Merge pull request #714 from DanielYang59/declare-opt-dependency

Declare required and optional dependency

.github/workflows/test.yml

@@ -5,6 +5,7 @@ on: [push, pull_request, workflow_call]
 jobs:
   build:
     strategy:
+      fail-fast: false
       max-parallel: 20
       matrix:
         os: [ubuntu-latest, macos-14, windows-latest]

pyproject.toml

@@ -19,31 +19,37 @@ classifiers = [
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
 dependencies = [
-
+  "ruamel.yaml",
+  "numpy<2.0.0",
 ]
 version = "2024.7.30"
 
 [project.optional-dependencies]
 ci = [
-    "pytest>=8",
-    "pytest-cov>=4",
-    "coverage",
-    "numpy<2.0.0",
-    "ruamel.yaml",
-    "msgpack",
-    "tqdm",
-    "pymongo",
-    "pandas",
-    "pint",
-    "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"]
@@ -101,3 +107,4 @@ lint.select = [
 ]
 
 lint.isort.required-imports = ["from __future__ import annotations"]
+lint.isort.known-first-party = ["monty"]

src/monty/dev.py

@@ -231,9 +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/io.py

@@ -9,11 +9,7 @@
 import errno
 import gzip
 import io
-
-try:
-    import lzma
-except ImportError:
-    lzma = None  # type: ignore[assignment]
+import lzma
 import mmap
 import os
 import subprocess
@@ -49,7 +45,7 @@ def zopen(filename: Union[str, Path], *args, **kwargs) -> IO:
         return bz2.open(filename, *args, **kwargs)
     if ext in {".GZ", ".Z"}:
         return gzip.open(filename, *args, **kwargs)
-    if lzma is not None and ext in {".XZ", ".LZMA"}:
+    if ext in {".XZ", ".LZMA"}:
         return lzma.open(filename, *args, **kwargs)
     return open(filename, *args, **kwargs)
 

src/monty/itertools.py

@@ -7,10 +7,7 @@
 import itertools
 from typing import TYPE_CHECKING
 
-try:
-    import numpy as np
-except ImportError:
-    np = None
+import numpy as np
 
 if TYPE_CHECKING:
     from typing import Iterable

src/monty/json.py

@@ -21,10 +21,8 @@
 from typing import Any
 from uuid import UUID, uuid4
 
-try:
-    import numpy as np
-except ImportError:
-    np = None
+import numpy as np
+from ruamel.yaml import YAML
 
 try:
     import pydantic
@@ -41,17 +39,11 @@
 except ImportError:
     bson = None
 
-try:
-    from ruamel.yaml import YAML
-except ImportError:
-    YAML = None
-
 try:
     import orjson
 except ImportError:
     orjson = None
 
-
 try:
     import torch
 except ImportError:
@@ -599,23 +591,22 @@ def default(self, o) -> dict:
                 d["data"] = o.numpy().tolist()
             return d
 
-        if np is not None:
-            if isinstance(o, np.ndarray):
-                if str(o.dtype).startswith("complex"):
-                    return {
-                        "@module": "numpy",
-                        "@class": "array",
-                        "dtype": str(o.dtype),
-                        "data": [o.real.tolist(), o.imag.tolist()],
-                    }
+        if isinstance(o, np.ndarray):
+            if str(o.dtype).startswith("complex"):
                 return {
                     "@module": "numpy",
                     "@class": "array",
                     "dtype": str(o.dtype),
-                    "data": o.tolist(),
+                    "data": [o.real.tolist(), o.imag.tolist()],
                 }
-            if isinstance(o, np.generic):
-                return o.item()
+            return {
+                "@module": "numpy",
+                "@class": "array",
+                "dtype": str(o.dtype),
+                "data": o.tolist(),
+            }
+        if isinstance(o, np.generic):
+            return o.item()
 
         if _check_type(o, "pandas.core.frame.DataFrame"):
             return {
@@ -668,7 +659,7 @@ def default(self, o) -> dict:
                 and dataclasses.is_dataclass(o)
             ):
                 # This handles dataclasses that are not subclasses of MSONAble.
-                d = dataclasses.asdict(o)  # type: ignore[call-overload]
+                d = dataclasses.asdict(o)  # type: ignore[call-overload, arg-type]
             elif hasattr(o, "as_dict"):
                 d = o.as_dict()
             elif isinstance(o, Enum):
@@ -813,7 +804,7 @@ def process_decoded(self, d):
                         ).type(d["dtype"])
                     return torch.tensor(d["data"]).type(d["dtype"])  # pylint: disable=E1101
 
-                elif np is not None and modname == "numpy" and classname == "array":
+                elif modname == "numpy" and classname == "array":
                     if d["dtype"].startswith("complex"):
                         return np.array(
                             [
@@ -936,7 +927,8 @@ def jsanitize(
             )
             for i in obj
         ]
-    if np is not None and isinstance(obj, np.ndarray):
+
+    if isinstance(obj, np.ndarray):
         try:
             return [
                 jsanitize(
@@ -950,8 +942,10 @@ def jsanitize(
             ]
         except TypeError:
             return obj.tolist()
-    if np is not None and isinstance(obj, np.generic):
+
+    if isinstance(obj, np.generic):
         return obj.item()
+
     if _check_type(
         obj,
         (

src/monty/multiprocessing.py

@@ -9,8 +9,8 @@
 
 try:
     from tqdm.autonotebook import tqdm
-except ImportError:
-    tqdm = None
+except ImportError as exc:
+    raise ImportError("tqdm must be installed for this function.") from exc
 
 
 def imap_tqdm(nprocs: int, func: Callable, iterable: Iterable, *args, **kwargs) -> list:
@@ -28,8 +28,6 @@ def imap_tqdm(nprocs: int, func: Callable, iterable: Iterable, *args, **kwargs)
     Returns:
         Results of Pool.imap.
     """
-    if tqdm is None:
-        raise ImportError("tqdm must be installed for this function.")
     data = []
     with Pool(nprocs) as pool:
         try:

src/monty/serialization.py

@@ -9,10 +9,7 @@
 import os
 from typing import TYPE_CHECKING
 
-try:
-    from ruamel.yaml import YAML
-except ImportError:
-    YAML = None  # type: ignore[arg-type]
+from ruamel.yaml import YAML
 
 from monty.io import zopen
 from monty.json import MontyDecoder, MontyEncoder

tasks.py

@@ -11,6 +11,7 @@
 
 import requests
 from invoke import task
+
 from monty import __version__ as ver
 from monty.os import cd
 

tests/test_collections.py

@@ -3,6 +3,7 @@
 import os
 
 import pytest
+
 from monty.collections import AttrDict, FrozenAttrDict, Namespace, frozendict, tree
 
 TEST_DIR = os.path.join(os.path.dirname(__file__), "test_files")

tests/test_design_patterns.py

@@ -6,6 +6,7 @@
 from typing import Any
 
 import pytest
+
 from monty.design_patterns import cached_class, singleton
 
 

tests/test_dev.py

@@ -7,6 +7,7 @@
 from unittest.mock import patch
 
 import pytest
+
 from monty.dev import deprecated, install_excepthook, requires
 
 # Set all warnings to always be triggered.

tests/test_fractions.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import pytest
+
 from monty.fractions import gcd, gcd_float, lcm
 
 

tests/test_functools.py

@@ -5,6 +5,7 @@
 import unittest
 
 import pytest
+
 from monty.functools import (
     TimeoutError,
     lazy_property,

tests/test_io.py

@@ -5,6 +5,7 @@
 from unittest.mock import patch
 
 import pytest
+
 from monty.io import (
     FileLock,
     FileLockException,

tests/test_json.py

@@ -8,10 +8,19 @@
 from enum import Enum
 from typing import Union
 
-try:
-    import numpy as np
-except ImportError:
-    np = None
+import numpy as np
+import pytest
+
+from monty.json import (
+    MontyDecoder,
+    MontyEncoder,
+    MSONable,
+    _load_redirect,
+    jsanitize,
+    load,
+)
+
+from . import __version__ as TESTS_VERSION
 
 try:
     import pandas as pd
@@ -38,18 +47,6 @@
 except ImportError:
     ObjectId = None
 
-import pytest
-from monty.json import (
-    MontyDecoder,
-    MontyEncoder,
-    MSONable,
-    _load_redirect,
-    jsanitize,
-    load,
-)
-
-from . import __version__ as tests_version
-
 TEST_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "test_files")
 
 
@@ -320,7 +317,7 @@ def test_unsafe_hash(self):
     def test_version(self):
         obj = self.good_cls("Hello", "World", "Python")
         d = obj.as_dict()
-        assert d["@version"] == tests_version
+        assert d["@version"] == TESTS_VERSION
 
     def test_nested_to_from_dict(self):
         GMC = GoodMSONClass
@@ -564,7 +561,6 @@ def test_nan(self):
         d = json.loads(djson)
         assert isinstance(d[0], float)
 
-    @pytest.mark.skipif(np is None, reason="numpy not present")
     def test_numpy(self):
         x = np.array([1, 2, 3], dtype="int64")
         with pytest.raises(TypeError):
@@ -872,9 +868,7 @@ def test_jsanitize_pandas(self):
         clean = jsanitize(s)
         assert clean == s.to_dict()
 
-    @pytest.mark.skipif(
-        np is None or ObjectId is None, reason="numpy and bson not present"
-    )
+    @pytest.mark.skipif(ObjectId is None, reason="bson not present")
     def test_jsanitize_numpy_bson(self):
         d = {
             "a": ["b", np.array([1, 2, 3])],

tests/test_os.py

@@ -4,6 +4,7 @@
 from pathlib import Path
 
 import pytest
+
 from monty.os import cd, makedirs_p
 from monty.os.path import find_exts, zpath