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Update README, include rst version, bump version to 0.8.6
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‎README.md‎

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|mca_data |ec_results |
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|reaction name* |J_reaction name |
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|par_scan |do_par_scan |
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*reaction name refers to the naming of a reaction as it is defined in the model file.*
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*reaction name refers to the naming of a reaction as it is defined in the model file.
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**Symca**
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|save |save_session|
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|load |load_session|
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|par_scan |do_par_scan |
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*CCn refers to any of the additional result dictionaries that are created when an internal metabolite is fixed and the `internal_fixed` paramenter of `do_symca` is set to `True`
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**Data2D**

‎README.rst‎

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|Documentation Status|
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PySCeSToolbox
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=============
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This is a set of metabolic model analysis tools for PySCeS.
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PySCeSToolbox currently provides tools for:
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- Generalised supply-demand analysis.
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- Symbolic metabolic control analysis and control pattern analysis.
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- Generating model schemas from metabolic models.
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- Distinguishing between thermodynamic and kinetic contributions
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towards reaction rate.
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- Interactive plotting
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PySCeSToolbox was designed to be used within the Jupyter notebook, but
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most of the core features should work in a normal Python script.
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Documentation can be found at http://pyscestoolbox.readthedocs.org.
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While all major tools have been documented, the documentation is still a
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work in progress.
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Contents of README
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------------------
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- `Requirements <#requirements>`__
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- `Installation <#installation>`__
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- `Basic usage <#basic-usage>`__
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- `Important notices <#important-notices>`__
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- `Porting scripts to latest
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version <#porting-scripts-to-latest-version>`__
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Requirements
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------------
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An abbreviated list of requirements is given below. Python dependencies
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will be installed automatically when installing PySCeSToolbox via pip.
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For detailed operating system specific instructions on installing the
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requirements see the documentation at
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`http://pyscestoolbox.readthedocs.io/ <http://pyscestoolbox.readthedocs.io>`__,
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- A Python 2.7 installation
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- The full SciPy stack (see http://scipy.org/install.html)
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- PySCeS (see http://pysces.sourceforge.net/download.html or install
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using ``pip install pysces``)
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- Maxima (see http://maxima.sourceforge.net/download.html)
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- Jupyter Notebook (version in the 4.x.x series)
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**Notes:**
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Required packages should automatically download and install when using
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the commands specified under `Installation <#installation>`__ below.
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Maxima is only a requirement for SymCA.
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Installation
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------------
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The latest release of PySCeSToolbox can be installed from PyPi by
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running the following commands in the terminal (or Windows equivalent):
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.. code:: bash
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pip install pyscestoolbox
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The latest development version can be installed from GitHub with:
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.. code:: bash
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pip install git+https://github.com/exe0cdc/ipython-d3networkx.git
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pip install git+https://github.com/PySCeS/PySCeSToolbox.git
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For the pre-2015-11-11 version:
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.. code:: bash
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pip install git+https://github.com/exe0cdc/ipython-d3networkx.git
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pip install git+https://github.com/PySCeS/PySCeSToolbox.git@f63b5ab660f103105750159885608a5f48de1551
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Basic usage
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-----------
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To start a PySCeSToolbox session in a Jupyter notebook:
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1. Start up the Jupyter Notebook using the ``jupyter notebook`` command
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in the terminal
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2. Create a new notebook by clicking the ``New`` button on the top right
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of the window and selecting ``Python 2``
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3. Run the following three commands in the first cell:
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.. code:: python
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%matplotlib inline
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import pysces
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import psctb
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Model files must be placed in ``~/Pysces/psc/`` if using Linux or
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``C:\Pysces\psc\`` for Windows.
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Important notices
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-----------------
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For readers of "Tracing regulatory routes in metabolism using generalised supply-demand analysis" published in BMC Systems Biology on 03/12/2015:
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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To use the IPython notebook file included as "Additional file 5" in the
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paper, please install the **latest version** of PySCeSToolbox specified
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under `Installation <#installation>`__.
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The two PySCeS MDL model files included as "Addition file 1" and
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"Addition file 2" are required to run the notebook. They should be
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renamed to "Hoefnagel\_moiety\_ratio.psc" and "Curien.psc",
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respectively. Further instructions are included within the notebook and
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on this page.
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Firefox users should download these files using a different browser or
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switch to the new beta version of the BMC Systems Biology website.
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Changes:
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~~~~~~~~
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Because this project is still in its infancy, future changes might break
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older scripts. These types of changes will be kept to a minimum and will
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be documented here.
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Changes on 2017-02-09: Full cross compatibility
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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On 2017-02-09 Symca support via Maxima has been added to PySCeSToolbox
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on Windows. A configuration file located at
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``C:\Pysces\psctb_config.ini`` can be used to specify the path to
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``maxima.bat``. By default, however, PySCeSToolbox should detect the
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path to ``maxima.bat`` automatically if it has been installed using the
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default options. This change should have no impact on any older scripts
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save for making them platform independent.
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Changes on 2017-02-02: Dropped IPython Notebook 3.x.x support
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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As of 2017-02-02 IPython Notebook 3.x.x support has been dropped in
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favour of Jupyter 4.x.x. This should not affect the functioning of
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scripts (save for those based on versions before that of 2015-11-11).
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PySCeSToolbox will however require the Jupyter Notebook as of this date
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in order to use its interactive features. Note that ``ipywidgets`` (an
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automatically installed requirement for the Jupyter notebook) needs you
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to run the command
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"``jupyter nbextension enable --py --sys-prefix widgetsnbextension``"
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before enabling widgets in the notebook.
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Changes on 2015-11-11: API changes
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Major changes were made on 2015-11-11 that might break scripts coded
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before this date. These changes are related to the naming of methods and
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fields. For scripts older than 2015-11-11 we recommend using an older
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version of PySCeSToolbox (noted under `Installation <#installation>`__).
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Manual porting of scripts is also possible with details of necessary
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changes outlined under `Porting scripts to latest
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version <#porting-scripts-to-latest-version>`__.
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Porting scripts to latest version
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---------------------------------
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Method and variable names and the analysis objects they belong to that
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were changed on 2015-11-11 are documented in the tables below. To port
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any older script simply change the old name of any method/variable to
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the new name.
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**RateChar**
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+-------------------+-----------------+
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| Old name | New Name |
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+===================+=================+
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| save | save\_session |
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+-------------------+-----------------+
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| load | load\_session |
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+-------------------+-----------------+
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| plot\_data | scan\_results |
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+-------------------+-----------------+
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| mca\_data | mca\_results |
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+-------------------+-----------------+
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| plot\_decompose | do\_mca\_scan |
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+-------------------+-----------------+
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**Thermokin**
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+-------------------+---------------------+
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| Old name | New Name |
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+===================+=====================+
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| reactions | reaction\_results |
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+-------------------+---------------------+
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| mca\_data | ec\_results |
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+-------------------+---------------------+
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| reaction name\* | J\_reaction name |
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+-------------------+---------------------+
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| par\_scan | do\_par\_scan |
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+-------------------+---------------------+
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\*reaction name refers to the naming of a reaction as it is defined in
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the model file.
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**Symca**
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+-------------+------------------+
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| Old name | New Name |
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+=============+==================+
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| CC | cc\_results |
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+-------------+------------------+
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| CCn\* | cc\_results\_n |
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+-------------+------------------+
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| save | save\_session |
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+-------------+------------------+
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| load | load\_session |
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+-------------+------------------+
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| par\_scan | do\_par\_scan |
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+-------------+------------------+
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\*CCn refers to any of the additional result dictionaries that are
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created when an internal metabolite is fixed and the ``internal_fixed``
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paramenter of ``do_symca`` is set to ``True``
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**Data2D**
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+--------------+-----------------+
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| Old name | New Name |
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+==============+=================+
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| plot\_data | scan\_results |
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+--------------+-----------------+
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| save\_data | save\_results |
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+--------------+-----------------+
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.. |Documentation Status| image:: https://readthedocs.org/projects/pyscestoolbox/badge/?version=latest
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:target: http://pyscestoolbox.readthedocs.org/en/latest/?badge=latest

‎setup.py‎

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setup(
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name='PyscesToolbox',
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version='0.8.5',
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version='0.8.6',
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packages=packages,
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url='https://github.com/PySCeS/PyscesToolbox',
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download_url='https://github.com/PySCeS/PyscesToolbox/archive/0.8.5.tar.gz',
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download_url='http://github.com/PySCeS/PyscesToolbox/archive/0.8.6.tar.gz',
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license='BSD-3-Clause',
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author='Carl Christensen',
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author_email='carldc@sun.ac.za',

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