Fix typing_extension ImportError in downstream packages (#3752)

* guard from typing_extensions import Self with TYPE_CHECKING

in pymatgen/analysis/elasticity/stress.py, pymatgen/ext/optimade.py, and pymatgen/io/abinit/netcdf.py

* pymatgen/core/__init__.py drop ruff: noqa: PLC0414 and format imports

* remove ruff noqas and fix

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.5
+    rev: v0.3.7
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]

pymatgen/analysis/elasticity/stress.py

@@ -6,12 +6,15 @@
 from __future__ import annotations
 
 import math
+from typing import TYPE_CHECKING
 
 import numpy as np
-from typing_extensions import Self
 
 from pymatgen.core.tensors import SquareTensor
 
+if TYPE_CHECKING:
+    from typing_extensions import Self
+
 __author__ = "Joseph Montoya"
 __copyright__ = "Copyright 2012, The Materials Project"
 __credits__ = "Maarten de Jong, Mark Asta, Anubhav Jain"

pymatgen/core/__init__.py

@@ -1,4 +1,3 @@
-# ruff: noqa: PLC0414
 """This package contains core modules and classes for representing structures and operations on them."""
 
 from __future__ import annotations
@@ -10,25 +9,13 @@
 
 from ruamel.yaml import YAML
 
-from pymatgen.core.composition import Composition as Composition
-from pymatgen.core.lattice import Lattice as Lattice
-from pymatgen.core.operations import SymmOp as SymmOp
-from pymatgen.core.periodic_table import DummySpecie as DummySpecie
-from pymatgen.core.periodic_table import DummySpecies as DummySpecies
-from pymatgen.core.periodic_table import Element as Element
-from pymatgen.core.periodic_table import Species as Species
-from pymatgen.core.periodic_table import get_el_sp as get_el_sp
-from pymatgen.core.sites import PeriodicSite as PeriodicSite
-from pymatgen.core.sites import Site as Site
-from pymatgen.core.structure import IMolecule as IMolecule
-from pymatgen.core.structure import IStructure as IStructure
-from pymatgen.core.structure import Molecule as Molecule
-from pymatgen.core.structure import PeriodicNeighbor as PeriodicNeighbor
-from pymatgen.core.structure import SiteCollection as SiteCollection
-from pymatgen.core.structure import Structure as Structure
-from pymatgen.core.units import ArrayWithUnit as ArrayWithUnit
-from pymatgen.core.units import FloatWithUnit as FloatWithUnit
-from pymatgen.core.units import Unit as Unit
+from pymatgen.core.composition import Composition
+from pymatgen.core.lattice import Lattice
+from pymatgen.core.operations import SymmOp
+from pymatgen.core.periodic_table import DummySpecie, DummySpecies, Element, Species, get_el_sp
+from pymatgen.core.sites import PeriodicSite, Site
+from pymatgen.core.structure import IMolecule, IStructure, Molecule, PeriodicNeighbor, SiteCollection, Structure
+from pymatgen.core.units import ArrayWithUnit, FloatWithUnit, Unit
 
 __author__ = "Pymatgen Development Team"
 __email__ = "pymatgen@googlegroups.com"

pymatgen/ext/optimade.py

@@ -5,16 +5,19 @@
 import logging
 import sys
 from collections import namedtuple
+from typing import TYPE_CHECKING
 from urllib.parse import urljoin, urlparse
 
 import requests
 from tqdm import tqdm
-from typing_extensions import Self
 
 from pymatgen.core import DummySpecies, Structure
 from pymatgen.util.due import Doi, due
 from pymatgen.util.provenance import StructureNL
 
+if TYPE_CHECKING:
+    from typing_extensions import Self
+
 # TODO: importing optimade-python-tool's data structures will make more sense
 Provider = namedtuple("Provider", ["name", "base_url", "description", "homepage", "prefix"])
 

pymatgen/io/abinit/netcdf.py

@@ -7,18 +7,21 @@
 import logging
 import os.path
 import warnings
+from typing import TYPE_CHECKING
 
 import numpy as np
 from monty.collections import AttrDict
 from monty.dev import requires
 from monty.functools import lazy_property
 from monty.string import marquee
-from typing_extensions import Self
 
 from pymatgen.core.structure import Structure
 from pymatgen.core.units import ArrayWithUnit
 from pymatgen.core.xcfunc import XcFunc
 
+if TYPE_CHECKING:
+    from typing_extensions import Self
+
 try:
     import netCDF4
 except ImportError:

tests/io/test_packmol.py

@@ -12,11 +12,12 @@
 from pymatgen.io.packmol import PackmolBoxGen
 from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest
 
-# ruff: noqa: PT011
-
-
 TEST_DIR = f"{TEST_FILES_DIR}/packmol"
-
+# error message is different in CI for unknown reasons (as of 2024-04-12)
+# macOS: "Packmol failed with error code 173 and stderr: b'STOP 173\\n'"
+# CI: "Packmol failed with return code 0 and stdout: Packmol was unable to
+# put the molecules in the desired regions even without"
+ERR_MSG_173 = "Packmol failed with "
 
 if which("packmol") is None:
     pytest.skip("packmol executable not present", allow_module_level=True)
@@ -110,7 +111,7 @@ def test_control_params(self):
             input_string = file.read()
             assert "maxit 0" in input_string
             assert "nloop 0" in input_string
-        with pytest.raises(ValueError):
+        with pytest.raises(ValueError, match=ERR_MSG_173):
             input_set.run(self.tmp_path)
 
     def test_timeout(self):
@@ -141,7 +142,7 @@ def test_no_return_and_box(self):
         with open(f"{self.tmp_path}/packmol.inp") as file:
             input_string = file.read()
             assert "inside box 0 0 0 2 2 2" in input_string
-        with pytest.raises(ValueError):
+        with pytest.raises(ValueError, match=ERR_MSG_173):
             pw.run(self.tmp_path)
 
     def test_chdir_behavior(self):
@@ -159,7 +160,8 @@ def test_chdir_behavior(self):
             box=[0, 0, 0, 2, 2, 2],
         )
         pw.write_input(self.tmp_path)
-        with pytest.raises(ValueError):
+
+        with pytest.raises(ValueError, match=ERR_MSG_173):
             pw.run(self.tmp_path)
         assert str(Path.cwd()) == start_dir
 

tests/transformations/test_standard_transformations.py

@@ -1,4 +1,3 @@
-# ruff: noqa: N806
 from __future__ import annotations
 
 import functools