Single source of truth for optional deps in pyproject.toml (#1036)

* ruff

* fix PYI063 Use PEP 570 syntax for positional-only arguments

* single source of truth for optional deps in pyproject.toml

* revert to mace-torch==0.3.6, 0.3.7 still unreleased

* fix typo defects -> phonons

* lint

---------

Co-authored-by: Aaron Kaplan <[email protected]>
Co-authored-by: esoteric-ephemera <[email protected]>

Author: janosh

pyproject.toml

@@ -41,7 +41,7 @@ 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>=2.0.0"]
 lobster = ["ijson>=3.2.2", "lobsterpy>=0.4.0"]
@@ -94,30 +94,6 @@ tests = [
     "pytest-xdist==3.8.0",
     "pytest==8.4.1",
 ]
-strict = [
-    "PyYAML==6.0.2",
-    "ase==3.26.0",
-    "cclib==1.8.1",
-    "click==8.2.1",
-    "custodian==2025.8.13",
-    "dscribe==2.1.1",
-    "emmet-core==v0.84.10rc2",
-    "ijson==3.4.0",
-    "jobflow==0.2.0",
-    "lobsterpy==0.5.7",
-    "monty==2025.3.3",
-    "mp-api==0.45.8",
-    "numpy",
-    "phonopy==2.30.1",
-    "pydantic-settings==2.10.1",
-    "pydantic==2.11.7",
-    "pymatgen-analysis-defects==2025.1.18",
-    "pymatgen==2025.6.14",
-    "pymongo==4.10.1",
-    "python-ulid==3.1.0",
-    "seekpath==2.1.0",
-    "typing-extensions==4.14.1",
-]
 strict-openff = [
     "mdanalysis==2.9.0",
     "monty==2025.3.3",
@@ -135,6 +111,9 @@ strict-forcefields = [
     "torch==2.2.0",
     "torchdata==0.7.1",                            # TODO: remove when issue fixed
 ]
+strict = [
+    "atomate2[strict-forcefields, docs, cclib, phonons, lobster, openmm, mp, defects, ase, ase-ext]",
+]
 
 [project.scripts]
 atm = "atomate2.cli:cli"

src/atomate2/ase/jobs.py

@@ -4,7 +4,7 @@
 
 import logging
 import time
-from abc import ABCMeta, abstractmethod
+from abc import ABC, abstractmethod
 from dataclasses import dataclass, field
 from typing import TYPE_CHECKING
 
@@ -31,7 +31,7 @@
 
 
 @dataclass
-class AseMaker(Maker, metaclass=ABCMeta):
+class AseMaker(Maker, ABC):
     """
     Define basic template of ASE-based jobs.
 

src/atomate2/ase/md.py

@@ -8,7 +8,7 @@
 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
@@ -82,7 +82,7 @@ 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

@@ -103,7 +103,7 @@ class AseBaseModel(BaseModel):
     structure: Structure | None = Field(None, description="The structure at this step.")
     molecule: Molecule | None = 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
 
@@ -160,6 +160,7 @@ def make(
                 deformed_structures[index].final_structure,
                 prev_dir=None,
             )
+
             relaxed_vol = len(working_outputs["relax"]["volume"])
             md_job.name = f"{self.name} {md_job.name} {relaxed_vol + 1}"
 
@@ -180,7 +181,7 @@ 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:
@@ -391,7 +392,7 @@ 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/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

@@ -124,7 +124,7 @@ 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