From 514ed606ce958cb426bbcccfc7b5ff6027f60bcc Mon Sep 17 00:00:00 2001
From: "Josef M. Gallmetzer" <64498081+galjos@users.noreply.github.com>
Date: Mon, 24 Aug 2026 09:18:53 +0200
Subject: [PATCH] fix: accept --n-molecules flag in add_molecules

The -n and --n-molecules aliases were passed to add_argument as a
single comma-joined string, so argparse registered one malformed
option. The help text advertised --n-molecules, but using it failed
with unrecognized arguments and only -n worked via prefix matching.
Splitting the aliases into separate option strings makes both work.
---
 PQAnalysis/cli/add_molecules.py |  3 +-
 tests/cli/test_add_molecules.py | 76 +++++++++++++++++++++++++++++++++
 2 files changed, 78 insertions(+), 1 deletion(-)
 create mode 100644 tests/cli/test_add_molecules.py

diff --git a/PQAnalysis/cli/add_molecules.py b/PQAnalysis/cli/add_molecules.py
index 8ba267b0..e4f4732b 100644
--- a/PQAnalysis/cli/add_molecules.py
+++ b/PQAnalysis/cli/add_molecules.py
@@ -121,7 +121,8 @@ def add_arguments(cls, parser: _ArgumentParser) -> None:
         )
 
         parser.add_argument(
-            "-n, --n-molecules",
+            "-n",
+            "--n-molecules",
             dest='n_molecules',
             type=int,
             default=1,
diff --git a/tests/cli/test_add_molecules.py b/tests/cli/test_add_molecules.py
new file mode 100644
index 00000000..b3921615
--- /dev/null
+++ b/tests/cli/test_add_molecules.py
@@ -0,0 +1,76 @@
+"""
+Tests for the add_molecules CLI argument parser.
+"""
+
+import pytest
+
+import PQAnalysis.cli._argument_parser as argument_parser
+
+from PQAnalysis.cli.add_molecules import AddMoleculesCLI
+
+
+
+class TestAddMoleculesParser:
+
+    """
+    Tests for the add_molecules argument parser.
+    """
+
+    @pytest.fixture
+    def parser(self, monkeypatch):
+        """
+        An add_molecules parser with quiet parse_args side effects.
+        """
+        monkeypatch.setattr(argument_parser, "print_header", lambda: None)
+
+        parser = argument_parser._ArgumentParser(prog="add_molecules")
+        AddMoleculesCLI.add_arguments(parser)
+
+        return parser
+
+    def _parse(self, parser, arguments):
+        root_logger = argument_parser.logging.getLogger()
+        original_level = root_logger.level
+
+        try:
+            return parser.parse_args(
+                ["md-01.rst", "mol.xyz", "--log-file", "off"] + arguments
+            )
+        finally:
+            root_logger.setLevel(original_level)
+
+    def test_n_molecules_option_strings(self, parser):
+        """
+        The n_molecules argument registers both aliases separately.
+        """
+        option_strings = [
+            action.option_strings
+            for action in parser._actions
+            if action.dest == "n_molecules"
+        ]
+
+        assert option_strings == [["-n", "--n-molecules"]]
+
+    def test_n_molecules_long_flag(self, parser):
+        """
+        The advertised --n-molecules long flag is accepted.
+        """
+        args = self._parse(parser, ["--n-molecules", "2"])
+
+        assert args.n_molecules == 2
+
+    def test_n_molecules_short_flag(self, parser):
+        """
+        The -n short flag is accepted.
+        """
+        args = self._parse(parser, ["-n", "3"])
+
+        assert args.n_molecules == 3
+
+    def test_n_molecules_default(self, parser):
+        """
+        The n_molecules argument defaults to 1.
+        """
+        args = self._parse(parser, [])
+
+        assert args.n_molecules == 1