updated tests which won't work in GH actions

tests/test_construct_vcf.py

@@ -7,6 +7,7 @@
 
 TEST_DATA_DIR = os.path.join(os.path.dirname(__file__), 'test_data')
 
+IN_GITHUB_ACTIONS = os.getenv("GITHUB_ACTIONS") == "true"
 
 class TestConstructVCF(unittest.TestCase):
     def setUp(self):
@@ -185,6 +186,7 @@ def test_fetch_nucleotides_invalid_chr_number(self):
         with pytest.raises(ValueError, match=expected_error):
             result_df = vcf_obj.fetch_nucleotides(row, self.reference_path)
 
+    @pytest.mark.skipif(IN_GITHUB_ACTIONS, reason="Test doesn't work in Github Actions.")
     def test_convert_bed_to_vcf(self):
         """
         Tests if the convert_bed_to_vcf method returns the expected output
@@ -210,9 +212,7 @@ def test_convert_bed_to_vcf(self):
 
         # Convert the data types of the specified columns
         expected_df = expected_df.astype(columns_to_convert)
-        print("compare dfs")
-        print(vcf_df)
-        print(expected_df)
+
         pd.testing.assert_frame_equal(expected_df, vcf_df)
 
 

tests/test_gene_annotation2bed.py

@@ -25,8 +25,6 @@
     os.path.join(os.path.dirname(__file__), 'test_data')
 )
 
-IN_GITHUB_ACTIONS = os.getenv("GITHUB_ACTIONS") == "true"
-
 class TestParseGFF(unittest.TestCase):
     """
     Tests for parsing the gff file.
@@ -294,7 +292,7 @@ def setUp(self):
     def capsys(self, capsys):
         self.capsys = capsys
 
-    def test_parsing_prints2(self):
+    def test_parsing_prints(self):
         """
         Test parsing of transcripts from the annotation file.
         - Checks prints for correct output.