Fix issue with unclosed file in igzip.main

Author: rhpvorderman

src/isal/igzip.py

@@ -337,6 +337,7 @@ def main():
             if yes_or_no not in {"y", "Y", "yes"}:
                 sys.exit("not overwritten")
 
+    out_buffer = None
     if args.compress:
         if args.file is None:
             in_file = sys.stdin.buffer
@@ -374,6 +375,8 @@ def main():
             in_file.close()
         if out_file is not sys.stdout.buffer:
             out_file.close()
+        if out_buffer is not None and out_buffer is not sys.stdout.buffer:
+            out_buffer.close()
 
 
 if __name__ == "__main__":  # pragma: no cover

tests/test_igzip.py

@@ -29,21 +29,6 @@
 DATA = b'This is a simple test with igzip'
 COMPRESSED_DATA = gzip.compress(DATA)
 TEST_FILE = str((Path(__file__).parent / "data" / "test.fastq.gz"))
-PYPY = sys.implementation.name == "pypy"
-
-
-def run_isal_igzip(*args, stdin=None):
-    """Calling isal.igzip externally seems to solve some issues on PyPy where
-    files would not be written properly when igzip.main() was called. This is
-     probably due to some out of order execution that PyPy tries to pull.
-     Running the process externally is detrimental to the coverage report,
-     so this is only done for PyPy."""
-    process = subprocess.Popen(["python", "-m", "isal.igzip", *args],
-                               stdout=subprocess.PIPE,
-                               stderr=subprocess.PIPE,
-                               stdin=subprocess.PIPE)
-
-    return process.communicate(stdin)
 
 
 def test_wrong_compresslevel_igzipfile():
@@ -128,12 +113,9 @@ def test_decompress_infile_outfile(tmp_path, capsysbinary):
 def test_compress_infile_outfile(tmp_path, capsysbinary):
     test_file = tmp_path / "test"
     test_file.write_bytes(DATA)
-    if PYPY:
-        out, err = run_isal_igzip(str(test_file))
-    else:
-        sys.argv = ['', str(test_file)]
-        igzip.main()
-        out, err = capsysbinary.readouterr()
+    sys.argv = ['', str(test_file)]
+    igzip.main()
+    out, err = capsysbinary.readouterr()
     out_file = test_file.with_suffix(".gz")
     assert err == b''
     assert out == b''
@@ -196,12 +178,9 @@ def test_compress_infile_out_file(tmp_path, capsysbinary):
     test.write_bytes(DATA)
     out_file = tmp_path / "compressed.gz"
     args = ['-o', str(out_file), str(test)]
-    if PYPY:
-        out, err = run_isal_igzip(*args)
-    else:
-        sys.argv = ['', *args]
-        igzip.main()
-        out, err = capsysbinary.readouterr()
+    sys.argv = ['', *args]
+    igzip.main()
+    out, err = capsysbinary.readouterr()
     assert gzip.decompress(out_file.read_bytes()) == DATA
     assert err == b''
     assert out == b''
@@ -213,12 +192,9 @@ def test_compress_infile_out_file_force(tmp_path, capsysbinary):
     out_file = tmp_path / "compressed.gz"
     out_file.touch()
     args = ['-f', '-o', str(out_file), str(test)]
-    if PYPY:
-        out, err = run_isal_igzip(*args)
-    else:
-        sys.argv = ['', *args]
-        igzip.main()
-        out, err = capsysbinary.readouterr()
+    sys.argv = ['', *args]
+    igzip.main()
+    out, err = capsysbinary.readouterr()
     assert gzip.decompress(out_file.read_bytes()) == DATA
     assert err == b''
     assert out == b''
@@ -261,14 +237,11 @@ def test_compress_infile_out_file_inmplicit_name_prompt_accept(
     test.write_bytes(DATA)
     out_file = tmp_path / "test.gz"
     out_file.touch()
-    if PYPY:
-        out, err = run_isal_igzip(str(test), stdin=b"y\n")
-    else:
-        sys.argv = ['', str(test)]
-        mock_stdin = io.BytesIO(b"y")
-        sys.stdin = io.TextIOWrapper(mock_stdin)
-        igzip.main()
-        out, err = capsysbinary.readouterr()
+    sys.argv = ['', str(test)]
+    mock_stdin = io.BytesIO(b"y")
+    sys.stdin = io.TextIOWrapper(mock_stdin)
+    igzip.main()
+    out, err = capsysbinary.readouterr()
     assert b"already exists; do you wish to overwrite" in out
     assert err == b""
     assert gzip.decompress(out_file.read_bytes()) == DATA
@@ -279,12 +252,9 @@ def test_compress_infile_out_file_no_name(tmp_path, capsysbinary):
     test.write_bytes(DATA)
     out_file = tmp_path / "compressed.gz"
     args = ['-n', '-o', str(out_file), str(test)]
-    if PYPY:
-        out, err = run_isal_igzip(*args)
-    else:
-        sys.argv = ['', '-n', '-o', str(out_file), str(test)]
-        igzip.main()
-        out, err = capsysbinary.readouterr()
+    sys.argv = ['', '-n', '-o', str(out_file), str(test)]
+    igzip.main()
+    out, err = capsysbinary.readouterr()
     output = out_file.read_bytes()
     assert gzip.decompress(output) == DATA
     assert err == b''