[med-svn] [Git][med-team/garli][master] 6 commits: debhelper 11

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / garli


Commits:
48ac431b by Andreas Tille at 2018-09-04T10:38:49Z
debhelper 11

- - - - -
9798bf64 by Andreas Tille at 2018-09-04T10:38:53Z
Point Vcs fields to salsa.debian.org

- - - - -
2883f49d by Andreas Tille at 2018-09-04T10:38:53Z
Standards-Version: 4.2.1

- - - - -
cba93b1d by Andreas Tille at 2018-09-04T12:09:55Z
Fix installation

- - - - -
c1d7a502 by Andreas Tille at 2018-09-04T12:48:00Z
Better documentation of MPI version

- - - - -
eadfefee by Andreas Tille at 2018-09-04T13:20:25Z
Upload to unstable

- - - - -


8 changed files:

- debian/README.Debian
- debian/changelog
- debian/compat
- debian/control
- debian/garli-mpi.1
- + debian/garli-mpi.install
- debian/garli.install
- debian/rules


Changes:

=====================================
debian/README.Debian
=====================================
@@ -16,4 +16,17 @@ and was reported upstream.
 
 Please check this issue on Github for further information.
 
+
+The MPI version claims to be 32 bit based on this test in src/garlimain.cpp:
+
+	//I'm not sure that this is dependable or portable, but it is only for screen output, so isn't that important
+	int ptrSize = sizeof(int *);
+	if(ptrSize == 8)
+		is64bit = true;
+	else
+		is64bit = false;
+
+I think that test is simply wrong since compilation is 64 bit on amd64.
+
+
  -- Andreas Tille <tille at debian.org>  Tue, 04 Sep 2018 11:09:43 +0200


=====================================
debian/changelog
=====================================
@@ -1,12 +1,15 @@
-garli (2.1-3) UNRELEASED; urgency=medium
+garli (2.1-3) unstable; urgency=medium
 
   * d/rules: Fix random seed before running tests to get (mostly!) reproducible
     results
     Addresses: #907905 (since the FTBFS issue is solved severity will be reset
     to minor but I leave the bug open for further discussion)
   * Provide additional MPI version in separate package
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
 
- -- Andreas Tille <tille at debian.org>  Tue, 04 Sep 2018 11:09:43 +0200
+ -- Andreas Tille <tille at debian.org>  Tue, 04 Sep 2018 15:04:01 +0200
 
 garli (2.1-2) unstable; urgency=medium
 


=====================================
debian/compat
=====================================
@@ -1 +1 @@
-10
+11


=====================================
debian/control
=====================================
@@ -3,14 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                libncl-dev,
                libopenmpi-dev,
                ncl-tools,
                bc
-Standards-Version: 4.1.1
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/garli.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/garli.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/garli
+Vcs-Git: https://salsa.debian.org/med-team/garli.git
 Homepage: https://github.com/Ashod/garli
 
 Package: garli
@@ -29,7 +29,8 @@ Description: phylogenetic analysis of molecular sequence data using maximum-like
 Package: garli-mpi
 Architecture: any
 Depends: ${shlibs:Depends},
-         ${misc:Depends}
+         ${misc:Depends},
+         openmpi-bin
 Description: phylogenetic analysis of molecular sequence data using maximum-likelihood (MPI)
  GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for
  inferring phylogenetic trees. Using an approach similar to a classical


=====================================
debian/garli-mpi.1
=====================================
@@ -3,8 +3,7 @@
 .SH NAME
 garli \- phylogenetic analysis of molecular sequence data using maximum-likelihood (MPI version)
 .SH SYNOPSIS
-.B garli
-[\fI\,OPTION\/\fR] [\fI\,config filename\/\fR]
+\fBmpirun\fR [\fIMPI OPTIONS\fR] \fBgarli-mpi\fR -[# of times to execute config file] [\fI\,config filename\/\fR]
 .SH DESCRIPTION
 GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for
 inferring phylogenetic trees. Using an approach similar to a classical


=====================================
debian/garli-mpi.install
=====================================
@@ -0,0 +1 @@
+debian/mpi/*	usr/lib/garli/bin


=====================================
debian/garli.install
=====================================
@@ -1,2 +1 @@
 usr/bin		usr/lib/garli
-# debian/bin	usr


=====================================
debian/rules
=====================================
@@ -11,8 +11,8 @@ override_dh_auto_configure:
 	# First build MPI version of Garli
 	dh_auto_configure -- --with-ncl=/usr --enable-mpi
 	dh_auto_build
-	mkdir -p debian/$(DEB_SOURCE)-mpi/usr/lib/$(DEB_SOURCE)/bin
-	mv src/Garli debian/$(DEB_SOURCE)-mpi/usr/lib/$(DEB_SOURCE)/bin/Garli-mpi
+	mkdir -p debian/mpi
+	mv src/Garli debian/mpi/Garli-mpi
 	make distclean
 	# Now build single processor binary
 	dh_auto_configure -- --with-ncl=/usr



View it on GitLab: https://salsa.debian.org/med-team/garli/compare/0271bccd209b9f5cd205ff4763c64e0785b7f208...eadfefeef220c5c000fd3e57f33b814c3e29d2eb

-- 
View it on GitLab: https://salsa.debian.org/med-team/garli/compare/0271bccd209b9f5cd205ff4763c64e0785b7f208...eadfefeef220c5c000fd3e57f33b814c3e29d2eb
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