added: tests for priming_prob.py and CLI

tests/test_cli_priming_prob.py

+"""Unit tests for module ``CLI_PrimingProb.py``."""
+import pytest
+from pathlib import Path
+from src.primingprob import cli_priming_prob as CPb
+from unittest.mock import patch, MagicMock
+
+PACKAGE_DIR = Path(__file__).resolve().parents[1]
+TEST_FILE = "./tests/resources/Energies_test.txt"
+
+
+class TestParseArgs:
+    """Test ``parse_args()`` function."""
+
+    def test_no_positional_args(self):
+        """Call without positional args."""
+        with pytest.raises(SystemExit) as exc:
+            CPb.parse_args()
+        assert exc.value.code != 0
+
+
+class TestMain:
+    """Test ``main()`` function."""
+
+    def test_without_args(self):
+        """Call without args."""
+        with pytest.raises(SystemExit) as exc:
+            CPb.main()
+        assert exc.value.code != 0
+
+    def test_last_line(self):
+        """Test name equals main."""
+        # Arrange
+        with patch.object(CPb, "main", MagicMock()) as mock_main:
+            with patch.object(CPb, "__name__", "__main__"):
+                # Act
+                CPb.init()
+
+        # Assert
+        mock_main.assert_called_once()

tests/test_priming_prob.py

+"""Unit tests for module ``PrimingProb_CI``."""
+import os
+from src.primingprob.priming_prob import Probability as Pbt
+
+Energy_file = "./tests/resources/Energies_test.txt"
+Fasta_file = "./tests/resources/transcript.fasta"
+Output_file = "./tests/resources/Potential_Priming_Sites.txt"
+
+
+def test_inter_para():
+    """Tests InterPara function."""
+    testdata = Pbt.inter_para(Energy_file)
+    assert len(testdata) == 3  # Number of interactions
+    assert type(testdata) is list
+    for i in range(0, len(testdata)):
+        assert testdata[i][0].isdigit()
+
+    return testdata
+
+
+testdata2 = test_inter_para()
+
+
+def test_inter_prob():
+    """Tests InterProb function."""
+    Pbt.inter_prob(testdata2, Fasta_file, Output_file)
+    assert os.path.exists(Output_file) is True  # Check whether file exists
+
+    mytestfile = open(Output_file, "r")  # Test whether gff file start with transcript ID
+    for mylinecounter in mytestfile:
+        assert mylinecounter.startswith("NW_005196756.1:c68260-66684")
+
+    with open(Output_file, "r") as tt:  # Check whether number of interactions is right
+        x = len(tt.readlines())
+        assert x == 3