Cleanup and v0.1.0 release

README.md

@@ -1,7 +1,7 @@
 # pyYAMB
 
-![Python versions](https://img.shields.io/pypi/pyversions/pyyamb.svg)
-![PyPI version](https://img.shields.io/pypi/v/pyyamb.svg)
+[![Python versions](https://img.shields.io/pypi/pyversions/pyyamb.svg)](https://pypi.org/project/pyYAMB/)
+[![PyPI version](https://img.shields.io/pypi/v/pyyamb.svg)](https://pypi.org/project/pyYAMB/)
 
 pyYAMB is an implementation of [YAMB](https://github.com/laxeye/YAMB/) (Yet another metagenome binner) on Python (>=3.8). Originally YAMB was described in the preprint https://www.biorxiv.org/content/10.1101/521286.abstract and it's main point is the use of tSNE and HDBSCAN to process tetramer frequencies and coverage depth of metagenome fragments. pyYAMB strives for parallel computing wherever possible, currently coverage depth extraction is single threaded and takes the most time.
 

pyyamb/__init__.py

@@ -1 +1 @@
-__version__ = '0.1.0b0'
+__version__ = '0.1.0'

pyyamb/pyyamb.py

@@ -16,23 +16,22 @@
 from pyyamb.map import sort_mapping_file
 from pyyamb.utils import write_records_to_fasta
 from pyyamb.tetra import kmer_freq_table
+from pyyamb import __version__
 
 
 def parse_args():
 	logger = logging.getLogger()
 	parser = argparse.ArgumentParser(prog="pyYAMB",
-		description="pyYAMB metagenome binner",
+		description=f"pyYAMB metagenome binner ver. {__version__}",
 		formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
 	general_args = parser.add_argument_group(title="General options", description="")
 	general_args.add_argument("--task", required=True,
-		choices=["all", "cut", "tetra", "clustering", "map", "make_bins"],
+		choices=["all", "cut", "tetra", "map", "clustering", "make_bins"],
 		help="Task of pipeline: cut (discard short contigs and cut longer), "
 		+ "map (map reads or process mapping file)")
 	general_args.add_argument("-o", "--output", type=str, required=True,
 		help="Output directory")
-	'''general_args.add_argument("--mapper", help="Mapping software, currently minimap2 only",
-		choices=["minimap2"], default="minimap2")'''
 	general_args.add_argument("--min-length", default=1000, type=int,
 		help="Minimum contig length")
 	general_args.add_argument("--fragment-length", default=10000, type=int,

setup.py

@@ -1,3 +1,4 @@
+import pyyamb
 import setuptools
 
 with open("README.md", "r") as fh: