CLI + complete linting & coverage

tests/test_frag.py

@@ -2,19 +2,19 @@
 import pytest
 from Bio import SeqIO
 
-from term_frag_sel.fragmentation import fragmentation
+from term_frag_sel.fragmentation import fragmentation  # type: ignore
 
-with open("./test_files/test.fasta", "r") as handle:
+with open("tests/test_files/test.fasta", "r", encoding="utf-8") as handle:
     fasta = SeqIO.parse(handle, "fasta")
 
 # have to create the counts file
 
-mu = 100
-std = 10
-a_prob = 0.22
-c_prob = 0.28
-t_prob = 0.25
-g_prob = 0.25
+MU = 100
+STD = 10
+A_PROB = 0.22
+C_PROB = 0.28
+T_PROB = 0.25
+G_PROB = 0.25
 
 
 def test_frag():

tests/test_utils.py

 """Test utils.py functions."""
-import pytest
 import argparse
+import pytest
 
-from term_frag_sel.utils import check_positive, check_prob
+from term_frag_sel.utils import check_positive, check_prob  # type: ignore
 
 
 def test_positive():
     """Test check_positive function."""
     assert check_positive("1") == 1
     assert check_positive("100") == 100
-    assert check_positive("0") == 100
     assert check_positive("2.2") == 2
     assert check_positive("2.6") == 3
+    with pytest.raises(argparse.ArgumentTypeError):
+        check_positive("0")
     with pytest.raises(argparse.ArgumentTypeError):
         check_positive("-1")
     with pytest.raises(argparse.ArgumentTypeError):
@@ -30,7 +31,7 @@ def test_prob():
         check_prob("10")
     with pytest.raises(argparse.ArgumentTypeError):
         check_prob("-1")
-    with pytest.raises(argparse.ArgumentTypeError):
+    with pytest.raises(ValueError):
         check_prob("string")
-    with pytest.raises(argparse.ArgumentTypeError):
+    with pytest.raises(ValueError):
         check_prob("")