Fixed pytests

.vscode/settings.json

@@ -1,4 +1,9 @@
 {
     "python.analysis.autoImportCompletions": true,
-    "python.analysis.typeCheckingMode": "basic"
+    "python.analysis.typeCheckingMode": "basic",
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
 }

fastqwiper/fastq_wiper.py

@@ -7,7 +7,7 @@
 from enum import auto, Enum
 from pathlib import Path
 from typing import Pattern, TextIO
-from wipertool_abstract import WiperTool
+from fastqwiper.wipertool_abstract import WiperTool
 
 
 # region Variables for final report
@@ -65,6 +65,7 @@ def file_choices(choices, fname):
                 if ext not in choices:
                     parser.error(
                         f"File '{fname}' doesn't end with one of {choices}")
+                    raise ValueError(f"File '{fname}' doesn't end with one of {choices}")
                 return fname
 
             parser.add_argument("-i", "--fastq_in", help="FASTQ file to be wiped", type=lambda s: file_choices(
@@ -188,7 +189,7 @@ def open_fastq_file(self, file_path: str) -> None | TextIO:
                 fastq_file_handler = codecs.open(
                     file_path, encoding="utf-8", errors="replace"
                 )
-
+        
         return fastq_file_handler
 
     def read_next_line(self, fin: TextIO, log_frequency: int) -> str:

tests/test_fastq_wiper.py

@@ -40,34 +40,35 @@ def fw_bad_fastq(fw):
 def fw_parser():
     fastq_in: str = "./tests/testdata/bad.fastq"
     fastq_out: str = "./tests/testdata/bad_wiped.fastq"
-    log_out: str = "./tests/testdata/bad.log"
+    report: str = "./tests/testdata/bad.report"
     log_frequency: int = 100
     alphabet: str = "ACGTN"
 
     return argparse.Namespace(
         fastq_in=fastq_in,
         fastq_out=fastq_out,
-        log_out=log_out,
+        report=report,
         log_frequency=log_frequency,
         alphabet=alphabet,
     )
 
+
 @pytest.fixture
 def fw_run(fw, fw_parser):
     fw.run(fw_parser)
 
     print("\nSetting up resources...")
     with open("./tests/testdata/bad_wiped.fastq", "r") as file:
         data = file.read()
-    with open("./tests/testdata/bad.log", "r") as file_log:
+    with open("./tests/testdata/bad.report", "r") as file_log:
         data_log = file_log.read()
 
     # Execute the actual test
     yield (data, data_log)
 
     print("\nTearing down resources...")
     os.remove("./tests/testdata/bad_wiped.fastq")
-    os.remove("./tests/testdata/bad.log")
+    os.remove("./tests/testdata/bad.report")
 
 
 def test_set_parser(fw, fw_parser):
@@ -76,6 +77,14 @@ def test_set_parser(fw, fw_parser):
     # print(f"\n{excinfo.value}")
 
 
+def test_set_parser_bad_argument_ext(fw, fw_parser):
+    fw_parser.fastq_out = "wrong_ext.txt"
+
+    with pytest.raises(ValueError):
+        fw.set_parser(fw_parser)
+    # print(f"\n{excinfo.value}")
+
+
 def test_run(fw_run):
     with open("./tests/testdata/bad_wiped_test.fastq", "r") as file_test:
         data_test = file_test.read()
@@ -91,16 +100,8 @@ def test_run_wrong_filein(fw, fw_parser):
     # print(f"\n{excinfo.value}")
 
 
-def test_run_wrong_fileout(fw, fw_parser):
-    fw_parser.fastq_out = "wrong_file.txt"
-
-    with pytest.raises(ValueError):
-        fw.run(fw_parser)
-    # print(f"\n{excinfo.value}")
-
-
-def test_summary(fw_run):
-    with open("./tests/testdata/bad_test.log", "r") as file_log_test:
+def test_report(fw_run):
+    with open("./tests/testdata/bad_test.report", "r") as file_log_test:
         data_test = file_log_test.read()
 
         assert fw_run[1] == data_test

tests/testdata/bad_test.log → tests/testdata/bad_test.report

@@ -1,8 +1,9 @@
-FASTQWIPER SUMMARY:
+FASTQWIPER REPORT:
 
 Total lines: 60
 Well-formed lines: 16 (26.67%)
-Clean reads: 4Bad headers or misplaced lines: 10 (16.67%) of which 4 fixed
+Clean reads: 4
+Bad headers or misplaced lines: 10 (16.67%) of which 4 fixed
 BAD SEQ lines: 2 (3.33%)
 BAD '+' lines: 2 (3.33%)
 BAD QUAL lines: 2 (3.33%)

tests/testdata/summary1.log → tests/testdata/summary1.report

@@ -1,4 +1,4 @@
-FASTQWIPER SUMMARY:
+FASTQWIPER REPORT:
 
 Total lines: 30
 Well-formed lines: 8 (26.67%)

tests/testdata/summary2.log → tests/testdata/summary2.report

@@ -1,4 +1,4 @@
-FASTQWIPER SUMMARY:
+FASTQWIPER REPORT:
 
 Total lines: 12
 Well-formed lines: 2 (16.67%)