diff --git a/INSTALLATION.rst b/INSTALLATION.rst index 52b96d0516..f4bfe5f852 100644 --- a/INSTALLATION.rst +++ b/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/ --------------- diff --git a/README.rst b/README.rst index 3c7a8048f2..250081d5a0 100644 --- a/README.rst +++ b/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 . 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 . 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 diff --git a/documentation/ADMINISTRATA.rst b/documentation/ADMINISTRATA.rst index 6daa70087a..0a669d28d5 100644 --- a/documentation/ADMINISTRATA.rst +++ b/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/ diff --git a/documentation/FAQ.rst b/documentation/FAQ.rst index 7979681e62..4d8c59edc0 100644 --- a/documentation/FAQ.rst +++ b/documentation/FAQ.rst @@ -561,4 +561,4 @@ What if my question isn't answered here? Please post your question to the mailing list -or file a Tracker request at . +or file an issue at . diff --git a/documentation/GIT.rst b/documentation/GIT.rst index 8b41ede904..27dfd3b228 100644 --- a/documentation/GIT.rst +++ b/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 `` 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/ \ No newline at end of file diff --git a/documentation/USAGE.rst b/documentation/USAGE.rst index d46859ec77..4edc221f03 100644 --- a/documentation/USAGE.rst +++ b/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 or you can `download the latest manual`_ from -. Alternatively, +. 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 diff --git a/documentation/_templates/index.html b/documentation/_templates/index.html index 8ba1f920db..aa6f4a4e1e 100644 --- a/documentation/_templates/index.html +++ b/documentation/_templates/index.html @@ -103,18 +103,18 @@

Applications

-

FiPy@MatForge

+

Download

+ +

FiPy@GitHub

Download

+ href="/cgi-bin/redirect.py?url=https://github.com/usnistgov/fipy">Source Code

Source Code

+ href="/cgi-bin/redirect.py?url=https://github.com/usnistgov/fipy/issues">Reporting Bugs

wiki

-

Reporting Bugs

+ href="/cgi-bin/redirect.py?url=https://github.com/usnistgov/fipy/wiki">wiki

diff --git a/documentation/_templates/indexsidebar.html b/documentation/_templates/indexsidebar.html index be9a4cd9c5..cb7e103f94 100644 --- a/documentation/_templates/indexsidebar.html +++ b/documentation/_templates/indexsidebar.html @@ -32,5 +32,5 @@

Questions? Suggestions?

You can also open an issue at the - tracker.

+ tracker.

diff --git a/fipy/meshes/cylindricalNonUniformGrid1D.py b/fipy/meshes/cylindricalNonUniformGrid1D.py index c8c6de68c8..8c05182f15 100644 --- a/fipy/meshes/cylindricalNonUniformGrid1D.py +++ b/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) diff --git a/fipy/meshes/cylindricalNonUniformGrid2D.py b/fipy/meshes/cylindricalNonUniformGrid2D.py index 4a9d1a317c..fc2075f4b0 100644 --- a/fipy/meshes/cylindricalNonUniformGrid2D.py +++ b/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) diff --git a/fipy/meshes/cylindricalUniformGrid1D.py b/fipy/meshes/cylindricalUniformGrid1D.py index 0799d44b9f..45fb93fab3 100644 --- a/fipy/meshes/cylindricalUniformGrid1D.py +++ b/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) diff --git a/fipy/meshes/cylindricalUniformGrid2D.py b/fipy/meshes/cylindricalUniformGrid2D.py index f5f9debe23..5f1a19eba6 100644 --- a/fipy/meshes/cylindricalUniformGrid2D.py +++ b/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) diff --git a/fipy/meshes/nonUniformGrid1D.py b/fipy/meshes/nonUniformGrid1D.py index a79def7c57..074cd67893 100644 --- a/fipy/meshes/nonUniformGrid1D.py +++ b/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) diff --git a/fipy/meshes/nonUniformGrid2D.py b/fipy/meshes/nonUniformGrid2D.py index a88fd39f73..f7c9b8f1a9 100644 --- a/fipy/meshes/nonUniformGrid2D.py +++ b/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) diff --git a/fipy/meshes/nonUniformGrid3D.py b/fipy/meshes/nonUniformGrid3D.py index 3e9db32bc6..19fcfa89cb 100644 --- a/fipy/meshes/nonUniformGrid3D.py +++ b/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) diff --git a/fipy/tools/__init__.py b/fipy/tools/__init__.py index 21f10e7d70..eb4d3cdf4d 100644 --- a/fipy/tools/__init__.py +++ b/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 ). 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 ). Try installing using 'easy_install mpi4py'.") from fipy.tools.comms.commWrapper import ParallelCommWrapper parallelComm = ParallelCommWrapper(Epetra=Epetra) diff --git a/fipy/variables/variable.py b/fipy/variables/variable.py index ffd2f138a4..df12aac281 100644 --- a/fipy/variables/variable.py +++ b/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 for more explanation. + ## See for more explanation. subscriber()._markStale() def _markFresh(self):