debian/changelog

+python-intervaltree-bio (1.0.1-3) unstable; urgency=medium
+
+  * Team upload.
+  * Fix autopkgtest
+    Closes: #920545
+  * debhelper 12
+  * Standards-Version: 4.3.0
+  * Secure URI in copyright format
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Remove trailing whitespace in debian/copyright
+
+ -- Andreas Tille <tille@debian.org>  Sun, 27 Jan 2019 00:10:54 +0100
+
 python-intervaltree-bio (1.0.1-2) unstable; urgency=medium
 
   * Team upload.

debian/compat

-11
+12

debian/control

@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Afif Elghraoui <afif@debian.org>
 Section: python
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
                dh-python,
                python-all,
                python-setuptools,
@@ -14,7 +14,7 @@ Build-Depends: debhelper (>= 11~),
 # Test-Depends:
                python-pytest,
                python3-pytest
-Standards-Version: 4.1.5
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/python-intervaltree-bio
 Vcs-Git: https://salsa.debian.org/med-team/python-intervaltree-bio.git
 Homepage: https://github.com/konstantint/intervaltree-bio

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: python-intervaltree-bio
 Upstream-Contact: Konstantin Tretyakov <kt@ut.ee>
 Source: https://github.com/konstantint/intervaltree-bio

debian/patches/0001-Replace-all-.search-calls-with-.overlap-in-tests-and.patch

+From: Hilko Bengen <bengen@debian.org>
+Date: Sat, 26 Jan 2019 22:56:49 +0100
+Bug-Debian: https://bugs.debian.org/920545
+Subject: [PATCH] Replace all .search() calls with .overlap()  in tests and
+ documentation
+
+---
+ README.rst                       |  2 +-
+ intervaltree_bio/__init__.py     | 10 +++++-----
+ tests/genomeintervaltree_test.py |  4 ++--
+ 3 files changed, 8 insertions(+), 8 deletions(-)
+
+--- a/README.rst
++++ b/README.rst
+@@ -34,7 +34,7 @@ The core example is loading the transcri
+ 
+ It is then possible to use the data structure to search known genes within given intervals::
+ 
+-    >> result = knownGene[b'chr1'].search(100000, 138529)
++    >> result = knownGene[b'chr1'].overlap(100000, 138529)
+     
+ It is possible to load other UCSC tables besides ``knownGene`` or specify custom URL or file to read the table from.
+ Consult the docstring of the ``GenomeIntervalTree.from_table`` method for more details.
+--- a/intervaltree_bio/__init__.py
++++ b/intervaltree_bio/__init__.py
+@@ -125,10 +125,10 @@ class GenomeIntervalTree(defaultdict):
+             >>> gtree = GenomeIntervalTree.from_bed(BytesIO(data))
+             >>> len(gtree)
+             1732
+-            >>> assert gtree[b'chr10'].search(22610878) == set([Interval(22610878, 22611813, [b'.', b'1000', b'.', b'471.725544438908', b'-1', b'3.21510858105313', b'389']), Interval(22610878, 22611813, [b'.', b'791', b'.', b'123.885507169449', b'-1', b'3.21510858105313', b'596'])])
+-            >>> assert gtree[b'chr10'].search(22611813) == set([])
+-            >>> assert gtree[b'chr1'].search(145036590, 145036594) == set([Interval(145036593, 145037123, [b'.', b'247', b'.', b'38.6720804428054', b'-1', b'3.06233123683911', b'265'])])
+-            >>> assert gtree[b'chr10'].search(145036594, 145036595) == set([])
++            >>> assert gtree[b'chr10'].overlap(22610878) == set([Interval(22610878, 22611813, [b'.', b'1000', b'.', b'471.725544438908', b'-1', b'3.21510858105313', b'389']), Interval(22610878, 22611813, [b'.', b'791', b'.', b'123.885507169449', b'-1', b'3.21510858105313', b'596'])])
++            >>> assert gtree[b'chr10'].overlap(22611813) == set([])
++            >>> assert gtree[b'chr1'].overlap(145036590, 145036594) == set([Interval(145036593, 145037123, [b'.', b'247', b'.', b'38.6720804428054', b'-1', b'3.06233123683911', b'265'])])
++            >>> assert gtree[b'chr10'].overlap(145036594, 145036595) == set([])
+             
+         '''
+         # We collect all intervals into a set of lists, and then put them all at once into the tree structures
+@@ -187,7 +187,7 @@ class GenomeIntervalTree(defaultdict):
+         >> knownGene = GenomeIntervalTree.from_table()
+         >> len(knownGene)
+         82960
+-        >> result = knownGene[b'chr1'].search(100000, 138529)
++        >> result = knownGene[b'chr1'].overlap(100000, 138529)
+         >> len(result)
+         1
+         >> list(result)[0].data['name']
+--- a/tests/genomeintervaltree_test.py
++++ b/tests/genomeintervaltree_test.py
+@@ -23,7 +23,7 @@ def test_knownGene(base_url):
+     knownGene_localurl = 'file:///%s' % os.path.abspath(knownGene_file)
+     knownGene = GenomeIntervalTree.from_table(url=knownGene_localurl, decompress=True) # Py3 downloads .gz files to local files with names not ending with .gz
+     assert len(knownGene) == 82960
+-    result = knownGene[b'chr1'].search(100000, 138529)
++    result = knownGene[b'chr1'].overlap(100000, 138529)
+     assert len(result) == 1
+     assert list(result)[0].data['name'] == b'uc021oeg.2'
+     
+@@ -33,7 +33,7 @@ def test_knownGene(base_url):
+     
+     knownGene = GenomeIntervalTree.from_table(url=knownGene_localurl, mode='exons', decompress=True)
+     assert len(knownGene) == 742493
+-    result = list(knownGene[b'chr1'].search(134772, 140566))
++    result = list(knownGene[b'chr1'].overlap(134772, 140566))
+     assert len(result) == 3
+     assert result[0].data == result[1].data and result[0].data == result[2].data
+     

debian/patches/series

 offline-test-data.patch
 disable-doctests.patch
 setup-cfg-deprecation.patch
+0001-Replace-all-.search-calls-with-.overlap-in-tests-and.patch

debian/rules

@@ -11,4 +11,6 @@ export PYBUILD_NAME=intervaltree-bio
 	dh $@ --with python2,python3 --buildsystem=pybuild
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	dh_auto_test -- --test-args "--verbose --datadir $(CURDIR)/debian/data"
+endif