PyPI readme

pypi-readme.rst

@@ -0,0 +1,76 @@
+BioPrinter
+==========
+
+.. image:: https://travis-ci.org/Edinburgh-Genome-Foundry/bioprinter.svg?branch=master
+   :target: https://travis-ci.org/Edinburgh-Genome-Foundry/bioprinter
+   :alt: Travis CI build status (Python 3)
+
+.. image:: https://coveralls.io/repos/github/Edinburgh-Genome-Foundry/bioprinter/badge.svg?branch=master
+   :target: https://coveralls.io/github/Edinburgh-Genome-Foundry/bioprinter?branch=master
+
+
+Bioprinter (webpage here_) is a Python package for producing living art. It transforms an image into files that a liquid dispenser can use to *print* the image to a plate using pigmented yeast or bacteria.
+
+Here are two examples of bio-art:
+
+.. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/bioprint_dolly.jpeg
+    :align: center
+
+    Dolly drawn with baker yeast (white), violacein-producing yeast (black), and carotene-producing yeast (orange).
+
+
+.. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/bioprint_england.jpeg
+    :align: center
+
+    British flag drawn with 3 different strains of the bacterium *E. coli*.
+
+These bio-prints (and many others!) were presented at the University of Edinburgh's SynthSys Open days 2016 (strain selection and acoustic printing by Paulina Kanigowska).
+
+Bioprinter is released on Github_ under the MIT licence (Copyright 2015 Edinburgh Genome Foundry), everyone is welcome to contribute!
+
+Bioprinter was written at the Edinburgh Genome Foundry by Zulko_ after an original idea and Matlab code by Mike Shen (`project on Github <https://github.com/mshen5/BioPointillism>`_).
+
+Installation
+------------
+
+If you have PIP installed: ::
+
+    (sudo) pip install ez_setup bioprinter
+
+Or unzip the source code in a directory and type in a terminal: ::
+
+    sudo python setup.py install
+
+
+Usage
+-----
+
+The image file to be printed can have any resolution, but note that the width/height ratio of the plate the image is printed on is 1.5. Ensure that a specific color is used to mark the un-pigmented background of the image, here we use blue:
+
+.. figure:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/bioprinter/master/docs/_static/images/dolly.jpeg
+    :align: center
+
+Run the following code in Python or save in ``dolly.py``:
+
+.. code:: python
+
+    from bioprinter import bioprint
+
+    bioprint(
+        image_filename="/path/to/image/dolly.jpeg",
+        output_filename="dolly.csv",
+        bg_color=[0, 0, 255],  # blue background represents empty wells
+        pigments_wells={"A1": [0, 0, 0],        # black yeast in source well A1
+                        "A2": [250, 120, 10],   # orange yeast in well A2
+                        "A3": [255, 255, 255]}, # white yeast in well A3
+        quantified_image_filename="dolly_preview.jpeg"
+    )
+
+The saved script can be executed in a terminal with ``python dolly.py``. This will produce a ``dolly.csv`` file as well as a preview image of the final printing (so that you can check if the image looks good at this low resolution).
+
+Prepare a source plate with the right pigmented yeasts in wells A1, A2, A3, use an agar plate as the destination plate, and feed ``dolly.csv`` to the `Labcyte Echo Acoustic Liquid Handler <https://www.labcyte.com/products/liquid-handling/echo-liquid-handlers>`_ (tested with Labcyte Echo 555 Series). Once the printing is finished, incubate 2 days at 30C (it would be one day at 37C for bacteria). Enjoy the result!
+
+
+.. _here: http://edinburgh-genome-foundry.github.io/bioprinter/
+.. _Zulko: https://github.com/Zulko/
+.. _Github: https://github.com/Edinburgh-Genome-Foundry/bioprinter

setup.py

@@ -11,7 +11,7 @@
     version=__version__,
     author="Zulko",
     description="",
-    long_description=open("README.rst").read(),
+    long_description=open("pypi-readme.rst").read(),
     license="MIT",
     url="https://github.com/Edinburgh-Genome-Foundry/bioprinter",
     keywords="bioprinter pointillism living art",