[med-svn] [Git][med-team/python-pyfaidx][master] 5 commits: New upstream version 0.8.1.2

[Étienne Mollier (@emollier)]

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 <emollier at debian.org>  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
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