Docs: huge update following migration to GitHub

CITATION.rst

@@ -0,0 +1,33 @@
+.. GaudiMM: Genetic Algorithms with Unrestricted
+   Descriptors for Intuitive Molecular Modeling
+   
+   https://github.com/insilichem/gaudi
+  
+   Copyright 2017 Jaime Rodriguez-Guerra, Jean-Didier Marechal
+   
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+   
+        http://www.apache.org/licenses/LICENSE-2.0
+   
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+
+
+How to cite this software
+=========================
+
+GaudiMM is scientific software, funded by public research grants. If you make use of GaudiMM in scientific publications, please cite it. It will help measure the impact of our research and future funding!
+
+.. code-block:: latex
+
+   @preamble{ " \newcommand{\noop}[1]{} " }
+   @article{GaudiMM2017,
+      title = {GaudiMM: A Modular Multi-Objective Platform for Molecular Modeling},
+      author = {Rodr{\'i}guez-Guerra Pedregal, Jaime and Sciortino, Giuseppe and Guasp, Jordi and Municoy, Mart{\'i} and Mar{\'e}chal, Jean-Didier},
+      year = {\noop{2017}submitted},
+   }

MANIFEST.in

@@ -1,4 +1,5 @@
 include README.rst
+include CITATION.rst
 include LICENSE
 include environment.yml
 include .gitignore

README.rst

@@ -1,7 +1,7 @@
 .. GaudiMM: Genetic Algorithms with Unrestricted
    Descriptors for Intuitive Molecular Modeling
    
-   http://bitbucket.org/insilichem/gaudi
+   https://github.com/insilichem/gaudi
   
    Copyright 2017 Jaime Rodriguez-Guerra, Jean-Didier Marechal
    
@@ -17,65 +17,50 @@
    See the License for the specific language governing permissions and
    limitations under the License.
 
+
 GaudiMM
 =======
 
 GaudiMM: Genetic Algorithms with Unrestricted Descriptors for Intuitive Molecular Modeling provides a novel method in design essays by combining several chemostructural criteria, along with energy-like optimization.
 
+
 Features
 --------
 
-**True multi-objective optimization**
-
-- Feel free to optimize H bonds, hydrophobic interactions, desolvation effects, distances between given sets of atoms, rotamers and more.
-
-**Force-field-less approach**
+**Full multi-objective optimization**
 
-- Metal complexes are more than welcome.
+- Feel free to optimize H bonds, hydrophobic interactions, desolvation effects, distances between given sets of atoms, rotamers and more, without compromises.
 
 **Unprecedented customizability**
 
-- Each objective can be switched off upon demand, and multi-instantiated.
-
-
-Documentation
--------------
-
-Quick installation:
+- Every gene and objective is a separate module, so they can be called on demand one or more times. This flexible approach allows very different calculations with the same mindset: exploration and evaluation.
 
-1 - Download the `latest stable copy of UCSF Chimera <http://www.cgl.ucsf.edu/chimera/download.html>`_ and install it with:
+**Developer friendly**
 
-::
+- If the provided genes and objectives are not enough, you can always code your own ones. Check out the `developer docs <http://gaudi.readthedocs.io/en/latest/developers.html>`_!
 
-  chmod +x chimera-*.bin && sudo ./chimera-*.bin
 
-2 - Install `Miniconda Python 2.7 Distribution <http://conda.pydata.org/miniconda.html>`_ for your platform and install it with:
+Documentation and support
+-------------------------
 
-::
+Documentation source is available in ``docs/`` subdirectory, and also compiled as HTML at `this webpage <http://gaudi.readthedocs.io/>`_
 
-  bash Miniconda2*.sh
+If you need help with GaudiMM, please use the `issues page <https://github.com/insilichem/gaudi/issues>`_ of our `GitHub repo <https://github.com/insilichem/gaudi>`_. You can drop me a message at `jaime.rodriguezguerra@uab.cat <mailto:jaime.rodriguezguerra@uab.cat>`_ too.
 
-3 - Grab the `environment.yml <https://bitbucket.org/insilichem/gaudi/raw/HEAD/environment.yml>`_ file and create the GAUDI environment with:
+License
+-------
 
-::
+GaudiMM is licensed under the Apache License, Version 2.0. Check the details in the ``LICENSE`` file.
 
-  conda env create -f /path/to/downloaded/environment.yml
-
-4 - Activate the new environment as proposed:
-
-::
-
-  source activate gaudi
-
-5 - Run it!
-
-::
-
-  gaudi
+Citation
+--------
 
-You can also check the (outdated) docs `here <docs/>`_.
+GaudiMM is scientific software, funded by public research grants (Spanish MINECO's project ``CTQ2014-54071-P``, Generalitat de Catalunya's project ``2014SGR989`` and research grant ``2015FI_B00768``, COST Action ``CM1306``). If you make use of GaudiMM in scientific publications, please cite it. It will help measure the impact of our research and future funding!
 
-Bug reports and contact
------------------------
+.. code-block:: latex
 
-Please, use the `issues page <https://bitbucket.org/jrgp/gaudi/issues>`_ of our `Bitbucket repo <https://bitbucket.org/jrgp/gaudi>`_. You can drop me a message at `jaime@klingon.uab.cat <mailto:jaime@klingon.uab.cat>`_ too.
+  @article{GaudiMM2017,
+      title = {GaudiMM: A Modular Multi-Objective Platform for Molecular Modeling},
+      author = {Rodr{\'i}guez-Guerra Pedregal, Jaime and Sciortino, Giuseppe and Guasp, Jordi and Municoy, Mart{\'i} and Mar{\'e}chal, Jean-Didier},
+      year = {2017},
+  }

conda-recipe/meta.yaml

@@ -6,7 +6,7 @@ package:
                               ) }}
 
 about:
-  home: https://bitbucket.org/insilichem/gaudi
+  home: https://github.com/insilichem/gaudi
   license: Apache 2.0
   summary: Genetic Algorithms with Unrestricted Descriptors for Intuitive Molecular Modeling
 

docs/Makefile

@@ -52,7 +52,7 @@ clean:
 	rm -rf $(BUILDDIR)/*
 
 html:
-	pychimera $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	python $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 

docs/api/gaudi.cli.rst

@@ -1,7 +1,7 @@
 .. GaudiMM: Genetic Algorithms with Unrestricted
    Descriptors for Intuitive Molecular Modeling
    
-   http://bitbucket.org/insilichem/gaudi
+   https://github.com/insilichem/gaudi
   
    Copyright 2017 Jaime Rodriguez-Guerra, Jean-Didier Marechal
    
@@ -17,10 +17,9 @@
    See the License for the specific language governing permissions and
    limitations under the License.
 
-Command line interfaces
-=======================
-
-Located in ``gaudi.cli``.
+=========
+gaudi.cli
+=========
 
 .. automodule:: gaudi.cli
     :members:

docs/api/gaudi.genes.rst

@@ -1,7 +1,7 @@
 .. GaudiMM: Genetic Algorithms with Unrestricted
    Descriptors for Intuitive Molecular Modeling
    
-   http://bitbucket.org/insilichem/gaudi
+   https://github.com/insilichem/gaudi
   
    Copyright 2017 Jaime Rodriguez-Guerra, Jean-Didier Marechal
    
@@ -19,8 +19,9 @@
 
 .. _api.gaudi.genes:
 
-Genes
-=====
+===========
+gaudi.genes
+===========
 
 These are the built-in genes in GAUDI. You can also build your own, but these are ready to use.
 

docs/api/gaudi.objectives.rst

@@ -1,7 +1,7 @@
 .. GaudiMM: Genetic Algorithms with Unrestricted
    Descriptors for Intuitive Molecular Modeling
    
-   http://bitbucket.org/insilichem/gaudi
+   https://github.com/insilichem/gaudi
   
    Copyright 2017 Jaime Rodriguez-Guerra, Jean-Didier Marechal
    
@@ -19,8 +19,9 @@
 
 .. _api.gaudi.objectives:
 
-Objectives 
-==========
+================
+gaudi.objectives
+================
 
 These are the built-in objectives in GAUDI. You can also build your own, but these are ready to use.
 

docs/api/gaudi.rst

@@ -1,7 +1,7 @@
 .. GaudiMM: Genetic Algorithms with Unrestricted
    Descriptors for Intuitive Molecular Modeling
    
-   http://bitbucket.org/insilichem/gaudi
+   https://github.com/insilichem/gaudi
   
    Copyright 2017 Jaime Rodriguez-Guerra, Jean-Didier Marechal
    
@@ -17,6 +17,7 @@
    See the License for the specific language governing permissions and
    limitations under the License.
 
+=================
 API documentation
 =================
 
@@ -25,80 +26,81 @@ API documentation
     :undoc-members:
     :show-inheritance:
 
+.. toctree::
+
+    gaudi.cli
+
+.. toctree::
+
+    gaudi.genes
+
+
+.. toctree::
+
+    gaudi.objectives
+
 
 gaudi.algorithms
-----------------
+================
 
 .. automodule:: gaudi.algorithms
     :members:
     :undoc-members:
     :show-inheritance:
 
 gaudi.base
-----------
+==========
 
 .. automodule:: gaudi.base
     :members:
     :undoc-members:
     :show-inheritance:
 
 gaudi.box
----------
+=========
 
 .. automodule:: gaudi.box
     :members:
     :undoc-members:
     :show-inheritance:
 
 gaudi.exceptions
-----------------
+================
 
 .. automodule:: gaudi.exceptions
     :members:
     :undoc-members:
     :show-inheritance:
 
 gaudi.parse
------------
+===========
 
 .. automodule:: gaudi.parse
     :members:
     :undoc-members:
     :show-inheritance:
 
 gaudi.plugin
-------------
+============
 
 .. automodule:: gaudi.plugin
     :members:
     :undoc-members:
     :show-inheritance:
 
 gaudi.similarity
-----------------
+================
 
 .. automodule:: gaudi.similarity
     :members:
     :undoc-members:
     :show-inheritance:
 
-Genes, Objectives and CLI
--------------------------
-
-.. toctree::
-
-    gaudi.genes
-    gaudi.objectives
-    gaudi.cli
-
-
-Private modules
----------------
 
 gaudi._cpdrift
-~~~~~~~~~~~~~~
+==============
 
 .. automodule:: gaudi._cpdrift
     :members:
     :undoc-members:
-    :show-inheritance:
+    :show-inheritance: