diff --git a/CHANGES.rst b/CHANGES.rst index 45916a8..0715c4c 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -6,7 +6,7 @@ Version 1.6.0 * swarm updated to version 2.1.12; * Now the mergepairs command allows merging staggered reads by default. With the new option ``-n/--nostagger`` the command produces the same - results of the previous versions (<=1.5.0); + results of the previous versions (<=1.5); * classify and tabletotax commands now strip the ``D_X__`` prefix from the Silva taxonomy files; * Documentation updated; diff --git a/README.rst b/README.rst index 5177486..6287576 100644 --- a/README.rst +++ b/README.rst @@ -20,13 +20,12 @@ software. Key features: * supports **single-end** (Roche 454, Illumina MiSeq/HiSeq ,Ion - Torren) as well **overlapping paired-end** reads (Illumina MiSeq/HiSeq); -* **multithread** de novo greedy clustering -* **closed-reference**, **open-reference** and **swarm** OTU picking protocols; -* **state-of-the-art taxonomic classification** algorithms are - available (RDP and consensus-based classifier); -* fast (multithread) and and memory efficient implementation of the - **NAST** multiple sequence alignment (MSA); + Torrent) and **overlapping paired-end** reads (Illumina MiSeq/HiSeq); +* **multithread** de novo greedy, closed-reference, open-reference and swarm OTU + picking protocols; +* **state-of-the-art taxonomic classification** algorithms (RDP and + consensus-based classifier); +* fast and and memory efficient **NAST** multiple sequence alignment (MSA); * filters low quality sequences according to the maximum allowed **expected error (EE) rate** %; * runs on **Linux**, **Mac OS X** and **MS Windows** (through Docker @@ -52,5 +51,5 @@ cited** if they are used: * MUSCLE (doi: 10.1093/nar/gkh340) used in ``msa`` and ``tree`` commands * FastTree (doi: 10.1371/journal.pone.0009490) used in the ``tree`` command * Cutadapt (doi: 10.14806/ej.17.1.200) used in the ``trim`` command -* RDP classifier (doi:10.1128/AEM.00062-07) used in the ``classify`` command -* swarm (10.7717/peerj.593, doi: 10.7717/peerj.1420) used in the ``otu`` command +* RDP classifier (doi: 10.1128/AEM.00062-07) used in the ``classify`` command +* swarm (doi: 10.7717/peerj.1420) used in the ``otu`` command diff --git a/micca/__init__.py b/micca/__init__.py index 2ede160..2356b24 100644 --- a/micca/__init__.py +++ b/micca/__init__.py @@ -1,5 +1,21 @@ import os -__version__ = "1.6.0" +# PEP0440 compatible formatted version, see: +# https://www.python.org/dev/peps/pep-0440/ +# +# Generic release markers: +# X.Y +# X.Y.Z # For bugfix releases +# +# Admissible pre-release markers: +# X.YaN # Alpha release +# X.YbN # Beta release +# X.YrcN # Release Candidate +# X.Y # Final release +# +# Dev branch marker is: 'X.Y.dev' or 'X.Y.devN' where N is an integer. +# 'X.Y.dev0' is the canonical version of 'X.Y.dev' +# +__version__ = "1.6" THIRDPARTY_BIN_PATH = os.path.join(os.path.dirname(__file__), "thirdparty_bin")