[med-svn] [circlator] 01/07: Remove code to support now unnecessary second tarball

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository circlator.

commit 18c214d8c18d84f7bd31abfcf0a853fe27722948
Author: Afif Elghraoui <afif at debian.org>
Date:   Mon Aug 15 20:51:26 2016 -0700

    Remove code to support now unnecessary second tarball
    
    bioassembly-refinement is no longer needed.
---
 debian/README.source                       | 24 ------------------------
 debian/patches/bundle-bioassemblyref.patch | 23 -----------------------
 debian/patches/series                      |  1 -
 debian/rules                               | 11 -----------
 debian/watch                               |  8 +-------
 5 files changed, 1 insertion(+), 66 deletions(-)

diff --git a/debian/README.source b/debian/README.source
deleted file mode 100644
index 7f677ae..0000000
--- a/debian/README.source
+++ /dev/null
@@ -1,24 +0,0 @@
-circlator for Debian
--------------------
-
-The circlator package currently bundles bio_assembly_refinement,
-another Python package that does not warrant independent packaging.
-Circlator upstream declared an intent to bundle the necessary parts
-of it in an eventual release of Circlator, while the author of
-bio_assembly_refinement confirmed that it does not warrant an
-independent package [1].
-
-This package is thus currently built using multi-upstream tarballs.
-The secondary tarball is checked into the pristine-tar branch, but
-gbp will probably not handle it automatically for you.
-You can pull it out with pristine-tar checkout.
-It must be extracted into the top source directory with the
-extracted folder renamed as "bioassemblyrefinement".
-The compressed tarball should be placed next to the primary tarball
-in the source's parent directory.
-
-1. See the thread beginning at
-   https://lists.debian.org/debian-med/2016/03/msg00031.html
-
- -- Afif Elghraoui <afif at debian.org>, Fri, 18 Mar 2016 01:03:13 -0700
-
diff --git a/debian/patches/bundle-bioassemblyref.patch b/debian/patches/bundle-bioassemblyref.patch
deleted file mode 100644
index bbb7392..0000000
--- a/debian/patches/bundle-bioassemblyref.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-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 >= 3.12.1',
-         'pysam >= 0.8.1, <= 0.8.3',
-         'pymummer>=0.7.1',
--        'bio_assembly_refinement>=0.5.1',
-     ],
-     license='GPLv3',
-     classifiers=[
diff --git a/debian/patches/series b/debian/patches/series
index f9719e0..fe47d41 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
-bundle-bioassemblyref.patch
 spades-call.patch
 pysam-maxversion.patch
diff --git a/debian/rules b/debian/rules
index 5019b20..4f96279 100755
--- a/debian/rules
+++ b/debian/rules
@@ -8,16 +8,5 @@ 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
-	$(RM) bio_assembly_refinement
-
 override_dh_auto_test:
-	PYTHONPATH=$(CURDIR)/bioassemblyrefinement \
-	nosetests3 -v \
-	--where=bioassemblyrefinement/bio_assembly_refinement/tests
 	PYTHONPATH=$(CURDIR) nosetests3 -v --where=circlator/tests
diff --git a/debian/watch b/debian/watch
index 0a9d39e..d61a45f 100644
--- a/debian/watch
+++ b/debian/watch
@@ -2,10 +2,4 @@ version=4
 
 opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%circlator-$1.tar.gz%" \
     https://github.com/sanger-pathogens/circlator/releases \
-    (?:.*/)?v?(\d[\d\.]*)\.tar\.gz \
-    debian
-
-opts="component=bioassemblyrefinement" \
-    https://github.com/sanger-pathogens/bio_assembly_refinement/tags \
-    (?:.*/)?v?(\d[\d\.]*)\.tar\.gz \
-    ignore uupdate
+    (?:.*/)?v?(\d[\d\.]*)\.tar\.gz

-- 
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