Commit 2f4b5a3c authored by Nicholas Breen's avatar Nicholas Breen

* Apply DEP-3 headers to patches.

* Bump Standars-Version to 3.9.3.
parent 0d50e9fd
gromacs (4.5.5-3) UNRELEASED; urgency=low
[ Andreas Tille ]
* debian/upstream:
- copied citations from tasks/bio to debian/upstream
- make last citation conform to BibTeX syntax
[ Nicholas Breen ]
* patches/*: Tidy up with DEP-3 headers.
* rules: Remove more obsolete dpatch verbiage.
* control: Update to Standards-Version 3.9.3, no changes required.
-- Andreas Tille <tille@debian.org> Thu, 29 Mar 2012 16:29:18 +0200
gromacs (4.5.5-2) unstable; urgency=low
......
......@@ -4,7 +4,7 @@ Priority: extra
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders: Nicholas Breen <nbreen@debian.org>
Build-Depends: debhelper (>= 7.0.0), libfftw3-dev, libmpich2-dev, libopenmpi-dev (>= 1.2.4-5) [alpha amd64 armel armhf i386 ia64 powerpc powerpcspe sparc sparc64 kfreebsd-i386 kfreebsd-amd64 hurd-i386], lesstif2-dev, libx11-dev, zlib1g-dev, libgsl0-dev, gfortran [alpha], libxml2-dev, cmake
Standards-Version: 3.9.2
Standards-Version: 3.9.3
Homepage: http://www.gromacs.org/
Vcs-Browser: http://svn.debian.org/wsvn/debichem/
Vcs-Svn: svn://svn.debian.org/svn/debichem/unstable/gromacs/
......
#! /bin/sh /usr/share/dpatch/dpatch-run
## 11_readme.dpatch by Nicholas Breen <nbreen@ofb.net>
##
## All lines beginning with `## DP:' are a description of the patch.
## DP: Edit README to explain that this is not an official upstream build
Description: Edit README to explain that this is not an official upstream build
Origin: vendor
Author: Nicholas Breen <nbreen@debian.org>
@DPATCH@
diff -Nru gromacs-4.5-orig/README gromacs-4.5/README
--- gromacs-4.5-orig/README.orig 2010-08-11 17:36:13.817033358 -0700
+++ gromacs-4.5/README 2010-08-11 17:36:58.051395506 -0700
Index: gromacs-4.5.5/README
===================================================================
--- gromacs-4.5.5.orig/README 2011-09-21 18:48:00.298864534 -0700
+++ gromacs-4.5.5/README 2011-12-04 15:08:50.338009669 -0800
@@ -1,5 +1,5 @@
- Welcome to the official version of GROMACS!
+ Welcome to the Debian version of GROMACS!
If you are familiar with unix, it should be fairly trivial to compile and
install GROMACS. Installation instructions are available in the INSTALL file,
@@ -39,6 +39,13 @@
install GROMACS. Installation instructions are available in the INSTALL.*
@@ -41,6 +41,13 @@
under GPL, and that it must clearly be labeled as derived work. It should
not use the name "official GROMACS", and make sure support questions are
directed to you instead of the GROMACS developers.
......
#! /bin/sh /usr/share/dpatch/dpatch-run
## 31_manpages.dpatch by Nicholas Breen <nbreen@ofb.net>
##
## All lines beginning with `## DP:' are a description of the patch.
## DP: Minor spelling and header fixes for various man pages.
Description: Minor spelling and header fixes for various man pages.
Origin: vendor
Author: Nicholas Breen <nbreen@debian.org>
@DPATCH@
diff -Nru gromacs-4.5.4.orig/man/man1/g_analyze.1 gromacs-4.5.4/man/man1/g_analyze.1
--- gromacs-4.5.4.orig/man/man1/g_analyze.1 2011-04-25 12:27:52.705534377 -0700
+++ gromacs-4.5.4/man/man1/g_analyze.1 2011-04-25 12:28:40.016493755 -0700
Index: gromacs-4.5.5/man/man1/g_analyze.1
===================================================================
--- gromacs-4.5.5.orig/man/man1/g_analyze.1 2011-12-04 15:09:40.913982645 -0800
+++ gromacs-4.5.5/man/man1/g_analyze.1 2011-12-04 15:09:46.549979674 -0800
@@ -127,7 +127,7 @@
\&Option \fB \-gem\fR fits bimolecular rate constants ka and kb
\&(and optionally kD) to the hydrogen bond autocorrelation function
......@@ -18,9 +15,10 @@ diff -Nru gromacs-4.5.4.orig/man/man1/g_analyze.1 gromacs-4.5.4/man/man1/g_analy
\&O. Markovitch, J. Chem. Phys. 129:084505, 2008.
diff -Nru gromacs-4.5.4.orig/man/man1/g_dist.1 gromacs-4.5.4/man/man1/g_dist.1
--- gromacs-4.5.4.orig/man/man1/g_dist.1 2011-04-25 12:27:52.711534370 -0700
+++ gromacs-4.5.4/man/man1/g_dist.1 2011-04-25 12:28:54.983486921 -0700
Index: gromacs-4.5.5/man/man1/g_dist.1
===================================================================
--- gromacs-4.5.5.orig/man/man1/g_dist.1 2011-12-04 15:09:40.921982638 -0800
+++ gromacs-4.5.5/man/man1/g_dist.1 2011-12-04 15:09:46.549979674 -0800
@@ -31,7 +31,7 @@
\&With options \fB \-lt\fR and \fB \-dist\fR the number of contacts
\&of all atoms in group 2 that are closer than a certain distance
......@@ -30,9 +28,10 @@ diff -Nru gromacs-4.5.4.orig/man/man1/g_dist.1 gromacs-4.5.4/man/man1/g_dist.1
\&Other programs that calculate distances are \fB g_mindist\fR
diff -Nru gromacs-4.5.4.orig/man/man1/g_hydorder.1 gromacs-4.5.4/man/man1/g_hydorder.1
--- gromacs-4.5.4.orig/man/man1/g_hydorder.1 2011-04-25 12:27:52.714534366 -0700
+++ gromacs-4.5.4/man/man1/g_hydorder.1 2011-04-25 12:31:09.113551562 -0700
Index: gromacs-4.5.5/man/man1/g_hydorder.1
===================================================================
--- gromacs-4.5.5.orig/man/man1/g_hydorder.1 2011-12-04 15:09:40.929982634 -0800
+++ gromacs-4.5.5/man/man1/g_hydorder.1 2011-12-04 15:09:46.549979674 -0800
@@ -1,6 +1,6 @@
.TH g_hydorder 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
......@@ -41,9 +40,10 @@ diff -Nru gromacs-4.5.4.orig/man/man1/g_hydorder.1 gromacs-4.5.4/man/man1/g_hydo
.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_hydorder\fP
diff -Nru gromacs-4.5.4.orig/man/man1/g_mindist.1 gromacs-4.5.4/man/man1/g_mindist.1
--- gromacs-4.5.4.orig/man/man1/g_mindist.1 2011-04-25 12:27:52.716534364 -0700
+++ gromacs-4.5.4/man/man1/g_mindist.1 2011-04-25 12:29:45.817486302 -0700
Index: gromacs-4.5.5/man/man1/g_mindist.1
===================================================================
--- gromacs-4.5.5.orig/man/man1/g_mindist.1 2011-12-04 15:09:40.941982629 -0800
+++ gromacs-4.5.5/man/man1/g_mindist.1 2011-12-04 15:09:46.549979674 -0800
@@ -38,7 +38,7 @@
\&(between any pair of atoms from the respective groups)
\&and the number of contacts within a given
......@@ -53,9 +53,10 @@ diff -Nru gromacs-4.5.4.orig/man/man1/g_mindist.1 gromacs-4.5.4/man/man1/g_mindi
\&with multiple atoms in the first group is counted as one contact
\&instead of as multiple contacts.
\&With \fB \-or\fR, minimum distances to each residue in the first
diff -Nru gromacs-4.5.4.orig/man/man1/g_tune_pme.1 gromacs-4.5.4/man/man1/g_tune_pme.1
--- gromacs-4.5.4.orig/man/man1/g_tune_pme.1 2011-04-25 12:27:52.725534353 -0700
+++ gromacs-4.5.4/man/man1/g_tune_pme.1 2011-04-25 12:29:55.888492125 -0700
Index: gromacs-4.5.5/man/man1/g_tune_pme.1
===================================================================
--- gromacs-4.5.5.orig/man/man1/g_tune_pme.1 2011-12-04 15:09:40.949982623 -0800
+++ gromacs-4.5.5/man/man1/g_tune_pme.1 2011-12-04 15:09:46.549979674 -0800
@@ -410,7 +410,7 @@
If non\-negative, perform this many steps in the real run (overwrites nsteps from \fB .tpr\fR, add \fB .cpt\fR steps)
......@@ -65,9 +66,10 @@ diff -Nru gromacs-4.5.4.orig/man/man1/g_tune_pme.1 gromacs-4.5.4/man/man1/g_tune
.BI "\-deffnm" " string" " "
Set the default filename for all file options at launch time
diff -Nru gromacs-4.5.4.orig/man/man1/g_wham.1 gromacs-4.5.4/man/man1/g_wham.1
--- gromacs-4.5.4.orig/man/man1/g_wham.1 2011-04-25 12:27:52.726534352 -0700
+++ gromacs-4.5.4/man/man1/g_wham.1 2011-04-25 12:30:06.400498844 -0700
Index: gromacs-4.5.5/man/man1/g_wham.1
===================================================================
--- gromacs-4.5.5.orig/man/man1/g_wham.1 2011-12-04 15:09:40.957982619 -0800
+++ gromacs-4.5.5/man/man1/g_wham.1 2011-12-04 15:09:46.549979674 -0800
@@ -155,7 +155,7 @@
\&to the file defined with \fB \-oiact\fR. In verbose mode, all
\&autocorrelation functions (ACFs) are written to \fB hist_autocorr.xvg\fR.
......@@ -77,9 +79,10 @@ diff -Nru gromacs-4.5.4.orig/man/man1/g_wham.1 gromacs-4.5.4/man/man1/g_wham.1
\&reaction coordinate with a Gaussian (sigma provided with \fB \-acsig\fR,
\&see output in \fB iact.xvg\fR). Note that the IACTs are estimated by simple
\&integration of the ACFs while the ACFs are larger 0.05.
diff -Nru gromacs-4.5.5.orig//src/kernel/hizzie.c gromacs-4.5.5//src/kernel/hizzie.c
--- gromacs-4.5.5.orig//src/kernel/hizzie.c 2011-09-21 05:34:32.000000000 -0700
+++ gromacs-4.5.5//src/kernel/hizzie.c 2011-09-21 18:49:32.291850466 -0700
Index: gromacs-4.5.5/src/kernel/hizzie.c
===================================================================
--- gromacs-4.5.5.orig/src/kernel/hizzie.c 2011-12-04 15:09:40.969982613 -0800
+++ gromacs-4.5.5/src/kernel/hizzie.c 2011-12-04 15:09:46.549979674 -0800
@@ -211,7 +211,7 @@
/* A histidine residue exists that requires automated assignment, so
* doing the analysis of donors and acceptors is worthwhile. */
......@@ -89,9 +92,10 @@ diff -Nru gromacs-4.5.5.orig//src/kernel/hizzie.c gromacs-4.5.5//src/kernel/hizz
" protonation.");
snew(donor,natom);
diff -Nru gromacs-4.5.5.orig//src/kernel/readir.c gromacs-4.5.5//src/kernel/readir.c
--- gromacs-4.5.5.orig//src/kernel/readir.c 2011-09-21 18:01:47.814687957 -0700
+++ gromacs-4.5.5//src/kernel/readir.c 2011-09-21 18:49:53.900080215 -0700
Index: gromacs-4.5.5/src/kernel/readir.c
===================================================================
--- gromacs-4.5.5.orig/src/kernel/readir.c 2011-12-04 15:09:40.977982609 -0800
+++ gromacs-4.5.5/src/kernel/readir.c 2011-12-04 15:09:46.549979674 -0800
@@ -924,7 +924,7 @@
EETYPE("DispCorr", ir->eDispCorr, edispc_names);
CTYPE ("Extension of the potential lookup tables beyond the cut-off");
......@@ -101,9 +105,10 @@ diff -Nru gromacs-4.5.5.orig//src/kernel/readir.c gromacs-4.5.5//src/kernel/read
STYPE ("energygrp_table", egptable, NULL);
CTYPE ("Spacing for the PME/PPPM FFT grid");
RTYPE ("fourierspacing", opts->fourierspacing,0.12);
diff -Nru gromacs-4.5.5.orig//src/tools/gmx_genpr.c gromacs-4.5.5//src/tools/gmx_genpr.c
--- gromacs-4.5.5.orig//src/tools/gmx_genpr.c 2011-09-21 18:01:47.814687957 -0700
+++ gromacs-4.5.5//src/tools/gmx_genpr.c 2011-09-21 18:49:03.063538595 -0700
Index: gromacs-4.5.5/src/tools/gmx_genpr.c
===================================================================
--- gromacs-4.5.5.orig/src/tools/gmx_genpr.c 2011-12-04 15:09:40.989982602 -0800
+++ gromacs-4.5.5/src/tools/gmx_genpr.c 2011-12-04 15:09:46.549979674 -0800
@@ -134,7 +134,7 @@
nfn = opt2fn_null("-n",NFILE,fnm);
......
......@@ -5,7 +5,6 @@
# export DH_VERBOSE=1
PACKAGE := gromacs
include /usr/share/dpatch/dpatch.make
# OpenMPI is only supported on a subset of architectures at this time.
# This list should remain synced with the Build-Depends and the Architecture
......@@ -69,8 +68,8 @@ ifneq (,$(findstring alpha,$(DEB_HOST_ARCH)))
export F77=/usr/bin/gfortran
endif
configure: patch-stamp configure-stamp
configure-stamp: patch-stamp
configure: configure-stamp
configure-stamp:
dh_testdir
(mkdir -p build/basic; cd build/basic; cmake $(COMMON_CONFIG_PARAMS) -DGMX_MPI=OFF)
(mkdir -p build/basic-dp; cd build/basic-dp; cmake $(COMMON_CONFIG_PARAMS) -DGMX_MPI=OFF -DGMX_DOUBLE=ON)
......@@ -87,7 +86,7 @@ endif
touch $@
build: patch-stamp configure-stamp build-basic build-mpich build-openmpi
build: configure-stamp build-basic build-mpich build-openmpi
build-arch: build
build-indep: build
......@@ -119,12 +118,11 @@ endif
touch $@
clean: clean-patched unpatch
clean-patched:
clean:
dh_testdir
dh_testroot
rm -rf build
dh_clean patch-stamp build-basic build-mpich build-openmpi configure-stamp \
dh_clean build-basic build-mpich build-openmpi configure-stamp \
debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian
......@@ -256,7 +254,7 @@ endif
binary: binary-indep binary-arch
.PHONY: binary binary-arch binary-indep build clean clean-patched install install-basic install-mpich install-openmpi
.PHONY: binary binary-arch binary-indep build clean install install-basic install-mpich install-openmpi
# Because multiple versions of the same programs are created using the same source tree,
# the various build-* targets can't be compiled simultaneously.
......
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