%global _empty_manifest_terminate_build 0 Name: python-bsb Version: 3.10.5 Release: 1 Summary: A package for modelling morphologically detailed neuronal microcircuits. License: GPLv3 URL: https://github.com/dbbs-lab/bsb Source0: https://mirrors.nju.edu.cn/pypi/web/packages/92/24/d3e18dd8cb90e7d3666df368268ba25d0e548e51f2fdb536358ed2a322fb/bsb-3.10.5.tar.gz BuildArch: noarch Requires: python3-h5py Requires: python3-numpy Requires: python3-scipy Requires: python3-scikit-learn Requires: python3-plotly Requires: python3-colour Requires: python3-errr Requires: python3-rtree Requires: python3-psutil Requires: python3-sphinx Requires: python3-furo Requires: python3-pre-commit Requires: python3-black Requires: python3-nrn-subprocess Requires: python3-mpi4py Requires: python3-dbbs-models Requires: python3-nrn-patch %description [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Documentation Status](https://readthedocs.org/projects/bsb/badge/?version=latest)](https://bsb.readthedocs.io/en/latest/?badge=latest) [![Build Status](https://travis-ci.com/dbbs-lab/bsb.svg?branch=master)](https://travis-ci.com/dbbs-lab/bsb) [![codecov](https://codecov.io/gh/dbbs-lab/bsb/branch/master/graph/badge.svg)](https://codecov.io/gh/dbbs-lab/bsb) **Note:** The scaffold framework is still under heavy development. Please check the **_Known Issues_** section at the bottom for important issues that fell victim to our deadlines and will be solved at a later date. # BSB: A scaffold modelling framework This package is intended to facilitate spatially, topologically and morphologically detailed simulations of brain regions developed by the Department of Brain and Behavioral Sciences at the University of Pavia. ## Installation ### pip This software can be installed as a Python package from PyPI through pip: ``` pip install bsb ``` ### Developers Developers best use pip's *editable* install. This creates a live link between the installed package and the local git repository: ``` git clone git@github.com:dbbs-lab/bsb cd bsb pip install -e .[dev] pre-commit install ``` ## Usage The scaffold framework can be used through the command line interface or as a python package. ### Command line interface (CLI) Run the framework in the command line with subcommand `compile` to compile a network architecture. ``` bsb --config=mouse_cerebellum_cortex_noTouch.json compile -x=200 -z=200 -p ``` To run with different configurations, change the config argument to the relative path of a .json config file. The `-p` flag indicates that the compiled network should be plotted afterwards and can be omitted. ### Python package The central object is the `bsb.core.Scaffold` class. This object requires a `bsb.config.ScaffoldConfig` instance for its construction. To emulate the CLI functionality you can use the `JSONConfig` class and provide the relative path to the configuration file. ```python from bsb import Scaffold from bsb.config import JSONConfig config = new JSONConfig(file='mouse_cerebellum_cortex_noTouch.json') scaffoldInstance = new Scaffold(config) ``` This scaffold instance can then be used to perform the subcommands available in the CLI by calling their corresponding functions: ```python scaffoldInstance.compile_network() ``` #### Plotting network architecture After calling `compile_network` the scaffold instance can be plotted: ```python scaffoldInstance.plot_network_cache() ``` # Contributing All contributions are very much welcome. Take a look at the [contribution guide](CONTRIBUTING.md) # Known issues ## No configuration serialization When modifying the config object through scripts and then saving it to file, you'll store the original configuration file text, and you won't actually serialize the modified object We will fix this by version 4.0 ## If MPI is installed but mpi4py is not undefined behavior may occur The amount of NEST virtual processes is determined by using mpi4py to get the amount of MPI processes. But if the package is not installed it is assumed no MPI simulations will be ran and the amount of virtual processes might be lower than expected when used in combination with OpenMP. Be sure to `pip install` using the `[MPI]` requirement tag. %package -n python3-bsb Summary: A package for modelling morphologically detailed neuronal microcircuits. Provides: python-bsb BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-bsb [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Documentation Status](https://readthedocs.org/projects/bsb/badge/?version=latest)](https://bsb.readthedocs.io/en/latest/?badge=latest) [![Build Status](https://travis-ci.com/dbbs-lab/bsb.svg?branch=master)](https://travis-ci.com/dbbs-lab/bsb) [![codecov](https://codecov.io/gh/dbbs-lab/bsb/branch/master/graph/badge.svg)](https://codecov.io/gh/dbbs-lab/bsb) **Note:** The scaffold framework is still under heavy development. Please check the **_Known Issues_** section at the bottom for important issues that fell victim to our deadlines and will be solved at a later date. # BSB: A scaffold modelling framework This package is intended to facilitate spatially, topologically and morphologically detailed simulations of brain regions developed by the Department of Brain and Behavioral Sciences at the University of Pavia. ## Installation ### pip This software can be installed as a Python package from PyPI through pip: ``` pip install bsb ``` ### Developers Developers best use pip's *editable* install. This creates a live link between the installed package and the local git repository: ``` git clone git@github.com:dbbs-lab/bsb cd bsb pip install -e .[dev] pre-commit install ``` ## Usage The scaffold framework can be used through the command line interface or as a python package. ### Command line interface (CLI) Run the framework in the command line with subcommand `compile` to compile a network architecture. ``` bsb --config=mouse_cerebellum_cortex_noTouch.json compile -x=200 -z=200 -p ``` To run with different configurations, change the config argument to the relative path of a .json config file. The `-p` flag indicates that the compiled network should be plotted afterwards and can be omitted. ### Python package The central object is the `bsb.core.Scaffold` class. This object requires a `bsb.config.ScaffoldConfig` instance for its construction. To emulate the CLI functionality you can use the `JSONConfig` class and provide the relative path to the configuration file. ```python from bsb import Scaffold from bsb.config import JSONConfig config = new JSONConfig(file='mouse_cerebellum_cortex_noTouch.json') scaffoldInstance = new Scaffold(config) ``` This scaffold instance can then be used to perform the subcommands available in the CLI by calling their corresponding functions: ```python scaffoldInstance.compile_network() ``` #### Plotting network architecture After calling `compile_network` the scaffold instance can be plotted: ```python scaffoldInstance.plot_network_cache() ``` # Contributing All contributions are very much welcome. Take a look at the [contribution guide](CONTRIBUTING.md) # Known issues ## No configuration serialization When modifying the config object through scripts and then saving it to file, you'll store the original configuration file text, and you won't actually serialize the modified object We will fix this by version 4.0 ## If MPI is installed but mpi4py is not undefined behavior may occur The amount of NEST virtual processes is determined by using mpi4py to get the amount of MPI processes. But if the package is not installed it is assumed no MPI simulations will be ran and the amount of virtual processes might be lower than expected when used in combination with OpenMP. Be sure to `pip install` using the `[MPI]` requirement tag. %package help Summary: Development documents and examples for bsb Provides: python3-bsb-doc %description help [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Documentation Status](https://readthedocs.org/projects/bsb/badge/?version=latest)](https://bsb.readthedocs.io/en/latest/?badge=latest) [![Build Status](https://travis-ci.com/dbbs-lab/bsb.svg?branch=master)](https://travis-ci.com/dbbs-lab/bsb) [![codecov](https://codecov.io/gh/dbbs-lab/bsb/branch/master/graph/badge.svg)](https://codecov.io/gh/dbbs-lab/bsb) **Note:** The scaffold framework is still under heavy development. Please check the **_Known Issues_** section at the bottom for important issues that fell victim to our deadlines and will be solved at a later date. # BSB: A scaffold modelling framework This package is intended to facilitate spatially, topologically and morphologically detailed simulations of brain regions developed by the Department of Brain and Behavioral Sciences at the University of Pavia. ## Installation ### pip This software can be installed as a Python package from PyPI through pip: ``` pip install bsb ``` ### Developers Developers best use pip's *editable* install. This creates a live link between the installed package and the local git repository: ``` git clone git@github.com:dbbs-lab/bsb cd bsb pip install -e .[dev] pre-commit install ``` ## Usage The scaffold framework can be used through the command line interface or as a python package. ### Command line interface (CLI) Run the framework in the command line with subcommand `compile` to compile a network architecture. ``` bsb --config=mouse_cerebellum_cortex_noTouch.json compile -x=200 -z=200 -p ``` To run with different configurations, change the config argument to the relative path of a .json config file. The `-p` flag indicates that the compiled network should be plotted afterwards and can be omitted. ### Python package The central object is the `bsb.core.Scaffold` class. This object requires a `bsb.config.ScaffoldConfig` instance for its construction. To emulate the CLI functionality you can use the `JSONConfig` class and provide the relative path to the configuration file. ```python from bsb import Scaffold from bsb.config import JSONConfig config = new JSONConfig(file='mouse_cerebellum_cortex_noTouch.json') scaffoldInstance = new Scaffold(config) ``` This scaffold instance can then be used to perform the subcommands available in the CLI by calling their corresponding functions: ```python scaffoldInstance.compile_network() ``` #### Plotting network architecture After calling `compile_network` the scaffold instance can be plotted: ```python scaffoldInstance.plot_network_cache() ``` # Contributing All contributions are very much welcome. Take a look at the [contribution guide](CONTRIBUTING.md) # Known issues ## No configuration serialization When modifying the config object through scripts and then saving it to file, you'll store the original configuration file text, and you won't actually serialize the modified object We will fix this by version 4.0 ## If MPI is installed but mpi4py is not undefined behavior may occur The amount of NEST virtual processes is determined by using mpi4py to get the amount of MPI processes. But if the package is not installed it is assumed no MPI simulations will be ran and the amount of virtual processes might be lower than expected when used in combination with OpenMP. Be sure to `pip install` using the `[MPI]` requirement tag. %prep %autosetup -n bsb-3.10.5 %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-bsb -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Wed May 10 2023 Python_Bot - 3.10.5-1 - Package Spec generated