[med-svn] [pbgenomicconsensus] 02/07: Revert "Enable Arrow: add its dependency and enable its tests"

[Afif Elghraoui]

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commit 76d77845274114f8caf160048101f5b452cd0a49
Author: Afif Elghraoui <afif at debian.org>
Date:   Sat Jan 21 15:36:40 2017 -0800

    Revert "Enable Arrow: add its dependency and enable its tests"
    
    This reverts commit cc6cffdacf1afaaf3da376a1c93072d9732233ce.
    
    We don't have python-consensuscore2 anymore, so we can't enable
    Arrow.
    The quilt patch also needed a slight update.
---
 debian/control                           |  1 -
 debian/patches/disable-arrow-tests.patch | 25 +++++++++++++++++++++++++
 debian/patches/series                    |  1 +
 3 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 7b5afde..4938c3a 100644
--- a/debian/control
+++ b/debian/control
@@ -11,7 +11,6 @@ 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
new file mode 100644
index 0000000..3cca9b7
--- /dev/null
+++ b/debian/patches/disable-arrow-tests.patch
@@ -0,0 +1,25 @@
+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/Makefile
++++ pbgenomicconsensus/Makefile
+@@ -15,13 +15,13 @@
+ 	# 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
+ 	# down the development cycle, so aren't run by "tests"
+ 	# target.
+-	PATH=`pwd`:$(PATH) cram --verbose tests/cram/extra/*.t
++	PATH=`pwd`:$(PATH) cram --verbose ` ls tests/cram/extra/*.t | grep -v arrow`
+ 
+ internal-tests:
+ 	# Long running tests that depend on files located on PacBio internal NFS
diff --git a/debian/patches/series b/debian/patches/series
index 00448f4..9a84c11 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,5 @@
 spelling.patch
 verbose-testing.patch
+disable-arrow-tests.patch
 no-poa-convenience-script.patch
 missing-testdata.patch

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