From ffb33f61a9f32b6cdc431f6f7d075e89fb45abbb Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Mon, 4 Apr 2016 18:49:10 +0200 Subject: [PATCH 1/3] Switch to version 1.2.3 --- setup.py | 2 +- src/obitools/version.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 84cf849..264b23b 100644 --- a/setup.py +++ b/setup.py @@ -19,7 +19,7 @@ from os import path PACKAGE = "OBITools" -VERSION = "1.2.2" +VERSION = "1.2.3" AUTHOR = 'Eric Coissac' EMAIL = 'eric@coissac.eu' URL = 'metabarcoding.org/obitools' diff --git a/src/obitools/version.py b/src/obitools/version.py index 9570e9e..8270c25 100644 --- a/src/obitools/version.py +++ b/src/obitools/version.py @@ -1,5 +1,5 @@ major = 1 minor = 2 -serial= '2' +serial= '3' version = "%2d.%02d %s" % (major,minor,serial) From b2d2346eb7cb3ddde8bfde9808167d8fcf21a59f Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Wed, 6 Apr 2016 14:44:17 +0200 Subject: [PATCH 2/3] Set the Cython required version to 0.23 because of a bug in the 0.24 version --- requirements.txt | 2 +- setup.py | 2 +- src/obitools/version.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/requirements.txt b/requirements.txt index 6e5febb..1a80796 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ --extra-index-url https://pypi.python.org/simple/ -Cython>=0.21 +Cython==0.23 Sphinx>=1.2.0 wheel>=0.24.0 virtualenv>=1.11.0 diff --git a/setup.py b/setup.py index 264b23b..b935926 100644 --- a/setup.py +++ b/setup.py @@ -19,7 +19,7 @@ from os import path PACKAGE = "OBITools" -VERSION = "1.2.3" +VERSION = "1.2.4" AUTHOR = 'Eric Coissac' EMAIL = 'eric@coissac.eu' URL = 'metabarcoding.org/obitools' diff --git a/src/obitools/version.py b/src/obitools/version.py index 8270c25..42d4494 100644 --- a/src/obitools/version.py +++ b/src/obitools/version.py @@ -1,5 +1,5 @@ major = 1 minor = 2 -serial= '3' +serial= '4' version = "%2d.%02d %s" % (major,minor,serial) From c395d7623100e6f6056c48abe06da92c281db0f7 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Wed, 6 Apr 2016 14:46:08 +0200 Subject: [PATCH 3/3] patch a bug in the sequence counting of obiselect --- src/obiselect.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/obiselect.py b/src/obiselect.py index e9700e0..0e05e82 100644 --- a/src/obiselect.py +++ b/src/obiselect.py @@ -231,8 +231,11 @@ if __name__ == '__main__': for seq in seqs[1:]: - s['count']+=seq['count'] - + if 'count' in seq: + s['count']+=seq['count'] + else: + s['count']+=1 + for key in mergedKey: if key=='taxid' and mergeIds: if 'taxid_dist' in seq: