Merge branch 'master' of github.com:materialsvirtuallab/monty

Author: shyuep

.github/workflows/test.yml

@@ -8,18 +8,18 @@ jobs:
       fail-fast: false
       max-parallel: 20
       matrix:
-        os: [ubuntu-latest, macos-14] #, windows-latest]
-        python-version: ["3.10", "3.12"]
+        os: [ubuntu-latest, macos-14, windows-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     runs-on: ${{ matrix.os }}
 
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python }}
+      - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python }}
+          python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: |

pyproject.toml

@@ -9,7 +9,7 @@ maintainers = [
 ]
 description = "Monty is the missing complement to Python."
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.10,<3.14"
 classifiers = [
     "Programming Language :: Python :: 3",
     "Development Status :: 4 - Beta",

src/monty/collections.py

@@ -89,7 +89,9 @@ def __setitem__(self, key, value) -> None:
 
     def update(self, *args, **kwargs) -> None:
         """Forbid adding or updating keys based on _allow_add and _allow_update."""
-        for key in dict(*args, **kwargs):
+
+        updates = dict(*args, **kwargs)
+        for key in updates:
             if key not in self.data and not self._allow_add:
                 raise TypeError(
                     f"Cannot add new key {key!r} using update, because add is disabled."
@@ -99,7 +101,7 @@ def update(self, *args, **kwargs) -> None:
                     f"Cannot update key {key!r} using update, because update is disabled."
                 )
 
-        super().update(*args, **kwargs)
+        super().update(updates)
 
     def setdefault(self, key, default=None) -> Any:
         """Forbid adding or updating keys based on _allow_add and _allow_update.

src/monty/io.py

@@ -61,7 +61,7 @@ def zopen(
     # TODO: remove default value of `mode` to force user to give one after deadline
     if mode is None:
         warnings.warn(
-            "We strongly discourage using a default `mode`, it would be"
+            "We strongly discourage using a default `mode`, it would be "
             f"set to `r` now but would not be allowed after {_deadline}",
             FutureWarning,
             stacklevel=2,

src/monty/json.py

@@ -905,7 +905,8 @@ def jsanitize(
             jsanitize will try to get the as_dict() attribute of the object. If
             no such attribute is found, an attribute error will be thrown. If
             strict is False, jsanitize will simply call str(object) to convert
-            the object to a string representation.
+            the object to a string representation.  If "skip" is provided,
+            jsanitize will skip and return the original object without modification.
         allow_bson (bool): This parameter sets the behavior when jsanitize
             encounters a bson supported type such as objectid and datetime. If
             True, such bson types will be ignored, allowing for proper
@@ -1009,7 +1010,7 @@ def jsanitize(
         except AttributeError:
             pass
 
-    if not strict:
+    if strict is False:
         return str(obj)
 
     if isinstance(obj, str):
@@ -1024,13 +1025,18 @@ def jsanitize(
             recursive_msonable=recursive_msonable,
         )
 
-    return jsanitize(
-        obj.as_dict(),
-        strict=strict,
-        allow_bson=allow_bson,
-        enum_values=enum_values,
-        recursive_msonable=recursive_msonable,
-    )
+    try:
+        return jsanitize(
+            obj.as_dict(),
+            strict=strict,
+            allow_bson=allow_bson,
+            enum_values=enum_values,
+            recursive_msonable=recursive_msonable,
+        )
+    except Exception as exc_:
+        if strict == "skip":
+            return obj
+        raise exc_
 
 
 def _serialize_callable(o):

tests/test_collections.py

@@ -62,6 +62,10 @@ def test_update_allowed(self):
         dct.update({"a": 3})
         assert dct["a"] == 3
 
+        # Test Iterator handling
+        dct.update(zip(["c", "d"], [11, 12]))
+        assert dct["c"] == 11
+
         dct.setdefault("a", 4)  # existing key
         assert dct["a"] == 3
 
@@ -122,6 +126,11 @@ def test_frozen_like(self):
         assert not dct._allow_add
         assert not dct._allow_update
 
+    def test_iterator_handling(self):
+        """Make sure iterators are handling correctly."""
+        c_dict = ControlledDict(zip(["c", "d"], [11, 12]))
+        assert c_dict["c"] == 11
+
 
 def test_frozendict():
     dct = frozendict({"hello": "world"})
@@ -157,7 +166,11 @@ def test_namespace_dict():
     dct["hello"] = "world"
     assert dct["key"] == "val"
 
-    # Test update (not allowed)
+    # Test use `update` to add new values
+    dct.update({"new_key": "new_value"})
+    assert dct["new_key"] == "new_value"
+
+    # Test add (not allowed)
     with pytest.raises(TypeError, match="update is disabled"):
         dct["key"] = "val"
 

tests/test_io.py

@@ -426,6 +426,7 @@ def test_lzw_files(self):
 
         # Cannot decompress a real LZW file
         with (
+            pytest.warns(FutureWarning, match="compress LZW-compressed files"),
             pytest.raises(gzip.BadGzipFile, match="Not a gzipped file"),
             zopen(f"{TEST_DIR}/real_lzw_file.txt.Z", "rt", encoding="utf-8") as f,
         ):

tests/test_json.py

@@ -875,6 +875,50 @@ def test_jsanitize(self):
         clean = jsanitize(d, strict=True)
         assert "@class" in clean["c"]
 
+    def test_unserializable_composite(self):
+        class Unserializable:
+            def __init__(self, a):
+                self._a = a
+
+            def __str__(self):
+                return "Unserializable"
+
+        class Composite(MSONable):
+            def __init__(self, name, unserializable, msonable):
+                self.name = name
+                self.unserializable = unserializable
+                self.msonable = msonable
+
+        composite_dictionary = {
+            "name": "test",
+            "unserializable": Unserializable(1),
+            "msonable": GoodMSONClass(1, 2, 3),
+        }
+
+        with pytest.raises(AttributeError):
+            jsanitize(composite_dictionary, strict=True)
+
+        composite_obj = Composite.from_dict(composite_dictionary)
+
+        with pytest.raises(AttributeError):
+            jsanitize(composite_obj, strict=True)
+
+        # Test that skip mode preserves unserializable objects
+        skipped_dict = jsanitize(composite_obj, strict="skip", recursive_msonable=True)
+        assert skipped_dict["name"] == "test", "String values should remain unchanged"
+        assert (
+            skipped_dict["unserializable"]._a == 1
+        ), "Unserializable object should be preserved in skip mode"
+        assert (
+            skipped_dict["msonable"]["a"] == 1
+        ), "MSONable object should be properly serialized"
+
+        # Test non-strict mode converts unserializable to string
+        dict_with_str = jsanitize(composite_obj, strict=False, recursive_msonable=True)
+        assert isinstance(
+            dict_with_str["unserializable"], str
+        ), "Unserializable object should be converted to string in non-strict mode"
+
     @pytest.mark.skipif(pd is None, reason="pandas not present")
     def test_jsanitize_pandas(self):
         s = pd.Series({"a": [1, 2, 3], "b": [4, 5, 6]})