Merge branch 'main' into neb_nn

.github/workflows/tests.yaml

@@ -13,11 +13,11 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.10", "3.12"]
         os: [ubuntu-latest, windows-latest]
         exclude:
           - os: windows-latest
-            python-version: "3.9"
+            python-version: "3.10"
 
     runs-on: ${{ matrix.os }}
     defaults:

CHANGELOG.md

@@ -4,6 +4,22 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project generally adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.11.5]
+
+### Added
+
+- Added support for atomate2>=0.0.15
+
+### Changed
+
+- The minimum supported Python version is now 3.10 in alignment with Pymatgen
+
+## [0.11.4]
+
+### Changed
+
+- Put a `<=` version pin on Atomate2 to resolve upstream breaking change
+
 ## [0.11.3]
 
 ### Added

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "quacc"
 description="A platform to enable high-throughput, database-driven quantum chemistry and computational materials science"
-version = "0.11.4"
+version = "0.11.5"
 readme = "README.md"
 license = { text = "BSD-3" }
 authors = [{ name = "Andrew S. Rosen", email = "[email protected]" }]
@@ -15,7 +15,6 @@ classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Science/Research",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -25,7 +24,7 @@ classifiers = [
     "Operating System :: Unix",
     "Operating System :: MacOS",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "ase>=3.23.0", # for Atoms object and calculators
     "custodian>=2024.3.12", # for automated error corrections
@@ -47,7 +46,7 @@ dask = ["dask[distributed]>=2023.12.1", "dask-jobqueue>=0.8.2"]
 defects = ["pymatgen-analysis-defects>=2023.8.22", "shakenbreak>=3.2.0"]
 jobflow = ["jobflow[fireworks]>=0.1.14", "jobflow-remote>=0.1.0"]
 mlp = ["matgl>=1.1.2", "chgnet>=0.3.3", "mace-torch>=0.3.3", "torch-dftd>=0.4.0"]
-mp = ["atomate2<=0.0.14"]
+mp = ["atomate2>=0.0.14"]
 newtonnet = ["newtonnet>=1.1"]
 parsl = ["parsl[monitoring]>=2024.5.27; platform_system!='Windows'"]
 phonons = ["phonopy>=2.20.0", "seekpath>=2.1.0"]

src/quacc/calculators/vasp/params.py

@@ -449,7 +449,11 @@ def convert_vasp_maker(self, VaspMaker: BaseVaspMaker) -> dict:
         )
         self.incar_dict = input_set.incar
         self.pmg_kpts = input_set.kpoints
-        self.potcar_symbols = input_set.potcar
+        self.potcar_symbols = (
+            input_set.potcar.split("\n")
+            if isinstance(input_set.potcar, str)
+            else input_set.potcar
+        )
         self.potcar_functional = input_set_generator.potcar_functional
         self.poscar = input_set.poscar
         return self._convert()

src/quacc/calculators/vasp/vasp.py

@@ -232,7 +232,7 @@ def _cleanup_params(self) -> None:
         # Allow the user to use setups='mysetups.yaml' to load in a custom
         # setups from a YAML file
         if (
-            isinstance(self.user_calc_params.get("setups"), (str, Path))
+            isinstance(self.user_calc_params.get("setups"), str | Path)
             and self.user_calc_params["setups"] not in ase_setups.setups_defaults
         ):
             self.user_calc_params["setups"] = load_vasp_yaml_calc(

src/quacc/recipes/emt/defects.py

@@ -21,7 +21,8 @@
 
 
 if TYPE_CHECKING:
-    from typing import Any, Callable
+    from collections.abc import Callable
+    from typing import Any
 
     from ase.atoms import Atoms
 

src/quacc/recipes/emt/elastic.py

@@ -10,7 +10,8 @@
 from quacc.wflow_tools.customizers import customize_funcs
 
 if TYPE_CHECKING:
-    from typing import Any, Callable
+    from collections.abc import Callable
+    from typing import Any
 
     from ase.atoms import Atoms
 

src/quacc/recipes/emt/phonons.py

@@ -10,7 +10,8 @@
 from quacc.wflow_tools.customizers import customize_funcs
 
 if TYPE_CHECKING:
-    from typing import Any, Callable
+    from collections.abc import Callable
+    from typing import Any
 
     from ase.atoms import Atoms
 

src/quacc/recipes/emt/slabs.py

@@ -10,7 +10,8 @@
 from quacc.wflow_tools.customizers import customize_funcs
 
 if TYPE_CHECKING:
-    from typing import Any, Callable
+    from collections.abc import Callable
+    from typing import Any
 
     from ase.atoms import Atoms
 

src/quacc/recipes/espresso/_base.py

@@ -258,7 +258,7 @@ def prepare_copy(
     dict
         Dictionary of files to copy.
     """
-    if isinstance(copy_files, (str, Path)):
+    if isinstance(copy_files, str | Path):
         copy_files = [copy_files]
 
     if isinstance(copy_files, list):

src/quacc/recipes/espresso/bands.py

@@ -18,7 +18,8 @@
 from quacc.wflow_tools.customizers import customize_funcs
 
 if TYPE_CHECKING:
-    from typing import Any, Callable
+    from collections.abc import Callable
+    from typing import Any
 
     from ase.atoms import Atoms
 

src/quacc/recipes/espresso/dos.py

@@ -12,7 +12,8 @@
 from quacc.wflow_tools.customizers import customize_funcs
 
 if TYPE_CHECKING:
-    from typing import Any, Callable
+    from collections.abc import Callable
+    from typing import Any
 
     from ase.atoms import Atoms
 

src/quacc/recipes/espresso/phonons.py

@@ -23,7 +23,8 @@
 
 if TYPE_CHECKING:
     from collections import UserDict
-    from typing import Any, Callable
+    from collections.abc import Callable
+    from typing import Any
 
     from quacc.types import (
         EspressoPhononDosSchema,

src/quacc/recipes/mlp/phonons.py

@@ -16,7 +16,8 @@
 has_seekpath = bool(find_spec("seekpath"))
 
 if TYPE_CHECKING:
-    from typing import Any, Callable, Literal
+    from collections.abc import Callable
+    from typing import Any, Literal
 
     from ase.atoms import Atoms
 

src/quacc/recipes/tblite/phonons.py

@@ -17,7 +17,8 @@
 has_seekpath = bool(find_spec("seekpath"))
 
 if TYPE_CHECKING:
-    from typing import Any, Callable
+    from collections.abc import Callable
+    from typing import Any
 
     from ase.atoms import Atoms
 

src/quacc/recipes/vasp/mp.py

@@ -31,7 +31,8 @@
     )
 
 if TYPE_CHECKING:
-    from typing import Any, Callable
+    from collections.abc import Callable
+    from typing import Any
 
     from ase.atoms import Atoms
 

src/quacc/recipes/vasp/slabs.py

@@ -10,7 +10,8 @@
 from quacc.wflow_tools.customizers import customize_funcs
 
 if TYPE_CHECKING:
-    from typing import Any, Callable
+    from collections.abc import Callable
+    from typing import Any
 
     from ase.atoms import Atoms
 

src/quacc/runners/ase.py

@@ -39,6 +39,7 @@
     pass
 
 if TYPE_CHECKING:
+    from collections.abc import Callable
     from pathlib import Path
     from typing import Any
 
@@ -206,7 +207,7 @@ def run_opt(
 
         # Handle optimizer kwargs
         if (
-            issubclass(optimizer, (SciPyOptimizer, MolecularDynamics))
+            issubclass(optimizer, SciPyOptimizer | MolecularDynamics)
             or optimizer.__name__ == "IRC"
         ):
             # https://gitlab.com/ase/ase/-/issues/1476
@@ -230,7 +231,7 @@ def run_opt(
             full_run_kwargs.pop("fmax")
         try:
             with traj, optimizer(self.atoms, **merged_optimizer_kwargs) as dyn:
-                if issubclass(optimizer, (SciPyOptimizer, MolecularDynamics)):
+                if issubclass(optimizer, SciPyOptimizer | MolecularDynamics):
                     # https://gitlab.coms/ase/ase/-/issues/1475
                     # https://gitlab.com/ase/ase/-/issues/1497
                     dyn.run(**full_run_kwargs)

src/quacc/runners/prep.py

@@ -74,7 +74,7 @@ def calc_setup(
 
     # Copy files to tmpdir and decompress them if needed
     if copy_files:
-        if isinstance(copy_files, (str, Path)):
+        if isinstance(copy_files, str | Path):
             copy_files = {copy_files: "*"}
 
         for source_directory, filenames in copy_files.items():

src/quacc/settings.py

@@ -16,7 +16,8 @@
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
 if TYPE_CHECKING:
-    from typing import Any, Callable
+    from collections.abc import Callable
+    from typing import Any
 
 _DEFAULT_CONFIG_FILE_PATH = Path("~", ".quacc.yaml").expanduser().resolve()
 

src/quacc/types.py

@@ -16,9 +16,10 @@ class DefaultSetting(BaseSettings):
 
 
 if TYPE_CHECKING:
+    from collections.abc import Callable
     from datetime import datetime
     from pathlib import Path
-    from typing import Any, Callable, Literal, Union
+    from typing import Any, Literal
 
     from ase.atoms import Atoms
     from ase.md.md import MolecularDynamics
@@ -41,8 +42,8 @@ class DefaultSetting(BaseSettings):
 
     # ----------- File handling -----------
 
-    Filenames = Union[str, Path, list[Union[str, Path]]]
-    SourceDirectory = Union[str, Path]
+    Filenames = str | Path | list[str | Path]
+    SourceDirectory = str | Path
 
     # ----------- k-point handling -----------
 

src/quacc/wflow_tools/customizers.py

@@ -9,7 +9,8 @@
 from quacc.utils.dicts import recursive_dict_merge
 
 if TYPE_CHECKING:
-    from typing import Any, Callable
+    from collections.abc import Callable
+    from typing import Any
 
 
 def strip_decorator(func: Callable) -> Callable:
@@ -66,7 +67,7 @@ def strip_decorator(func: Callable) -> Callable:
         from prefect import Flow as PrefectFlow
         from prefect import Task
 
-        if isinstance(func, (Task, PrefectFlow)):
+        if isinstance(func, Task | PrefectFlow):
             func = func.fn
         elif hasattr(func, "__wrapped__"):
             func = func.__wrapped__
@@ -182,9 +183,9 @@ def customize_funcs(
     decorators = decorators or {}
     updated_funcs = []
 
-    if not isinstance(names, (list, tuple)):
+    if not isinstance(names, list | tuple):
         names = [names]
-    if not isinstance(funcs, (list, tuple)):
+    if not isinstance(funcs, list | tuple):
         funcs = [funcs]
 
     if "all" in names:

src/quacc/wflow_tools/decorators.py

@@ -2,8 +2,9 @@
 
 from __future__ import annotations
 
+from collections.abc import Callable
 from functools import partial, wraps
-from typing import Any, Callable
+from typing import Any
 
 from quacc.settings import change_settings_wrap
 

src/quacc/wflow_tools/job_patterns.py

@@ -7,7 +7,8 @@
 from quacc.wflow_tools.decorators import job
 
 if TYPE_CHECKING:
-    from typing import Any, Callable
+    from collections.abc import Callable
+    from typing import Any
 
 
 @job

src/quacc/wflow_tools/prefect_utils.py

@@ -56,7 +56,7 @@ def _collect_futures(futures, expr, context):
             result = result.get()
         results.append(result)
 
-    states_by_future = dict(zip(futures, results))
+    states_by_future = dict(zip(futures, results, strict=False))
 
     def replace_futures_with_states(expr, context):
         # Expressions inside quotes should not be modified

tests/requirements-covalent.txt

@@ -1,4 +1,3 @@
 covalent==0.235.1rc0
 covalent-cloud==0.73.0
-covalent-hpc-plugin==0.0.8
 covalent-slurm-plugin==0.18.0

tests/requirements-dask.txt

@@ -1,2 +1,2 @@
-dask[distributed]==2024.8.2
+dask[distributed]==2024.9.0
 dask-jobqueue==0.9.0

tests/requirements-jobflow.txt

@@ -1,3 +1,3 @@
 jobflow==0.1.18
-jobflow-remote==0.1.3
+jobflow-remote==0.1.4
 fireworks==2.0.3

tests/requirements-parsl.txt

@@ -1 +1 @@
-parsl[monitoring]==2024.9.2
+parsl[monitoring]==2024.9.16

tests/requirements-phonons.txt

@@ -1,2 +1,2 @@
-phonopy==2.27.0
+phonopy==2.28.0
 seekpath==2.1.0

tests/requirements-prefect.txt

@@ -1,2 +1,2 @@
 dask-jobqueue==0.9.0
-prefect[dask]==3.0.1
+prefect[dask]==3.0.2

tests/requirements.txt

@@ -6,7 +6,7 @@ monty==2024.7.30
 numpy==1.26.4
 psutil==5.9.8
 pydantic==2.9.1
-pydantic-settings==2.4.0
-pymatgen==2024.7.18
+pydantic-settings==2.5.2
+pymatgen==2024.9.17
 ruamel.yaml==0.18.6
 typer==0.12.5