=========
pykinetic
=========
------------------------------------------------------------------
A python library and command line tools for microkinetic modelling
------------------------------------------------------------------
.. image:: https://zenodo.org/badge/333841133.svg
:target: https://zenodo.org/badge/latestdoi/333841133
.. project-description-start
Pykinetic is a project that aims to facilitate the automation and generation
of kinetic and microkinetic models. Pykinetic acts as an intermediate layer
between the user and the mathematical model that is then simulated to obtain the
kinetic data. This functionality can be done either through the use of the
pykinetic python library or through the use of the command line apps:
"pykinetic-model.py" and "pykinetic-scan.py". The minimal source code to run the
simulation is the output of pykinetic and currently python and c++ are supported.
Compiling and executing that code leads to the simulation of the chemical system.
.. project-description-end
.. contents::
:backlinks: none
:depth: 2
:local:
Getting Started
---------------
These instructions will get you a copy of the project up and running on your
local machine.
.. setup-instructions-start
Prerequisites
.............
- python >= 3.6 (3.7.3 or higher recommended)
- python library: setuptools
- python library: numpy (optional, needed to run the generated python scripts)
- python library: scipy (optional, needed to run the generated python scripts)
- c++ library: boost (optional, needed to run the generated c++ scripts)
Note: proper documentation installation of the c++ library is being
currently being reviewed.
Installing the dependencies
...........................
python3.7 installation in Ubuntu 18.04 LTS
.. code:: shell-session
$ sudo apt-get update
$ sudo apt-get install python3.7 python3.7-dev
If for any reason it is not reachable:
.. code:: shell-session
$ sudo add-apt-repository ppa:deadsnakes/ppa
$ sudo apt-get update
$ sudo apt-get install python3.7 python3.7-dev
Now you can skip the next step if you don't want to set up a virtual environment
the lines below correspond to python3.7 but can be also applied to python3.6 or
higher (Remember to change "my_venv" for the actual path of the directory where
you want the virtual environment)
.. code:: shell-session
$ sudo apt-get install python3.7-venv
$ python3.7 -m venv my_venv
$ source my_venv/bin/activate
In the case of creating a virtual environment and running the
previous "source" command, anytime you write "python" it will act as an alias
for "python3.7" or whichever python executable you used for the virtual environment.
(To leave the virtual environment run the "deactivate" command at anytime)
If you have not created a virtual environment, all the following commands must
explicitly use the python executable in which you are going to install the
the package.
Now we install the python default installer pip in our virtual environment
.. code:: shell-session
$ python -m pip install pip
$ python -m pip install --upgrade pip
$ python -m pip install setuptools
If it proceeded without any errors (pip and setuptools should already be
installed) otherwise please check the `pip`_ documentation
.. _pip: https://pip.pypa.io/en/stable/installing/
Now to install the optional dependencies (Skip if you do not want them):
.. code:: shell-session
$ python -m pip install numpy scipy
$ sudo apt-get install libboost-dev
Installing pykinetic
....................
Get the source code from github through git and install it.
.. code:: shell-session
$ git clone https://github.com/maserasgroup-repo/pykinetic.git pykinetic
$ python -m pip install pykinetic/
If you do not have git or do prefer to download manually the source
code as a .zip or .tar.gz do it install it.
.. code:: shell-session
$ python -m pip install pykinetic-0.1.0.tar.gz
..
Note: If you prefer to unpack it you can do it but it is not needed
Running the tests
.................
After installing you should be able to run the tests:
.. code:: shell-session
$ python -m unittest -v pykinetic.tests
Uninstalling pykinetic
......................
.. code:: shell-session
$ python -m pip uninstall pykinetic
.. setup-instructions-end
Developed with
--------------
- python 3.7.3
- Ubuntu 16.04 LTS and Ubuntu 18.04 LTS
Examples
--------
Please open the `Examples.rst <Examples.rst>`_ file in github to visualize the
basic usage examples or read the documentation.
Authors
-------
.. project-authors-start
List of main developers and contact emails:
* Raúl Pérez-Soto [
`ORCID <https://orcid.org/0000-0002-6237-2155>`__ ,
`Github <https://github.com/rperezsoto>`__ ,
`email <rperezsoto.research@gmail.com>`__ ]
* Sergio Pablo-García [
`ORCID <https://orcid.org/0000-0002-3327-9285>`__ ,
`Github <https://github.com/spgarcica>`__ ,
`email <spgarcica@gmail.com>`__]
* María Besora [
`ORCID <http://orcid.org/0000-0002-6656-5827>`__ ,
`Github <https://github.com/BesoraMaria>`__ ,
`email <maria.besora@urv.cat>`__ ]
* Feliu Maseras [
`ORCID <http://orcid.org/0000-0001-8806-2019>`__ ,
`Github <https://github.com/maserasgroup-repo>`__ ,
`email <fmaseras@iciq.es>`__]
.. project-authors-end
License
-------
.. project-license-start
pykinetic is freely available under an `MIT <https://opensource.org/licenses/MIT>`__ License
.. project-license-end
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"description": "=========\npykinetic\n=========\n\n------------------------------------------------------------------\nA python library and command line tools for microkinetic modelling\n------------------------------------------------------------------\n\n.. image:: https://zenodo.org/badge/333841133.svg\n :target: https://zenodo.org/badge/latestdoi/333841133\n\n.. project-description-start\n\nPykinetic is a project that aims to facilitate the automation and generation \nof kinetic and microkinetic models. Pykinetic acts as an intermediate layer \nbetween the user and the mathematical model that is then simulated to obtain the\nkinetic data. This functionality can be done either through the use of the \npykinetic python library or through the use of the command line apps: \n\"pykinetic-model.py\" and \"pykinetic-scan.py\". The minimal source code to run the \nsimulation is the output of pykinetic and currently python and c++ are supported. \nCompiling and executing that code leads to the simulation of the chemical system. \n\n.. project-description-end\n\n.. contents:: \n :backlinks: none\n :depth: 2\n :local:\n\n\nGetting Started\n---------------\n\nThese instructions will get you a copy of the project up and running on your\nlocal machine.\n\n.. setup-instructions-start\n\nPrerequisites\n.............\n\n- python >= 3.6 (3.7.3 or higher recommended)\n- python library: setuptools\n- python library: numpy (optional, needed to run the generated python scripts)\n- python library: scipy (optional, needed to run the generated python scripts)\n- c++ library: boost (optional, needed to run the generated c++ scripts)\n\n Note: proper documentation installation of the c++ library is being \n currently being reviewed.\n\nInstalling the dependencies\n...........................\n\npython3.7 installation in Ubuntu 18.04 LTS\n\n.. code:: shell-session\n\n $ sudo apt-get update\n $ sudo apt-get install python3.7 python3.7-dev\n\n\nIf for any reason it is not reachable:\n\n.. code:: shell-session\n\n $ sudo add-apt-repository ppa:deadsnakes/ppa\n $ sudo apt-get update\n $ sudo apt-get install python3.7 python3.7-dev\n\nNow you can skip the next step if you don't want to set up a virtual environment\nthe lines below correspond to python3.7 but can be also applied to python3.6 or \nhigher (Remember to change \"my_venv\" for the actual path of the directory where \nyou want the virtual environment)\n\n.. code:: shell-session\n\n $ sudo apt-get install python3.7-venv\n $ python3.7 -m venv my_venv\n $ source my_venv/bin/activate\n\nIn the case of creating a virtual environment and running the \nprevious \"source\" command, anytime you write \"python\" it will act as an alias \nfor \"python3.7\" or whichever python executable you used for the virtual environment.\n(To leave the virtual environment run the \"deactivate\" command at anytime)\n\nIf you have not created a virtual environment, all the following commands must \nexplicitly use the python executable in which you are going to install the \nthe package. \nNow we install the python default installer pip in our virtual environment\n\n.. code:: shell-session\n\n $ python -m pip install pip\n $ python -m pip install --upgrade pip\n $ python -m pip install setuptools\n\nIf it proceeded without any errors (pip and setuptools should already be \ninstalled) otherwise please check the `pip`_ documentation\n\n.. _pip: https://pip.pypa.io/en/stable/installing/\n\nNow to install the optional dependencies (Skip if you do not want them):\n\n.. code:: shell-session\n\n $ python -m pip install numpy scipy\n $ sudo apt-get install libboost-dev\n\nInstalling pykinetic\n....................\n\n\nGet the source code from github through git and install it.\n\n.. code:: shell-session\n\n $ git clone https://github.com/maserasgroup-repo/pykinetic.git pykinetic\n $ python -m pip install pykinetic/\n\nIf you do not have git or do prefer to download manually the source \ncode as a .zip or .tar.gz do it install it. \n\n.. code:: shell-session\n\n $ python -m pip install pykinetic-0.1.0.tar.gz\n\n.. \n \n Note: If you prefer to unpack it you can do it but it is not needed\n\nRunning the tests\n.................\n\nAfter installing you should be able to run the tests: \n\n.. code:: shell-session\n\n $ python -m unittest -v pykinetic.tests\n\nUninstalling pykinetic\n......................\n\n.. code:: shell-session\n\n $ python -m pip uninstall pykinetic\n\n.. setup-instructions-end\n\nDeveloped with\n--------------\n\n- python 3.7.3\n- Ubuntu 16.04 LTS and Ubuntu 18.04 LTS\n\n\nExamples\n--------\n\nPlease open the `Examples.rst <Examples.rst>`_ file in github to visualize the \nbasic usage examples or read the documentation.\n\nAuthors\n-------\n\n.. project-authors-start\n\nList of main developers and contact emails: \n\n* Ra\u00fal P\u00e9rez-Soto [\n `ORCID <https://orcid.org/0000-0002-6237-2155>`__ ,\n `Github <https://github.com/rperezsoto>`__ ,\n `email <rperezsoto.research@gmail.com>`__ ]\n* Sergio Pablo-Garc\u00eda [\n `ORCID <https://orcid.org/0000-0002-3327-9285>`__ , \n `Github <https://github.com/spgarcica>`__ , \n `email <spgarcica@gmail.com>`__]\n* Mar\u00eda Besora [\n `ORCID <http://orcid.org/0000-0002-6656-5827>`__ ,\n `Github <https://github.com/BesoraMaria>`__ ,\n `email <maria.besora@urv.cat>`__ ] \n* Feliu Maseras [\n `ORCID <http://orcid.org/0000-0001-8806-2019>`__ ,\n `Github <https://github.com/maserasgroup-repo>`__ , \n `email <fmaseras@iciq.es>`__] \n\n.. project-authors-end\n\nLicense\n-------\n\n.. project-license-start\n\npykinetic is freely available under an `MIT <https://opensource.org/licenses/MIT>`__ License\n\n.. project-license-end\n",
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