Keep subcommands using _ instead of - with click 7.0

Click 7.0 has changed so that subcommands named by function
convert _ to -. See http://click.palletsprojects.com/en/7.x/changelog/#version-7-0.

Updates version to 1.0.1.

HISTORY.md

@@ -1,4 +1,5 @@
-## 1.1.0 (in progress)
+## 1.0.1 
+- Add support for click 7.0.
 
 ## 1.0.0
 - Fix for min-length filtering with paired samples. Previously required only one read to be longer, fix requires both.

setup.py

@@ -8,7 +8,7 @@ def read(fname):
 
 setup(
         name='umis',
-        version='1.0.0',
+        version='1.0.1',
         description='Package for estimating UMI counts in Transcript Tag Counting data.',
         packages=find_packages(),
         install_requires=['click', 'pysam>=0.8.3', 'pandas', 'regex', 'scipy', 'toolz'],

umis/umis.py

@@ -24,7 +24,7 @@
 import scipy.io, scipy.sparse
 import click
 
-VERSION = "1.0.0"
+VERSION = "1.0.1"
 
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
@@ -1342,13 +1342,13 @@ def umis():
 umis.add_command(fastqtransform)
 umis.add_command(tagcount)
 umis.add_command(fasttagcount)
-umis.add_command(cb_histogram)
-umis.add_command(umi_histogram)
-umis.add_command(cb_filter)
-umis.add_command(sb_filter)
-umis.add_command(mb_filter)
-umis.add_command(add_uid)
+umis.add_command(cb_histogram, name="cb_histogram")
+umis.add_command(umi_histogram, name="umi_histogram")
+umis.add_command(cb_filter, name="cb_filter")
+umis.add_command(sb_filter, name="sb_filter")
+umis.add_command(mb_filter, name="mb_filter")
+umis.add_command(add_uid, name="add_uid")
 umis.add_command(kallisto)
 umis.add_command(bamtag)
-umis.add_command(demultiplex_samples)
-umis.add_command(subset_bamfile)
+umis.add_command(demultiplex_samples, name="demultiplex_samples")
+umis.add_command(subset_bamfile, name="subset_bamfile")