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 <[email protected]> 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 <[email protected]> -Uploaders: Andreas Tille <[email protected]> +Uploaders: Andreas Tille <[email protected]>, Nilesh Patra <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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