automatic import of python-cxsystem2openeuler20.03

3 files changed, 581 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
index e69de29..fc0d6b1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1 @@
+/cxsystem2-2.1.2.0.tar.gz
diff --git a/python-cxsystem2.spec b/python-cxsystem2.spec
new file mode 100644
index 0000000..e33b66c
--- /dev/null
+++ b/python-cxsystem2.spec
@@ -0,0 +1,579 @@
+%global _empty_manifest_terminate_build 0
+Name:		python-cxsystem2
+Version:	2.1.2.0
+Release:	1
+Summary:	A cerebral cortex simulation framework
+License:	GPL v3.0
+URL:		https://github.com/VisualNeuroscience-UH/CxSystem2
+Source0:	https://mirrors.aliyun.com/pypi/web/packages/6e/6a/e1fdd9b9acf7db78a83f6776ca3e0e8093e62dd9840118252f26b9ebb379/cxsystem2-2.1.2.0.tar.gz
+BuildArch:	noarch
+
+Requires:	python3-wheel
+Requires:	python3-requests
+Requires:	python3-asn1crypto
+Requires:	python3-bcrypt
+Requires:	python3-brian2
+Requires:	python3-brian2genn
+Requires:	python3-cffi
+Requires:	python3-cryptography
+Requires:	python3-cycler
+Requires:	python3-cython
+Requires:	python3-django
+Requires:	python3-django-extensions
+Requires:	python3-django-sslserver
+Requires:	python3-docopt
+Requires:	python3-ipython
+Requires:	python3-jinja2
+Requires:	python3-kiwisolver
+Requires:	python3-markupsafe
+Requires:	python3-matplotlib
+Requires:	python3-mpmath
+Requires:	python3-numpy
+Requires:	python3-pandas
+Requires:	python3-ping3
+Requires:	python3-paramiko
+Requires:	python3-pycparser
+Requires:	python3-pynacl
+Requires:	python3-pyopenssl
+Requires:	python3-pyparsing
+Requires:	python3-dateutil
+Requires:	python3-pytz
+Requires:	python3-scipy
+Requires:	python3-scp
+Requires:	python3-six
+Requires:	python3-sqlparse
+Requires:	python3-sympy
+Requires:	python3-werkzeug
+Requires:	python3-sphinx
+Requires:	python3-sphinx-rtd-theme
+Requires:	python3-pyyaml
+
+%description
+<a href="https://github.com/VisualNeuroscience-UH/CxSystem2/blob/master/README.md"><img src="https://github.com/VisualNeuroscience-UH/CxSystem2/blob/master/data_config/icon/cxsystem_logo.png?sanitize=true" width="50%"></a>
+
+# CxSystem2, A Flexible Cortical Simulation Framework
+> Warning: CxSystem2 BUI is developed for using in a local environment and should not be installed on a publicly accessible server unless extra security measures are added on top of it
+
+[![License](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/blob/master/LICENSE)
+[![Github Issues](http://img.shields.io/github/issues/VisualNeuroscience-UH/CxSystem2/bug.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/issues?q=is%3Aopen+is%3Aissue+label%3Abug)
+[![Github Issues](http://img.shields.io/github/issues/VisualNeuroscience-UH/CxSystem2/enhancement.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/issues?q=is%3Aopen+is%3Aissue+label%3Aenhancement)
+[![Github Issues](http://img.shields.io/github/issues-pr/VisualNeuroscience-UH/CxSystem2.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/pulls)
+[![Documentation Status](https://readthedocs.org/projects/cxsystem2/badge/?version=latest)](https://cxsystem2.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://badge.fury.io/py/cxsystem2.svg)](https://badge.fury.io/py/cxsystem2)
+[![Build Status](https://travis-ci.org/VisualNeuroscience-UH/CxSystem2.svg?branch=master)](https://travis-ci.org/VisualNeuroscience-UH/CxSystem2)
+
+## Table of Contents
+
+- [Synopsis](#synopsis)
+- [Installation](#installation)
+    * [Windows](#windows)
+    * [Linux/Mac](#linuxmac)
+    * [Development](#development)
+- [Interfaces](#interfaces)
+    * [Browser User Interface (BUI)](#browser-user-interface-bui)
+    * [Command Line Interface (CLI)](#command-line-interface-cli)
+- [Documentation](#documentation)
+- [Citation](#citation)
+- [Support](#support)
+- [Team](#team)
+- [License](#license)
+
+## Synopsis
+
+CxSystem is a cerebral cortex simulation framework, which operates on personal computers. We have tested the simulation software with a simplified version of a comprehensive cortical microcircuit model [1], which is available as configuration file. 
+
+The CxSystem aims at easy testing and buildup of diverse models at single cell resolution.  Implemented on the top of the Python-based [Brian2 simulator](https://github.com/brian-team/brian2), CxSystem supports the main goal of Brian, i.e. minimizing development time, by providing the user with a simplified interface.
+
+The preliminary version of this software has been developed at Aalto University 2012-2015 [2], and the full version at the Hospital District of Helsinki and Uusimaa and University of Helsinki 2013-2017. The software is distributed under the terms of the GNU General Public License, Copyright 2017 Vafa Andalibi, Henri Hokkanen and Simo Vanni.
+
+
+## Installation
+
+We highly recommend installing `CxSystem2` on a virtual environment. Use the following commands to install a Python3 virtual environment and install CxSystem: 
+
+### Windows
+
+ Make sure you have python 3.5 or above. To create activate a `venv` in windows at `~/CX2` (you can deactivate the environment with the command `deactivate` and reactivate later by running the second command):
+
+```shell
+C:\> python --version
+Python 3.7.4
+C:\> python3 -m venv %userprofile%\CX2
+C:\> %userprofile%\CX2\Scripts\activate
+(CX2) C:\> pip install --upgrade setuptools
+(CX2) C:\> pip install -U cxsystem2
+```
+
+Moreover, to use the C++ standalone device on Windows, install the [Visual C++ Build Tools 2015](https://www.microsoft.com/en-us/download/details.aspx?id=48159).
+
+### Linux/Mac
+
+Make sure you have python 3.5 or above. To create activate a `venv` in Linux/Mac at `~/CX2` (you can deactivate the environment with the command `deactivate` and reactivate later by running the second command):
+
+```shell
+$ python --version
+Python 3.7.4
+$ python3 -m venv ~/CX2
+$ source ~/CX2/bin/activate
+(CX2) $ pip install --upgrade setuptools
+(CX2) $ pip install -U cxsystem2
+```
+
+### Development
+
+To develop `CxSystem2`, after cloning the repository install it with the following commands:
+
+```shell
+(CX2) $ git clone https://github.com/VisualNeuroscience-UH/CxSystem2
+(CX2) $ cd CxSystem2
+(CX2) $ pip install --upgrade setuptools
+(CX2) $ pip install -r requirements.txt
+(CX2) $ pip install -U -e .
+```
+
+With this method any change to the code will be reflected on the package immediately.
+
+## Interfaces
+
+`CxSystem2` comes with two interfaces:
+
+### Browser User Interface (BUI)
+
+CxSystem's BUI is built to provide users with an interactive environment for changing the parameters for simulations.
+
+### Command Line Interface (CLI)
+
+Beside the BUI, Some of the main functionalities of the `CxSystem2` are available in terminal, including the BUI itself. All of the following commands have built-in documentations available with `-h` or `--help` flags:
+
+#### `cxsystem2`
+
+This command (all in lower letters and case sensitive) can be used to run a simulation locally using anatomy and physiology configuration files.
+
+#### `cxserver`
+
+This command will run the `CxSystem2` BUI django server.
+
+#### `cxconfig`
+
+CxSystem2 supports `csv` and `json` for importing/exporting configuration files. To convert the configuration files, use the `cxconfig` and pass the path to the configuration file path as its argument. This command recognizes the file type and convert it to the alternative extension.
+
+#### `cxcluster`
+
+Use `cxcluster` to download the results from the cluster. `cxcluster` takes in one argument which is the path to the metadata file saved as a result of cluster-run submission. For convenience, at the end of a cluster-run job submission, `CxSystem2` prints the command that should be run to retrieve the result.
+
+#### `cxvisualize`
+
+This command can be used to visualize the result of the simulation using `visimpl` visualizer. ViSimpl binaries are available at the Modeling and Virtual Reality Group [download page](https://vg-lab.es/visimpl/) at  Universidad Rey Juan Carlos and Universidad Politécnica de Madrid. This command can also be used to generate a pdf of rasterplots from a set of simulations.
+
+
+
+## Documentation
+
+You can access the documentation of the CxSystem2 at [cxsystem2.readthedocs.io](https://cxsystem2.readthedocs.io).
+
+## Citation
+
+If you use CxSystem2 for your work, we kindly ask you to cite any of our related articles:
+
+```
+Andalibi, V., Hokkanen, H., Vanni, S., Controlling complexity of cerebral cortex simulations—I: CxSystem, a flexible cortical simulation framework, 2019, Neural computation
+```
+<br>
+
+```
+Hokkanen, H., Andalibi, V., Vanni, S., Controlling complexity of cerebral cortex simulations—II: Streamlined microcircuits, 2019, Neural computation
+```
+
+## Support
+
+You are encouraged to use <a href="https://github.com/VisualNeuroscience-UH/CxSystem2/issues" target="_blank">Github's Issues</a> to report bugs, or request enhancements or new features.
+
+## Team
+
+- [Vafa Andalibi](https://www.andalibi.me)
+- [Henri Hokkanen](https://github.com/henhok)
+- [Simo Vanni](https://scholar.google.fi/citations?user=nRiUf30AAAAJ&hl=en)
+
+## License
+
+[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
+
+- **[GPL-3-Clause](https://www.gnu.org/licenses/gpl-3.0.en.html)**
+- Copyright 2019 © <a href="http://www.helsinki.fi/visualneuroscience/" target="_blank">HUS Helsinki University Hospital</a>.
+
+***
+<sub>[1] Markram, H., Muller, E., Ramaswamy, S., Reimann, M. W., Abdellah, M., Sanchez, C. A., … Schürmann, F. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell, 163(2), 456–492. http://doi.org/10.1016/j.cell.2015.09.029</sub>
+
+<sub>[2]Heikkinen, H., Sharifian, F., Vigário, R., & Vanni, S. (2015). Feedback to distal dendrites links fMRI signals to neural receptive fields in a spiking network model of the visual cortex. Journal of Neurophysiology, 114(1), 57–69. http://doi.org/10.1152/jn.00169.2015</sub>
+
+
+%package -n python3-cxsystem2
+Summary:	A cerebral cortex simulation framework
+Provides:	python-cxsystem2
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-cxsystem2
+<a href="https://github.com/VisualNeuroscience-UH/CxSystem2/blob/master/README.md"><img src="https://github.com/VisualNeuroscience-UH/CxSystem2/blob/master/data_config/icon/cxsystem_logo.png?sanitize=true" width="50%"></a>
+
+# CxSystem2, A Flexible Cortical Simulation Framework
+> Warning: CxSystem2 BUI is developed for using in a local environment and should not be installed on a publicly accessible server unless extra security measures are added on top of it
+
+[![License](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/blob/master/LICENSE)
+[![Github Issues](http://img.shields.io/github/issues/VisualNeuroscience-UH/CxSystem2/bug.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/issues?q=is%3Aopen+is%3Aissue+label%3Abug)
+[![Github Issues](http://img.shields.io/github/issues/VisualNeuroscience-UH/CxSystem2/enhancement.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/issues?q=is%3Aopen+is%3Aissue+label%3Aenhancement)
+[![Github Issues](http://img.shields.io/github/issues-pr/VisualNeuroscience-UH/CxSystem2.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/pulls)
+[![Documentation Status](https://readthedocs.org/projects/cxsystem2/badge/?version=latest)](https://cxsystem2.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://badge.fury.io/py/cxsystem2.svg)](https://badge.fury.io/py/cxsystem2)
+[![Build Status](https://travis-ci.org/VisualNeuroscience-UH/CxSystem2.svg?branch=master)](https://travis-ci.org/VisualNeuroscience-UH/CxSystem2)
+
+## Table of Contents
+
+- [Synopsis](#synopsis)
+- [Installation](#installation)
+    * [Windows](#windows)
+    * [Linux/Mac](#linuxmac)
+    * [Development](#development)
+- [Interfaces](#interfaces)
+    * [Browser User Interface (BUI)](#browser-user-interface-bui)
+    * [Command Line Interface (CLI)](#command-line-interface-cli)
+- [Documentation](#documentation)
+- [Citation](#citation)
+- [Support](#support)
+- [Team](#team)
+- [License](#license)
+
+## Synopsis
+
+CxSystem is a cerebral cortex simulation framework, which operates on personal computers. We have tested the simulation software with a simplified version of a comprehensive cortical microcircuit model [1], which is available as configuration file. 
+
+The CxSystem aims at easy testing and buildup of diverse models at single cell resolution.  Implemented on the top of the Python-based [Brian2 simulator](https://github.com/brian-team/brian2), CxSystem supports the main goal of Brian, i.e. minimizing development time, by providing the user with a simplified interface.
+
+The preliminary version of this software has been developed at Aalto University 2012-2015 [2], and the full version at the Hospital District of Helsinki and Uusimaa and University of Helsinki 2013-2017. The software is distributed under the terms of the GNU General Public License, Copyright 2017 Vafa Andalibi, Henri Hokkanen and Simo Vanni.
+
+
+## Installation
+
+We highly recommend installing `CxSystem2` on a virtual environment. Use the following commands to install a Python3 virtual environment and install CxSystem: 
+
+### Windows
+
+ Make sure you have python 3.5 or above. To create activate a `venv` in windows at `~/CX2` (you can deactivate the environment with the command `deactivate` and reactivate later by running the second command):
+
+```shell
+C:\> python --version
+Python 3.7.4
+C:\> python3 -m venv %userprofile%\CX2
+C:\> %userprofile%\CX2\Scripts\activate
+(CX2) C:\> pip install --upgrade setuptools
+(CX2) C:\> pip install -U cxsystem2
+```
+
+Moreover, to use the C++ standalone device on Windows, install the [Visual C++ Build Tools 2015](https://www.microsoft.com/en-us/download/details.aspx?id=48159).
+
+### Linux/Mac
+
+Make sure you have python 3.5 or above. To create activate a `venv` in Linux/Mac at `~/CX2` (you can deactivate the environment with the command `deactivate` and reactivate later by running the second command):
+
+```shell
+$ python --version
+Python 3.7.4
+$ python3 -m venv ~/CX2
+$ source ~/CX2/bin/activate
+(CX2) $ pip install --upgrade setuptools
+(CX2) $ pip install -U cxsystem2
+```
+
+### Development
+
+To develop `CxSystem2`, after cloning the repository install it with the following commands:
+
+```shell
+(CX2) $ git clone https://github.com/VisualNeuroscience-UH/CxSystem2
+(CX2) $ cd CxSystem2
+(CX2) $ pip install --upgrade setuptools
+(CX2) $ pip install -r requirements.txt
+(CX2) $ pip install -U -e .
+```
+
+With this method any change to the code will be reflected on the package immediately.
+
+## Interfaces
+
+`CxSystem2` comes with two interfaces:
+
+### Browser User Interface (BUI)
+
+CxSystem's BUI is built to provide users with an interactive environment for changing the parameters for simulations.
+
+### Command Line Interface (CLI)
+
+Beside the BUI, Some of the main functionalities of the `CxSystem2` are available in terminal, including the BUI itself. All of the following commands have built-in documentations available with `-h` or `--help` flags:
+
+#### `cxsystem2`
+
+This command (all in lower letters and case sensitive) can be used to run a simulation locally using anatomy and physiology configuration files.
+
+#### `cxserver`
+
+This command will run the `CxSystem2` BUI django server.
+
+#### `cxconfig`
+
+CxSystem2 supports `csv` and `json` for importing/exporting configuration files. To convert the configuration files, use the `cxconfig` and pass the path to the configuration file path as its argument. This command recognizes the file type and convert it to the alternative extension.
+
+#### `cxcluster`
+
+Use `cxcluster` to download the results from the cluster. `cxcluster` takes in one argument which is the path to the metadata file saved as a result of cluster-run submission. For convenience, at the end of a cluster-run job submission, `CxSystem2` prints the command that should be run to retrieve the result.
+
+#### `cxvisualize`
+
+This command can be used to visualize the result of the simulation using `visimpl` visualizer. ViSimpl binaries are available at the Modeling and Virtual Reality Group [download page](https://vg-lab.es/visimpl/) at  Universidad Rey Juan Carlos and Universidad Politécnica de Madrid. This command can also be used to generate a pdf of rasterplots from a set of simulations.
+
+
+
+## Documentation
+
+You can access the documentation of the CxSystem2 at [cxsystem2.readthedocs.io](https://cxsystem2.readthedocs.io).
+
+## Citation
+
+If you use CxSystem2 for your work, we kindly ask you to cite any of our related articles:
+
+```
+Andalibi, V., Hokkanen, H., Vanni, S., Controlling complexity of cerebral cortex simulations—I: CxSystem, a flexible cortical simulation framework, 2019, Neural computation
+```
+<br>
+
+```
+Hokkanen, H., Andalibi, V., Vanni, S., Controlling complexity of cerebral cortex simulations—II: Streamlined microcircuits, 2019, Neural computation
+```
+
+## Support
+
+You are encouraged to use <a href="https://github.com/VisualNeuroscience-UH/CxSystem2/issues" target="_blank">Github's Issues</a> to report bugs, or request enhancements or new features.
+
+## Team
+
+- [Vafa Andalibi](https://www.andalibi.me)
+- [Henri Hokkanen](https://github.com/henhok)
+- [Simo Vanni](https://scholar.google.fi/citations?user=nRiUf30AAAAJ&hl=en)
+
+## License
+
+[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
+
+- **[GPL-3-Clause](https://www.gnu.org/licenses/gpl-3.0.en.html)**
+- Copyright 2019 © <a href="http://www.helsinki.fi/visualneuroscience/" target="_blank">HUS Helsinki University Hospital</a>.
+
+***
+<sub>[1] Markram, H., Muller, E., Ramaswamy, S., Reimann, M. W., Abdellah, M., Sanchez, C. A., … Schürmann, F. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell, 163(2), 456–492. http://doi.org/10.1016/j.cell.2015.09.029</sub>
+
+<sub>[2]Heikkinen, H., Sharifian, F., Vigário, R., & Vanni, S. (2015). Feedback to distal dendrites links fMRI signals to neural receptive fields in a spiking network model of the visual cortex. Journal of Neurophysiology, 114(1), 57–69. http://doi.org/10.1152/jn.00169.2015</sub>
+
+
+%package help
+Summary:	Development documents and examples for cxsystem2
+Provides:	python3-cxsystem2-doc
+%description help
+<a href="https://github.com/VisualNeuroscience-UH/CxSystem2/blob/master/README.md"><img src="https://github.com/VisualNeuroscience-UH/CxSystem2/blob/master/data_config/icon/cxsystem_logo.png?sanitize=true" width="50%"></a>
+
+# CxSystem2, A Flexible Cortical Simulation Framework
+> Warning: CxSystem2 BUI is developed for using in a local environment and should not be installed on a publicly accessible server unless extra security measures are added on top of it
+
+[![License](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/blob/master/LICENSE)
+[![Github Issues](http://img.shields.io/github/issues/VisualNeuroscience-UH/CxSystem2/bug.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/issues?q=is%3Aopen+is%3Aissue+label%3Abug)
+[![Github Issues](http://img.shields.io/github/issues/VisualNeuroscience-UH/CxSystem2/enhancement.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/issues?q=is%3Aopen+is%3Aissue+label%3Aenhancement)
+[![Github Issues](http://img.shields.io/github/issues-pr/VisualNeuroscience-UH/CxSystem2.svg)](https://github.com/VisualNeuroscience-UH/CxSystem2/pulls)
+[![Documentation Status](https://readthedocs.org/projects/cxsystem2/badge/?version=latest)](https://cxsystem2.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://badge.fury.io/py/cxsystem2.svg)](https://badge.fury.io/py/cxsystem2)
+[![Build Status](https://travis-ci.org/VisualNeuroscience-UH/CxSystem2.svg?branch=master)](https://travis-ci.org/VisualNeuroscience-UH/CxSystem2)
+
+## Table of Contents
+
+- [Synopsis](#synopsis)
+- [Installation](#installation)
+    * [Windows](#windows)
+    * [Linux/Mac](#linuxmac)
+    * [Development](#development)
+- [Interfaces](#interfaces)
+    * [Browser User Interface (BUI)](#browser-user-interface-bui)
+    * [Command Line Interface (CLI)](#command-line-interface-cli)
+- [Documentation](#documentation)
+- [Citation](#citation)
+- [Support](#support)
+- [Team](#team)
+- [License](#license)
+
+## Synopsis
+
+CxSystem is a cerebral cortex simulation framework, which operates on personal computers. We have tested the simulation software with a simplified version of a comprehensive cortical microcircuit model [1], which is available as configuration file. 
+
+The CxSystem aims at easy testing and buildup of diverse models at single cell resolution.  Implemented on the top of the Python-based [Brian2 simulator](https://github.com/brian-team/brian2), CxSystem supports the main goal of Brian, i.e. minimizing development time, by providing the user with a simplified interface.
+
+The preliminary version of this software has been developed at Aalto University 2012-2015 [2], and the full version at the Hospital District of Helsinki and Uusimaa and University of Helsinki 2013-2017. The software is distributed under the terms of the GNU General Public License, Copyright 2017 Vafa Andalibi, Henri Hokkanen and Simo Vanni.
+
+
+## Installation
+
+We highly recommend installing `CxSystem2` on a virtual environment. Use the following commands to install a Python3 virtual environment and install CxSystem: 
+
+### Windows
+
+ Make sure you have python 3.5 or above. To create activate a `venv` in windows at `~/CX2` (you can deactivate the environment with the command `deactivate` and reactivate later by running the second command):
+
+```shell
+C:\> python --version
+Python 3.7.4
+C:\> python3 -m venv %userprofile%\CX2
+C:\> %userprofile%\CX2\Scripts\activate
+(CX2) C:\> pip install --upgrade setuptools
+(CX2) C:\> pip install -U cxsystem2
+```
+
+Moreover, to use the C++ standalone device on Windows, install the [Visual C++ Build Tools 2015](https://www.microsoft.com/en-us/download/details.aspx?id=48159).
+
+### Linux/Mac
+
+Make sure you have python 3.5 or above. To create activate a `venv` in Linux/Mac at `~/CX2` (you can deactivate the environment with the command `deactivate` and reactivate later by running the second command):
+
+```shell
+$ python --version
+Python 3.7.4
+$ python3 -m venv ~/CX2
+$ source ~/CX2/bin/activate
+(CX2) $ pip install --upgrade setuptools
+(CX2) $ pip install -U cxsystem2
+```
+
+### Development
+
+To develop `CxSystem2`, after cloning the repository install it with the following commands:
+
+```shell
+(CX2) $ git clone https://github.com/VisualNeuroscience-UH/CxSystem2
+(CX2) $ cd CxSystem2
+(CX2) $ pip install --upgrade setuptools
+(CX2) $ pip install -r requirements.txt
+(CX2) $ pip install -U -e .
+```
+
+With this method any change to the code will be reflected on the package immediately.
+
+## Interfaces
+
+`CxSystem2` comes with two interfaces:
+
+### Browser User Interface (BUI)
+
+CxSystem's BUI is built to provide users with an interactive environment for changing the parameters for simulations.
+
+### Command Line Interface (CLI)
+
+Beside the BUI, Some of the main functionalities of the `CxSystem2` are available in terminal, including the BUI itself. All of the following commands have built-in documentations available with `-h` or `--help` flags:
+
+#### `cxsystem2`
+
+This command (all in lower letters and case sensitive) can be used to run a simulation locally using anatomy and physiology configuration files.
+
+#### `cxserver`
+
+This command will run the `CxSystem2` BUI django server.
+
+#### `cxconfig`
+
+CxSystem2 supports `csv` and `json` for importing/exporting configuration files. To convert the configuration files, use the `cxconfig` and pass the path to the configuration file path as its argument. This command recognizes the file type and convert it to the alternative extension.
+
+#### `cxcluster`
+
+Use `cxcluster` to download the results from the cluster. `cxcluster` takes in one argument which is the path to the metadata file saved as a result of cluster-run submission. For convenience, at the end of a cluster-run job submission, `CxSystem2` prints the command that should be run to retrieve the result.
+
+#### `cxvisualize`
+
+This command can be used to visualize the result of the simulation using `visimpl` visualizer. ViSimpl binaries are available at the Modeling and Virtual Reality Group [download page](https://vg-lab.es/visimpl/) at  Universidad Rey Juan Carlos and Universidad Politécnica de Madrid. This command can also be used to generate a pdf of rasterplots from a set of simulations.
+
+
+
+## Documentation
+
+You can access the documentation of the CxSystem2 at [cxsystem2.readthedocs.io](https://cxsystem2.readthedocs.io).
+
+## Citation
+
+If you use CxSystem2 for your work, we kindly ask you to cite any of our related articles:
+
+```
+Andalibi, V., Hokkanen, H., Vanni, S., Controlling complexity of cerebral cortex simulations—I: CxSystem, a flexible cortical simulation framework, 2019, Neural computation
+```
+<br>
+
+```
+Hokkanen, H., Andalibi, V., Vanni, S., Controlling complexity of cerebral cortex simulations—II: Streamlined microcircuits, 2019, Neural computation
+```
+
+## Support
+
+You are encouraged to use <a href="https://github.com/VisualNeuroscience-UH/CxSystem2/issues" target="_blank">Github's Issues</a> to report bugs, or request enhancements or new features.
+
+## Team
+
+- [Vafa Andalibi](https://www.andalibi.me)
+- [Henri Hokkanen](https://github.com/henhok)
+- [Simo Vanni](https://scholar.google.fi/citations?user=nRiUf30AAAAJ&hl=en)
+
+## License
+
+[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
+
+- **[GPL-3-Clause](https://www.gnu.org/licenses/gpl-3.0.en.html)**
+- Copyright 2019 © <a href="http://www.helsinki.fi/visualneuroscience/" target="_blank">HUS Helsinki University Hospital</a>.
+
+***
+<sub>[1] Markram, H., Muller, E., Ramaswamy, S., Reimann, M. W., Abdellah, M., Sanchez, C. A., … Schürmann, F. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell, 163(2), 456–492. http://doi.org/10.1016/j.cell.2015.09.029</sub>
+
+<sub>[2]Heikkinen, H., Sharifian, F., Vigário, R., & Vanni, S. (2015). Feedback to distal dendrites links fMRI signals to neural receptive fields in a spiking network model of the visual cortex. Journal of Neurophysiology, 114(1), 57–69. http://doi.org/10.1152/jn.00169.2015</sub>
+
+
+%prep
+%autosetup -n cxsystem2-2.1.2.0
+
+%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-cxsystem2 -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Tue Jun 20 2023 Python_Bot <Python_Bot@openeuler.org> - 2.1.2.0-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..bdd8897
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+a755dec3d5f94850199a4fe6f449b851  cxsystem2-2.1.2.0.tar.gz