Add: --version CLI flag and fix version string inconsistency

Remove hardcoded __version__ = "0.1.0" in __init__.py that was
overwriting the canonical version from __version__.py. Add -V/--version
flag to the CLI entry point. Add test coverage for --version, --csv,
and --top CLI flags.

https://claude.ai/code/session_017K4SRdDU2vdt93ErnwYM8t

Author: claude

python/flexaidds/__init__.py

@@ -76,4 +76,3 @@
         "VibrationalEntropy",
     ])
 
-__version__ = "0.1.0"

python/flexaidds/__main__.py

@@ -19,6 +19,7 @@
 from pathlib import Path
 from typing import Optional
 
+from .__version__ import __version__
 from .results import load_results
 
 
@@ -27,6 +28,11 @@ def build_parser() -> argparse.ArgumentParser:
         prog="python -m flexaidds",
         description="Inspect FlexAID∆S docking result directories from Python.",
     )
+    parser.add_argument(
+        "-V", "--version",
+        action="version",
+        version=f"%(prog)s {__version__}",
+    )
     parser.add_argument("results_dir", type=Path, help="Directory containing docking result PDB files")
     parser.add_argument(
         "--json",

python/tests/test_cli.py

@@ -1,8 +1,11 @@
 """Tests for flexaidds.__main__ – CLI entry point.
 
-Covers build_parser() and the two output branches of main():
+Covers build_parser() and the output branches of main():
   - human-readable summary (default)
   - machine-readable JSON (--json flag)
+  - CSV export (--csv flag)
+  - top-N filtering (--top flag)
+  - version display (--version flag)
 """
 
 from __future__ import annotations
@@ -196,3 +199,110 @@ def test_json_source_dir_is_string(self, tmp_path, monkeypatch, capsys):
         main()
         parsed = json.loads(capsys.readouterr().out)
         assert isinstance(parsed["source_dir"], str)
+
+
+# ===========================================================================
+# --version flag
+# ===========================================================================
+
+class TestMainVersionOutput:
+    def test_version_flag_prints_version(self, capsys):
+        from flexaidds.__version__ import __version__
+        parser = build_parser()
+        with pytest.raises(SystemExit) as exc_info:
+            parser.parse_args(["--version"])
+        assert exc_info.value.code == 0
+        out = capsys.readouterr().out
+        assert __version__ in out
+
+    def test_short_version_flag(self, capsys):
+        from flexaidds.__version__ import __version__
+        parser = build_parser()
+        with pytest.raises(SystemExit) as exc_info:
+            parser.parse_args(["-V"])
+        assert exc_info.value.code == 0
+        out = capsys.readouterr().out
+        assert __version__ in out
+
+
+# ===========================================================================
+# main() – CSV output
+# ===========================================================================
+
+class TestMainCsvOutput:
+    def _make_dir(self, tmp_path: Path) -> Path:
+        _write_pdb(
+            tmp_path / "mode_1_pose_1.pdb",
+            ["binding_mode = 1", "pose_rank = 1", "CF = -42.5",
+             "free_energy = -41.0", "temperature = 300.0"],
+        )
+        _write_pdb(
+            tmp_path / "mode_2_pose_1.pdb",
+            ["binding_mode = 2", "pose_rank = 1", "CF = -35.0",
+             "temperature = 300.0"],
+        )
+        return tmp_path
+
+    def test_returns_zero(self, tmp_path, monkeypatch):
+        d = self._make_dir(tmp_path)
+        csv_out = tmp_path / "out.csv"
+        monkeypatch.setattr(sys, "argv", ["flexaidds", str(d), "--csv", str(csv_out)])
+        assert main() == 0
+
+    def test_creates_csv_file(self, tmp_path, monkeypatch):
+        d = self._make_dir(tmp_path)
+        csv_out = tmp_path / "out.csv"
+        monkeypatch.setattr(sys, "argv", ["flexaidds", str(d), "--csv", str(csv_out)])
+        main()
+        assert csv_out.exists()
+
+    def test_csv_has_header_and_rows(self, tmp_path, monkeypatch):
+        d = self._make_dir(tmp_path)
+        csv_out = tmp_path / "out.csv"
+        monkeypatch.setattr(sys, "argv", ["flexaidds", str(d), "--csv", str(csv_out)])
+        main()
+        lines = csv_out.read_text().strip().splitlines()
+        assert len(lines) == 3  # header + 2 modes
+        assert "mode_id" in lines[0]
+
+    def test_csv_confirmation_message(self, tmp_path, monkeypatch, capsys):
+        d = self._make_dir(tmp_path)
+        csv_out = tmp_path / "out.csv"
+        monkeypatch.setattr(sys, "argv", ["flexaidds", str(d), "--csv", str(csv_out)])
+        main()
+        out = capsys.readouterr().out
+        assert "2" in out  # n_modes in confirmation
+        assert str(csv_out) in out
+
+
+# ===========================================================================
+# main() – --top flag
+# ===========================================================================
+
+class TestMainTopFlag:
+    def _make_dir(self, tmp_path: Path) -> Path:
+        for i in range(1, 4):
+            _write_pdb(
+                tmp_path / f"mode_{i}_pose_1.pdb",
+                [f"binding_mode = {i}", "pose_rank = 1",
+                 f"CF = {-40.0 + i}", f"free_energy = {-39.0 + i}",
+                 "temperature = 300.0"],
+            )
+        return tmp_path
+
+    def test_top_limits_table_rows(self, tmp_path, monkeypatch, capsys):
+        d = self._make_dir(tmp_path)
+        monkeypatch.setattr(sys, "argv", ["flexaidds", str(d), "--top", "1"])
+        main()
+        out = capsys.readouterr().out
+        assert "Binding modes: 3" in out
+
+    def test_top_default_is_none(self, tmp_path):
+        parser = build_parser()
+        args = parser.parse_args([str(tmp_path)])
+        assert args.top is None
+
+    def test_top_parsed_as_int(self, tmp_path):
+        parser = build_parser()
+        args = parser.parse_args([str(tmp_path), "--top", "5"])
+        assert args.top == 5