[med-svn] [circlator] 01/04: Adjust setup.py and d/rules to install bundled module

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository circlator.

commit 016efd484c8ac88ba7e4d64e74d4d8c57cea7e63
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Tue Mar 15 00:59:31 2016 -0700

    Adjust setup.py and d/rules to install bundled module
---
 debian/patches/bundle-bioassemblyref.patch | 23 +++++++++++++++++++++++
 debian/patches/series                      |  1 +
 debian/rules                               | 16 ++++++++++++++++
 3 files changed, 40 insertions(+)

diff --git a/debian/patches/bundle-bioassemblyref.patch b/debian/patches/bundle-bioassemblyref.patch
new file mode 100644
index 0000000..78004a7
--- /dev/null
+++ b/debian/patches/bundle-bioassemblyref.patch
@@ -0,0 +1,23 @@
+Description: Modify setup.py to also install bio_assembly_refinement
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: not-needed
+Last-Update: 2016-03-15
+--- circlator.orig/setup.py
++++ circlator/setup.py
+@@ -14,7 +14,7 @@
+     author='Martin Hunt, Nishadi De Silva',
+     author_email='path-help at sanger.ac.uk',
+     url='https://github.com/sanger-pathogens/circlator',
+-    scripts=glob.glob('scripts/*'),
++    scripts=glob.glob('scripts/*')+glob.glob('bioassemblyrefinement/scripts/*'),
+     test_suite='nose.collector',
+     tests_require=['nose >= 1.3'],
+     install_requires=[
+@@ -22,7 +22,6 @@
+         'pyfastaq >= 3.10.0',
+         'pysam >= 0.8.1',
+         'pymummer>=0.6.1',
+-        'bio_assembly_refinement>=0.5.0',
+     ],
+     license='GPLv3',
+     classifiers=[
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..3ec7478
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+bundle-bioassemblyref.patch
diff --git a/debian/rules b/debian/rules
index 4a7e6cd..0a41e0c 100755
--- a/debian/rules
+++ b/debian/rules
@@ -3,5 +3,21 @@
 #DH_VERBOSE = 1
 #include /usr/share/dpkg/default.mk
 
+export LC_ALL=C.UTF-8
+
 %:
 	dh $@ --with python3 --buildsystem=pybuild
+
+override_dh_auto_configure:
+	ln -sf bioassemblyrefinement/bio_assembly_refinement .
+	dh_auto_configure
+
+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

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