Import mpgrafic_0.3.10-1.debian.tar.xz

[dgit import tarball mpgrafic 0.3.10-1 mpgrafic_0.3.10-1.debian.tar.xz]

diff --git a/README.Debian b/README.Debian
new file mode 100644 (file)
index 0000000..213c6b0
--- /dev/null
+++ b/README.Debian
@@ -0,0 +1,7 @@
+mpgrafic for Debian
+-------------------
+
+  * The --help option has an extra comment to help the user find
+    example files in /usr/share/doc/mpgrafic/examples.
+
+ -- Boud Roukema <boud-debian@cosmo.torun.pl>  Tue, 27 Dec 2016

diff --git a/changelog b/changelog
new file mode 100644 (file)
index 0000000..3260b54
--- /dev/null
+++ b/changelog
@@ -0,0 +1,94 @@
+mpgrafic (0.3.10-1) unstable; urgency=low
+
+  * Portability: Bypass fftw2/openmpi fortran-to-C
+    interfacing bug for s390x architecture by adding
+    fortran-to-C wrappers to directly call the fftw2 C function
+    called by src/mpgrafic.f90. This does not solve
+    Debian bug #851918 - openmpi and fftw2
+    have preprocessor macros MPI_COMM_F2C and FFTW_MPI_COMM_F2C,
+    respectively, which are supposed to handle this
+    cleanly, but at least on s390x, do not. However, version 0.3.10
+    should solve the bug from mpgrafic's point of view.
+    (Closes: #851923)
+
+ -- Boud Roukema <boud-debian@cosmo.torun.pl>  Sun, 29 Jan 2017 00:33:07 +0100
+
+mpgrafic (0.3.9-1) unstable; urgency=low
+
+  * portability: lower precision printed float mppower.f90;
+    partial code tidying based on strict compiler warnings;
+    iseed, seeds -> c_long -> up to 4e9 cores can run with different seeds
+    (if MaxParallelism is increased)
+
+ -- Boud Roukema <boud-debian@cosmo.torun.pl>  Mon, 23 Jan 2017 00:15:32 +0100
+
+mpgrafic (0.3.8-1) unstable; urgency=low
+
+  * v0.3.8  portability: reproducible lower precision printed floats;
+    iso_C_binding; avoid implementation-dependent integer sizes;
+    avoid implementation-dependent fortran kind values
+
+ -- Boud Roukema <boud-debian@cosmo.torun.pl>  Sun, 22 Jan 2017 03:32:46 +0100
+
+mpgrafic (0.3.7.8-1) unstable; urgency=low
+
+  * v0.3.7.7 regression test written but forgot to include it
+  * v0.3.7.8 regression test - precision requirements, 'kind' portability,
+    debian/rules - more diagnostic info
+
+ -- Boud Roukema <boud-debian@cosmo.torun.pl>  Fri, 20 Jan 2017 14:24:00 +0100
+
+mpgrafic (0.3.7.6-2) unstable; urgency=low
+
+  * debian/control vcs-* s/bitbucket/anonscm.debian/g ; metadata +bitbucket
+
+ -- Boud Roukema <boud-debian@cosmo.torun.pl>  Thu, 19 Jan 2017 14:53:29 +0100
+
+mpgrafic (0.3.7.6-1) UNRELEASED; urgency=low
+
+  * New upstream release
+  * v0.3.7.6 - correct shell error so that regression test logs output
+
+ -- Boud Roukema <boud-debian@cosmo.torun.pl>  Thu, 19 Jan 2017 12:25:06 +0100
+
+mpgrafic (0.3.7.5-1) unstable; urgency=low
+
+  * New upstream release
+  * v0.3.7.5 - revert allow-run-as-root changes;
+    drop foreign and 1.4 automake options;
+    downgrade debian status of regression test - log output but
+    continue the build, since failure is not (yet) evidence of a bug
+
+ -- Boud Roukema <boud-debian@cosmo.torun.pl>  Wed, 18 Jan 2017 20:30:22 +0100
+
+mpgrafic (0.3.7.4-1) unstable; urgency=low
+
+  * New upstream release
+  * v0.3.7.1 - configure.ac: prioritise mpifort over deprecated mpif90
+  * v0.3.7.2 - avoid mpirun running as root if possible
+  * v0.3.7.4 - allow running make check as root if openmpi@debian
+
+ -- Boud Roukema <boud-debian@cosmo.torun.pl>  Mon, 16 Jan 2017 23:18:27 +0100
+
+mpgrafic (0.3.7-1) unstable; urgency=low
+
+  * New upstream release
+  * v0.3.5 - regression test - fast full run should match v0.3.4 output
+  * v0.3.6 - minor configuration file simplifications
+  * v0.3.6.[1234] - regression test portability
+  * v0.3.7 - matches 0.3.6.4
+
+ -- Boud Roukema <boud-debian@cosmo.torun.pl>  Sun, 15 Jan 2017 02:06:54 +0100
+
+mpgrafic (0.3.4-1) unstable; urgency=low
+
+  * Minor upstream and debian changes to better satisfy debian standards
+  * Upstream replacement of use of obsolete pause command
+
+ -- Boud Roukema <boud-debian@cosmo.torun.pl>  Thu, 05 Jan 2017 23:47:21 +0100
+
+mpgrafic (0.3.2.1-1) unstable; urgency=low
+
+  * Initial release (Closes: #849427)
+
+ -- Boud Roukema <boud-debian@cosmo.torun.pl>  Tue, 27 Dec 2016 04:08:41 +0100

diff --git a/compat b/compat
new file mode 100644 (file)
index 0000000..ec63514
--- /dev/null
+++ b/compat
@@ -0,0 +1 @@
+9

diff --git a/control b/control
new file mode 100644 (file)
index 0000000..35f0a06
--- /dev/null
+++ b/control
@@ -0,0 +1,33 @@
+Source: mpgrafic
+Section: science
+Priority: optional
+Maintainer: Debian Astro Team <debian-astro-maintainers@lists.alioth.debian.org>
+Uploaders: Boud Roukema <boud-debian@cosmo.torun.pl>
+Build-Depends: debhelper (>= 9),
+               autotools-dev,
+               chrpath,
+               fftw-dev (>= 2.1.5),
+               libgsl-dev (>= 2.3),
+               gfortran,
+               mpi-default-dev,
+               mpi-default-bin,
+               perl
+Standards-Version: 3.9.8
+Homepage: http://www2.iap.fr/users/pichon/mpgrafic.html
+Vcs-Git: https://anonscm.debian.org/git/debian-astro/packages/mpgrafic.git
+Vcs-Browser: https://anonscm.debian.org/git/debian-astro/packages/mpgrafic.git
+
+Package: mpgrafic
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, mpi-default-bin
+Recommends: gnudatalanguage
+Description: MPI version of N-body initial conditions grafic package
+ mpgrafic produces initial conditions files for N-body simulations of
+ cosmological large-scale structure formation. It is a free-licensed,
+ MPI-parallelised, rewritten version of Ed Bertschinger's grafic-1
+ program, producing output files in the grafic format. It includes
+ options for an Eisenstein and Hu baryonic wiggles power spectrum, for
+ using a low-resolution map for large-scale modes in the spirit of
+ grafic-2, and together with constrfield, can be used for generating
+ constrained initial conditions. Details are given in Prunet et al
+ (2008) http://cdsads.u-strasbg.fr/abs/2008ApJS..178..179P.

diff --git a/copyright b/copyright
new file mode 100644 (file)
index 0000000..c1c79e5
--- /dev/null
+++ b/copyright
@@ -0,0 +1,30 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: mpgrafic
+Upstream-Contact: Boud Roukema  (boud cosmo.torun.pl)
+Source: https://broukema@bitbucket.org/broukema/mpgrafic.git
+
+Files: *
+Copyright: 2008-2016, Simon Prunet (prunet iap.fr)
+           2008-2016, Christophe Pichon
+           2016, Boud Roukema (boud-debian cosmo.torun.pl)
+License: GPL-2+
+ This program is free software; you can redistribute it
+ and/or modify it under the terms of the GNU General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later
+ version.
+ .
+ This program is distributed in the hope that it will be
+ useful, but WITHOUT ANY WARRANTY; without even the implied
+ warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE.  See the GNU General Public License for more
+ details.
+ .
+ You should have received a copy of the GNU General Public
+ License along with this package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA  02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL-2'.

diff --git a/docs b/docs
new file mode 100644 (file)
index 0000000..c17f037
--- /dev/null
+++ b/docs
@@ -0,0 +1,4 @@
+AUTHORS
+NEWS
+README
+TODO

diff --git a/mpgrafic.examples b/mpgrafic.examples
new file mode 100644 (file)
index 0000000..43721a8
--- /dev/null
+++ b/mpgrafic.examples
@@ -0,0 +1,8 @@
+Input.stdin
+Output.stdout
+gdl
+gdl/powerspec.pro
+gdl/read_grafic.pro
+gdl/read_white.pro
+gdl/write_grafic.pro
+idl

diff --git a/mpgrafic.manpages b/mpgrafic.manpages
new file mode 100644 (file)
index 0000000..05e6fd9
--- /dev/null
+++ b/mpgrafic.manpages
@@ -0,0 +1 @@
+mpgrafic.1

diff --git a/patches/01-find-debian-example-files.patch b/patches/01-find-debian-example-files.patch
new file mode 100644 (file)
index 0000000..5b0460a
--- /dev/null
+++ b/patches/01-find-debian-example-files.patch
@@ -0,0 +1,17 @@
+Description: Add an extra comment to the --help option so that the
+ user can more easily find example input/output files in
+ /usr/share/doc/mpgrafic/examples/. This is valid for debian, but not
+ for upstream in general.
+Forwarded: not-needed
+Author: Boud Roukema <boud-debian@cosmo.torun.pl>
+--- a/src/mpgrafic.f90
++++ b/src/mpgrafic.f90
+@@ -131,6 +131,8 @@
+         write(*,'(a)')'Most recent source code:'
+         write(*,'(a)')'git clone https://broukema@bitbucket.org/broukema/mpgrafic.git'
+         write(*,'(a)')''
++        write(*,'(a)')'Example input/output files: see /usr/share/doc/mpgrafic/examples/'
++        write(*,'(a)')''
+         write(*,'(a)')' -?, --help                 Give this help list'
+         write(*,'(a)')'     --np=INTEGER           Number of particles per dimension'
+         write(*,'(a)')'     --usage                Give a short usage message'

diff --git a/patches/02-force-regression-test-fail.patch b/patches/02-force-regression-test-fail.patch
new file mode 100644 (file)
index 0000000..fde0176
--- /dev/null
+++ b/patches/02-force-regression-test-fail.patch
@@ -0,0 +1,17 @@
+Description: Force the code regression test to fail by modifying
+ the random seed; this should normally not be included in debian/patches/series.
+ Use `quilt import <filename>' and later `quilt delete <filename>'
+ to temporarily apply this patch; `info quilt' for more info.
+Forwarded: not-needed
+Author: Boud Roukema <boud-debian@cosmo.torun.pl>
+--- a/Input.stdin
++++ b/Input.stdin
+@@ -12,7 +12,7 @@
+ 
+ 
+ 1
+-1234
++97531
+ white-outfile.dat
+ 0
+ noisefile_dummy.dat

diff --git a/patches/series b/patches/series
new file mode 100644 (file)
index 0000000..cd22ffe
--- /dev/null
+++ b/patches/series
@@ -0,0 +1 @@
+01-find-debian-example-files.patch

diff --git a/rules b/rules
new file mode 100755 (executable)
index 0000000..a75c6cf
--- /dev/null
+++ b/rules
@@ -0,0 +1,46 @@
+#!/usr/bin/make -f
+
+# Recommendations in https://wiki.debian.org/Hardening, motivated by lintian warnings.
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/buildflags.mk
+
+# To run the first test program in `make check', mpirun is called.
+# This may fail if run as root, e.g. during automated building in
+# a chroot gaol. So for debian builds, running mpirun - on a single
+# processor - is allowed.
+export MPI_ALLOW_RUN_AS_ROOT = --allow-run-as-root
+
+%:
+       dh $@  --with autotools-dev
+
+# https://lintian.debian.org/tags/binary-or-shlib-defines-rpath.html
+# https://wiki.debian.org/RpathIssue
+# TODO: Where is r(un)path inserted in upstream? [not obvious]
+override_dh_install:
+       chrpath -d $(CURDIR)/debian/mpgrafic/usr/bin/mpgrafic
+       dh_install
+
+# 2017-01-17: debian/0.3.7.5-1: Data on failures of the test script
+# regression-0.3.7.sh on various architectures is needed in order to
+# make both the source code and the test reproducible. This override
+# is intended to be temporary only, while obtaining data on failures
+# from the log files of builds.
+override_dh_auto_test:
+       # since v0.3.7.8: log a diagnostic, and then return a fail if
+       # dh_auto_test failed
+       if dh_auto_test ; then \
+        printf "+++regression test diagnostic+++\n"; \
+        grep ARCH_DEFAULT_MPI_IMPL /usr/share/mpi-default-dev/debian_defaults; \
+        printf "diff:\n"; \
+        diff -u Output.stdout.np32 Output.stdout.np32.tmp; \
+        printf "+++/regression test diagnostic+++\n"; else \
+        printf "+++regression test diagnostic+++\n"; \
+        grep ARCH_DEFAULT_MPI_IMPL /usr/share/mpi-default-dev/debian_defaults; \
+        printf "diff:\n"; \
+        diff -u Output.stdout.np32 Output.stdout.np32.tmp; \
+        uname -a; \
+        printf "Processors on this machine:\n"; \
+        grep processor /proc/cpuinfo; \
+        printf "+++/regression test diagnostic+++\n"; \
+        false ; fi

diff --git a/source/format b/source/format
new file mode 100644 (file)
index 0000000..163aaf8
--- /dev/null
+++ b/source/format
@@ -0,0 +1 @@
+3.0 (quilt)

diff --git a/source/options b/source/options
new file mode 100644 (file)
index 0000000..21f55ef
--- /dev/null
+++ b/source/options
@@ -0,0 +1 @@
+extend-diff-ignore = "(^|/)(config\.(sub|guess)|Makefile|src/.*\.mod|src/Makefile\.in|ic_.*[bxyz]|[pw].*\.dat|stamp-h1|test-suite\.log|Output.*\.tmp.*|reg.*sh\.[lt][or][gs])$"

diff --git a/upstream/metadata b/upstream/metadata
new file mode 100644 (file)
index 0000000..02ad943
--- /dev/null
+++ b/upstream/metadata
@@ -0,0 +1,16 @@
+ASCL-Id: 1304.014
+Name: mpgrafic
+Contact: boud-debian cosmo.torun.pl
+Repository: git@bitbucket.org:broukema/mpgrafic.git
+Repository-Browse: https://bitbucket.org/broukema/mpgrafic
+Bug-Database: https://bitbucket.org/broukema/mpgrafic/issues
+Reference:
+  Author: Prunet, S. and Pichon, C. and Aubert, D. and Pogosyan, D. and Teyssier, R. and Gottloeber, S.
+  Title: Initial Conditions For Large Cosmological Simulations
+  Journal: Astrophysical Journal Supplement Series
+  Year: 2008
+  Volume: 178
+  Pages: 179-188
+  DOI: 10.1086/590370
+  Eprint: https://arXiv.org/abs/0804.3536
+  URL: http://cdsads.u-strasbg.fr/abs/2008ApJS..178..179P

diff --git a/watch b/watch
new file mode 100644 (file)
index 0000000..18e82c8
--- /dev/null
+++ b/watch
@@ -0,0 +1,3 @@
+# watch control file for uscan
+version=3
+https://bitbucket.org/broukema/mpgrafic/downloads?tab=tags .*/v(\d\S+)\.tar\.gz debian uupdate