[med-svn] [circlator] 01/02: Enable build-time tests

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository circlator.

commit 4e5b6e9192b6d8bf6fe745b3914778def75e3317
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Fri Mar 18 00:51:36 2016 -0700

    Enable build-time tests
---
 debian/control                   |  1 +
 debian/patches/series            |  1 +
 debian/patches/spades-call.patch | 18 ++++++++++++++++++
 debian/rules                     | 10 +++++-----
 4 files changed, 25 insertions(+), 5 deletions(-)

diff --git a/debian/control b/debian/control
index 3a24e44..86c8fc2 100644
--- a/debian/control
+++ b/debian/control
@@ -15,6 +15,7 @@ Build-Depends:
 	python3-pymummer (>= 0.6.1),
 # Test-Depends:
 	python3-nose,
+	spades,
 Standards-Version: 3.9.7
 Homepage: http://sanger-pathogens.github.io/circlator/
 Vcs-Git: https://anonscm.debian.org/git/debian-med/circlator.git
diff --git a/debian/patches/series b/debian/patches/series
index 3ec7478..991a513 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 bundle-bioassemblyref.patch
+spades-call.patch
diff --git a/debian/patches/spades-call.patch b/debian/patches/spades-call.patch
new file mode 100644
index 0000000..b073a8e
--- /dev/null
+++ b/debian/patches/spades-call.patch
@@ -0,0 +1,18 @@
+Description: Fix the way spades is called by circlator
+ The wrapper script in the Debian packaged spades fails when called
+ as "python2 /usr/bin/spades.py". Our shebang lines handle the interpreter,
+ so circlator should only be concerned with calling spades directly.
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: no
+Last-Update: 2016-03-18
+--- circlator.orig/circlator/external_progs.py
++++ circlator/circlator/external_progs.py
+@@ -13,7 +13,7 @@
+ # This means we need to explicitly run SPAdes with python2.
+ class Spades(program.Program):
+     def exe(self):
+-        return 'python2 ' + shutil.which(self.path)
++        return shutil.which(self.path)
+ 
+ 
+ prog_to_env_var = {
diff --git a/debian/rules b/debian/rules
index 0a41e0c..5019b20 100755
--- a/debian/rules
+++ b/debian/rules
@@ -16,8 +16,8 @@ override_dh_auto_clean:
 	dh_auto_clean
 	$(RM) bio_assembly_refinement
 
-#override_dh_auto_test:
-#	PYBUILD_SYSTEM=custom \
-#	PYBUILD_TEST_ARGS="nosetests3 -v --where=bio_assembly_refinement/tests" dh_auto_test
-#	PYBUILD_SYSTEM=custom \
-#	PYBUILD_TEST_ARGS="nosetests3 -v --where=circlator/tests" dh_auto_test
+override_dh_auto_test:
+	PYTHONPATH=$(CURDIR)/bioassemblyrefinement \
+	nosetests3 -v \
+	--where=bioassemblyrefinement/bio_assembly_refinement/tests
+	PYTHONPATH=$(CURDIR) nosetests3 -v --where=circlator/tests

-- 
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