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

.github/workflows/lint.yml

@@ -9,7 +9,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
 

.github/workflows/test.yml

@@ -5,10 +5,11 @@ on: [push, pull_request, workflow_call]
 jobs:
   build:
     strategy:
+      fail-fast: false
       max-parallel: 20
       matrix:
         os: [ubuntu-latest, macos-14, windows-latest]
-        python-version: ["3.9", "3.x"]
+        python-version: ["3.9", "3.12"]
 
     runs-on: ${{ matrix.os }}
 

.pre-commit-config.yaml

@@ -32,7 +32,7 @@ repos:
     rev: v2.3.0
     hooks:
       - id: codespell
-        stages: [commit, commit-msg]
+        stages: [pre-commit, commit-msg]
         exclude_types: [html]
         additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
 

docs/Gemfile.lock

@@ -224,8 +224,8 @@ GEM
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
-    rexml (3.2.8)
-      strscan (>= 3.0.9)
+    rexml (3.3.6)
+      strscan
     rouge (3.26.0)
     ruby2_keywords (0.0.5)
     rubyzip (2.3.2)
@@ -251,7 +251,7 @@ GEM
       unf_ext
     unf_ext (0.0.8.2)
     unicode-display_width (1.8.0)
-    webrick (1.8.1)
+    webrick (1.8.2)
 
 PLATFORMS
   arm64-darwin-22

docs/changelog.md

@@ -1,5 +1,10 @@
 # Change log
 
+## 2024.7.29
+- Fix line ending in reverse_readfile/readline in Windows (@DanielYang59)
+- Add missing functools.wraps decorator to deprecated decorator and handle dataclass properly (@DanielYang59)
+- Add pint Quantity support to JSON (@rkingsbury)
+
 ## 2024.7.12
 - Make cached_class decorated classes picklable  (@janosh)
 - deprecated decorator allow replacement as string (@DanielYang59)

pyproject.toml

@@ -19,30 +19,37 @@ classifiers = [
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
 dependencies = [
-
+  "ruamel.yaml",
+  "numpy<2.0.0",
 ]
-version = "2024.7.12"
+version = "2024.7.30"
 
 [project.optional-dependencies]
 ci = [
-    "pytest>=8",
-    "pytest-cov>=4",
-    "coverage",
-    "numpy<2.0.0",
-    "ruamel.yaml",
-    "msgpack",
-    "tqdm",
-    "pymongo",
-    "pandas",
-    "orjson",
-    "types-orjson",
-    "types-requests",
-    "torch"
+  "coverage",
+  "monty[optional]",
+  "pytest>=8",
+  "pytest-cov>=4",
+  "types-requests",
 ]
+# dev is for "dev" module, not for development
+dev = ["ipython"]
 docs = [
     "sphinx",
     "sphinx_rtd_theme",
 ]
+json = [
+  "bson",
+  "orjson>=3.6.1",
+  "pandas",
+  "pydantic",
+  "pint",
+  "torch",
+]
+multiprocessing = ["tqdm"]
+optional = ["monty[dev,json,multiprocessing,serialization]"]
+serialization = ["msgpack"]
+task = ["requests", "invoke"]
 
 [tool.setuptools.packages.find]
 where = ["src"]
@@ -100,3 +107,4 @@ lint.select = [
 ]
 
 lint.isort.required-imports = ["from __future__ import annotations"]
+lint.isort.known-first-party = ["monty"]

src/monty/__init__.py

@@ -7,9 +7,16 @@
 
 from __future__ import annotations
 
+from importlib.metadata import PackageNotFoundError, version
+
 __author__ = "Shyue Ping Ong"
 __copyright__ = "Copyright 2014, The Materials Virtual Lab"
-__version__ = "2024.7.12"
 __maintainer__ = "Shyue Ping Ong"
 __email__ = "[email protected]"
 __date__ = "Oct 12 2020"
+
+try:
+    __version__ = version("monty")
+except PackageNotFoundError:  # pragma: no cover
+    # package is not installed
+    pass

src/monty/dev.py

@@ -12,6 +12,7 @@
 import subprocess
 import sys
 import warnings
+from dataclasses import is_dataclass
 from datetime import datetime
 from typing import TYPE_CHECKING
 
@@ -121,6 +122,7 @@ def craft_message(
         return msg
 
     def deprecated_function_decorator(old: Callable) -> Callable:
+        @functools.wraps(old)
         def wrapped(*args, **kwargs):
             msg = craft_message(old, replacement, message, _deadline)
             warnings.warn(msg, category=category, stacklevel=2)
@@ -129,14 +131,23 @@ def wrapped(*args, **kwargs):
         return wrapped
 
     def deprecated_class_decorator(cls: Type) -> Type:
-        original_init = cls.__init__
+        # Modify __post_init__ for dataclass
+        if is_dataclass(cls) and hasattr(cls, "__post_init__"):
+            original_init = cls.__post_init__
+        else:
+            original_init = cls.__init__
 
+        @functools.wraps(original_init)
         def new_init(self, *args, **kwargs):
             msg = craft_message(cls, replacement, message, _deadline)
             warnings.warn(msg, category=category, stacklevel=2)
             original_init(self, *args, **kwargs)
 
-        cls.__init__ = new_init
+        if is_dataclass(cls) and hasattr(cls, "__post_init__"):
+            cls.__post_init__ = new_init
+        else:
+            cls.__init__ = new_init
+
         return cls
 
     # Convert deadline to datetime type
@@ -220,9 +231,8 @@ def install_excepthook(hook_type: str = "color", **kwargs) -> int:
     """
     try:
         from IPython.core import ultratb  # pylint: disable=import-outside-toplevel
-    except ImportError:
-        warnings.warn("Cannot install excepthook, IPyhon.core.ultratb not available")
-        return 1
+    except ImportError as exc:
+        raise ImportError("Cannot install excepthook, IPython not installed") from exc
 
     # Select the hook.
     hook = dict(

src/monty/functools.py

@@ -84,7 +84,7 @@ def __init__(self, func: Callable) -> None:
             func: Function to decorate.
         """
         self.__func = func
-        wraps(self.__func)(self)  # type: ignore
+        wraps(self.__func)(self)  # type: ignore[arg-type]
 
     def __get__(self, inst: Any, inst_cls) -> Any:
         if inst is None:
@@ -95,7 +95,7 @@ def __get__(self, inst: Any, inst_cls) -> Any:
                 f"'{inst_cls.__name__}' object has no attribute '__dict__'"
             )
 
-        name = self.__name__  # type: ignore  # pylint: disable=E1101
+        name = self.__name__  # type: ignore[attr-defined]  # pylint: disable=E1101
         if name.startswith("__") and not name.endswith("__"):
             name = f"_{inst_cls.__name__}{name}"