From ed29afafe42e4a1a0b4c503f55078be4a55a106f Mon Sep 17 00:00:00 2001 From: Jonathan Guyer Date: Fri, 26 Sep 2014 14:38:22 -0400 Subject: [PATCH] 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 | 2 +- README.rst | 13 +++++------ documentation/ADMINISTRATA.rst | 27 +++++++--------------- documentation/FAQ.rst | 2 +- documentation/GIT.rst | 8 +++---- documentation/USAGE.rst | 13 +++++------ documentation/_templates/index.html | 12 +++++----- documentation/_templates/indexsidebar.html | 2 +- fipy/meshes/cylindricalNonUniformGrid1D.py | 2 +- fipy/meshes/cylindricalNonUniformGrid2D.py | 4 ++-- fipy/meshes/cylindricalUniformGrid1D.py | 2 +- fipy/meshes/cylindricalUniformGrid2D.py | 2 +- fipy/meshes/nonUniformGrid1D.py | 2 +- fipy/meshes/nonUniformGrid2D.py | 2 +- fipy/meshes/nonUniformGrid3D.py | 2 +- fipy/tools/__init__.py | 2 +- fipy/variables/variable.py | 2 +- 17 files changed, 43 insertions(+), 56 deletions(-) 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):