This contains the Reveal Chromatography project for exploring and generating Chromatography data and profiles. This exposes a C++ Chromatography process simulator, CADET [0], to generate chromatography simulations and compare them to experimental results observed in laboratories. Its goal is to provide a graphical user interface frontend for these explorations.

This README details how to use the project. Other documents discuss other aspect of the project: * See the CONTRIBUTING.txt document for how to contribute to this repository. * See the RELEASE.txt for details about the evolution of this project. * See the ROADMAP.txt document for details about where this project is going. To accelerate that effort, and steer the tool in directions you need, please contact us at release-support@kbibiopharma.com.

If you are not a developer, the easiest way to use Reveal Chromatography is to download a 1-click installed from https://www.kbibiopharma.com/capabilities/services/mechanistic-modeling-optimize-characterize-purification-process . If you are a developer, see the section below.

To develop on this project, you need a Python 2.7 environment that contains the right list of package dependencies. The list of dependencies and their precise versions are to be found in deploy/requirement_py27_**_x86_64.txt, where the ** should be replaced by the name of the OS you want to run on. Of course, in addition, this project must also be added to the developement environment by running:

python setup.py develop

or:

python setup.py install

To make sure the installation is successful, it is recommended to run the entire test suite, using `nose`:

nosetests -v kromatography

To launch the GUI tool, the entry point is in the app sub-package:

python kromatography/app/main.py

or use the entry point named reveal-chrom.

You are report issues using the Github issue tracker or submit contributions to the code base using Github's Pull Requests. Please review the CONTRIBUTING document before doing so.

To develop on the PICTS tools, you will need a "bootstrap" python environment to create the development environment. It will need to be based on Python version 2.7. That environment can created using Enthought's EDM (https://www.enthought.com/products/edm/). Note that EDM is an environment management tool, and a python, so once installed, a 2.7 environment can be created by running `bash edm environments create bootstrap --version 2.7 To make subsequent commands easier, it is recommended to add the path to the new environment to the `PATH environment variable. For example on UNIX like systems, the following should be added to the ~/.bashrc or `~/.bash_profile`:

export PATH="~/.edm/envs/bootstrap/bin":$PATH

That environment also will need to contain the following packages: fabric, and `hatcher`:

edm install hatcher fabric -e bootstrap

Using that environment, you will need create an Enthought (hatcher) token following [this](http://pythonhosted.org/hatcher/user-guide/getting-started.html#token-authentication) :

hatcher -U you@kbibiopharma.com -u https://packages.enthought.com api-tokens create YOUR_NAME

Note that this will require for your email to be registered with Enthought.

You will also need to edit the EDM file ~/.edm.yaml to include kbi/kromatography in the list of repositories. Also the following must be added to the bottom of the file:

authentication:
    api_token: <YOUR HATCHER TOKER HERE>

After that, you can install ci-tools (pulled from the kbi repository):

edm install ci_tools 0.1.2.dev0-2 -e bootstrap

Note that this will require for your Enthought account to be added to the list of accounts authorized to see KBI's private repository.

Once the bootstrap environment has all the needed dependencies (fabric and ci-tools), a python 2.7 development environment can be created using:

fab build_devenv

Once you have an environment set up, you need to install the Kromatography project itself into it. First, activate the development environment (see above). Then you can install the Kromatography package as a standalone install or as a development version.

To install the latest stable release of kromatography, simply activate the environment (see section above) and run:

edm install kromatography

To see the list of available versions, run edm search kromatography.

To install Kromatography in the development environment and develop on it, from the top of the kromatography repository, run:

~/.edm/env/kromatography/bin/python setup.py develop

or on Windows, from the HOME directory:

.edm\envs\kromatography\python.exe setup.py develop

Of course, you can omit the path if the EDM environment has been activated. See below for uninstalling kromatography.

The source files for the documentation are stored in the docs/sources folder. After doing some modifications, the HTML documentation can be regenerated, by running fab build_docs from the home folder. That will regenerate the docs and copy the webpage structure into the project's doc/ sub-package.

Run the GUI application using:

fab run

Note that this requires that whatever default python on your system has the fabric package installed.

It is also possible to pass a study file (excel file) to open on startup, using:

fab run:PATH/TO/FILE

This is equivalent to invoking the krom_app application launcher automatically from the devenv python executable:

~/.edm/env/kromatography/bin/python kromatography/app/krom_app.py -i PATH/TO/FILE

If you have installed the latest stable release of kromatography, simply activate the environment (see section above) and run:

edm environments remove kromatography

Building an MSI installer relies on an open source tool called WIXToolset [1]. To build an installer refer to the steps described in the RELEASE.rst document.

The project contains a unit test suite. It can be run using:

fab test

[0] https://github.com/modsim/CADET [1] http://wixtoolset.org/