rathann pushed to gromacs (f22). "Merge branch 'master' into f22"
notifications at fedoraproject.org
notifications at fedoraproject.org
Mon Jun 15 09:37:56 UTC 2015
From 91cb199e0737d267a622f6f004fe3c8e621ab7dd Mon Sep 17 00:00:00 2001
From: Dominik 'Rathann' Mierzejewski <dominik at greysector.net>
Date: Mon, 15 Jun 2015 10:33:10 +0200
Subject: update to 5.0.5
- fix path to packaged dssp
- drop upstreamed patch
- move the large manual into a separate -doc subpackage
diff --git a/.gitignore b/.gitignore
index e698f45..88e87d9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -22,3 +22,5 @@ manual-4.0.pdf
/manual-4.6.5.pdf
/gromacs-5.0.4.tar.gz
/manual-5.0.4.pdf
+/gromacs-5.0.5.tar.gz
+/manual-5.0.5.pdf
diff --git a/gromacs-dssp-path.patch b/gromacs-dssp-path.patch
new file mode 100644
index 0000000..0ea4f19
--- /dev/null
+++ b/gromacs-dssp-path.patch
@@ -0,0 +1,21 @@
+diff -up gromacs-5.0.5/src/gromacs/gmxana/gmx_do_dssp.c.dssp gromacs-5.0.5/src/gromacs/gmxana/gmx_do_dssp.c
+--- gromacs-5.0.5/src/gromacs/gmxana/gmx_do_dssp.c.dssp 2015-05-06 23:18:00.000000000 +0200
++++ gromacs-5.0.5/src/gromacs/gmxana/gmx_do_dssp.c 2015-06-14 01:10:16.556983504 +0200
+@@ -441,7 +441,7 @@ int gmx_do_dssp(int argc, char *argv[])
+ "calling the dssp program. If you do not have the dssp program,",
+ "get it from http://swift.cmbi.ru.nl/gv/dssp. [THISMODULE] assumes ",
+ "that the dssp executable is located in ",
+- "[TT]/usr/local/bin/dssp[tt]. If this is not the case, then you should",
++ "[TT]/usr/bin/mkdssp[tt]. If this is not the case, then you should",
+ "set an environment variable [TT]DSSP[tt] pointing to the dssp",
+ "executable, e.g.: [PAR]",
+ "[TT]setenv DSSP /opt/dssp/bin/dssp[tt][PAR]",
+@@ -586,7 +586,7 @@ int gmx_do_dssp(int argc, char *argv[])
+
+ if ((dptr = getenv("DSSP")) == NULL)
+ {
+- dptr = "/usr/local/bin/dssp";
++ dptr = "/usr/bin/mkdssp";
+ }
+ if (!gmx_fexist(dptr))
+ {
diff --git a/gromacs-issue1716.patch b/gromacs-issue1716.patch
deleted file mode 100644
index 5711bfa..0000000
--- a/gromacs-issue1716.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-diff -up gromacs-5.0.4/src/gromacs/trajectoryanalysis/tests/angle.cpp.issue1716 gromacs-5.0.4/src/gromacs/trajectoryanalysis/tests/angle.cpp
---- gromacs-5.0.4/src/gromacs/trajectoryanalysis/tests/angle.cpp.issue1716 2014-07-07 15:03:16.000000000 +0200
-+++ gromacs-5.0.4/src/gromacs/trajectoryanalysis/tests/angle.cpp 2015-04-23 13:47:59.539750157 +0200
-@@ -184,21 +184,4 @@ TEST_F(AngleModuleTest, HandlesOneVsMult
- runTest(CommandLine(cmdline));
- }
-
--TEST_F(AngleModuleTest, HandlesOneVsMultipleVectorGroupsAngles)
--{
-- const char *const cmdline[] = {
-- "angle",
-- "-g1", "vector",
-- "-group1",
-- "resname RV1 and name A1 A2",
-- "resname RV3 RV4 and name A1 A2",
-- "-g2", "plane",
-- "-group2",
-- "resname RP1 RP2 and name A1 A2 A3",
-- "-binw", "60"
-- };
-- setTopology("angle.gro");
-- runTest(CommandLine(cmdline));
--}
--
- } // namespace
diff --git a/gromacs.spec b/gromacs.spec
index 48f8e43..8af90b2 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -5,7 +5,7 @@
%endif
Name: gromacs
-Version: 5.0.4
+Version: 5.0.5
Release: 1%{?dist}
Summary: Fast, Free and Flexible Molecular Dynamics
Group: Applications/Engineering
@@ -15,9 +15,9 @@ URL: http://www.gromacs.org
Source0: ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz
Source1: ftp://ftp.gromacs.org/pub/manual/manual-%{version}.pdf
Source6: gromacs-README.fedora
-# disable only the failing tests on i686
-# http://redmine.gromacs.org/issues/1716
-Patch0: gromacs-issue1716.patch
+# fix path to packaged dssp
+# https://bugzilla.redhat.com/show_bug.cgi?id=1203754
+Patch0: gromacs-dssp-path.patch
BuildRequires: cmake
BuildRequires: atlas-devel >= 3.10.1
@@ -66,7 +66,21 @@ It is developed for biomolecules like proteins, but the extremely high
performance means it is used also in several other field like polymer chemistry
and solid state physics.
-This package includes architecture independent data and documentation.
+This package includes architecture independent data and HTML documentation.
+
+
+%package doc
+Summary: GROMACS manual
+BuildArch: noarch
+
+%description doc
+GROMACS is a versatile and extremely well optimized package to perform
+molecular dynamics computer simulations and subsequent trajectory analysis.
+It is developed for biomolecules like proteins, but the extremely high
+performance means it is used also in several other field like polymer chemistry
+and solid state physics.
+
+This package the manual in PDF format.
%package devel
@@ -252,9 +266,7 @@ script.
%prep
%setup -q
-%ifarch i686
-%patch0 -p1 -b .issue1716
-%endif
+%patch0 -p1 -b .dssp
mkdir {serial,mpich,openmpi}{,_d}
%build
@@ -350,9 +362,11 @@ make DESTDIR=%{buildroot} INSTALL="install -p" install
cd ..
done
+mkdir -p %{buildroot}%{_docdir}/gromacs
+install -pm 644 AUTHORS COPYING README %{buildroot}%{_docdir}/gromacs
# Install manual & packager's note
-install -cpm 644 %{SOURCE1} manual.pdf
-install -cpm 644 %{SOURCE6} README.fedora
+install -cpm 644 %{SOURCE1} %{buildroot}%{_docdir}/gromacs/manual.pdf
+install -cpm 644 %{SOURCE6} %{buildroot}%{_docdir}/gromacs/README.fedora
pushd %{buildroot}
# Fix GMXRC file permissions
@@ -424,15 +438,19 @@ done
%{_bindir}/g_*
%files common
-%doc AUTHORS COPYING README manual.pdf README.fedora
+%{_docdir}/gromacs
+%exclude %{_docdir}/gromacs/manual.pdf
%config(noreplace) %{_sysconfdir}/bash_completion.d/gmx-completion*
%{_bindir}/GMXRC
%{_bindir}/GMXRC.bash
%{_mandir}/man1/gmx*.1*
%{_mandir}/man7/gromacs.7*
-%{_datadir}/%{name}/
+%{_datadir}/%{name}
%exclude %{_datadir}/%{name}/template
+%files doc
+%{_docdir}/gromacs/manual.pdf
+
%files libs
%{_libdir}/libgromacs*.so.*
@@ -469,6 +487,12 @@ done
%{_bindir}/GMXRC.csh
%changelog
+* Sat Jun 13 2015 Dominik 'Rathann' Mierzejewski <rpm at greysector.net> - 5.0.5-1
+- update to 5.0.5
+- fix path to packaged dssp
+- drop upstreamed patch
+- move the large manual into a separate -doc subpackage
+
* Tue Apr 14 2015 Dominik 'Rathann' Mierzejewski <rpm at greysector.net> - 5.0.4-1
- update to 5.0.4
- switch Motif library to original Motif (as it's in Fedora since long)
diff --git a/sources b/sources
index 2c791a9..d445cfe 100644
--- a/sources
+++ b/sources
@@ -1,2 +1,2 @@
-c177ae5fd6d71e2bec7369bc66cd082e gromacs-5.0.4.tar.gz
-c3767b2e05a07bd2fc3c1feec6e93805 manual-5.0.4.pdf
+206884042be656dc06fb73847a9af97f gromacs-5.0.5.tar.gz
+2927e4617c0eaefd0940c5af6dae87fa manual-5.0.5.pdf
--
cgit v0.10.2
http://pkgs.fedoraproject.org/cgit/gromacs.git/commit/?h=f22&id=03b21a0b9240e6d27fac51ad1682566fd0db7723
More information about the scm-commits
mailing list