Merge branch 'master' into new-moulder

Conflicts:
	README.md

MANIFEST.in

@@ -1,5 +1,5 @@
 include LICENSE.txt
-include README.md
+include README.rst
 include CITATION.rst
 include MANIFEST.in
 recursive-include cookbook *

README.rst

@@ -0,0 +1,108 @@
+|title|
+=======
+
+.. |title| image:: https://raw.githubusercontent.com/fatiando/logo/master/fatiando-banner-long.png
+    :alt: Fatiando a Terra
+
+`Website <http://www.fatiando.org>`__ |
+`Docs <http://fatiando.readthedocs.org>`__ |
+`Mailing list <https://groups.google.com/d/forum/fatiando>`__ |
+`Google+ <https://plus.google.com/+FatiandoOrg>`__
+
+A Python package for modeling and inversion in geophysics.
+
+.. image:: http://img.shields.io/pypi/v/fatiando.svg?style=flat
+    :alt: Latest PyPI version
+    :target: https://crate.io/packages/fatiando
+.. image:: http://img.shields.io/pypi/dm/fatiando.svg?style=flat
+    :alt: Number of PyPI downloads
+    :target:  https://crate.io/packages/fatiando/
+.. image:: http://img.shields.io/badge/license-BSD-lightgrey.svg?style=flat
+    :alt: BSD 3 clause license
+    :target: https://github.com/fatiando/fatiando/blob/master/LICENSE.txt
+.. image:: http://img.shields.io/travis/fatiando/fatiando.svg?style=flat
+    :alt: Travis CI build status
+    :target: https://travis-ci.org/fatiando/fatiando
+.. image:: http://img.shields.io/coveralls/fatiando/fatiando.svg?style=flat
+    :alt: Test coverage status
+    :target: https://coveralls.io/r/fatiando/fatiando?branch=master
+.. image:: http://img.shields.io/badge/doi-10.6084/m9.figshare.1115194-blue.svg?style=flat
+    :alt: doi:10.6084/m9.figshare.1115194
+    :target: http://dx.doi.org/10.6084/m9.figshare.1115194
+
+Dependencies
+------------
+
+For the moment, Fatiando runs and is tested in Python 2.7.
+To install and run Fatiando, you'll need the following packages:
+
+* numpy >= 1.8
+* scipy >= 0.14
+* matplotlib >= 1.3
+* IPython >= 2.0.0
+* mayavi >= 4.3
+* PIL >= 1.1.7
+* basemap >= 1.0.7
+* gcc >= 4.8.2
+
+You can get all of these on Linux, Mac, and Windows through
+the `Anaconda distribution <http://continuum.io/downloads>`__.
+See file ``requirements.txt`` and the
+`documentation <http://fatiando.readthedocs.org>`__.
+
+**Windows users**: See the
+`install docs <http://fatiando.readthedocs.org/en/latest/install.html>`__
+for special instructions on getting the dependencies installed.
+
+Installing
+----------
+
+Download and install the latest release of Fatiando from
+`PyPI <https://pypi.python.org/pypi/fatiando>`__::
+
+    pip install fatiando
+
+or get the latest development version from Github::
+
+    pip install --upgrade https://github.com/fatiando/fatiando/archive/master.zip
+
+**Note**: ``fatiando.__version__`` has the current version number. If you install
+from PyPI, this will be something like ``'0.2'``. If you installed from Github,
+this will be the latest commit hash. This way you can track exactly what
+version of Fatiando generated your results.
+
+Citing
+------
+
+Fatiando is research software. If you use it in your research,
+please **cite it** in your publications as::
+
+    Uieda, L, Oliveira Jr, V C, Ferreira, A, Santos, H B; Caparica Jr, J F (2014),
+    Fatiando a Terra: a Python package for modeling and inversion in geophysics.
+    figshare. doi: 10.6084/m9.figshare.1115194
+
+Some of the methods implemented here are also **original research** by some of
+the developers. Please **also cite the method papers**.
+See the
+`CITATION.rst <https://github.com/fatiando/fatiando/blob/master/CITATION.rst>`__
+file for more information.
+
+Read `this blog post by Robin Wilson
+<http://www.software.ac.uk/blog/2013-09-02-encouraging-citation-software-introducing-citation-files>`__
+if you haven't heard of CITATION files.
+
+Documentation
+-------------
+
+The latest documentation is available at ReadTheDocs. The docs reflects the
+*master* branch on Github.
+
+http://fatiando.readthedocs.org
+
+
+License
+-------
+
+Fatiando a Terra is free software: you can redistribute it and/or modify it
+under the terms of the **BSD License**. A copy of this license is provided in
+`LICENSE.txt`.

doc/develop.rst

@@ -61,12 +61,14 @@ copy this checklist to the PR description
 `khmer docs
 <http://khmer.readthedocs.org/en/v1.1/development.html#checklist>`__)::
 
-    Checklist:
+    ## Checklist:
+
     - [ ] Make tests for new code
     - [ ] Create/update docstrings
     - [ ] Code follows PEP8 style conventions
     - [ ] Code and docs have been spellchecked
     - [ ] Changelog entry
+    - [ ] Include new dependencies in docs, requirements.txt, README
     - [ ] Documentation builds properly
     - [ ] All tests pass
     - [ ] Can be merged

doc/install.rst

@@ -143,7 +143,7 @@ information:
 .. _Python: http://www.python.org/
 .. _pip: http://www.pip-installer.org
 .. _MinGW: http://www.mingw.org/
-.. _mailing list: https://groups.google.com/forum/#!forum/fatiando
+.. _mailing list: https://groups.google.com/d/forum/fatiando
 .. _Leonardo Uieda: http://fatiando.org/people/uieda/
 .. _Continuum Analytics: http://continuum.io/
 .. _Anaconda: http://continuum.io/downloads

fatiando/gravmag/talwani.py

@@ -26,7 +26,7 @@
 from fatiando.constants import G, SI2MGAL
 
 
-def gz(xp, zp, polygons):
+def gz(xp, zp, polygons, dens=None):
     """
     Calculates the :math:`g_z` gravity acceleration component.
 
@@ -43,6 +43,9 @@ def gz(xp, zp, polygons):
         Polygons must have the property ``'density'``. Polygons that don't have
         this property will be ignored in the computations. Elements of
         *polygons* that are None will also be ignored.
+    * dens : float or None
+        If not None, will use this value instead of the ``'density'`` property
+        of the polygons. Use this, e.g., for sensitivity matrix building.
 
         .. note:: The y coordinate of the polygons is used as z!
 
@@ -56,9 +59,13 @@ def gz(xp, zp, polygons):
         raise ValueError("Input arrays xp and zp must have same shape!")
     res = numpy.zeros_like(xp)
     for polygon in polygons:
-        if polygon is None or 'density' not in polygon.props:
+        if polygon is None or ('density' not in polygon.props
+                               and dens is None):
             continue
-        density = polygon.props['density']
+        if dens is None:
+            density = polygon.props['density']
+        else:
+            density = dens
         x = polygon.x
         z = polygon.y
         nverts = polygon.nverts

setup.py

@@ -19,7 +19,7 @@
 DESCRIPTION = "Modeling and inversion for geophysics"
 VERSION = versioneer.get_version()
 CMDCLASS = versioneer.get_cmdclass()
-with open("README.md") as f:
+with open("README.rst") as f:
     LONG_DESCRIPTION = ''.join(f.readlines())
 PACKAGES = ['fatiando',
             'fatiando.gravmag',