[med-svn] [Git][med-team/python-intervaltree-bio][master] 7 commits: Fix autopkgtest

Andreas Tille gitlab at salsa.debian.org
Sat Jan 26 23:14:58 GMT 2019 

Andreas Tille pushed to branch master at Debian Med / python-intervaltree-bio


Commits:
c3d0bbb7 by Andreas Tille at 2019-01-26T23:09:11Z
Fix autopkgtest

- - - - -
a7156987 by Andreas Tille at 2019-01-26T23:09:33Z
debhelper 12

- - - - -
a5f103d5 by Andreas Tille at 2019-01-26T23:09:36Z
Standards-Version: 4.3.0

- - - - -
db415d34 by Andreas Tille at 2019-01-26T23:09:36Z
Secure URI in copyright format

- - - - -
1c55981c by Andreas Tille at 2019-01-26T23:10:54Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test target

- - - - -
57f37c6c by Andreas Tille at 2019-01-26T23:10:54Z
Remove trailing whitespace in debian/copyright

- - - - -
ff0b3164 by Andreas Tille at 2019-01-26T23:14:20Z
Upload to unstable

- - - - -


7 changed files:

- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- + debian/patches/0001-Replace-all-.search-calls-with-.overlap-in-tests-and.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+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 at debian.org>  Sun, 27 Jan 2019 00:10:54 +0100
+
 python-intervaltree-bio (1.0.1-2) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/compat
=====================================
@@ -1 +1 @@
-11
+12


=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Afif Elghraoui <afif at 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
=====================================
@@ -1,4 +1,4 @@
-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 at ut.ee>
 Source: https://github.com/konstantint/intervaltree-bio
@@ -26,6 +26,6 @@ License: MIT
  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
  IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
- CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, 
- TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
  SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.


=====================================
debian/patches/0001-Replace-all-.search-calls-with-.overlap-in-tests-and.patch
=====================================
@@ -0,0 +1,69 @@
+From: Hilko Bengen <bengen at 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
=====================================
@@ -1,3 +1,4 @@
 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



View it on GitLab: https://salsa.debian.org/med-team/python-intervaltree-bio/compare/c8f73b76c262462f29be9be1e2a41ed073bb7f1a...ff0b316465ef27021020403c57cbf19d793efeb8

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View it on GitLab: https://salsa.debian.org/med-team/python-intervaltree-bio/compare/c8f73b76c262462f29be9be1e2a41ed073bb7f1a...ff0b316465ef27021020403c57cbf19d793efeb8
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