Fix NumPy Serialization

[ax3l]

Fix #67

• add test with reproducer for MultipoleP
• add fix for MultipoleP
• develop a more generic serializer that can be used for any location where we have floats and lists

[ax3l]

cc @ruisardkj @adb-xkc85723 NumPy fix attempt :)

[EZoni]

First review batch to suggest using pytest's tmp_path fixture to avoid polluting and cleaning the root directory (no try/finally, no os.remove, etc.). I think we should do this in pre-existing tests as well, in a separate PR.

[EZoni]

We could use pytest's tmp_path fixture to avoid polluting and cleaning the root directory (no try/finally, no os.remove, etc.):

Suggested change

	def test_yaml_roundtrip_with_numpy():
	"""Regression test for issue #67: writing YAML with numpy-typed values
	must not produce !!python/object tags, and round-tripping must yield
	Python-native floats with the correct numeric values."""
	np = pytest.importorskip("numpy")
	line = _build_numpy_lattice(np)
	yaml_file = "numpy_roundtrip.pals.yaml"
	line.to_file(yaml_file)
	try:
	with open(yaml_file, "r") as f:
	text = f.read()
	# The bug symptom: YAML contains opaque numpy object tags.
	assert "!!python/object" not in text, (
	f"YAML output still contains unsafe numpy object tags:\n{text}"
	)
	assert "numpy" not in text, f"YAML output still references numpy:\n{text}"
	loaded = pals.BeamLine.from_file(yaml_file)
	loaded_quad = loaded.line[0]
	assert loaded_quad.MagneticMultipoleP.Bn1 == -26.0
	assert type(loaded_quad.MagneticMultipoleP.Bn1) is float
	assert loaded_quad.MagneticMultipoleP.Bs1 == 0.5
	assert loaded_quad.MagneticMultipoleP.Kn0 == -1
	loaded_oct = loaded.line[1]
	assert loaded_oct.ElectricMultipoleP.En3 == 0.75
	assert type(loaded_oct.ElectricMultipoleP.En3) is float
	finally:
	if os.path.exists(yaml_file):
	os.remove(yaml_file)
	def test_yaml_roundtrip_with_numpy(tmp_path):
	"""Regression test for issue #67: writing YAML with numpy-typed values
	must not produce !!python/object tags, and round-tripping must yield
	Python-native floats with the correct numeric values."""
	np = pytest.importorskip("numpy")
	line = _build_numpy_lattice(np)
	yaml_file = str(tmp_path / "numpy_roundtrip.pals.yaml")
	line.to_file(yaml_file)
	with open(yaml_file, "r") as f:
	text = f.read()
	# The bug symptom: YAML contains opaque numpy object tags.
	assert "!!python/object" not in text, (
	f"YAML output still contains unsafe numpy object tags:\n{text}"
	)
	assert "numpy" not in text, f"YAML output still references numpy:\n{text}"
	loaded = pals.BeamLine.from_file(yaml_file)
	loaded_quad = loaded.line[0]
	assert loaded_quad.MagneticMultipoleP.Bn1 == -26.0
	assert type(loaded_quad.MagneticMultipoleP.Bn1) is float
	assert loaded_quad.MagneticMultipoleP.Bs1 == 0.5
	assert loaded_quad.MagneticMultipoleP.Kn0 == -1
	loaded_oct = loaded.line[1]
	assert loaded_oct.ElectricMultipoleP.En3 == 0.75
	assert type(loaded_oct.ElectricMultipoleP.En3) is float

[EZoni]

For convenience, the diff without whitespace would be:

-def test_yaml_roundtrip_with_numpy():
+def test_yaml_roundtrip_with_numpy(tmp_path):
     """Regression test for issue #67: writing YAML with numpy-typed values
     must not produce !!python/object tags, and round-tripping must yield
     Python-native floats with the correct numeric values."""
     np = pytest.importorskip("numpy")
 
     line = _build_numpy_lattice(np)
-    yaml_file = "numpy_roundtrip.pals.yaml"
+    yaml_file = str(tmp_path / "numpy_roundtrip.pals.yaml")
     line.to_file(yaml_file)
-    try:
+
     with open(yaml_file, "r") as f:
         text = f.read()
 
@@ -384,25 +384,19 @@ def test_yaml_roundtrip_with_numpy():
     loaded_oct = loaded.line[1]
     assert loaded_oct.ElectricMultipoleP.En3 == 0.75
     assert type(loaded_oct.ElectricMultipoleP.En3) is float
-    finally:
-        if os.path.exists(yaml_file):
-            os.remove(yaml_file)

[EZoni]

We could use pytest's tmp_path fixture to avoid polluting and cleaning the root directory (no try/finally, no os.remove, etc.):

Suggested change

	def test_json_roundtrip_with_numpy():
	"""JSON path also needs to handle numpy values cleanly (defense-in-depth)."""
	np = pytest.importorskip("numpy")
	line = _build_numpy_lattice(np)
	json_file = "numpy_roundtrip.pals.json"
	line.to_file(json_file)
	try:
	loaded = pals.BeamLine.from_file(json_file)
	loaded_quad = loaded.line[0]
	assert loaded_quad.MagneticMultipoleP.Bn1 == -26.0
	assert type(loaded_quad.MagneticMultipoleP.Bn1) is float
	loaded_oct = loaded.line[1]
	assert loaded_oct.ElectricMultipoleP.En3 == 0.75
	finally:
	if os.path.exists(json_file):
	os.remove(json_file)
	def test_json_roundtrip_with_numpy(tmp_path):
	"""JSON path also needs to handle numpy values cleanly (defense-in-depth)."""
	np = pytest.importorskip("numpy")
	line = _build_numpy_lattice(np)
	json_file = str(tmp_path / "numpy_roundtrip.pals.json")
	line.to_file(json_file)
	loaded = pals.BeamLine.from_file(json_file)
	loaded_quad = loaded.line[0]
	assert loaded_quad.MagneticMultipoleP.Bn1 == -26.0
	assert type(loaded_quad.MagneticMultipoleP.Bn1) is float
	loaded_oct = loaded.line[1]
	assert loaded_oct.ElectricMultipoleP.En3 == 0.75

[EZoni]

For convenience, the diff without whitespace would be:

-def test_json_roundtrip_with_numpy():
+def test_json_roundtrip_with_numpy(tmp_path):
     """JSON path also needs to handle numpy values cleanly (defense-in-depth)."""
     np = pytest.importorskip("numpy")
 
     line = _build_numpy_lattice(np)
-    json_file = "numpy_roundtrip.pals.json"
+    json_file = str(tmp_path / "numpy_roundtrip.pals.json")
     line.to_file(json_file)
-    try:
+
     loaded = pals.BeamLine.from_file(json_file)
     loaded_quad = loaded.line[0]
     assert loaded_quad.MagneticMultipoleP.Bn1 == -26.0
     assert type(loaded_quad.MagneticMultipoleP.Bn1) is float
     loaded_oct = loaded.line[1]
     assert loaded_oct.ElectricMultipoleP.En3 == 0.75
-    finally:
-        if os.path.exists(json_file):
-            os.remove(json_file)