Merge branch 'master' of github.com:choderalab/assaytools

README.md

@@ -1,5 +1,8 @@
 [![Build Status](https://travis-ci.org/choderalab/assaytools.png)](https://travis-ci.org/choderalab/assaytools)
+[![Anaconda Badge](https://anaconda.org/omnia/assaytools/badges/version.svg)](https://anaconda.org/omnia/assaytools)
+[![Anaconda-Server Badge](https://anaconda.org/omnia/assaytools/badges/downloads.svg)](https://anaconda.org/omnia/assaytools)
 [![ReadTheDocs Status](https://readthedocs.org/projects/assaytools/badge/?version=latest)](https://readthedocs.org/projects/assaytools/?badge=latest)
+[![DOI](https://zenodo.org/badge/29434469.svg)](https://zenodo.org/badge/latestdoi/29434469)
 
 assaytools
 ==========
@@ -17,6 +20,7 @@ See some [examples](https://github.com/choderalab/assaytools/tree/master/example
 ## Authors
 * John D. Chodera `<john.chodera@choderalab.org>`
 * Sonya M. Hanson `<sonya.hanson@choderalab.org>`
+* Mehtap Isik `<mehtap.isik@choderalab.org>`
 
 ## Acknowledgments
-* Many thanks to the authors of the [MDTraj](http://mdtraj.org) project on which much of the modern project skeleton is based.
+* Many thanks to the authors of the [MDTraj](http://mdtraj.org) project on which much of the modern project skeleton is based.

docs/conf.py

@@ -166,7 +166,7 @@
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-html_logo = '_static/assaytools_logo-small.png'
+html_logo = '_static/assaytools_logo-small.jpeg'
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32

docs/getting_started.rst

@@ -4,89 +4,42 @@
 Installation
 ************
 
-Platforms
-=========
+.. highlight:: bash
 
-`AssayTools` runs on CPython 2.7, 3.3, and 3.4.
-
-Install with Conda
+Install with conda
 ------------------
 .. _install-with-conda:
 
-`conda <http://www.continuum.io/blog/conda>`_ is a python package manager built for scientific python.
-Unlike ``easy_install`` or ``pip``, it handles binaries and binary dependencies, which are critical for most scientific workflows.
-If you're a ``conda`` user, you can install MDTraj by adding the omnia channel.
-If you're not a conda user, you should look into it. ::
-
-To install `AssayTools` with conda, use the following commands ::
+To install `AssayTools` with `conda <conda.pydata.org>`_`, use the following commands:
 
-  $ conda config --add channels choderalab
-  $ conda install assaytools
+::
+   $ conda install -c omnia assaytools
 
-.. note:: ``conda`` will automatically all of the tricky dependencies from binary packages automatically!
-This includes :mod:`pytables`, :mod:`numpy`, :mod:`scipy`, :mod:`pandas`, and :mod:`pymc`!
-The easiest way to get ``conda`` is with the `Anaconda python distribution <https://store.continuum.io/cshop/anaconda/>`_, or its smaller version `Miniconda <http://conda.pydata.org/miniconda.html>`_.
+.. note::
+   ``conda`` will automatically all of the tricky dependencies from binary packages automatically!
+   This includes :mod:`pytables`, :mod:`numpy`, :mod:`scipy`, :mod:`pandas`, and :mod:`pymc`!
+   The easiest way to get ``conda`` is with the `Anaconda python distribution <https://store.continuum.io/cshop/anaconda/>`_, or its smaller version `Miniconda <http://conda.pydata.org/miniconda.html>`_.
 
-Install from Source
+Install from source
 -------------------
-Clone the source code repository from github::
-
-  $ git clone git://github.com/choderalab/assaytools.git
-
-If you don't have ``git``, you can download the source code as a zip file ::
-
-  https://github.com/choderalab/assaytools/archive/master.zip
-
-Then, in the directory containing the source code, you can install it with ::
-
-  $ python setup.py install
-
-Dependencies
-============
-
-To use `AssayTools`, the following libraries and software will need to be installed.
-
-    Linux, Mac OS X or Windows operating system
-        We develop mainly on 64-bit Linux and Mac machines. Windows is not
-        well supported.
+.. _install-from-source
 
-    `Python <http://python.org>`_ >= 2.6
-        The development package (``python-dev`` or ``python-devel``
-        on most Linux distributions) is recommended.
+You can install the latest development version of ``AssayTools`` from github via ``pip``:
 
-    `NumPy <http://numpy.scipy.org/>`_ >= 1.6.0
-        Numpy is the base package for numerical computing in python.
-
-    `PyMC <http://pymc-devs.github.io/pymc/>`_ >= 2.3.3
-        PyMC is used as the underlying Markov chain Monte Carlo (MCMC) based Bayesian inference engine for AssayTools.
-
-Optional packages:
-
-    `Pandas <http://pandas.pydata.org>`_ >= 0.9.0
-        Some functionality requires pandas.
-
-Avoid Hassles with Anaconda or Canopy
--------------------------------------
-
-The easiest way to get all of the dependencies is to install via :ref:`conda <install-with-conda>`.
-
-.. note:: We really recommend Continuum's Anaconda.
-
-Manually Installing the Dependencies
-------------------------------------
-
-Oh, please don't!
+::
+   $ pip install git+https://github.com/choderalab/assaytools.git
 
 Testing Your Installation
 =========================
-Running the tests is a great way to verify that everything is working.
-The test suite uses `nose <https://nose.readthedocs.org/en/latest/>`_, which you can pick up via ``conda`` if you don't already have it. ::
+.. _testing-your-installation
 
-  $ conda install nose
+Running the tests is a great way to verify that everything is working.
+The test suite uses `nose <https://nose.readthedocs.org/en/latest/>`_, which you can install via ``conda``:
 
-Then, to run the tests, open a python shell and do ::
+::
+   $ conda install nose
 
-  >>> import assaytools
-  >>> assaytools.test()
+Then, to run the tests:
 
-From the source directory, you can also run the tests with ``nosetests assaytools`` on the command line.
+::
+   $ nosetests -vv assaytools

docs/index.rst

@@ -6,37 +6,26 @@ AssayTools
 AssayTools is a python library that allows users to model automated assays and analyze assay data using powerful Bayesian techniques that allow complete characterization of the uncertainty in fit models.
 With AssayTools, you can
 
- - Create models of experimental assays (e.g. fluorescence assays of ligand binding from titration curves prepared by automated liquid handlers)
- - Analyze data from these assays usijng powerful Bayesian techniques
+ - Create models of experimental assays (e.g. fluorescence or absorbance assays of ligand binding from titration curves prepared by automated liquid handlers)
+ - Analyze data from these assays using powerful Bayesian techniques
  - Derive parameters for these experimental assays from real data to use in modeling
  - Model new assay configurations to determine expected accuracy and bias across a range of ligand affinities
 
-The library also ships with a command-line application for visualizing Tecan Infinite plate XML output.
+The library also ships with a command-line application for visualizing [Tecan Infinite](http://lifesciences.tecan.com/products/reader_and_washer/microplate_readers/infinite_m1000_pro) plate reader XML output.
 When you install AssayTools, the script will be installed under the name ``xml2png``.
 
+ - `Download the code <https://github.com/choderalab/assaytools/releases/latest>`_
+ - `See it in action <https://github.com/choderalab/assaytools/tree/master/examples>`_
+ - `Get involved <https://github.com/assaytools/assaytools/issues>`_
+
 .. raw:: html
 
-  <div>
-      <h2 style="display: inline; float:left; margin-left:5em">
-          <a href="https://github.com/choderalab/assaytools/releases/latest">
-          Download the Code</a>
-      </h2>
-      <h2 style="display: inline; float:right; margin-right:5em">
-         <a href="https://github.com/choderalab/assaytools/tree/master/examples/fluorescence-binding-assay">
-          See it in Action</a>
-      </h2>
-      <div style="clear:both"></div>
-      <h2 style="display: inline; float:right; margin-right:7em">
-          <a href="https://github.com/assaytools/assaytools/issues">
-          Get Involved</a>
-      </h2>
-  </div>
+  <!-- robot video -->
   <br/>
   <iframe id="player" type="text/html" width="500" height="300" style="display:block; margin:auto"
   src="http://www.youtube.com/embed/H6zIcMst4lY"/>
   frameborder="0"></iframe>
-
-
+  <br/>
 
 .. raw:: html
 
@@ -53,39 +42,17 @@ Documentation
 
    getting_started
    theory
-..   examples/index
-   whatsnew
-   faq
-..   Discussion Forums <http://discourse.mdtraj.org>
 
 API Reference
 -------------
 
 .. toctree::
    :maxdepth: 1
 
-..   load_functions
-..   atom_selection
    analysis
-..   api/trajectory_files
-..   api/reporters
-..   api/utils
-   xml2png
-
-
-Developing
-----------
-
-.. toctree::
-   :maxdepth: 1
-
-   building_docs
-
 
 --------------------------------------------------------------------------------
 
-.. raw:: html
-
    </div>
 
 License

setup.py

@@ -46,7 +46,7 @@
 
 
 ##########################
-VERSION = "0.2.0"
+VERSION = "0.2.1"
 ISRELEASED = False
 __version__ = VERSION
 ##########################