[med-svn] [Git][med-team/garli][master] 4 commits: Fix random seed before running tests to get (mostly!) reproducible results

Andreas Tille gitlab at salsa.debian.org
Tue Sep 4 11:38:35 BST 2018 

Andreas Tille pushed to branch master at Debian Med / garli


Commits:
6803ef08 by Andreas Tille at 2018-09-04T09:10:49Z
Fix random seed before running tests to get (mostly!) reproducible results

- - - - -
1be4eea8 by Andreas Tille at 2018-09-04T09:23:02Z
Leave bug open and document in README.Debian

- - - - -
f1c4df5f by Andreas Tille at 2018-09-04T09:33:51Z
Provide additional MPI version in separate package

- - - - -
0271bccd by Andreas Tille at 2018-09-04T09:56:39Z
Fix typo

- - - - -


9 changed files:

- + debian/README.Debian
- debian/changelog
- debian/control
- + debian/garli-mpi.1
- + debian/garli-mpi.links
- + debian/garli-mpi.manpages
- + debian/garli.manpages
- − debian/manpages
- debian/rules


Changes:

=====================================
debian/README.Debian
=====================================
@@ -0,0 +1,19 @@
+Garli for Debian
+================
+
+When building the package the build time test suite is run.  It has turned
+out that it does not pass for each random number initialisation, which is
+documented in a bug log
+
+    https://bugs.debian.org/907905
+
+To enable relieable package builds randseed was set from -1 to 1 in all
+test configurations.  It might be worth detailed inspection why there are
+random test failures.  Unfortunately this goes beyond the Debian packaging
+and was reported upstream.
+
+    https://github.com/Ashod/garli/issues/1
+
+Please check this issue on Github for further information.
+
+ -- Andreas Tille <tille at debian.org>  Tue, 04 Sep 2018 11:09:43 +0200


=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+garli (2.1-3) UNRELEASED; 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
+
+ -- Andreas Tille <tille at debian.org>  Tue, 04 Sep 2018 11:09:43 +0200
+
 garli (2.1-2) unstable; urgency=medium
 
   * Add some copyright holders


=====================================
debian/control
=====================================
@@ -5,6 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 10),
                libncl-dev,
+               libopenmpi-dev,
                ncl-tools,
                bc
 Standards-Version: 4.1.1
@@ -25,6 +26,21 @@ Description: phylogenetic analysis of molecular sequence data using maximum-like
  sequence evolution, and runs on all platforms. The latest version adds
  support for partitioned models and morphology-like datatypes.
 
+Package: garli-mpi
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+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
+ genetic algorithm, it rapidly searches the space of evolutionary trees
+ and model parameters to find the solution maximizing the likelihood
+ score. It implements nucleotide, amino acid and codon-based models of
+ sequence evolution, and runs on all platforms. The latest version adds
+ support for partitioned models and morphology-like datatypes.
+ .
+ This version of Garli is using MPI.
+
 Package: garli-examples
 Architecture: all
 Depends: ${misc:Depends}


=====================================
debian/garli-mpi.1
=====================================
@@ -0,0 +1,44 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH GARLI "1" "June 2016" "garli 2.1" "User Commands"
+.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]
+.SH DESCRIPTION
+GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for
+inferring phylogenetic trees. Using an approach similar to a classical
+genetic algorithm, it rapidly searches the space of evolutionary trees
+and model parameters to find the solution maximizing the likelihood
+score. It implements nucleotide, amino acid and codon-based models of
+sequence evolution, and runs on all platforms. The latest version adds
+support for partitioned models and morphology-like datatypes.
+.
+This is the MPI version of Garli.
+.SH OPTIONS
+.TP
+\fB\-i\fR, \fB\-\-interactive\fR
+interactive mode (allow and/or expect user feedback)
+.TP
+\fB\-b\fR, \fB\-\-batch\fR
+batch mode (do not expect user input)
+(batch is the default for the version you are running)
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+print version information and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+print this help and exit
+.TP
+\fB\-t\fR
+run internal tests (requires dataset and config file)
+.TP
+\fB\-V\fR
+validate: load config file and data, validate config file, data, starting trees
+and constraint files, print required memory and selected model, then exit
+.P
+NOTE: If no config filename is passed on the command line the program
+will look in the current directory for a file named "garli.conf"
+.PP
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.


=====================================
debian/garli-mpi.links
=====================================
@@ -0,0 +1 @@
+usr/lib/garli/bin/Garli-mpi	usr/bin/garli-mpi


=====================================
debian/garli-mpi.manpages
=====================================
@@ -0,0 +1 @@
+debian/garli-mpi.1


=====================================
debian/garli.manpages
=====================================
@@ -0,0 +1 @@
+debian/garli.1


=====================================
debian/manpages deleted
=====================================
@@ -1 +0,0 @@
-debian/*.1


=====================================
debian/rules
=====================================
@@ -2,8 +2,28 @@
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
+include /usr/share/dpkg/default.mk
+
 %:
 	dh $@
 
 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
+	make distclean
+	# Now build single processor binary
 	dh_auto_configure -- --with-ncl=/usr
+
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	cp -a tests tests.bak
+	# get (mostly!) reproducible test results and avoid failures as described in bug #907905
+	find tests -name "*.conf" -exec sed -i~ 's/randseed *= *-1/randseed = 1/' \{\} \;
+	dh_auto_test
+	# restore original test dir
+	rm -rf tests
+	mv tests.bak tests
+endif



View it on GitLab: https://salsa.debian.org/med-team/garli/compare/3757307062c53be19e20cf4cfb500a0a53054639...0271bccd209b9f5cd205ff4763c64e0785b7f208

-- 
View it on GitLab: https://salsa.debian.org/med-team/garli/compare/3757307062c53be19e20cf4cfb500a0a53054639...0271bccd209b9f5cd205ff4763c64e0785b7f208
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