Point FiPy website links at GitHub

cherry-picked e3f9cc4^..0e1df48

matforge -> github

Change links to reflect hosting at GitHub rather than MatForge

catch SystemExit

sphinx-doc/sphinx@edb8fd9 moved `sys.exit()`
from __init__.py to sphinx.build(), so we need to catch it. Probably want
to shift to "make mode" at some point.

change reST extension from .txt to .rst

GitHub automatically renders reST in files ending in .rst, but not .txt

Addresses #416

INSTALLATION.rst

@@ -87,7 +87,7 @@ with Git_.
    to :term:`FiPy` become available (upgrades via Git_ will handle
    this issue automatically).
 
-.. _Git:       http://matforge.org/fipy/browserfipy
+.. _Git:       https://github.com/usnistgov/fipy
 .. _compressed archive:      http://www.ctcms.nist.gov/fipy/download/
 
 ---------------

README.rst

@@ -144,17 +144,16 @@ Support
 -------
 
 You can communicate with the :term:`FiPy` developers and with other
-users via our `mailing list`_ and we welcome you to use the `tracking
-system`_ for bugs, support requests, feature requests and patch
-submissions <http://matforge.org/fipy/report>. We also monitor 
+users via our `mailing list`_ and we welcome you to use the `issue
+tracker`_ for bugs, support requests, feature requests and patch
+submissions <https://github.com/usnistgov/fipy/issues>. We also monitor 
 StackOverflow_ for questions tagged with "fipy". We welcome
 collaborative efforts on this project.
 
 :term:`FiPy` is a member of MatForge_, a project of the `Materials
 Digital Library Pathway`_. This National Science Foundation funded
-service provides management of our public source code repository, our
-bug tracking system, and a "wiki" space for public contributions of
-code snippets, discussions, and tutorials.
+service provides a "wiki" space for public contributions of
+code snippets, discussions, and tutorials and hosts our testing framework.
 
 .. toctree::
 
@@ -236,7 +235,7 @@ or a
 .. _MSED:                 http://www.nist.gov/mml/msed/
 .. _NIST:                 http://www.nist.gov/
 .. _compressed archive:   http://www.ctcms.nist.gov/fipy/download/FiPy-1.1.tar.gz
-.. _tracking system:      http://matforge.org/fipy/report
+.. _issue tracker:        https://github.com/usnistgov/fipy/issues
 .. _mailing list:         http://www.ctcms.nist.gov/fipy/documentation/MAIL.html
 .. _Sourceforge:          http://www.sourceforge.net/projects/fipy
 .. _Materials Digital Library Pathway: http://matdl.org

documentation/ADMINISTRATA.rst

@@ -9,9 +9,9 @@ Branches
 --------
 
 Whether fixing a bug or adding a feature, all work on FiPy should be based 
-on a reported `Trac ticket`_. Assuming ticket number 12345, branch the code::
+on a reported `GitHub issue`_. Assuming issue number 12345, branch the code::
 
-    $ BRANCH=ticket12345-Summary_of_what_branch_addresses
+    $ BRANCH=issue12345-Summary_of_what_branch_addresses
     $ git checkout -b $BRANCH develop
 
 Edit and add to branch::
@@ -44,7 +44,7 @@ Submit branch for code review
 
    **Administrators Only!**
 
-   Push the code to matforge for automated testing::
+   Push the code to GitHub for automated testing::
 
        $ git push origin $BRANCH
 
@@ -89,7 +89,7 @@ Refactoring complete: merge branch to develop
 
        $ python setup.py test
 
-   Push the code to matforge for automated testing::
+   Push the code to GitHub for automated testing::
 
        $ git push origin develop
 
@@ -146,7 +146,7 @@ Make sure ``develop`` is ready for release::
 
    $ git checkout develop
 
-Check items in the tickets_ and update the :file:`README.txt`::
+Check items in the issues_ and update the :file:`README.txt`::
 
    $ git commit README.txt -m "REL: update new features for release"
 
@@ -240,24 +240,13 @@ Upload
 
 Tag the repository as appropriate (see `SVN practices`_ above).
 
-Upload the build products and documentation from :file:`dist/` to MatForge and 
+Upload the build products and documentation from :file:`dist/` and 
 the web site to CTCMS ::
 
     $ export FIPY_WWWHOST=bunter:/u/WWW/wd15/fipy
     $ export FIPY_WWWACTIVATE=updatewww
     $ python setup.py upload_products --pdf --html --tarball --winzip
 
-.. note::
-
-   You will need to manually upload the files
-
-     * http://matforge.org/fipy/admin/general/downloader
-
-   and, if appropriate, update the links to current files:
-
-     * http://matforge.org/fipy/wiki/FiPyDownloadCurrent?action=edit
-     * http://matforge.org/fipy/wiki/FiPyManual?action=edit
-
 .. warning:: Some versions of ``rsync`` on Mac OS X have caused problems
    when they try to upload erroneous ``\rsrc`` directories. Version 2.6.2
    does not have this problem.
@@ -267,8 +256,8 @@ Make an announcement to `fipy@nist.gov`_
 Build (``python setup.py bdist --formats=wininst``) a Windows `PyVTK`_
 executable and upload to download page.
 
-.. _Trac ticket: http://matforge.org/fipy/newticket
-.. _tickets: http://matforge.org/fipy/report
+.. _GitHub issue: https://github.com/usnistgov/fipy/issues/new
+.. _issues: https://github.com/usnistgov/fipy/issues
 .. _Buildbot: http://build.cmi.kent.edu:8010/tgrid
 .. _fipy@nist.gov: mailto:fipy@nist.gov
 .. _PyVTK: http://cens.ioc.ee/projects/pyvtk/

documentation/FAQ.rst

@@ -561,4 +561,4 @@ What if my question isn't answered here?
 
 Please post your question to the
 mailing list <http://www.ctcms.nist.gov/fipy/mail.html>
-or file a Tracker request at <http://matforge.org/fipy/report>.
+or file an issue at <https://github.com/usnistgov/fipy/issues/new>.

documentation/GIT.rst

@@ -3,8 +3,8 @@ Git usage
 ---------
 
 All stages of :term:`FiPy` development are archived in a Git
-repository at MatForge_. You can browse through the code at
-http://matforge.org/fipy/browser/fipy and, using a `Git client`_, you can
+repository at GitHub_. You can browse through the code at
+https://github.com/usnistgov/fipy and, using a `Git client`_, you can
 download various tagged revisions of :term:`FiPy` depending on your needs. 
 
 .. attention:: 
@@ -35,7 +35,7 @@ development to track.
 
 A fresh copy of the :term:`FiPy` source code  can be obtained with::
 
-   $ git clone git://code.matforge.org/nist/fipy.git
+   $ git clone https://github.com/usnistgov/fipy.git
 
 An existing Git checkout of FiPy can be shifted to a different `<branch>` of
 development by issuing the command::
@@ -87,6 +87,6 @@ The `Pro Git book`_ :cite:`ProGit` is particularly instructive.
 
 .. _Pro Git book: http://git-scm.com/book
 
-.. _MatForge: http://matforge.org/fipy
+.. _GitHub: https://github.com/usnistgov/fipy
 
 .. _a successful Git branching model: http://nvie.com/posts/a-successful-git-branching-model/

documentation/USAGE.rst

@@ -86,13 +86,12 @@ We have a few known, intermittent failures:
     have an effect on actual simulations.
 
 Although the test suite may show warnings, there should be no other errors.
-Any errors should be investigated or reported on the `tracking
-system`_. Users can see if there are any known problems for the latest
-:term:`FiPy` distribution by checking `FiPy's automated test
-display`_.
+Any errors should be investigated or reported on the `issue tracker`_.
+Users can see if there are any known problems for the latest :term:`FiPy`
+distribution by checking `FiPy's automated test display`_.
 
 .. _FiPy's automated test display: http://build.cmi.kent.edu:8010/console
-.. _tracking system: http://matforge.org/fipy/newticket
+.. _issue tracker: https://github.com/usnistgov/fipy/issues/new
 
 Below are a number of common `Command-line Flags`_ for testing various
 :term:`FiPy` configurations.
@@ -648,7 +647,7 @@ Manual
 
 You can view the manual online at <http://www.ctcms.nist.gov/fipy> or you 
 can `download the latest manual`_ from 
-<http://matforge.org/fipy/wiki/FiPyManual>. Alternatively,
+<http://www.ctcms.nist.gov/fipy/download/>. Alternatively,
 it may be possible to build a fresh copy by issuing the following
 command in the base directory::
 
@@ -680,7 +679,7 @@ command in the base directory::
    $ pip install -e git+git@github.com:mcmtroffaes/pybtex-docutils.git#egg=pybtex-docutils
    $ pip install -e git+git@github.com:mcmtroffaes/sphinxcontrib-bibtex.git#egg=sphinxcontrib-bibtex
 
-.. _download the latest manual:  http://matforge.org/fipy/wiki/FiPyManual
+.. _download the latest manual:  http://www.ctcms.nist.gov/fipy/download/
 .. _hg: http://mercurial.selenic.com
 .. _bzr: http://bazaar.canonical.com
 .. _git: http://git-scm.com

documentation/_templates/index.html

@@ -103,18 +103,18 @@ <h2>Applications</h2>
      </td></tr>
    </table>
 
-   <h2><a href="/cgi-bin/redirect.py?url=http://matforge.org/fipy">FiPy@MatForge</a></h2>
+   <h2><a href="download">Download</a></h2>
+
+   <h2><a href="/cgi-bin/redirect.py?url=https://github.com/usnistgov/fipy">FiPy@GitHub</a></h2>
    <table class="contentstable" align="center"><tr>
      <td width="50%">
        <p class="biglink"><a class="biglink" 
-       href="/cgi-bin/redirect.py?url=http://matforge.org/fipy/wiki/FiPyDownloadCurrent">Download</a></p>
+       href="/cgi-bin/redirect.py?url=https://github.com/usnistgov/fipy">Source Code</a></p>
        <p class="biglink"><a class="biglink" 
-       href="/cgi-bin/redirect.py?url=http://matforge.org/fipy/browser">Source Code</a></p>
+       href="/cgi-bin/redirect.py?url=https://github.com/usnistgov/fipy/issues">Reporting Bugs</a></p>
      </td><td width="50%">
        <p class="biglink"><a class="biglink" 
-       href="/cgi-bin/redirect.py?url=http://matforge.org/fipy">wiki</a></p>
-       <p class="biglink"><a class="biglink" 
-       href="/cgi-bin/redirect.py?url=http://matforge.org/fipy/report">Reporting Bugs</a></p>
+       href="/cgi-bin/redirect.py?url=https://github.com/usnistgov/fipy/wiki">wiki</a></p>
      </td></tr>
    </table>
 

documentation/_templates/indexsidebar.html

@@ -32,5 +32,5 @@ <h3>Questions? Suggestions?</h3>
 <iframe src="http://blog.gmane.org/recent.php?group=gmane.comp.python.fipy&type=topics&content=subject&table.font-size=small" width="100%"></iframe>
 </p>
 <p>You can also open an issue at the
-  <a href="http://matforge.org/fipy/report">tracker</a>.</p>
+  <a href="/cgi-bin/redirect.py?url=https://github.com/usnistgov/fipy/issues">tracker</a>.</p>
 </div>

fipy/meshes/cylindricalNonUniformGrid1D.py

@@ -118,7 +118,7 @@ def _test(self):
             >>> var = CellVariable(mesh=mesh)
             >>> DiffusionTerm().solve(var)
 
-        This test is for http://matforge.org/fipy/ticket/513. Cell
+        This test is for https://github.com/usnistgov/fipy/issues/372. Cell
         volumes were being returned as binOps rather than arrays.
 
             >>> m = CylindricalNonUniformGrid1D(dx=(1., 2., 3., 4.), nx=4)

fipy/meshes/cylindricalNonUniformGrid2D.py

@@ -288,7 +288,7 @@ def _test(self):
             >>> print fp.CellVariable(mesh=mesh, value=mesh.cellVolumes).globalValue
             [ 1.5  6. ]
 
-        This test is for http://matforge.org/fipy/ticket/513. Cell
+        This test is for https://github.com/usnistgov/fipy/issues/372. Cell
         volumes were being returned as binOps rather than arrays.
 
             >>> m = CylindricalNonUniformGrid2D(dx=(1., 2.), dy=(1., 2.))
@@ -302,7 +302,7 @@ def _test(self):
             >>> print isinstance(fp.CellVariable(mesh=m).arithmeticFaceValue.divergence.value, numerix.ndarray)
             True
             
-        Test for http://matforge.org/fipy/ticket/650. exteriorFaces were
+        Test for https://github.com/usnistgov/fipy/issues/393. exteriorFaces were
         ndarrays rather than FaceVariables.
         
             >>> print isinstance(m.facesTop, fp.FaceVariable)

fipy/meshes/cylindricalUniformGrid1D.py

@@ -96,7 +96,7 @@ def _test(self):
             >>> var = CellVariable(mesh=mesh)
             >>> DiffusionTerm().solve(var)
 
-        This test is for http://matforge.org/fipy/ticket/513. Cell
+        This test is for https://github.com/usnistgov/fipy/issues/372. Cell
         volumes were being returned as binOps rather than arrays.
 
             >>> m = CylindricalUniformGrid1D(dx=1., nx=4)

fipy/meshes/cylindricalUniformGrid2D.py

@@ -312,7 +312,7 @@ def _test(self):
             >>> var = CellVariable(mesh=mesh)
             >>> DiffusionTerm().solve(var, solver=DummySolver())
 
-        This test is for http://matforge.org/fipy/ticket/513. Cell
+        This test is for https://github.com/usnistgov/fipy/issues/372. Cell
         volumes were being returned as binOps rather than arrays.
 
             >>> m = CylindricalUniformGrid2D(dx=1., dy=1, nx=4, ny=4)

fipy/meshes/nonUniformGrid1D.py

@@ -118,7 +118,7 @@ def _test(self):
             >>> var = CellVariable(mesh=mesh)
             >>> DiffusionTerm().solve(var, solver=DummySolver())
 
-        Test for ticket http://matforge.org/fipy/ticket/490.
+        Test for ticket https://github.com/usnistgov/fipy/issues/364.
 
             >>> from fipy.meshes.nonUniformGrid1D import NonUniformGrid1D
             >>> m = NonUniformGrid1D(nx=9, overlap=1)

fipy/meshes/nonUniformGrid2D.py

@@ -266,7 +266,7 @@ def _test(self):
             >>> print numerix.allclose(mesh.cellCenters, unpickledMesh.cellCenters)
             True
 
-        Test for http://matforge.org/fipy/ticket/490.
+        Test for https://github.com/usnistgov/fipy/issues/364.
             
             >>> from fipy.meshes.nonUniformGrid2D import NonUniformGrid2D
             >>> m = NonUniformGrid2D(nx=1, ny=9, overlap=1)

fipy/meshes/nonUniformGrid3D.py

@@ -389,7 +389,7 @@ def _test(self):
             >>> NonUniformGrid3D(nx=2, ny=2, nz=2, dx=(1., 2.), dy=(1., 2.), dz=(1., 2.))
             NonUniformGrid3D(dx=(1.0, 2.0), nx=2, dy=(1.0, 2.0), ny=2, dz=(1.0, 2.0), nz=2)
 
-        Test for http://matforge.org/fipy/ticket/490.
+        Test for https://github.com/usnistgov/fipy/issues/364.
             
             >>> from fipy.meshes.nonUniformGrid3D import NonUniformGrid3D
             >>> m = NonUniformGrid3D(nx=1, ny=1, nz=9, overlap=1)

fipy/tools/__init__.py

@@ -49,7 +49,7 @@ def _parallelImport():
             try:
                 from mpi4py import MPI
             except ImportError:
-                raise Exception("Could not import mpi4py. The package mpi4py is a required package if you are using Trilinos on a Debian platform with Trilinos version 10.0.4 due to a Trilinos bug (see <http://matforge.org/fipy/ticket/420>). Try installing using 'easy_install mpi4py'.")
+                raise Exception("Could not import mpi4py. The package mpi4py is a required package if you are using Trilinos on a Debian platform with Trilinos version 10.0.4 due to a Trilinos bug (see <https://github.com/usnistgov/fipy/issues/301>). Try installing using 'easy_install mpi4py'.")
 
     from fipy.tools.comms.commWrapper import ParallelCommWrapper
     parallelComm = ParallelCommWrapper(Epetra=Epetra)

fipy/variables/variable.py

@@ -873,7 +873,7 @@ def __markStale(self):
                 ## vagaries of garbage collection and the possibility that 
                 ## later subscribedVariables were removed, changing the 
                 ## dependencies of this subscriber. 
-                ## See <https://www.matforge.org/fipy/ticket/118> for more explanation.
+                ## See <https://github.com/usnistgov/fipy/issues/103> for more explanation.
                 subscriber()._markStale()
 
     def _markFresh(self):