[med-svn] [Git][med-team/python-pyfaidx][upstream] New upstream version 0.8.1.2

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream 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
- - - - -


3 changed files:

- − codecov.yml
- pyfaidx/__init__.py
- pyproject.toml


Changes:

=====================================
codecov.yml deleted
=====================================
@@ -1,4 +0,0 @@
-comment: false
-coverage:
-  status:
-    patch: false


=====================================
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/-/commit/4ceb37365bfcd5955c73649709bf72e7ca4a0120

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View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/commit/4ceb37365bfcd5955c73649709bf72e7ca4a0120
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