I still don't know how this works

term_frag_sel/utils.py

@@ -28,8 +28,7 @@ def check_positive(value: str) -> int:
 
 
 def check_prob(value: str) -> float:
-    """
-    Check probability value is within ]0,1] range.
+    """Check probability value is within ]0,1] range.
 
     Args:
         value (str): command line parameter
@@ -42,6 +41,6 @@ def check_prob(value: str) -> float:
     """
     pvalue = float(value)
     if pvalue <= 0 or pvalue > 1:
-        raise argparse.ArgumentTypeError("""%s is an invalid positive int
-                                         value""" % value)
+        raise argparse.ArgumentTypeError("""Expected a positive float between
+                                         0 and 1, but got {value}""")
     return pvalue

tests/test_cli.py

+"""Test cli.py functions."""
+import pytest
+# from Bio import SeqIO
+
+from term_frag_sel.cli import file_validation  # type: ignore
+
+FASTA_FILE = "tests/test_files/test.fasta"
+
+
+def test_file():
+    """Test check_positive function."""
+    with pytest.raises(FileNotFoundError):
+        file_validation("", "", ",")

tests/test_frag.py

+"""Test utils.py functions."""
+import pytest
+from Bio import SeqIO
+
+from term_frag_sel.fragmentation import fragmentation  # type: ignore
+
+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
+
+
+def test_frag():
+    """Test fragmentation function."""
+    with pytest.raises(TypeError):
+        fragmentation()

tests/test_utils.py

 """Test utils.py functions."""
+<<<<<<< HEAD
 import pytest
 
 from 
+=======
+import argparse
+import pytest
+
+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("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):
+        check_positive("string")
+    with pytest.raises(argparse.ArgumentTypeError):
+        check_positive("")
+
+
+def test_prob():
+    """Test check_prob function."""
+    assert check_prob("0.1") == 0.1
+    assert check_prob("1") == 1.0
+    with pytest.raises(argparse.ArgumentTypeError):
+        check_prob("0")
+    with pytest.raises(argparse.ArgumentTypeError):
+        check_prob("10")
+    with pytest.raises(argparse.ArgumentTypeError):
+        check_prob("-1")
+    with pytest.raises(ValueError):
+        check_prob("string")
+    with pytest.raises(ValueError):
+        check_prob("")
+>>>>>>> hugo_new