Merge branch 'develop' into ticket460-import-fipy-without-solvers-rebase

.gitignore

@@ -0,0 +1,10 @@
+*.pyc
+*.pyo
+.*~ 
+*~
+.DS_Store
+FiPy.egg-info
+dist/
+documentation/_build/
+documentation/tutorial/package/generated/
+examples/reactiveWetting/generated/

INSTALLATION.txt

@@ -39,9 +39,9 @@ installing packages:
 
  * Use the operating system package manager, if possible.
  * Use the 
-   `pip installs python <http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.pip-installer.org/>`_ 
+   `pip installs python <http://www.pip-installer.org/>`_ 
    (:term:`pip`) tool to obtain software from the 
-   `Python Package Index <http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://pypi.python.org/pypi>`_ 
+   `Python Package Index <http://pypi.python.org/pypi>`_ 
    (:term:`PyPI`) repository::
 
      $ pip install package
@@ -74,20 +74,20 @@ given in the respective packages' :file:`README` and
 Obtaining FiPy
 --------------
 
-:term:`FiPy` is freely available for download via Subversion_ or as a
+:term:`FiPy` is freely available for download via Git_ or as a
 compressed archive from
 <http://www.ctcms.nist.gov/fipy/download>. Please see
-:ref:`documentation:SVN` for instructions on obtaining :term:`FiPy`
-with Subversion_.
+:ref:`documentation:GIT` for instructions on obtaining :term:`FiPy`
+with Git_.
 
 .. warning::
 
    Keep in mind that if you choose to download the `compressed
    archive`_ you will then need to preserve your changes when upgrades
-   to :term:`FiPy` become available (upgrades via Subversion_ will handle
+   to :term:`FiPy` become available (upgrades via Git_ will handle
    this issue automatically).
 
-.. _Subversion:       http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://matforge.org/fipy/browser
+.. _Git:       http://matforge.org/fipy/browserfipy
 .. _compressed archive:      http://www.ctcms.nist.gov/fipy/download/
 
 ---------------
@@ -170,7 +170,7 @@ If necessary, you can download_ and install it for your platform
    :term:`FiPy` requires at least version 2.4.x of :term:`Python`. See
    the specialized instructions if you wish to :ref:`RunUnderPython3`.
 
-.. _download: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.python.org/download/
+.. _download: http://www.python.org/download/
 
 :term:`Python` along with many of :term:`FiPy`'s required and optional
 packages is available with one of the following distributions.
@@ -251,6 +251,44 @@ details), via the :mod:`scipy.weave` module.
     A handful of test cases use functions from the :term:`SciPy`
     library and will throw errors if it is missing.
 
+------------------
+Level Set Packages
+------------------
+
+To use the level set components of :ref:`FiPy` one of the following is
+required.
+
+.. _SCIKITFMM:
+
+Scikit-fmm
+==========
+
+http://packages.python.org/scikit-fmm/
+
+Scikit-fmm_ is a python extension module which implements the fast
+marching method.
+
+.. _Scikit-fmm: http://packages.python.org/scikit-fmm/
+
+.. _LSMLIBDOC:
+
+LSMLIB
+======
+
+http://ktchu.serendipityresearch.org/software/lsmlib/index.html
+
+The Level Set Method Library (LSMLIB_) provides support for the serial
+and parallel simulation of implicit surface and curve dynamics in two-
+and three-dimensions.
+
+Install LSMLIB_ as per the instructions on the website. Additionally
+PyLSMLIB_ is required. To install, follow the instructions on the
+website,
+https://github.com/ktchu/LSMLIB/tree/master/pylsmlib#pylsmlib.
+
+.. _PyLSMLIB: https://github.com/ktchu/LSMLIB/tree/master/pylsmlib#pylsmlib
+.. _LSMLIB: http://ktchu.serendipityresearch.org/software/lsmlib/index.html
+
 ------------------------------
 Platform-Specific Instructions
 ------------------------------
@@ -297,9 +335,9 @@ We presently find that the combination of Homebrew_ and :term:`pip` is a
 pretty straightforward way to get most of :term:`FiPy`'s prerequesites. 
 See the `Miscellaneous Build Recipes`_ for up-to-date directions.
 
-.. _Fink: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.finkproject.org/
-.. _MacPorts: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.macports.org/
-.. _Homebrew: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://mxcl.github.com/homebrew/
+.. _Fink: http://www.finkproject.org/
+.. _MacPorts: http://www.macports.org/
+.. _Homebrew: http://mxcl.github.com/homebrew/
 
 Windows Installation
 ====================
@@ -324,15 +362,15 @@ downloaded from <http://www.ctcms.nist.gov/fipy/download>. Simply run::
 to install. The `.deb` includes dependencies for all of the
 :ref:`REQUIREDPACKAGES` and :ref:`OPTIONALPACKAGES`.
 
-.. _tested regularly: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://matforge.org/fipy/build
-.. _Mac OS X: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.apple.com/macosx/
-.. _Debian Linux: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.debian.org/
-.. _RedHat Linux: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.redhat.com/
-.. _OpenSUSE Linux: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.opensuse.org/
-.. _Ubuntu Linux: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.ubuntu.com/
-.. _Solaris: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://oracle.com/solaris
-.. _Windows: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.microsoft.com/windows/
-.. _Windows XP: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.microsoft.com/windowsxp/
+.. _tested regularly: http://matforge.org/fipy/build
+.. _Mac OS X: http://www.apple.com/macosx/
+.. _Debian Linux: http://www.debian.org/
+.. _RedHat Linux: http://www.redhat.com/
+.. _OpenSUSE Linux: http://www.opensuse.org/
+.. _Ubuntu Linux: http://www.ubuntu.com/
+.. _Solaris: http://oracle.com/solaris
+.. _Windows: http://www.microsoft.com/windows/
+.. _Windows XP: http://www.microsoft.com/windowsxp/
 
 Miscellaneous Build Recipes
 ===========================
@@ -349,11 +387,11 @@ We often post miscellaneous installation instructions on the
     We encourange you to contribute your own build recipes on the wiki_
     if they are significantly different.
 
-.. _Installing FiPy on Mac OS X using Homebrew: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://matforge.org/fipy/wiki/InstallFiPy/MacOSX/HomeBrew
-.. _Building a 64-bit scientific python environment for FiPy from source: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://matforge.org/fipy/wiki/InstallFiPy/MacOSX/SnowLeopard
-.. _Installing FiPy with pip: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://matforge.org/fipy/wiki/InstallFiPy/PipInstallsPython
-.. _wiki: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://matforge.org/fipy
-.. _blog: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://matforge.org/fipy/blog
+.. _Installing FiPy on Mac OS X using Homebrew: http://matforge.org/fipy/wiki/InstallFiPy/MacOSX/HomeBrew
+.. _Building a 64-bit scientific python environment for FiPy from source: http://matforge.org/fipy/wiki/InstallFiPy/MacOSX/SnowLeopard
+.. _Installing FiPy with pip: http://matforge.org/fipy/wiki/InstallFiPy/PipInstallsPython
+.. _wiki: http://matforge.org/fipy
+.. _blog: http://matforge.org/fipy/blog
 
 .. _ENVIRONMENT:
 
@@ -398,9 +436,9 @@ variable.  See the `Alternate Installation`_ section of the
 in which you should use :option:`--prefix` instead of
 :option:`--home`.
 
-.. _Alternate Installation: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://docs.python.org/inst/alt-install-windows.html
+.. _Alternate Installation: http://docs.python.org/inst/alt-install-windows.html
 
-.. _Installing Python Modules: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://docs.python.org/inst/
+.. _Installing Python Modules: http://docs.python.org/inst/
 
 An alternative to setting the :envvar:`PYTHONPATH` is to employ one of the
 utilities that manage packages and their dependencies independently of
@@ -429,8 +467,8 @@ requires admin privileges, but thereafter, creating new virtual
 environments and installing packages into them does not require admin
 privileges.
 
-.. _Virtualenvwrapper: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.doughellmann.com/projects/virtualenvwrapper
+.. _Virtualenvwrapper: http://www.doughellmann.com/projects/virtualenvwrapper
 
-.. _documentation:SVN:
+.. _documentation:GIT:
 
-.. include:: documentation/SVN.txt
+.. include:: documentation/GIT.txt

LICENSE.txt

@@ -20,4 +20,4 @@ they have been modified.
 
 .. _National Institute of Standards and Technology: http://www.nist.gov/
 .. _NIST:                 http://www.nist.gov/
-.. _title 17 section 105: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://uscode.house.gov/uscode-cgi/fastweb.exe?getdoc+uscview+t17t20+9+0++
+.. _title 17 section 105: http://uscode.house.gov/uscode-cgi/fastweb.exe?getdoc+uscview+t17t20+9+0++

README.txt

@@ -4,12 +4,13 @@ Overview
 
 .. only:: latex
 
-   :term:`FiPy` is an object oriented, partial differential equation (PDE) solver,
-   written in :term:`Python`, based on a standard finite volume (FV)
-   approach.  The framework has been developed in the `Metallurgy Division`_
-   and Center for Theoretical and Computational Materials Science (CTCMS_), in
-   the Material Measurement Laboratory (MML_) at the National
-   Institute of Standards and Technology (NIST_).
+   :term:`FiPy` is an object oriented, partial differential equation (PDE)
+   solver, written in :term:`Python`, based on a standard finite volume
+   (FV) approach. The framework has been developed in the Materials Science
+   and Engineering Division (MSED_) and Center for Theoretical and
+   Computational Materials Science (CTCMS_), in the Material Measurement
+   Laboratory (MML_) at the National Institute of Standards and Technology
+   (NIST_).
 
    The solution of coupled sets of PDEs is ubiquitous to the numerical
    simulation of science problems.  Numerous PDE solvers exist, using a
@@ -249,15 +250,14 @@ or a
 
 .. _MML:                  http://www.nist.gov/mml/
 .. _CTCMS:                http://www.ctcms.nist.gov/
-.. _Metallurgy Division:  http://www.nist.gov/mml/metallurgy/
+.. _MSED:                 http://www.nist.gov/mml/msed/
 .. _NIST:                 http://www.nist.gov/
-.. _Subversion:           http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://matforge.org/fipy/browser
 .. _compressed archive:   http://www.ctcms.nist.gov/fipy/download/FiPy-1.1.tar.gz
-.. _tracking system:      http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://matforge.org/fipy/report
+.. _tracking system:      http://matforge.org/fipy/report
 .. _mailing list:         http://www.ctcms.nist.gov/fipy/mail.html
-.. _Sourceforge:          http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://www.sourceforge.net/projects/fipy
-.. _Materials Digital Library Pathway: http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://matdl.org
-.. _MatForge:             http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://matforge.org/
+.. _Sourceforge:          http://www.sourceforge.net/projects/fipy
+.. _Materials Digital Library Pathway: http://matdl.org
+.. _MatForge:             http://matforge.org/
 
 .. bibmissing:: /documentation/refs.bib
     :sort: