[Python-modules-commits] [petsc4py] 01/01: new upstream tarball 3.6.0
Drew Parsons
dparsons at moszumanska.debian.org
Fri Oct 30 15:36:14 UTC 2015
This is an automated email from the git hooks/post-receive script.
dparsons pushed a commit to branch upstream
in repository petsc4py.
commit 0383b0003d7bf3e950408c63146314a1fea96a31
Author: Drew Parsons <dparsons at debian.org>
Date: Fri Oct 30 23:32:14 2015 +0800
new upstream tarball 3.6.0
https://bitbucket.org/petsc/petsc4py
https://bitbucket.org/petsc/petsc4py/downloads/petsc4py-3.6.0.tar.gz
---
CHANGES.rst | 195 +
DESCRIPTION.rst | 52 +
HISTORY.txt | 83 -
LICENSE.rst | 33 +
LICENSE.txt | 12 -
MANIFEST.in | 15 +-
PKG-INFO | 68 +-
README.rst | 25 +
README.txt | 38 -
conf/baseconf.py | 770 +
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conf/cythonize.py | 110 +-
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conf/epydocify.py | 16 +
conf/metadata.py | 6 +-
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demo/binary-io/matvecio.py | 47 +
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demo/bratu3d/bratu3d.py | 146 +-
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demo/kspsolve/makefile | 25 +
demo/kspsolve/petsc-cg.tex | 21 -
demo/kspsolve/petsc-ksp.py | 2 +-
demo/kspsolve/petsc-mat.py | 6 +-
demo/kspsolve/test_mat_cg.py | 52 +-
demo/kspsolve/test_mat_ksp.py | 46 +-
demo/makefile | 11 +
demo/ode/ce.py | 7 +-
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demo/perftest/driver.py | 130 +
demo/perftest/makefile | 33 +
demo/perftest/makefile.f2py | 13 +
demo/perftest/makefile.petsc | 24 +
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demo/poisson3d/poisson3d.py | 28 +-
demo/taosolve/chwirut.py | 81 +
demo/taosolve/rosenbrock.py | 136 +
demo/wrap-cython/Bratu3D.pyx | 33 +
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src/PETSc/petscvec.pxi | 316 +-
src/PETSc/petscvwr.pxi | 70 +-
src/__init__.py | 17 +-
src/{help.py => __main__.py} | 51 +-
src/include/arraynpy.h | 126 -
src/include/compat.h | 39 +-
src/include/compat/232/private/kspimpl.h | 130 -
src/include/compat/232/private/matimpl.h | 994 -
src/include/compat/232/private/snesimpl.h | 145 -
src/include/compat/232/private/tsimpl.h | 89 -
src/include/compat/hdf5.h | 31 +
src/include/compat/mpi.h | 43 +-
src/include/compat/petsc.h | 88 -
src/include/compat/petscda.h | 56 -
src/include/compat/petscis.h | 156 -
src/include/compat/petscksp.h | 156 -
src/include/compat/petscmat.h | 724 -
src/include/compat/petscpc.h | 28 -
src/include/compat/petscsnes.h | 279 -
src/include/compat/petscsys.h | 15 -
src/include/compat/petscts.h | 163 -
src/include/compat/petscvec.h | 118 -
src/include/compat/petscviewer.h | 76 -
src/include/context.h | 174 -
src/include/custom.h | 1033 +-
src/include/cython.h | 53 +
src/include/initpkg.h | 90 +-
src/include/pep3118.h | 99 +
src/include/petsc4py/PETSc.pxd | 105 +-
src/include/petsc4py/numpy.h | 61 +
src/include/petsc4py/petsc4py.PETSc.h | 164 +-
src/include/petsc4py/petsc4py.PETSc_api.h | 330 +-
src/include/petsc4py/petsc4py.h | 10 -
src/include/petsc4py/petsc4py.i | 256 +-
src/include/petsc4py/petsc4py_PETSc_npy.h | 30 -
src/include/scalar.h | 28 +-
src/lib/__init__.py | 6 +-
src/libpetsc4py.c | 5 +
src/libpetsc4py.h | 16 +
src/libpetsc4py/custom.h | 113 +
src/libpetsc4py/libpetsc4py.c | 28047 ++
src/libpetsc4py/libpetsc4py.h | 40 +
src/libpetsc4py/libpetsc4py.pyx | 2560 +
src/petsc4py.PETSc.c | 323499 +++++++++++++-----
src/petsc4py.PETSc.pyx | 1 +
src/source/libpetsc4py.c | 44 -
src/source/libpetsc4py.h | 136 -
src/source/src/inline/python.h | 300 -
src/source/src/ksp/ksp/impls/python/makefile | 18 -
src/source/src/ksp/ksp/impls/python/python.c | 405 -
src/source/src/ksp/pc/impls/python/makefile | 18 -
src/source/src/ksp/pc/impls/python/python.c | 496 -
src/source/src/mat/impls/python/makefile | 18 -
src/source/src/mat/impls/python/python.c | 869 -
src/source/src/snes/impls/python/GNUmakefile | 14 -
src/source/src/snes/impls/python/ex1.c | 72 -
src/source/src/snes/impls/python/ex1.py | 39 -
src/source/src/snes/impls/python/makefile | 19 -
src/source/src/snes/impls/python/mysolver.py | 105 -
src/source/src/snes/impls/python/python.c | 764 -
src/source/src/ts/impls/python/makefile | 18 -
src/source/src/ts/impls/python/python.c | 788 -
test/runtests.py | 280 +-
test/test_comm.py | 17 +-
test/test_da.py | 135 -
test/test_dmda.py | 388 +
test/test_dmplex.py | 169 +
test/test_dmshell.py | 218 +
test/test_gc.py | 10 +-
test/test_is.py | 38 +-
test/test_ksp.py | 143 +-
test/test_ksp_py.py | 112 +
test/test_lgmap.py | 78 +-
test/test_mat_aij.py | 517 +-
test/test_mat_dense.py | 21 +-
test/test_mat_fact.py | 13 +-
test/test_mat_py.py | 62 +-
test/test_nsp.py | 4 +-
test/test_object.py | 70 +-
test/test_optdb.py | 8 +-
test/test_pc_py.py | 37 +-
test/test_snes.py | 125 +-
test/test_snes_py.py | 103 +
test/test_sys.py | 2 +
test/test_tao.py | 63 +
test/test_ts.py | 204 +-
test/test_ts_py.py | 119 +-
test/test_vec.py | 46 +-
463 files changed, 298424 insertions(+), 113306 deletions(-)
diff --git a/CHANGES.rst b/CHANGES.rst
new file mode 100644
index 0000000..9dcb782
--- /dev/null
+++ b/CHANGES.rst
@@ -0,0 +1,195 @@
+=========================
+CHANGES: PETSc for Python
+=========================
+
+:Author: Lisandro Dalcin
+:Contact: dalcinl at gmail.com
+
+
+Release 3.6.0
+=============
+
+- Update to PETSc 3.6 release.
+
+
+Release 3.5.1
+=============
+
+- Add ``Log.{begin|view|destroy}()``.
+- Add ``Mat.SOR()`` and ``Mat.SORType``.
+- Add ``DMPlex.createCoarsePointIS()``.
+- Add ``LGMap.createSF()``.
+- Add ``SNES.getVIInactiveSet()``.
+- Add ``Vec.isaxpy()``.
+- Add ``PC.setReusePreconditioner()``.
+- Return correct type in ``DM.getCoordinateDM()``.
+- Fix SWIG wrappers to handle 64bit ``PetscInt``.
+- Fix linker flags for Python from Fink.
+
+
+Release 3.5
+===========
+
+- Update to PETSc 3.5 release.
+
+
+Release 3.4
+===========
+
+- Update to PETSc 3.4 release.
+
+- Add support for ``DMComposite`` and ``DMPlex``.
+
+- Change ``Mat.getSizes()`` to return ``((m,M),(n,N))``.
+
+
+Release 3.3.1
+=============
+
+- Fix ``Options.getAll()`` mishandling values with negative numbers.
+
+- Minor backward compatibility fix for PETSc 3.2 .
+
+- Minor bugfix for TSPYTHON subtype.
+
+
+Release 3.3
+===========
+
+- Update to PETSc 3.3 release.
+
+- Change ``Vec.getLocalForm()`` to ``Vec.localForm()`` for use with
+ context manager and add ``Vec.setMPIGhost()``.
+
+- Add ``AO.createMemoryScalable()`` and ``LGMap.block()`` /
+ ``LGMap.unblock()``
+
+- Add ``Object.handle`` property (C pointer as a Python integer). Can
+ be used with ``ctypes`` to pass a PETSc handle.
+
+- Add ``Comm.tompi4py()`` to get a ``mpi4py`` communicator instance.
+
+
+Release 1.2
+===========
+
+- Update to PETSc 3.2 release.
+
+- Add new ``DM`` class , make ``DA`` inherit from ``DM``.
+
+- Better support for inplace LU/ILU and Cholesky/ICC factorization and
+ factor PC subtypes.
+
+- Now the ``Mat``/``PC``/``KSP``/``SNES``/``TS`` Python subtypes are
+ implemented with Cython.
+
+- Better interaction between Python garbage collector and PETSc
+ objects.
+
+- Support for PEP 3118 and legacy Python's buffer interface.
+
+
+Release 1.1.2
+=============
+
+This is a new-features and bug-fix release.
+
+- Add support for copying and computing complements in ``IS``
+ (``IS.copy()`` and ``IS.complement()``).
+
+- Add support for coarsening in ``DA`` (``DA.coarsen()``).
+
+- Support for shallow copy and deep copy operations (use ``copy.copy``
+ and ``copy.deepcopy``). Deep copy is only supported for a bunch of
+ types (``IS``, ``Scatter``, ``Vec``, ``Mat``)
+
+- Support for ``pip install petsc4py`` to download and install PETSc.
+
+
+Release 1.1.1
+=============
+
+This is a new-features and bug-fix release.
+
+- Support for setting PETSC_COMM_WORLD before PETSc initialization.
+
+- Support for coordinates, refinement and interpolation in DA. Many
+ thanks to Blaise Bourdin.
+
+- Workaround build failures when PETSc is built with *mpiuni*.
+
+- Workaround GIL-related APIs for non-threaded Python builds.
+
+
+Release 1.1
+===========
+
+- Update for API cleanups, changes, and new calls in PETSc 3.1 and
+ some other missing features.
+
+- Add support for Jed Brown's THETA an GL timestepper implementations.
+
+- Fix the annoying issues related to Open MPI shared libraries
+ dependencies and Python dynamic loading.
+
+- Many minor bug-fixes. Many thanks to Ethan Coon, Dmitry Karpeev,
+ Juha Jaykka, and Michele De Stefano.
+
+
+Release 1.0.3
+=============
+
+This is a bug-fix release.
+
+- Added a quick fix to solve build issues. The macro __SDIR__ is no
+ longer passed to the compiler in the command line.
+
+
+Release 1.0.2
+=============
+
+This is a new-features and bug-fix release.
+
+- Now ``petsc4py`` works against core PETSc built with complex
+ scalars.
+
+- Added support for PETSc logging features like stages, classes and
+ events. Stages and events support the context manager interface
+ (``with`` statement).
+
+- Documentation generated with Epydoc and Sphinx is now included in
+ the release tarball.
+
+- Removed enumeration-like classes from the ``petsc4py.PETSc`` module
+ namespace. For example, now you have to use ``PETSc.KSP.Type``
+ instead of ``PETSc.KSPType``.
+
+- The ``PETSc.IS`` to ``numpy.ndarray`` conversion now works for
+ stride and block index sets.
+
+- Implemented a more robust import machinery for multi-arch
+ ``petsc4py`` installations. Now a wrong value in the ``PETSC_ARCH``
+ environmental variable emit a warning (instead of failing) at import
+ time.
+
+- The unittest-based testsuite now can run under ``nose`` with its
+ default options.
+
+- Removed the dependency on ``numpy.distutils``, just use core Python
+ ``distutils``.
+
+
+Release 1.0.1
+=============
+
+This is a bug-fix release. Compile Cython-generated C sources with
+``-Wwrite-strings`` removed, as this flag (inherited from PETSc) made
+GCC emit a lot of (harmless but annoying) warnings about conversion of
+string literals to non-const char pointers.
+
+
+Release 1.0.0
+=============
+
+This is the fist release of the all-new, Cython-based, implementation
+of *PETSc for Python*.
diff --git a/DESCRIPTION.rst b/DESCRIPTION.rst
new file mode 100644
index 0000000..7ace2b0
--- /dev/null
+++ b/DESCRIPTION.rst
@@ -0,0 +1,52 @@
+PETSc for Python
+================
+
+Python bindings for PETSc.
+
+Install
+-------
+
+If you have a working MPI implementation and the ``mpicc`` compiler
+wrapper is on your search path, it highly recommended to install
+``mpi4py`` first::
+
+ $ pip install mpi4py
+
+Ensure you have NumPy installed::
+
+ $ pip install numpy
+
+and finally::
+
+ $ pip install petsc petsc4py
+
+You can also install the in-development version of petsc4py with::
+
+ $ pip install Cython numpy mpi4py
+ $ pip install --no-deps git+https://bitbucket.org/petsc/petsc
+ $ pip install --no-deps git+https://bitbucket.org/petsc/petsc4py
+
+or::
+
+ $ pip install Cython numpy mpi4py
+ $ pip install --no-deps https://bitbucket.org/petsc/petsc/get/master.tar.gz
+ $ pip install --no-deps https://bitbucket.org/petsc/petsc4py/get/master.tar.gz
+
+
+Citations
+---------
+
+If PETSc for Python been significant to a project that leads to an
+academic publication, please acknowledge that fact by citing the
+project.
+
+* L. Dalcin, P. Kler, R. Paz, and A. Cosimo,
+ *Parallel Distributed Computing using Python*,
+ Advances in Water Resources, 34(9):1124-1139, 2011.
+ http://dx.doi.org/10.1016/j.advwatres.2011.04.013
+
+* S. Balay, S. Abhyankar, M.F. Adams, J. Brown, P. Brune, K. Buschelman,
+ L. Dalcin, V. Eijkhout, W.D. Gropp, D. Kaushik, M.G. Knepley,
+ L. Curfman McInnes, K. Rupp, B.F. Smith, S. Zampini, and H. Zhang,
+ *PETSc Users Manual*, ANL-95/11 - Revision 3.6, 2015.
+ http://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf
diff --git a/HISTORY.txt b/HISTORY.txt
deleted file mode 100644
index 3401ad9..0000000
--- a/HISTORY.txt
+++ /dev/null
@@ -1,83 +0,0 @@
-=========================
-HISTORY: PETSc for Python
-=========================
-
-:Author: Lisandro Dalcin
-:Contact: dalcinl at gmail.com
-:Web Site: http://petsc4py.googlecode.com/
-:Organization: CIMEC <http://www.cimec.org.ar>
-:Address: PTLC, 3000 Santa Fe, Argentina
-
-
-Release 1.1
-===========
-
-- Update for API cleanups, changes, and new calls in PETSc 3.1 and
- some other missing features.
-
-- Add support for Jed Brown's THETA an GL timestepper implementations.
-
-- Fix the annoying issues related to Open MPI shared libraries
- dependencies and Python dynamic loading.
-
-- Many minor bug-fixes. Many thanks to Ethan Coon, Dmitry Karpeev,
- Juha Jaykka, and Michele De Stefano.
-
-
-Release 1.0.3
-=============
-
-This is a bug-fix release.
-
-- Added a quick fix to solve build issues. The macro __SDIR__ is no
- longer passed to the compiler in the command line.
-
-
-Release 1.0.2
-=============
-
-This is a new-features and bug-fix release.
-
-- Now ``petsc4py`` works against core PETSc built with complex
- scalars.
-
-- Added support for PETSc logging features like stages, classes and
- events. Stages and events support the context manager interface
- (``with`` statement).
-
-- Documentation generated with Epydoc and Sphinx is now included in
- the release tarball.
-
-- Removed enumeration-like classes from the ``petsc4py.PETSc`` module
- namespace. For example, now you have to use ``PETSc.KSP.Type``
- instead of ``PETSc.KSPType``.
-
-- The ``PETSc.IS`` to ``numpy.ndarray`` conversion now works for
- stride and block index sets.
-
-- Implemented a more robust import machinery for multi-arch
- ``petsc4py`` installations. Now a wrong value in the ``PETSC_ARCH``
- environmental variable emit a warning (instead of failing) at import
- time.
-
-- The unittest-based testsuite now can run under ``nose`` with its
- default options.
-
-- Removed the dependency on ``numpy.distutils``, just use core Python
- ``distutils``.
-
-
-Release 1.0.1
-=============
-
-This is a bug-fix release. Compile Cython-generated C sources with
-``-Wwrite-strings`` removed, as this flag (inherited from PETSc) made
-GCC emit a lot of (harmless but annoying) warnings about conversion of
-string literals to non-const char pointers.
-
-
-Release 1.0.0
-=============
-
-This is the fist release of the all-new, Cython-based, implementation
-of *PETSc for Python*.
diff --git a/LICENSE.rst b/LICENSE.rst
new file mode 100644
index 0000000..79b7447
--- /dev/null
+++ b/LICENSE.rst
@@ -0,0 +1,33 @@
+=========================
+LICENSE: PETSc for Python
+=========================
+
+:Author: Lisandro Dalcin
+:Contact: dalcinl at gmail.com
+
+
+Copyright (c) 2015, Lisandro Dalcin.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+
+* Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/LICENSE.txt b/LICENSE.txt
deleted file mode 100644
index 949943d..0000000
--- a/LICENSE.txt
+++ /dev/null
@@ -1,12 +0,0 @@
-=========================
-LICENSE: PETSc for Python
-=========================
-
-:Author: Lisandro Dalcin
-:Contact: dalcinl at gmail.com
-:Web Site: http://petsc4py.googlecode.com/
-:Organization: CIMEC <http://www.cimec.org.ar>
-:Address: PTLC, 3000 Santa Fe, Argentina
-
-
-This package has been placed in the public domain.
diff --git a/MANIFEST.in b/MANIFEST.in
index a1227e4..6cc4bb1 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,16 +1,17 @@
-include MANIFEST.in
-include *.py *.cfg *.txt
-include [M,m]akefile
+include setup*.py *.cfg *.rst
-recursive-include demo *.txt *.tex *.py *.h *.c *.f90 [M,m]akefile*
+recursive-include demo [M,m]akefile* *.py *.pyx *.i *.[hc]
+recursive-include demo .f2py_f2cmap *.pyf *.[fF]90
recursive-include conf *.py *.cfg
recursive-include src *.py *.pyx *.px[di] *.h *.c *.i *.cfg
recursive-include test *.py
recursive-include * [M,m]akefile
-recursive-include docs *.html
-recursive-include docs *.pdf
-recursive-include docs *.rst
+include docs/*.html
+include docs/*.pdf
+include docs/*.info
+include docs/*.[137]
+include docs/*.rst
recursive-include docs/usrman *
recursive-include docs/apiref *
recursive-include docs/source *
diff --git a/PKG-INFO b/PKG-INFO
index 532f041..3c194b3 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1,16 +1,68 @@
Metadata-Version: 1.1
Name: petsc4py
-Version: 1.1
+Version: 3.6.0
Summary: PETSc for Python
-Home-page: http://petsc4py.googlecode.com/
+Home-page: https://bitbucket.org/petsc/petsc4py/
Author: Lisandro Dalcin
Author-email: dalcinl at gmail.com
-License: Public Domain
-Download-URL: http://petsc4py.googlecode.com/files/petsc4py-1.1.tar.gz
-Description: Python bindings for PETSc libraries.
+License: BSD
+Download-URL: https://bitbucket.org/petsc/petsc4py/downloads/petsc4py-3.6.0.tar.gz
+Description: PETSc for Python
+ ================
+
+ Python bindings for PETSc.
+
+ Install
+ -------
+
+ If you have a working MPI implementation and the ``mpicc`` compiler
+ wrapper is on your search path, it highly recommended to install
+ ``mpi4py`` first::
+
+ $ pip install mpi4py
+
+ Ensure you have NumPy installed::
+
+ $ pip install numpy
+
+ and finally::
+
+ $ pip install petsc petsc4py
+
+ You can also install the in-development version of petsc4py with::
+
+ $ pip install Cython numpy mpi4py
+ $ pip install --no-deps git+https://bitbucket.org/petsc/petsc
+ $ pip install --no-deps git+https://bitbucket.org/petsc/petsc4py
+
+ or::
+
+ $ pip install Cython numpy mpi4py
+ $ pip install --no-deps https://bitbucket.org/petsc/petsc/get/master.tar.gz
+ $ pip install --no-deps https://bitbucket.org/petsc/petsc4py/get/master.tar.gz
+
+
+ Citations
+ ---------
+
+ If PETSc for Python been significant to a project that leads to an
+ academic publication, please acknowledge that fact by citing the
+ project.
+
+ * L. Dalcin, P. Kler, R. Paz, and A. Cosimo,
+ *Parallel Distributed Computing using Python*,
+ Advances in Water Resources, 34(9):1124-1139, 2011.
+ http://dx.doi.org/10.1016/j.advwatres.2011.04.013
+
+ * S. Balay, S. Abhyankar, M.F. Adams, J. Brown, P. Brune, K. Buschelman,
+ L. Dalcin, V. Eijkhout, W.D. Gropp, D. Kaushik, M.G. Knepley,
+ L. Curfman McInnes, K. Rupp, B.F. Smith, S. Zampini, and H. Zhang,
+ *PETSc Users Manual*, ANL-95/11 - Revision 3.6, 2015.
+ http://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf
+
Keywords: scientific computing,parallel computing,PETSc,MPI
Platform: POSIX
-Classifier: License :: Public Domain
+Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
@@ -18,8 +70,10 @@ Classifier: Programming Language :: C
Classifier: Programming Language :: C++
Classifier: Programming Language :: Cython
Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 2
+Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Classifier: Development Status :: 3 - Alpha
+Classifier: Development Status :: 5 - Production/Stable
Requires: numpy
Provides: petsc4py
diff --git a/README.rst b/README.rst
... 462656 lines suppressed ...
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