6273(16)30265-3?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0896627316302653%3Fshowall%3Dtrue)
2. **Comparison of neurons based on connectivity**: Science. 2012 Jul 27;337(6093):437-44. doi: 10.1126/science.1221762.
*The connectome of a decision-making neural network.*
Jarrell TA, Wang Y, Bloniarz AE, Brittin CA, Xu M, Thomson JN, Albertson DG, Hall DH, Emmons SW.
[link](http://science.sciencemag.org/content/337/6093/437.long)
3. **Comparison of neurons based on synapse distribution**: eLife. doi: 10.7554/eLife.16799
*Synaptic transmission parallels neuromodulation in a central food-intake circuit.*
Schlegel P, Texada MJ, Miroschnikow A, Schoofs A, Hückesfeld S, Peters M, … Pankratz MJ.
[link](https://elifesciences.org/content/5/e16799)
4. **Synapse flow centrality and segregation index**: eLife. doi: 10.7554/eLife.12059
*Quantitative neuroanatomy for connectomics in Drosophila.*
Schneider-Mizell CM, Gerhard S, Longair M, Kazimiers T, Li, Feng L, Zwart M … Cardona A.
[link](https://elifesciences.org/articles/12059)
## Contributing
1. Fork this repository
2. `git clone` it to your local machine
3. Install the full development dependencies with `pip install -r requirements.txt`
4. Install the package in editable mode with `pip install -e ".[all]"`
5. Create, `git add`, `git commit`, `git push`, and pull request your changes.
Run the tests locally with `pytest -v`.
Docstrings should use the [numpydoc](https://numpydoc.readthedocs.io/en/latest/format.html) format,
and make sure you include any relevant links and citations.
Unit tests should be [doctests](https://docs.python.org/3/library/doctest.html)
and/or use [pytest](https://docs.pytest.org/en/stable/) in the `./tests` directory.
Doctests have access to the `tmp_dir: pathlib.Path` variable,
which should be used if any files need to be written.
%package help
Summary: Development documents and examples for navis
Provides: python3-navis-doc
%description help
[](http://navis.readthedocs.io/en/latest/?badge=latest) [](https://github.com/navis-org/navis/actions/workflows/test-package.yml) [](https://github.com/navis-org/navis/actions/workflows/notebooktest-package.yml) [](https://coveralls.io/github/navis-org/navis?branch=master) [](https://colab.research.google.com/github/navis-org/navis/blob/master/examples/colab.ipynb) [](https://zenodo.org/badge/latestdoi/168142416) [](https://pepy.tech/project/navis)
<img src="https://github.com/navis-org/navis/raw/master/docs/_static/favicon.png" height="60">
NAVis is a Python 3 (3.7 or later) library for **N**euron **A**nalysis and **Vis**ualization.
## Documentation
NAVis is on [ReadTheDocs](http://navis.readthedocs.io/ "NAVis ReadTheDocs").
## Features
* works as Jupyter notebook, script or from terminal
* support for various neuron types: **skeletons**, **meshes**, **dotprops**, **voxels**
* 2D (matplotlib) and 3D (vispy, plotly or k3d) **plotting**
* neuron **surgery**: cutting, stitching, pruning, rerooting, intersections, ...
* **morphometrics**: Strahler analysis, cable length, volume, tortuosity, ...
* compare & cluster by morphology (e.g. **NBLAST**, persistence, form factor) and connectivity
* **transform** data between template brains (support for e.g. HDF5, CMTK, Elastix and thin plate spline transforms)
* load neurons directly from [neuPrint](https://neuprint.janelia.org), [neuromorpho.org](http://neuromorpho.org) and others
* simulate neurons and networks using the **NEURON** simulator
* interface with **Blender 3D** for high quality [renderings](https://youtu.be/wl3sFG7WQJc)
* interface with **R** neuron libraries (e.g. [nat](https://github.com/jefferis/nat), [rcatmaid](https://github.com/jefferis/rcatmaid), [elmr](https://github.com/jefferis/elmr))
* import-export from/to **SWC**, neuroglancer's ["**precomputed**"](https://github.com/google/neuroglancer/tree/master/src/neuroglancer/datasource/precomputed) format and more
* scalable thanks to out-of-the-box support for multiprocessing
* designed to be **extensible** - see for example [pymaid](https://pymaid.readthedocs.io/en/latest/)
## Getting started
See the [documentation](http://navis.readthedocs.io/ "NAVis ReadTheDocs") for detailed installation instructions, tutorials and examples. For the impatient:
```sh
pip3 install 'navis[all]'
```
which includes all optional extras providing features and/or performance improvements.
Currently, this is
`igraph`,
`pathos`,
`shapely`,
`kdtree`,
`hash`,
`flybrains`,
`cloudvolume`,
`meshes`,
and `vispy-default`.
3D plotting from a python REPL is provided by `vispy`, which has a choice of backends.
Different backends work best on different combinations of hardware, OS, python distribution, and REPL, so there may be some trial and error involved.
`vispy`'s backends are [listed here](https://vispy.org/installation.html#backend-requirements), and each can be installed as a navis extra, e.g. `pip3 install 'navis[vispy-pyqt6]'`.
## Changelog
A summary of changes can be found
[here](https://navis.readthedocs.io/en/latest/source/whats_new.html).
## NAVis & friends
<p align="center">
<img src="https://github.com/navis-org/navis/blob/master/docs/_static/navis_ecosystem.png?raw=true" width="700">
</p>
NAVis comes with batteries included but is also highly extensible. Some
libraries built on top of NAVis:
* [flybrains](https://github.com/navis-org/navis-flybrains) provides templates and transforms to use with navis
* [pymaid](https://pymaid.readthedocs.io/en/latest/) pulls and pushes data from/to CATMAID servers
* [fafbseg](https://fafbseg-py.readthedocs.io/en/latest/index.html) contains tools to work with autosegmented data for the FAFB EM dataset
## License
This code is under GNU GPL V3
## Acknowledgments
NAVis is inspired by and inherits much of its design from the excellent
[natverse](http://natverse.org) R packages by
[Greg Jefferis](https://github.com/jefferis), [Alex Bates](https://github.com/alexanderbates),
[James Manton](https://github.com/ajdm) and others.
## References
NAVis implements or provides interfaces with algorithms described in:
1. **Comparison of neurons based on morphology**: Neuron. 2016 doi: 10.1016/j.neuron.2016.06.012
*NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases.*
Costa M, Manton JD, Ostrovsky AD, Prohaska S, Jefferis GSXE.
[link](https://www.cell.com/neuron/fulltext/S0896-6273(16)30265-3?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0896627316302653%3Fshowall%3Dtrue)
2. **Comparison of neurons based on connectivity**: Science. 2012 Jul 27;337(6093):437-44. doi: 10.1126/science.1221762.
*The connectome of a decision-making neural network.*
Jarrell TA, Wang Y, Bloniarz AE, Brittin CA, Xu M, Thomson JN, Albertson DG, Hall DH, Emmons SW.
[link](http://science.sciencemag.org/content/337/6093/437.long)
3. **Comparison of neurons based on synapse distribution**: eLife. doi: 10.7554/eLife.16799
*Synaptic transmission parallels neuromodulation in a central food-intake circuit.*
Schlegel P, Texada MJ, Miroschnikow A, Schoofs A, Hückesfeld S, Peters M, … Pankratz MJ.
[link](https://elifesciences.org/content/5/e16799)
4. **Synapse flow centrality and segregation index**: eLife. doi: 10.7554/eLife.12059
*Quantitative neuroanatomy for connectomics in Drosophila.*
Schneider-Mizell CM, Gerhard S, Longair M, Kazimiers T, Li, Feng L, Zwart M … Cardona A.
[link](https://elifesciences.org/articles/12059)
## Contributing
1. Fork this repository
2. `git clone` it to your local machine
3. Install the full development dependencies with `pip install -r requirements.txt`
4. Install the package in editable mode with `pip install -e ".[all]"`
5. Create, `git add`, `git commit`, `git push`, and pull request your changes.
Run the tests locally with `pytest -v`.
Docstrings should use the [numpydoc](https://numpydoc.readthedocs.io/en/latest/format.html) format,
and make sure you include any relevant links and citations.
Unit tests should be [doctests](https://docs.python.org/3/library/doctest.html)
and/or use [pytest](https://docs.pytest.org/en/stable/) in the `./tests` directory.
Doctests have access to the `tmp_dir: pathlib.Path` variable,
which should be used if any files need to be written.
%prep
%autosetup -n navis-1.4.0
%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-navis -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Wed May 31 2023 Python_Bot <Python_Bot@openeuler.org> - 1.4.0-1
- Package Spec generated
|
