Étienne Mollier pushed to branch master at Debian Med / python-pyfaidx
Commits: 4ceb3736 by Étienne Mollier at 2024-08-11T19:14:40+02:00 New upstream version 0.8.1.2 - - - - - d54c3031 by Étienne Mollier at 2024-08-11T19:14:41+02:00 Update upstream source from tag 'upstream/0.8.1.2' Update to upstream version '0.8.1.2' with Debian dir 4c63617892c467916926d6567467b7d9ed9954ff - - - - - 77ce4b35 by Étienne Mollier at 2024-08-11T19:15:36+02:00 d/control: declare compliance to standards version 4.7.0. - - - - - 6c02089d by Étienne Mollier at 2024-08-11T19:19:40+02:00 d/python3-pyfaidx.lintian-overrides: delete. The false positive is not flagged anymore by new lintian versions. - - - - - f1e3f1dd by Étienne Mollier at 2024-08-11T19:20:43+02:00 Ready to upload to unstable. - - - - - 6 changed files: - − codecov.yml - debian/changelog - debian/control - − debian/python3-pyfaidx.lintian-overrides - pyfaidx/__init__.py - pyproject.toml Changes: ===================================== codecov.yml deleted ===================================== @@ -1,4 +0,0 @@ -comment: false -coverage: - status: - patch: false ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +python-pyfaidx (0.8.1.2-1) unstable; urgency=medium + + * New upstream version 0.8.1.2 + * d/control: declare compliance to standards version 4.7.0. + * d/python3-pyfaidx.lintian-overrides: delete. + The false positive is not flagged anymore by new lintian versions. + + -- Étienne Mollier <[email protected]> Sun, 11 Aug 2024 19:20:33 +0200 + python-pyfaidx (0.8.1.1-2) unstable; urgency=medium * Team upload. ===================================== debian/control ===================================== @@ -19,7 +19,7 @@ Build-Depends: debhelper-compat (= 13), python3-pytest <!nocheck>, samtools <!nocheck>, tabix <!nocheck> -Standards-Version: 4.6.2 +Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/python-pyfaidx Vcs-Git: https://salsa.debian.org/med-team/python-pyfaidx.git Homepage: https://github.com/mdshw5/pyfaidx ===================================== debian/python3-pyfaidx.lintian-overrides deleted ===================================== @@ -1,2 +0,0 @@ -# top_level.txt is not particularly documentation and looks needed there. -python3-pyfaidx: package-contains-documentation-outside-usr-share-doc [usr/lib/python3/dist-packages/pyfaidx-0.0.0.dist-info/top_level.txt] ===================================== pyfaidx/__init__.py ===================================== @@ -1134,9 +1134,9 @@ class Fasta(object): return sum(len(record) for record in self) def get_seq(self, name, start, end, rc=False): - """Return a sequence by record name and interval [start, end). + """Return a sequence by record name and interval [start, end]. - Coordinates are 1-based, end-exclusive. + Coordinates are 1-based, closed interval. If rc is set, reverse complement will be returned. """ # Get sequence from real genome object and save result. @@ -1245,9 +1245,9 @@ class FastaVariant(Fasta): str(self.gt_type)) def get_seq(self, name, start, end): - """Return a sequence by record name and interval [start, end). + """Return a sequence by record name and interval [start, end]. Replace positions with polymorphism with variant. - Coordinates are 0-based, end-exclusive. + Coordinates are 1-based, closed interval. """ seq = self.faidx.fetch(name, start, end) if self.faidx.as_raw: ===================================== pyproject.toml ===================================== @@ -28,7 +28,8 @@ classifiers = [ ] dependencies = [ "setuptools", - "importlib_metadata" + "importlib_metadata", + "packaging" ] dynamic = ["version"] View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/compare/d146d3de1455b1aac3de9c7a4e22719b68085749...f1e3f1ddbcb10e31ca3ba7ad91f5f48fbed2c70c -- View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/compare/d146d3de1455b1aac3de9c7a4e22719b68085749...f1e3f1ddbcb10e31ca3ba7ad91f5f48fbed2c70c You're receiving this email because of your account on salsa.debian.org.
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