[med-svn] [Git][med-team/python-treetime][master] 5 commits: New upstream version 0.8.1

[Nilesh Patra]

Nilesh Patra pushed to branch master at Debian Med / python-treetime


Commits:
28bc86c7 by Nilesh Patra at 2021-01-09T16:15:26+05:30
New upstream version 0.8.1
- - - - -
dec82133 by Nilesh Patra at 2021-01-09T16:15:54+05:30
Update upstream source from tag 'upstream/0.8.1'

Update to upstream version '0.8.1'
with Debian dir 32c8c2c95ffc6daffebbe1998b87d4824f6b5696
- - - - -
432b2e17 by Nilesh Patra at 2021-01-09T16:16:43+05:30
Declare compliance with policy 4.5.1

- - - - -
7d7f56f1 by Nilesh Patra at 2021-01-09T16:24:34+05:30
Add myself to uploaders

- - - - -
0d6e050e by Nilesh Patra at 2021-01-09T16:24:56+05:30
Update changelog

- - - - -


6 changed files:

- changelog.md
- debian/changelog
- debian/control
- treetime/__init__.py
- treetime/seq_utils.py
- treetime/treeanc.py


Changes:

=====================================
changelog.md
=====================================
@@ -1,3 +1,5 @@
+# 0.8.1 -- bug fixe amino acid profile map.
+
 # 0.8.0 -- drop python 2.7 support, bug fixes.
 
 # 0.7.6 -- catch of distributions are too short for calculating confidence intervals.


=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+python-treetime (0.8.1-1) unstable; urgency=medium
+
+  * Update changelog
+  * New upstream version 0.8.1
+  * Declare compliance with policy 4.5.1
+
+ -- Nilesh Patra <npatra974 at gmail.com>  Sat, 09 Jan 2021 16:16:56 +0530
+
 python-treetime (0.8.0-1) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/control
=====================================
@@ -1,6 +1,6 @@
 Source: python-treetime
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>, Nilesh Patra <npatra974 at gmail.com>
 Section: science
 Testsuite: autopkgtest-pkg-python
 Priority: optional
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-pandas,
                python3-scipy,
                python3-setuptools
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
 Vcs-Browser: https://salsa.debian.org/med-team/python-treetime
 Vcs-Git: https://salsa.debian.org/med-team/python-treetime.git
 Homepage: https://github.com/neherlab/treetime


=====================================
treetime/__init__.py
=====================================
@@ -1,5 +1,5 @@
 from __future__ import print_function, division, absolute_import
-version="0.8.0"
+version="0.8.1"
 
 class TreeTimeError(Exception):
     """TreeTimeError class"""


=====================================
treetime/seq_utils.py
=====================================
@@ -83,7 +83,7 @@ profile_maps = {
     'V': np.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0], dtype='float'), #Valine          Val
     'W': np.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0], dtype='float'), #Tryptophan      Trp
     'Y': np.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0], dtype='float'), #Tyrosine        Tyr
-    '*': np.array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0], dtype='float'), #stop
+    '*': np.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0], dtype='float'), #stop
     '-': np.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1], dtype='float'), #gap
     'X': np.array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], dtype='float'), #not specified/any
     'B': np.array([0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], dtype='float'), #Asparagine/Aspartic Acid    Asx


=====================================
treetime/treeanc.py
=====================================
@@ -1611,8 +1611,10 @@ class TreeAnc(object):
         else:
             if (not reconstructed) and (node.name in self.data.aln):
                 tmp_seq = self.data.aln[node.name]
-            else:
+            elif node.cseq is not None:
                 tmp_seq = self.data.compressed_to_full_sequence(node.cseq, as_string=False)
+            else:
+                tmp_seq = np.array([self.gtr.ambiguous or 'N']*self.data.compressed_length)
 
         return "".join(tmp_seq) if as_string else np.copy(tmp_seq)
 



View it on GitLab: https://salsa.debian.org/med-team/python-treetime/-/compare/751ac72303d6b03d64b0a6834154fa3dc0f3b9ae...0d6e050eca82f0afa91759d8ae7a552b64810b7e

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-treetime/-/compare/751ac72303d6b03d64b0a6834154fa3dc0f3b9ae...0d6e050eca82f0afa91759d8ae7a552b64810b7e
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