Single source of truth for optional deps in pyproject.toml

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.6.9
+  rev: v0.7.1
   hooks:
   - id: ruff
     args: [--fix]
@@ -17,7 +17,7 @@ repos:
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/asottile/blacken-docs
-  rev: 1.18.0
+  rev: 1.19.1
   hooks:
   - id: blacken-docs
     additional_dependencies: [black]
@@ -30,7 +30,7 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.11.2
+  rev: v1.13.0
   hooks:
   - id: mypy
     files: ^src/

pyproject.toml

@@ -40,7 +40,7 @@ dependencies = [
 [project.optional-dependencies]
 abinit = ["abipy>=0.9.3"]
 amset = ["amset>=0.4.15", "pydash"]
-cclib = ["cclib"]
+cclib = ["cclib>=1.8.1"]
 mp = ["mp-api>=0.37.5"]
 phonons = ["phonopy>=1.10.8", "seekpath"]
 lobster = ["ijson>=3.2.2", "lobsterpy>=0.4.0"]
@@ -51,16 +51,26 @@ defects = [
 ]
 forcefields = [
     "ase>=3.23.0",
-    "calorine<=2.2.1",
+    "calorine>=3.0",
     "chgnet>=0.2.2",
     "mace-torch>=0.3.3",
-    "torchdata<=0.7.1",
     "matgl>=1.1.3",
+    "torchdata<=0.7.1",
     # quippy-ase support for py3.12 tracked in https://github.com/libAtoms/QUIP/issues/645
     "quippy-ase>=0.9.14; python_version < '3.12'",
     "sevenn>=0.9.3",
     "torchdata<=0.7.1",                            # TODO: remove when issue fixed
 ]
+strict-forcefields = [
+    "calorine==3.0",
+    "chgnet==0.4.0",
+    "mace-torch==0.3.6",
+    "matgl==1.1.3",
+    "quippy-ase==0.9.14; python_version < '3.12'",
+    "sevenn==0.10.0",
+    "torch==2.5.0",
+    "torchdata==0.7.1",                            # TODO: remove when issue fixed
+]
 ase = ["ase>=3.23.0"]
 # tblite py3.12 support tracked in https://github.com/tblite/tblite/issues/198
 ase-ext = ["tblite>=0.3.0; python_version < '3.12'"]
@@ -92,41 +102,7 @@ tests = [
     "pytest==8.3.3",
 ]
 strict = [
-    "PyYAML==6.0.2",
-    "ase==3.23.0",
-    "cclib==1.8.1",
-    "click==8.1.7",
-    "custodian==2024.10.16",
-    "dscribe==2.1.1",
-    "emmet-core==0.84.2",
-    "ijson==3.3.0",
-    "jobflow==0.1.18",
-    "lobsterpy==0.4.9",
-    "mdanalysis==2.7.0",
-    "monty==2024.7.30",
-    "mp-api==0.42.2",
-    "numpy",
-    "openmm-mdanalysis-reporter==0.1.0",
-    "openmm==8.1.1",
-    "phonopy==2.27.0",
-    "pydantic-settings==2.6.0",
-    "pydantic==2.9.2",
-    "pymatgen-analysis-defects==2024.7.19",
-    "pymatgen==2024.10.3",
-    "python-ulid==3.0.0",
-    "seekpath==2.1.0",
-    "tblite==0.3.0; python_version < '3.12'",
-    "typing-extensions==4.12.2",
-]
-strict-forcefields = [
-    "calorine==3.0",
-    "chgnet==0.4.0",
-    "mace-torch>=0.3.6",
-    "matgl==1.1.3",
-    "quippy-ase==0.9.14; python_version < '3.12'",
-    "sevenn==0.10.0",
-    "torch==2.5.0",
-    "torchdata==0.7.1",                            # TODO: remove when issue fixed
+    "atomate2[forcefields, docs, cclib, phonons, lobster, openmm, mp, defects, ase, ase-ext]",
 ]
 
 [project.scripts]

src/atomate2/ase/jobs.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 import logging
-from abc import ABCMeta, abstractmethod
+from abc import ABC, abstractmethod
 from dataclasses import dataclass, field
 from typing import TYPE_CHECKING
 
@@ -29,7 +29,7 @@
 
 
 @dataclass
-class AseMaker(Maker, metaclass=ABCMeta):
+class AseMaker(Maker, ABC):
     """
     Define basic template of ASE-based jobs.
 

src/atomate2/ase/md.py

@@ -7,7 +7,7 @@
 import os
 import sys
 import time
-from abc import ABCMeta, abstractmethod
+from abc import ABC, abstractmethod
 from collections.abc import Sequence
 from dataclasses import dataclass, field
 from enum import Enum
@@ -79,7 +79,7 @@ class DynamicsPresets(Enum):
 
 
 @dataclass
-class AseMDMaker(AseMaker, metaclass=ABCMeta):
+class AseMDMaker(AseMaker, ABC):
     """
     Perform MD with the Atomic Simulation Environment (ASE).
 

src/atomate2/ase/schemas.py

@@ -99,7 +99,7 @@ class AseBaseModel(BaseModel):
     )
     molecule: Optional[Molecule] = Field(None, description="The molecule at this step.")
 
-    def model_post_init(self, __context: Any) -> None:
+    def model_post_init(self, context: Any, /) -> None:
         """Establish alias to structure and molecule fields."""
         if self.structure is None and isinstance(self.mol_or_struct, Structure):
             self.structure = self.mol_or_struct

src/atomate2/common/flows/mpmorph.py

@@ -13,7 +13,7 @@
 
 from __future__ import annotations
 
-from abc import ABCMeta, abstractmethod
+from abc import ABC, abstractmethod
 from dataclasses import dataclass, field
 from typing import TYPE_CHECKING, Literal
 
@@ -165,9 +165,8 @@ def make(
                 structure=deformed_structures[index].final_structure,
                 prev_dir=None,
             )
-            md_job.name = (
-                f"{self.name} {md_job.name} {len(working_outputs['relax']['volume'])+1}"
-            )
+            n_volumes = len(working_outputs["relax"]["volume"]) + 1
+            md_job.name = f"{self.name} {md_job.name} {n_volumes}"
 
             working_outputs["relax"]["energies"].append(md_job.output.output.energy)
             working_outputs["relax"]["volume"].append(md_job.output.structure.volume)
@@ -186,7 +185,7 @@ def make(
 
 
 @dataclass
-class MPMorphMDMaker(Maker, metaclass=ABCMeta):
+class MPMorphMDMaker(Maker, ABC):
     """Base MPMorph flow for amorphous solid equilibration.
 
     This flow uses NVT molecular dynamics to:
@@ -399,7 +398,7 @@ def make(
 
 
 @dataclass
-class SlowQuenchMaker(Maker, metaclass=ABCMeta):
+class SlowQuenchMaker(Maker, ABC):
     """Slow quench from high to low temperature structures.
 
     Quenches a provided structure with a molecular dynamics

src/atomate2/common/jobs/eos.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from abc import ABCMeta, abstractmethod
+from abc import ABC, abstractmethod
 from typing import TYPE_CHECKING
 
 import numpy as np
@@ -23,7 +23,7 @@
     from pymatgen.core import Structure
 
 
-class EOSPostProcessor(MSONable, metaclass=ABCMeta):
+class EOSPostProcessor(MSONable, ABC):
     """
     Fit data to an EOS.
 

src/atomate2/common/jobs/mpmorph.py

@@ -261,7 +261,7 @@ def get_entry_from_dict(chem_env: str) -> dict | None:
     for ielt in range(2, len(composition)):
         for combo in combinations(composition, ielt):
             chem_env_key = _get_chem_env_key_from_composition(
-                Composition({spec: 1 for spec in combo}),
+                Composition(dict.fromkeys(combo, 1)),
                 ignore_oxi_states=ignore_oxi_states,
             )
 

src/atomate2/forcefields/schemas.py

@@ -22,7 +22,7 @@ class ForcefieldResult(AseResult):
         None, description="The structure in the final trajectory frame."
     )
 
-    def model_post_init(self, __context: Any) -> None:
+    def model_post_init(self, context: Any, /) -> None:
         """Populate final_structure attr."""
         self.final_structure = getattr(
             self, "final_structure", self.final_mol_or_struct

src/atomate2/vasp/flows/ferroelectric.py

@@ -125,8 +125,7 @@ def make(
             add_interp_flow.output,
         )
 
-        jobs.append(add_interp_flow)
-        jobs.append(pol_analysis)
+        jobs += (add_interp_flow, pol_analysis)
 
         return Flow(
             jobs=jobs,

tests/forcefields/flows/test_mpmorph.py

@@ -132,7 +132,7 @@ def test_mpmorph_mlff_maker(ff_name, si_structure, test_dir, clean_dir):
         )
     task_docs = {}
     for uuid, job_name in uuids.items():
-        for _i, mp_job_name in enumerate(main_mp_morph_job_names):
+        for mp_job_name in main_mp_morph_job_names:
             if mp_job_name in job_name:
                 task_docs[mp_job_name] = response[uuid][1].output
                 break

tests/vasp/flows/test_mpmorph.py

@@ -147,7 +147,7 @@ def test_vasp_mpmorph(
     assert all(
         task_docs[
             "MP Morph VASP Equilibrium Volume Maker "
-            f"Convergence MPMorph VASP MD Maker {1+idx}"
+            f"Convergence MPMorph VASP MD Maker {1 + idx}"
         ].output.energy
         == pytest.approx(ref_eos["energy"][idx])
         for idx in range(3)
@@ -156,7 +156,7 @@ def test_vasp_mpmorph(
     assert all(
         task_docs[
             "MP Morph VASP Equilibrium Volume Maker "
-            f"Convergence MPMorph VASP MD Maker {1+idx}"
+            f"Convergence MPMorph VASP MD Maker {1 + idx}"
         ].output.structure.volume
         == pytest.approx(ref_eos["volume"][idx])
         for idx in range(3)

tests/vasp/test_sets.py

@@ -83,13 +83,13 @@ def test_user_incar_settings():
     static_set_generator = StaticSetGenerator(user_incar_settings=uis)
     incar = static_set_generator.get_input_set(structure, potcar_spec=True)["INCAR"]
 
-    for key in uis:
+    for key, val in uis.items():
         if isinstance(incar[key], str):
-            assert incar[key].lower() == uis[key].lower()
-        elif isinstance(uis[key], dict):
-            assert incar[key] == [uis[key][str(site.specie)] for site in structure]
+            assert incar[key].lower() == val.lower()
+        elif isinstance(val, dict):
+            assert incar[key] == [val[str(site.specie)] for site in structure]
         else:
-            assert incar[key] == uis[key]
+            assert incar[key] == val
 
 
 @pytest.mark.parametrize(