Add main entry to find_maximum_overlap script

micall/main.py

@@ -88,6 +88,7 @@
     "micall/monitor/update_qai.py",
     "micall/monitor/micall_watcher.py",
     "micall/tcr/igblast.py",
+    "micall/utils/find_maximum_overlap.py",
 ]
 
 

micall/tests/test_find_maximum_overlap.py

@@ -1,5 +1,5 @@
 import pytest
-from micall.utils.find_maximum_overlap import find_maximum_overlap, show_maximum_overlap
+from micall.utils.find_maximum_overlap import find_maximum_overlap, show_maximum_overlap, cli_main
 
 
 @pytest.mark.parametrize(
@@ -27,8 +27,7 @@ def test_maximum_overlap_cases(left, right, expected):
             find_maximum_overlap(left, right)
 
 
-@pytest.mark.parametrize(
-    "left, right, expected",
+print_cases = \
     [
         ('tttttxxxxx', 'uuuuuxxx', '''\
 tttttxxxxx
@@ -67,15 +66,18 @@ def test_maximum_overlap_cases(left, right, expected):
 tttttxxxxpppppppppppppppppppp-----------
 ------xxxuuuuuuuuuuuuuuuuuuuuuuuuuuuuuuu
 '''),
-    ],
-)
+]
+
+
+@pytest.mark.parametrize("left, right, expected", print_cases)
 def test_print(left, right, expected):
     shift = find_maximum_overlap(left, right)
     ret = show_maximum_overlap(left, right, shift)
-    if ret != expected:
-        print()
-        print()
-        print(ret)
-        print()
-        print()
+    assert ret == expected
+
+
+@pytest.mark.parametrize("left, right, expected", print_cases)
+def test_main(left, right, expected, capsys):
+    cli_main([left, right])
+    ret = capsys.readouterr().out
     assert ret == expected

micall/utils/find_maximum_overlap.py

@@ -1,4 +1,7 @@
+#! /usr/bin/env python
 
+import argparse
+import sys
 import numpy as np
 from typing import Sequence
 from itertools import chain
@@ -85,3 +88,27 @@ def show_maximum_overlap(arr1: Sequence[object],
              for x in [arr1_line, arr2_line])
 
     return '\n'.join(chain(lines, ['']))
+
+
+def main(seq1: str, seq2: str) -> int:
+    shift = find_maximum_overlap(seq1, seq2)
+    ret = show_maximum_overlap(seq1, seq2, shift)
+    print(ret, end='')
+    return 0
+
+
+def get_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser("Find maximum overlap between two sequences.")
+    parser.add_argument('seq1')
+    parser.add_argument('seq2')
+    return parser
+
+
+def cli_main(argv: Sequence[str]) -> int:
+    parser = get_parser()
+    args = parser.parse_args(argv)
+    return main(args.seq1, args.seq2)
+
+
+if __name__ == '__main__':
+    sys.exit(cli_main(sys.argv[1:]))