1.0.0 and added --version

Author: jordisr

poreover/__main__.py

@@ -2,6 +2,7 @@
 PoreOver
 '''
 import argparse, sys, glob, os, logging, progressbar
+from pkg_resources import get_distribution
 
 from poreover.network.network import call, train
 from poreover.decoding.decode import decode
@@ -31,6 +32,7 @@ def main():
     parser_train.add_argument('--num_neurons', type=int, default=128, help='Number of neurons in RNN layers')
     parser_train.add_argument('--kernel_size', type=int, default=9, help='Kernel size in Conv1D layer')
     parser_train.add_argument('--filters', type=int, default=256, help='Number of filters in Conv1D layer')
+    parser_train.add_argument('-v', '--version', action='version', version=get_distribution("poreover").version)
 
     # Call
     parser_call = subparsers.add_parser('call', help='Run basecalling forward pass on set of FAST5 reads', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
@@ -44,6 +46,7 @@ def main():
     parser_call.add_argument('--window', type=int, default=1000, help='Call read using chunks of this size')
     parser_call.add_argument('--format', choices=['csv', 'npy'], default='npy', help='Save softmax probabilities to CSV file or logits to binarized NumPy format')
     parser_call.add_argument('--no_stack', default=False, action='store_true', help='Basecall [1xSIGNAL_LENGTH] tensor instead of splitting it into windows (slower)')
+    parser_call.add_argument('-v', '--version', action='version', version=get_distribution("poreover").version)
 
     # Decode
     parser_decode = subparsers.add_parser('decode', help='Decode basecaller probabilities to a FASTA file')
@@ -55,10 +58,12 @@ def main():
     parser_decode.add_argument('--window', type=int, default=400, help='Use chunks of this size for prefix search')
     parser_decode.add_argument('--beam_width', type=int, default=25, help='Width for beam search')
     parser_decode.add_argument('--threads', type=int, default=1, help='Processes to use')
+    parser_decode.add_argument('-v', '--version', action='version', version=get_distribution("poreover").version)
 
     # Pair decode
     parser_pair= subparsers.add_parser('pair-decode', help='1D2 consensus decoding of two output probabilities', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser_pair.set_defaults(func=pair_decode)
+    parser_pair.add_argument('-v', '--version', action='version', version=get_distribution("poreover").version)
     # general options
     parser_pair.add_argument('in', nargs='+', help='Softmax probabilities to decode (either .npy from PoreOver, or HDF5/FAST5 from Flappie or Guppy) or list of read pairs')
     parser_pair.add_argument('--dir', default='.', help='Base directory to look in for basecaller probabilities')

poreover/network/network.py

@@ -7,6 +7,7 @@
 import progressbar
 import pathlib
 from pathlib import Path
+from pkg_resources import get_distribution
 
 INPUT_DIM=1
 
@@ -132,7 +133,7 @@ def train(args):
     # print software message, should incorporate to other subroutines as well
     coffee_emoji = u'\U00002615'
     dna_emoji = u'\U0001F9EC'
-    print('{0:2}{1:3}{0:2} {2:^30} {0:2}{1:3}{0:2}'.format(coffee_emoji, dna_emoji,'PoreOver train (version 0.0)'), file=sys.stderr)
+    print('{0:2}{1:3}{0:2} {2:^30} {0:2}{1:3}{0:2}'.format(coffee_emoji, dna_emoji,'PoreOver train'), file=sys.stderr)
 
     # directory for model checkpoints and logging
     out_dir = "{}_{}_{}".format(args.model, args.name, datetime.datetime.now().strftime("%Y-%m-%d_%H-%M"))

setup.py

@@ -20,7 +20,7 @@
 
 setup(
     name="poreover",
-    version="0.0.0",
+    version="1.0.0",
     packages=setuptools.find_namespace_packages(),
     ext_modules = cythonize(ext_modules, annotate=True),
     entry_points={'console_scripts':['poreover = poreover.__main__:main']}