--- python-scientific-2.4.11.orig/Src/MPI/compile.py +++ python-scientific-2.4.11/Src/MPI/compile.py @@ -12,10 +12,24 @@ mpicompiler = 'mpicc' sources='mpipython.c Scientific_mpi.c' +mpicompiler = 'mpicc' +mpiinclude = '/usr/include/lam' +executable = 'mpipython' + +if os.environ.has_key('USE_LAM'): + mpicompiler = 'mpicc.lam' + mpiinclude = '/usr/include/lam' + executable = 'mpipython.lam' +if os.environ.has_key('USE_MPICH'): + mpicompiler = 'mpicc.mpich' + mpiinclude = '/usr/lib/mpich/include' + executable = 'mpipython.mpich' -cmd = '%s %s -o mpipython -I%s %s -L%s -lpython%s %s %s' % \ +cmd = '%s %s -o %s -I../../Include -I%s -I%s %s -L%s -lpython%s %s %s' % \ (mpicompiler, cfgDict['LINKFORSHARED'], + executable, + mpiinclude, cfgDict['INCLUDEPY'], sources, cfgDict['LIBPL'], --- python-scientific-2.4.11.orig/Src/Scientific_netcdf.c +++ python-scientific-2.4.11/Src/Scientific_netcdf.c @@ -547,7 +547,7 @@ Py_XDECREF(self->attributes); Py_XDECREF(self->name); Py_XDECREF(self->mode); - PyMem_DEL(self); + PyObject_DEL(self); } /* Create file object */ @@ -1142,7 +1142,7 @@ free(self->name); Py_XDECREF(self->file); Py_XDECREF(self->attributes); - PyMem_DEL(self); + PyObject_DEL(self); } /* Create variable object */ --- python-scientific-2.4.11.orig/debian/copyright +++ python-scientific-2.4.11/debian/copyright @@ -0,0 +1,20 @@ +This package was debianized by Matthias Klose doko@debian.org on +Tue, 10 Mar 1998 12:43:50 +0100. + +It was downloaded from http://starship.python.net/crew/hinsen/scientific.html + +Copyright 1997-1999 by Konrad Hinsen. All Rights Reserved. + +Permission to use, copy, modify, and distribute this software and its +documentation for any purpose and without fee is hereby granted, +provided that the above copyright notice appear in all copies and that +both that copyright notice and this permission notice appear in +supporting documentation. + +THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, +INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO +EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, INDIRECT OR +CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF +USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR +OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR +PERFORMANCE OF THIS SOFTWARE. --- python-scientific-2.4.11.orig/debian/mpipython.1 +++ python-scientific-2.4.11/debian/mpipython.1 @@ -0,0 +1,12 @@ +.TH MPIPYTHON 1 "" "mpipython" +.SH NAME +mpipython \- Python interpreter with MPI support +.SH SYNOPSIS +.B mpipython +[\fIoptions\fR] \fIarguments \fR... +.SH DESCRIPTION +Python interpreter built with MPI support (MPI initialization must occur +before Python starts up, so a separate binary is needed). +.PP +.SH "SEE ALSO" +\fBpython\fP(1), \fBMPI\fP(1). --- python-scientific-2.4.11.orig/debian/lampython.postinst +++ python-scientific-2.4.11/debian/lampython.postinst @@ -0,0 +1,10 @@ +#! /bin/sh -e + +update-alternatives \ + --install /usr/bin/mpipython mpipython /usr/bin/mpipython.lam 30 \ + --slave /usr/share/man/man1/mpipython.1.gz mpipython.1.gz \ + /usr/share/man/man1/mpipython.lam.1.gz + +#DEBHELPER# + +exit 0 --- python-scientific-2.4.11.orig/debian/lampython.prerm +++ python-scientific-2.4.11/debian/lampython.prerm @@ -0,0 +1,9 @@ +#! /bin/sh -e + +if [ "$1" != "upgrade" ]; then + update-alternatives --remove mpipython /usr/bin/mpipython.lam +fi + +#DEBHELPER# + +exit 0 --- python-scientific-2.4.11.orig/debian/README +++ python-scientific-2.4.11/debian/README @@ -0,0 +1,14 @@ +python-scientific (ScientificPython) for DEBIAN +----------------------------------------------- + +This is the ScientificPython package (including the netCDF module) for +python, packaged for Debian GNU/Linux by Matthias Klose . + +Install the python-scientic-doc package for the documentation (located +in /usr/doc/python-scientific). + +MPI enabled python interpreters can be found in the mpipython (MPICH +based) and in the lampython (LAM based) packages. The executable +mpipython is handles by alternatives. + +Matthias Klose , Fri, 18 Apr 2003 09:16:57 +0200 --- python-scientific-2.4.11.orig/debian/changelog +++ python-scientific-2.4.11/debian/changelog @@ -0,0 +1,233 @@ +python-scientific (2.4.11-1ubuntu1) gutsy; urgency=low + + * NetCDF file causing invalid pointer error (LP: #113803) + * Changed maintainer to MOTU + * Added python-central (>= 0.5) to the build-depends field in debian/control + + -- Edoardo Batini Sun, 13 May 2007 22:44:54 +0200 + + +python-scientific (2.4.11-1build1) feisty; urgency=low + + * Rebuild for python2.5 as the default python version. + + -- Matthias Klose Mon, 15 Jan 2007 17:54:27 +0000 + +python-scientific (2.4.11-1) unstable; urgency=low + + * New upstream version. + + -- Matthias Klose Sun, 22 Oct 2006 02:09:13 +0000 + +python-scientific (2.4.9-6) unstable; urgency=low + + * Fix python-scientific / python-netcdf dependency. Closes: #374801. + + -- Matthias Klose Wed, 21 Jun 2006 19:25:28 +0000 + +python-scientific (2.4.9-5) unstable; urgency=low + + * Convert to the updated Python policy. Closes: #373351. + ... makes Scientific available for different python versions. + Closes: #319384. + + -- Matthias Klose Fri, 16 Jun 2006 22:02:26 +0000 + +python-scientific (2.4.9-4) unstable; urgency=low + + * python-scientific-doc: Install doc-base file (closes: #306514). + * python-netcdf: Add dependency on python-scientific, needed by + the Scientific/IO/NetCDF module (closes: #344090). + * Rebuild to fix dependency on libnetcdf3 (closes: #352232). + * Rebuild to fix dependency on lam4c2 (closes: #323414). + + -- Matthias Klose Sun, 12 Feb 2006 21:46:50 +0000 + +python-scientific (2.4.9-3) unstable; urgency=low + + * Rebuild for C++ ABI change. + + -- Matthias Klose Fri, 2 Sep 2005 20:16:53 +0000 + +python-scientific (2.4.9-2) unstable; urgency=low + + * python-mpi: Add dependency on python-scientific (thanks Yu Huang). + + -- Matthias Klose Sun, 3 Apr 2005 16:45:47 +0200 + +python-scientific (2.4.9-1) unstable; urgency=low + + * New upstream version. + + -- Matthias Klose Wed, 24 Nov 2004 07:18:34 +0100 + +python-scientific (2.4.6-2) unstable; urgency=low + + * Both mpichpython and lampython now provide 'mpipython' (closes: 268940). + * Change priority of lampython to extra. + * Update HTML docs (closes: #268256). + + -- Matthias Klose Tue, 21 Sep 2004 07:42:15 +0200 + +python-scientific (2.4.6-1) unstable; urgency=low + + * New upstream version. + + -- Matthias Klose Tue, 6 Jul 2004 01:07:07 +0200 + +python-scientific (2.4.5-2) unstable; urgency=low + + * lampython: depend on lam-runtime (closes: #236997). + + -- Matthias Klose Tue, 9 Mar 2004 21:00:34 +0100 + +python-scientific (2.4.5-1) unstable; urgency=low + + * New upstream version. + + -- Matthias Klose Sat, 24 Jan 2004 20:46:43 +0100 + +python-scientific (2.4.3-4) unstable; urgency=low + + * Update package description (closes: #209940). + + -- Matthias Klose Fri, 26 Sep 2003 10:31:29 +0200 + +python-scientific (2.4.3-3) unstable; urgency=low + + * Upload for python2.3 as the default python version. + * Add mpipython and lampython packages to handle both LAM based and + MPICH based setups (closes: #196962). + + -- Matthias Klose Fri, 8 Aug 2003 09:22:49 +0200 + +python-scientific (2.4.3-2) unstable; urgency=low + + * Build python-mpi package (Michael Banck). Closes: #186923. + + -- Matthias Klose Fri, 18 Apr 2003 08:30:48 +0200 + +python-scientific (2.4.3-1.1) unstable; urgency=low + + * Added a mpipython package including + - mpipython, as a replacement for the python executable + - the Scientific/MPI modules + - the mpi.py example file (formerly in the python-netcdf package) + * Added appropriate -I flags to Src/MPI/compile.py + * Remove stamp-build in debian/rules' clean-target + + -- Michael Banck Mon, 31 Mar 2003 04:50:21 +0200 + +python-scientific (2.4.3-1) unstable; urgency=low + + * New upstream version (closes: #179232). + + -- Matthias Klose Sun, 16 Mar 2003 15:17:06 +0100 + +python-scientific (2.4.1-1) unstable; urgency=low + + * New upstream version. + * Use python2.2 (closes: #160650). + * TODO: package BSPlib (http://www.bsp-worldwide.org/). + + -- Matthias Klose Thu, 12 Sep 2002 22:36:48 +0200 + +python-scientific (2.2-5) unstable; urgency=low + + * Add dependency to python-numeric-ext (closes: #127187). + + -- Matthias Klose Tue, 1 Jan 2002 18:01:32 +0100 + +python-scientific (2.2-4) unstable; urgency=low + + * Adapt dependencies to proposed python policy. + + -- Matthias Klose Sun, 11 Nov 2001 18:12:26 +0100 + +python-scientific (2.2-3) unstable; urgency=low + + * Only support one python version (2.1). Drop python2-scientific package. + + -- Matthias Klose Sat, 20 Oct 2001 18:39:57 +0200 + +python-scientific (2.2-2) unstable; urgency=low + + * Fix name of python2 interpreter in postinst (closes: #106860, #111183, + #111186). + + -- Matthias Klose Sat, 8 Sep 2001 15:47:16 +0200 + +python-scientific (2.2-1) unstable; urgency=low + + * New upstream release. + * No MPI support (yet). + + -- Matthias Klose Mon, 9 Apr 2001 18:29:16 +0200 + +python-scientific (2.0.1-2) unstable; urgency=low + + * Add build dependency (fixes #66392). + + -- Matthias Klose Wed, 5 Jul 2000 18:13:40 +0200 + +python-scientific (2.0.1-1) unstable; urgency=low + + * New upstream release. + + -- Matthias Klose Mon, 26 Jun 2000 17:59:03 +0200 + +python-scientific (2.0-2) unstable; urgency=low + + * Import math in Statistics.__init__.py (fixes #62604). + + -- Matthias Klose Thu, 4 May 2000 01:39:51 +0200 + +python-scientific (2.0-1) unstable; urgency=low + + * Final release. + + -- Matthias Klose Sat, 19 Feb 2000 13:21:58 +0100 + +python-scientific (2.0-0pre2) unstable; urgency=low + + * usr/doc -> usr/share/doc transition + + -- Matthias Klose Fri, 7 Jan 2000 16:12:35 +0100 + +python-scientific (2.0-0pre1) frozen unstable; urgency=low + + * New upstream version ScientificPython 2.0b1 (include python-netcdf). + + -- Matthias Klose Fri, 20 Aug 1999 20:51:39 +0200 + +python-netcdf (1.03-3) frozen unstable; urgency=low + + * Recompiled with new libc. + * Make lintian happy. + + -- Matthias Klose Thu, 26 Nov 1998 22:40:11 +0200 + +python-netcdf (1.03-2) frozen unstable; urgency=low + + * Adopted python policy to install in /usr/lib/python1.5/site-packages. + + -- Matthias Klose Wed, 29 Apr 1998 12:30:25 +0200 + +python-netcdf (1.03-1) unstable; urgency=low + + * Maintainer change + * new "upstream patch" fixes core dump when reading netCDF files + + -- Matthias Klose Fri, 20 Mar 1998 10:18:57 +0100 + +python-netcdf (1.0-2) unstable; urgency=low + + * Temporary maintainer change. + + -- Gregor Hoffleit Sun, 15 Mar 1998 12:44:37 +0100 + +python-netcdf (1.0-1) unstable; urgency=low + + * Initial Release. + + -- Matthias Klose Tue, 10 Mar 1998 12:43:50 +0100 --- python-scientific-2.4.11.orig/debian/mpichpython.postinst +++ python-scientific-2.4.11/debian/mpichpython.postinst @@ -0,0 +1,10 @@ +#! /bin/sh -e + +update-alternatives \ + --install /usr/bin/mpipython mpipython /usr/bin/mpipython.mpich 10 \ + --slave /usr/share/man/man1/mpipython.1.gz mpipython.1.gz \ + /usr/share/man/man1/mpipython.mpich.1.gz + +#DEBHELPER# + +exit 0 --- python-scientific-2.4.11.orig/debian/mpichpython.prerm +++ python-scientific-2.4.11/debian/mpichpython.prerm @@ -0,0 +1,9 @@ +#! /bin/sh -e + +if [ "$1" != "upgrade" ]; then + update-alternatives --remove mpipython /usr/bin/mpipython.mpich +fi + +#DEBHELPER# + +exit 0 --- python-scientific-2.4.11.orig/debian/watch +++ python-scientific-2.4.11/debian/watch @@ -0,0 +1,3 @@ +version=2 +http://starship.python.net/~hinsen/ScientificPython/ \ + .*ScientificPython-([\d\.]*)\.tar\.gz --- python-scientific-2.4.11.orig/debian/python-scientific-doc.doc-base +++ python-scientific-2.4.11/debian/python-scientific-doc.doc-base @@ -0,0 +1,14 @@ +Document: python-scientific-doc +Title: ScientificPython User's Guide +Author: Konrad Hinsen +Abstract: ScientificPython is a collection of Python modules that are useful + for scientific computing. This manual describes version 2.4 of + ScientificPython. +Section: Apps/Programming + +Format: html +Index: /usr/share/doc/python-scientific/HTML/Scientific.html +Files: /usr/share/doc/python-scientific/HTML + +Format: pdf +Files: /usr/share/doc/python-scientific/PDF/manual.pdf --- python-scientific-2.4.11.orig/debian/control +++ python-scientific-2.4.11/debian/control @@ -0,0 +1,69 @@ +Source: python-scientific +Section: python +Priority: optional +Maintainer: Ubuntu MOTU Developers +XSBC-Original-Maintainer: Matthias Klose +Standards-Version: 3.7.2 +XS-Python-Version: all +Build-Depends: debhelper (>= 5.0.37.1), python-all-dev (>= 2.3.5-9), netcdfg-dev, python-numeric-ext (> 24.2-3), libmpich1.0-dev, lam4-dev | lam-dev, python-central (>= 0.5) + +Package: python-scientific +Architecture: all +Depends: ${python:Depends}, python-numeric-ext (>= 24.2-3), python-netcdf (>= 2.4.11) +Recommends: python-tk (>= 2.4.3) +Suggests: python-scientific-doc +Provides: ${python:Provides} +XB-Python-Version: ${python:Versions} +Description: Python modules useful for scientific computing + ScientificPython is a collection of Python modules that are + useful for scientific computing. Most modules are rather general, + others belong to specific domains and will be of interest to only a + small number of users (e.g. the module Scientific.IO.PDB). Almost all + modules make extensive use of Numerical Python (NumPy) + +Package: python-netcdf +Architecture: any +Depends: ${python:Depends}, python-numeric-ext (>= 24.2-3), ${shlibs:Depends}, python-scientific (>= ${Source-Version}) +Provides: ${python:Provides} +XB-Python-Version: ${python:Versions} +Description: A netCDF interface for Python + A Python module to access netCDF files. NetCDF (network Common Data Form) + is an interface for scientific data access and a freely-distributed + software library that provides an implementation of the interface. + +Package: python-scientific-doc +Architecture: all +Section: doc +Depends: python-numeric (>= 24.2-3) +Description: Python modules useful for scientific computing + ScientificPython is a collection of Python modules that are + useful for scientific computing. Most modules are rather general, + others belong to specific domains and will be of interest to only a + small number of users (e.g. the module Scientific.IO.PDB). Almost all + modules make extensive use of Numerical Python (NumPy) + +Package: python-mpi +Architecture: all +Depends: ${python:Depends}, python-scientific (= ${Source-Version}) +XB-Python-Version: ${python:Versions} +Description: MPI module for Python + MPI (Message Passing Interface, message-based parallel programming) + support for Python. + +Package: mpichpython +Architecture: any +Depends: ${python:Depends}, python-mpi (>= ${Source-Version}), ${shlibs:Depends} +Conflicts: python-mpi (<< 2.4.3-3) +Provides: mpipython +Description: MPI-enhanced Python interpreter (MPICH based version) + Provides a python interpreter with MPI (Message Passing Interface, + message-based parallel programming) support. + +Package: lampython +Architecture: any +Priority: extra +Depends: ${python:Depends}, python-mpi (>= ${Source-Version}), lam-runtime, ${shlibs:Depends} +Provides: mpipython +Description: MPI-enhanced Python interpreter (LAM based version) + Provides a python interpreter with MPI (Message Passing Interface, + message-based parallel programming) support. --- python-scientific-2.4.11.orig/debian/rules +++ python-scientific-2.4.11/debian/rules @@ -0,0 +1,157 @@ +#!/usr/bin/make -f +# Made with the aid of debmake, by Christoph Lameter, +# based on the sample debian/rules file for GNU hello by Ian Jackson. + +export SHELL=bash + +pv = $(shell pyversions -vd) +PYVERS = $(shell pyversions -vs) +PYTHON = /usr/bin/python #$(pv) + +p_sci = python-scientific +p_cdf = python-netcdf +p_doc = $(p_sci)-doc +p_mpi = python-mpi +p_pympi = mpichpython +p_pylam = lampython + +d_sci = debian/$(p_sci) +d_cdf = debian/$(p_cdf) +d_doc = debian/$(p_doc) +d_mpi = debian/$(p_mpi) +d_pympi = debian/$(p_pympi) +d_pylam = debian/$(p_pylam) + +build: stamp-build +stamp-build: + dh_testdir + set -e; \ + for v in $(PYVERS); do \ + python$$v setup.py build; \ + done + rm -f Src/MPI/*.o + cd Src/MPI && USE_LAM=yes $(PYTHON) compile.py + rm -f Src/MPI/*.o + cd Src/MPI && USE_MPICH=yes $(PYTHON) compile.py + touch stamp-build + +cdf_dirs = \ + usr/lib/python$(pv)/site-packages \ + usr/include/python$(pv) \ + usr/share/doc/$(p_cdf)/examples + +sci_dirs = \ + usr/lib/python$(pv)/site-packages \ + usr/share/doc/$(p_sci) + +doc_dirs = \ + usr/share/doc/$(p_sci) \ + usr/share/doc/$(p_doc) + +mpi_dirs = \ + usr/lib/python$(pv)/site-packages \ + usr/share/doc/$(p_mpi)/examples \ + usr/bin + +pympi_dirs = \ + usr/share/doc/ \ + usr/bin \ + usr/share/man/man1 + +pylam_dirs = \ + usr/share/doc/ \ + usr/bin \ + usr/share/man/man1 + +install: build + dh_testdir + dh_testroot + dh_clean -k + + dh_installdirs -p$(p_sci) $(sci_dirs) + dh_installdirs -p$(p_doc) $(doc_dirs) + dh_installdirs -p$(p_cdf) $(cdf_dirs) + dh_installdirs -p$(p_mpi) $(mpi_dirs) + dh_installdirs -p$(p_pympi) $(pympi_dirs) + dh_installdirs -p$(p_pylam) $(pylam_dirs) + + set -e; \ + for v in $(PYVERS); do \ + mkdir -p $(d_sci)/usr/lib/python$(pv)/site-packages; \ + mkdir -p $(d_cdf)/usr/lib/python$(pv)/site-packages; \ + python$$v setup.py install --prefix=`pwd`/$(d_sci)/usr; \ + done + -find debian -name '*.py[co]' | xargs rm -f + + DH_COMPAT=2 dh_movefiles -v -p$(p_mpi) --sourcedir=$(d_sci) \ + usr/lib/python*/site-packages/Scientific/MPI \ + usr/include/python*/Scientific/{PyMPI_API.h,mpimodule.h} + + install -m775 Src/MPI/mpipython.mpich $(d_pympi)/usr/bin/ + install -m775 Src/MPI/mpipython.lam $(d_pylam)/usr/bin/ + cp -p debian/mpipython.1 $(d_pympi)/usr/share/man/man1/mpipython.mpich.1 + cp -p debian/mpipython.1 $(d_pylam)/usr/share/man/man1/mpipython.lam.1 + + -find $(d_sci) $(d_sci2) -name '*.py[co]' | xargs rm -f + + DH_COMPAT=2 dh_movefiles -v -p$(p_cdf) --sourcedir=$(d_sci) \ + usr/lib/python*/site-packages/Scientific/linux2 \ + usr/include/python*/Scientific/netcdfmodule.h + + rm -rf $(d_sci)/usr/include + +clean: + dh_testdir + rm -f stamp-build + rm -rf `find -name build -type d` + rm -f `find . -name '*.py[co]'` + rm -f Src/MPI/mpipython{,.lam,.mpich} Src/MPI/*.o + dh_clean + +binary-indep: install + dh_testdir + dh_testroot + + cp -a Doc/* \ + $(d_doc)/usr/share/doc/$(p_sci)/. + + dh_installdocs -p$(p_sci) -p$(p_doc) README + dh_installdocs -p$(p_mpi) README.MPI debian/README + dh_installchangelogs -i + cp -p Examples/mpi.py $(d_mpi)/usr/share/doc/$(p_mpi)/examples/. + dh_compress -i -X.py -X.c -X.pdf + dh_fixperms -i + dh_pycentral -i + dh_python -i + dh_installdeb -i + dh_shlibdeps -i + dh_gencontrol -i + dh_makeshlibs -i + dh_md5sums -i + dh_builddeb -i + +binary-arch: install + dh_testdir + dh_testroot + + dh_installdocs -p$(p_cdf) README + ln -sf $(p_mpi) $(d_pympi)/usr/share/doc/$(p_pympi) + ln -sf $(p_mpi) $(d_pylam)/usr/share/doc/$(p_pylam) + + dh_installchangelogs -a + dh_installexamples -p$(p_cdf) Examples/* + rm -f $(d_cdf)/usr/share/doc/$(p_cdf)/examples/mpi.py + dh_strip -a + dh_compress -a -X.py -X.c + dh_fixperms -a + dh_pycentral -a + dh_installdeb -a + dh_shlibdeps -a + dh_gencontrol -a + dh_makeshlibs -a + dh_md5sums -a + dh_builddeb -a + +binary: binary-indep binary-arch + +.PHONY: binary binary-arch binary-indep clean checkroot --- python-scientific-2.4.11.orig/debian/compat +++ python-scientific-2.4.11/debian/compat @@ -0,0 +1 @@ +5 \ No newline at end of file