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}"