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 <[email protected]> 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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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