test: add gff3_merge CLI coverage

Cover gff3_merge argument validation, conflict handling, user-defined parsing, and default output/report routing.

Assisted-by: GitHub Copilot (GPT-5.4)

Author: ChrisChilders-USDA

tests/unit/test_gff3_merge_cli.py

@@ -0,0 +1,147 @@
+import io
+import unittest
+from argparse import Namespace
+from unittest import mock
+
+from gff3tool.bin import gff3_merge
+
+
+class TestGff3MergeCli(unittest.TestCase):
+    def test_script_main_exits_when_gff_file1_missing(self):
+        args = Namespace(
+            gff_file1=None,
+            gff_file2="ref.gff3",
+            fasta="ref.fa",
+            user_defined_file1=None,
+            user_defined_file2=None,
+            output_gff="merged.gff",
+            report_file="report.txt",
+            all=False,
+            auto_assignment=True,
+        )
+        stdin = mock.Mock()
+        stdin.isatty.return_value = True
+
+        with mock.patch("argparse.ArgumentParser.parse_args", return_value=args), \
+            mock.patch("sys.stdin", stdin), \
+            mock.patch("argparse.ArgumentParser.print_help") as print_help, \
+            self.assertRaises(SystemExit) as exc:
+            gff3_merge.script_main()
+
+        print_help.assert_called_once()
+        self.assertEqual(exc.exception.code, 1)
+
+    def test_script_main_exits_when_gff_file2_missing(self):
+        args = Namespace(
+            gff_file1="new.gff3",
+            gff_file2=None,
+            fasta="ref.fa",
+            user_defined_file1=None,
+            user_defined_file2=None,
+            output_gff="merged.gff",
+            report_file="report.txt",
+            all=False,
+            auto_assignment=True,
+        )
+        stdin = mock.Mock()
+        stdin.isatty.return_value = True
+
+        with mock.patch("argparse.ArgumentParser.parse_args", return_value=args), \
+            mock.patch("sys.stdin", stdin), \
+            mock.patch("argparse.ArgumentParser.print_help") as print_help, \
+            self.assertRaises(SystemExit) as exc:
+            gff3_merge.script_main()
+
+        print_help.assert_called_once()
+        self.assertEqual(exc.exception.code, 2)
+
+    def test_script_main_exits_on_conflicting_all_and_no_auto(self):
+        args = Namespace(
+            gff_file1="new.gff3",
+            gff_file2="ref.gff3",
+            fasta="ref.fa",
+            user_defined_file1=None,
+            user_defined_file2=None,
+            output_gff="merged.gff",
+            report_file="report.txt",
+            all=True,
+            auto_assignment=False,
+        )
+
+        with mock.patch("argparse.ArgumentParser.parse_args", return_value=args), \
+            self.assertRaises(SystemExit) as exc:
+            gff3_merge.script_main()
+
+        self.assertEqual(exc.exception.code, 0)
+
+    def test_script_main_parses_user_defined_files_and_calls_main(self):
+        args = Namespace(
+            gff_file1="new.gff3",
+            gff_file2="ref.gff3",
+            fasta="ref.fa",
+            user_defined_file1="u1.txt",
+            user_defined_file2="u2.txt",
+            output_gff="out.gff3",
+            report_file="report.txt",
+            all=False,
+            auto_assignment=True,
+        )
+
+        def open_side_effect(path, mode="r", *args, **kwargs):
+            if path == "u1.txt":
+                return io.StringIO("gene mRNA\ngene mRNA\n")
+            if path == "u2.txt":
+                return io.StringIO("gene mRNA\n")
+            if path == "report.txt":
+                return io.StringIO()
+            raise AssertionError(path)
+
+        with mock.patch("argparse.ArgumentParser.parse_args", return_value=args), \
+            mock.patch("builtins.open", side_effect=open_side_effect), \
+            mock.patch.object(gff3_merge, "main", autospec=True) as main_mock:
+            gff3_merge.script_main()
+
+        main_mock.assert_called_once_with(
+            "new.gff3",
+            "ref.gff3",
+            "ref.fa",
+            mock.ANY,
+            "out.gff3",
+            False,
+            True,
+            [["gene", "mRNA"]],
+            [["gene", "mRNA"]],
+            logger=mock.ANY,
+        )
+
+    def test_script_main_uses_default_report_and_output_names(self):
+        args = Namespace(
+            gff_file1="new.gff3",
+            gff_file2="ref.gff3",
+            fasta="ref.fa",
+            user_defined_file1=None,
+            user_defined_file2=None,
+            output_gff=None,
+            report_file=None,
+            all=False,
+            auto_assignment=True,
+        )
+
+        def open_side_effect(path, mode="r", *args, **kwargs):
+            if path == "merge_report.txt":
+                return io.StringIO()
+            raise AssertionError(path)
+
+        with mock.patch("argparse.ArgumentParser.parse_args", return_value=args), \
+            mock.patch("builtins.open", side_effect=open_side_effect), \
+            mock.patch.object(gff3_merge, "main", autospec=True) as main_mock:
+            gff3_merge.script_main()
+
+        called = main_mock.call_args
+        self.assertEqual(called.args[4], "merged.gff")
+        self.assertEqual(called.args[5], False)
+        self.assertEqual(called.args[6], True)
+
+
+if __name__ == "__main__":
+    unittest.main()