diff options
| author | CoprDistGit <infra@openeuler.org> | 2023-05-10 04:30:04 +0000 |
|---|---|---|
| committer | CoprDistGit <infra@openeuler.org> | 2023-05-10 04:30:04 +0000 |
| commit | 57173283b95291ebfbbf692adc909fb8894a3127 (patch) | |
| tree | 3aa7b0fe9b2c691193791fbd39b9f771f2791ed8 /python-bsb.spec | |
| parent | a3d2a050957c10aa2b0f0bda1534dfa9a05ab180 (diff) | |
automatic import of python-bsbopeneuler20.03
Diffstat (limited to 'python-bsb.spec')
| -rw-r--r-- | python-bsb.spec | 404 |
1 files changed, 404 insertions, 0 deletions
diff --git a/python-bsb.spec b/python-bsb.spec new file mode 100644 index 0000000..88e5a6c --- /dev/null +++ b/python-bsb.spec @@ -0,0 +1,404 @@ +%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 +[](https://github.com/psf/black) +[](https://bsb.readthedocs.io/en/latest/?badge=latest) +[](https://travis-ci.com/dbbs-lab/bsb) +[](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 +[](https://github.com/psf/black) +[](https://bsb.readthedocs.io/en/latest/?badge=latest) +[](https://travis-ci.com/dbbs-lab/bsb) +[](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 +[](https://github.com/psf/black) +[](https://bsb.readthedocs.io/en/latest/?badge=latest) +[](https://travis-ci.com/dbbs-lab/bsb) +[](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 <Python_Bot@openeuler.org> - 3.10.5-1 +- Package Spec generated |