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commit cc6cffdacf1afaaf3da376a1c93072d9732233ce Author: Afif Elghraoui <[email protected]> Date: Sat Jul 23 20:51:08 2016 -0700 Enable Arrow: add its dependency and enable its tests This version of GenomicConsensus is now compatible with the version of consensuscore2 packaged in Debian. --- debian/control | 1 + debian/patches/disable-arrow-tests.patch | 28 ---------------------------- debian/patches/series | 1 - 3 files changed, 1 insertion(+), 29 deletions(-) diff --git a/debian/control b/debian/control index 888c5e1..107d5a3 100644 --- a/debian/control +++ b/debian/control @@ -11,6 +11,7 @@ Build-Depends: python-all, python-setuptools, python-pbconsensuscore (>= 1.0.1), + python-consensuscore2, python-pbcore (>= 1.2.9), python-pbcommand (>= 0.3.20), python-h5py (>= 2.0.1), diff --git a/debian/patches/disable-arrow-tests.patch b/debian/patches/disable-arrow-tests.patch deleted file mode 100644 index 73c4d69..0000000 --- a/debian/patches/disable-arrow-tests.patch +++ /dev/null @@ -1,28 +0,0 @@ -Description: Disable tests for Arrow - These tests need ConsensusCore2, and the version currently packaged in - Debian is newer than this GenomicConsensus version and not compatible. - The tests are thus expected to fail in this situation. -Author: Afif Elghraoui <[email protected]> -Forwarded: not-needed -Last-Update: 2016-07-08 ---- pbgenomicconsensus.orig/tests/unit/test_tool_contract.py -+++ pbgenomicconsensus/tests/unit/test_tool_contract.py -@@ -36,6 +36,7 @@ - self.assertTrue(isinstance(ds, ContigSet)) - - [email protected]("Compatible version of ConsensusCore2 isn't available") - class TestVariantCallerArrow(TestVariantCaller): - TASK_OPTIONS = { - "genomic_consensus.task_options.algorithm": "arrow", ---- pbgenomicconsensus.orig/Makefile -+++ pbgenomicconsensus/Makefile -@@ -15,7 +15,7 @@ - # Unit tests - nosetests -v --with-xunit tests/unit - # End-to-end tests -- PATH=`pwd`:$(PATH) cram --verbose tests/cram/*.t -+ PATH=`pwd`:$(PATH) cram --verbose `ls tests/cram/*.t | grep -v -e arrow -e bad_input` - - extra-tests: - # Tests that need to be run by Jenkins but are slowing diff --git a/debian/patches/series b/debian/patches/series index 95723a6..7db6f24 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,4 +1,3 @@ spelling.patch verbose-testing.patch -disable-arrow-tests.patch no-poa-convenience-script.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbgenomicconsensus.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
