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 <[email protected]> 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 <[email protected]. Uploaders: Afif Elghraoui <[email protected]> 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 <[email protected]> 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 <[email protected]> +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 -- View it on GitLab: https://salsa.debian.org/med-team/python-intervaltree-bio/compare/c8f73b76c262462f29be9be1e2a41ed073bb7f1a...ff0b316465ef27021020403c57cbf19d793efeb8 You're receiving this email because of your account on salsa.debian.org.
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