[med-svn] [pbgenomicconsensus] 04/05: Enable Arrow: add its dependency and enable its tests

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository pbgenomicconsensus.

commit cc6cffdacf1afaaf3da376a1c93072d9732233ce
Author: Afif Elghraoui <afif at debian.org>
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 <afif at debian.org>
-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))
- 
- 
-+ at unittest.skip("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

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