bump ruff and fix errors

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.7
+    rev: v0.1.9
     hooks:
       - id: ruff
         args: [--fix]
@@ -21,7 +21,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.7.1
+    rev: v1.8.0
     hooks:
       - id: mypy
 

README.md

@@ -1,32 +1,36 @@
 <h1 align="center">
-  <img src="https://github.com/materialsvirtuallab/matcalc/assets/30958850/89486f2f-73fb-40fb-803a-dfafe510eb6d" width="150" height="150" alt="MatCalc logo" style="vertical-align: middle;" />
+  <img src="https://github.com/materialsvirtuallab/matcalc/assets/30958850/89486f2f-73fb-40fb-803a-dfafe510eb6d" width="100" alt="MatCalc logo" style="vertical-align: middle;" /><br>
   MatCalc
 </h1>
 
+<h4 align="center">
+
 [![GitHub license](https://img.shields.io/github/license/materialsvirtuallab/matcalc)](https://github.com/materialsvirtuallab/matcalc/blob/main/LICENSE)
 [![Linting](https://github.com/materialsvirtuallab/matcalc/workflows/Linting/badge.svg)](https://github.com/materialsvirtuallab/matcalc/workflows/Linting/badge.svg)
 [![Testing](https://github.com/materialsvirtuallab/matcalc/workflows/Testing/badge.svg)](https://github.com/materialsvirtuallab/matcalc/workflows/Testing/badge.svg)
 [![codecov](https://codecov.io/gh/materialsvirtuallab/matcalc/branch/main/graph/badge.svg?token=OR7Z9WWRRC)](https://codecov.io/gh/materialsvirtuallab/matcalc)
 [![Requires Python 3.8+](https://img.shields.io/badge/Python-3.8+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads)
 [![PyPI](https://img.shields.io/pypi/v/matcalc?logo=pypi&logoColor=white)](https://pypi.org/project/matcalc?logo=pypi&logoColor=white)
 
+</h4>
+
 ## Docs
 
 [materialsvirtuallab.github.io/matcalc](https://materialsvirtuallab.github.io/matcalc)
 
 ## Introduction
 
-MatCalc is a Python library for calculating materials properties from the potential energy surface (PES). The
-PES can be from DFT or, more commonly, from machine learning interatomic potentials (MLIPs).
+MatCalc is a Python library for calculating material properties from the potential energy surface (PES). The
+PES can come from DFT or, more commonly, from machine learning interatomic potentials (MLIPs).
 
-Calculating various materials properties can require relatively involved setup of various simulation codes. The
+Calculating material properties often requires involved setups of various simulation codes. The
 goal of MatCalc is to provide a simplified, consistent interface to access these properties with any
 parameterization of the PES.
 
 ## Outline
 
 The main base class in MatCalc is `PropCalc` (property calculator). [All `PropCalc` subclasses](https://github.com/search?q=repo%3Amaterialsvirtuallab%2Fmatcalc%20%22(PropCalc)%22) should implement a
-`calc(pymatgen.Structure) -> dict` method that returns a dict of properties.
+`calc(pymatgen.Structure) -> dict` method that returns a dictionary of properties.
 
 In general, `PropCalc` should be initialized with an ML model or ASE calculator, which is then used by either ASE,
 LAMMPS or some other simulation code to perform calculations of properties.

matcalc/base.py

@@ -2,7 +2,7 @@
 from __future__ import annotations
 
 import abc
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Any
 
 from joblib import Parallel, delayed
 
@@ -29,7 +29,7 @@ def calc(self, structure: Structure) -> dict:
         """
 
     def calc_many(
-        self, structures: Sequence[Structure], n_jobs: None | int = None, **kwargs
+        self, structures: Sequence[Structure], n_jobs: None | int = None, **kwargs: Any
     ) -> Generator[dict, None, None]:
         """
         Performs calc on many structures. The return type is a generator given that the calc method can potentially be

matcalc/elasticity.py

@@ -15,6 +15,7 @@
     from collections.abc import Sequence
 
     from ase.calculators.calculator import Calculator
+    from numpy.typing import ArrayLike
     from pymatgen.core import Structure
 
 
@@ -48,11 +49,11 @@ def __init__(
         self.norm_strains = tuple(np.array([1]) * np.asarray(norm_strains))
         self.shear_strains = tuple(np.array([1]) * np.asarray(shear_strains))
         if len(self.norm_strains) == 0:
-            raise ValueError("norm_strains must be nonempty")
+            raise ValueError("norm_strains is empty")
         if len(self.shear_strains) == 0:
-            raise ValueError("shear_strains must be nonempty")
+            raise ValueError("shear_strains is empty")
         if 0 in self.norm_strains or 0 in self.shear_strains:
-            raise ValueError("Strains must be nonzero")
+            raise ValueError("strains must be non-zero")
         self.relax_structure = relax_structure
         self.fmax = fmax
         if len(self.norm_strains) > 1 and len(self.shear_strains) > 1:
@@ -112,11 +113,11 @@ def calc(self, structure: Structure) -> dict[str, Any]:
 
     def _elastic_tensor_from_strains(
         self,
-        strains,
-        stresses,
-        eq_stress=None,
+        strains: ArrayLike,
+        stresses: ArrayLike,
+        eq_stress: ArrayLike = None,
         tol: float = 1e-7,
-    ):
+    ) -> tuple[ElasticTensor, float]:
         """
         Slightly modified version of Pymatgen function
         pymatgen.analysis.elasticity.elastic.ElasticTensor.from_independent_strains;

matcalc/neb.py

@@ -2,7 +2,7 @@
 from __future__ import annotations
 
 import os
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Any
 
 from ase.io import Trajectory
 from ase.neb import NEB, NEBTools
@@ -27,8 +27,8 @@ def __init__(
         traj_folder: str | None = None,
         interval: int = 1,
         climb: bool = True,
-        **kwargs,
-    ):
+        **kwargs: Any,
+    ) -> None:
         """
         Args:
             images(list): A list of pymatgen structures as NEB image structures.
@@ -65,8 +65,8 @@ def from_end_images(
         n_images: int = 7,
         interpolate_lattices: bool = False,
         autosort_tol: float = 0.5,
-        **kwargs,
-    ):
+        **kwargs: Any,
+    ) -> NEBCalc:
         """
         Initialize a NEBCalc from end images.
 
@@ -94,7 +94,7 @@ def from_end_images(
 
     def calc(  # type: ignore[override]
         self, fmax: float = 0.1, max_steps: int = 1000
-    ) -> float:
+    ) -> tuple[float, float]:
         """
         Perform NEB calculation.
 

matcalc/utils.py

@@ -4,7 +4,7 @@
 
 import functools
 from inspect import isclass
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Any
 
 import ase.optimize
 from ase.optimize.optimize import Optimizer
@@ -23,7 +23,7 @@
 
 
 @functools.lru_cache
-def get_universal_calculator(name: str | Calculator, **kwargs) -> Calculator:
+def get_universal_calculator(name: str | Calculator, **kwargs: Any) -> Calculator:
     """
     Helper method to get some well-known **universal** calculators.
     Imports should be inside if statements to ensure that all models are optional dependencies.

pyproject.toml

@@ -51,51 +51,34 @@ packages = ["matcalc"]
 [tool.ruff]
 target-version = "py39"
 line-length = 120
-select = [
-    "B",    # flake8-bugbear
-    "C4",   # flake8-comprehensions
-    "D",    # pydocstyle
-    "E",    # pycodestyle error
-    "EXE",  # flake8-executable
-    "F",    # pyflakes
-    "I",    # isort
-    "ICN",  # flake8-import-conventions
-    "ISC",  # flake8-implicit-str-concat
-    "PD",   # pandas-vet
-    "PERF", # perflint
-    "PIE",  # flake8-pie
-    "PL",   # pylint
-    "PT",   # flake8-pytest-style
-    "PYI",  # flakes8-pyi
-    "Q",    # flake8-quotes
-    "RET",  # flake8-return
-    "RSE",  # flake8-raise
-    "RUF",  # Ruff-specific rules
-    "SIM",  # flake8-simplify
-    "SLOT", # flake8-slots
-    "TCH",  # flake8-type-checking
-    "TID",  # tidy imports
-    "TID",  # flake8-tidy-imports
-    "UP",   # pyupgrade
-    "W",    # pycodestyle warning
-    "YTT",  # flake8-2020
-]
+select = ["ALL"]
 ignore = [
+    "ANN101",
+    "ANN102",
+    "ANN401",
     "B019",    # functools.lru_cache on methods can lead to memory leaks
+    "COM812",  # trailing comma missing
     "D105",    # Missing docstring in magic method
     "D205",    # 1 blank line required between summary line and description
     "D212",    # Multi-line docstring summary should start at the first line
+    "EM101",
+    "EM102",
+    "FBT001",
+    "FBT002",
     "PLR",     # pylint refactor
     "PLW0603", # Using the global statement to update variables is discouraged
+    "PTH",     # prefer Path to os.path
     "SIM105",  # Use contextlib.suppress(OSError) instead of try-except-pass
+    "TRY003",
 ]
+exclude = ["docs/conf.py"]
 pydocstyle.convention = "google"
 isort.required-imports = ["from __future__ import annotations"]
 
 [tool.ruff.per-file-ignores]
 "__init__.py" = ["F401"]
-"tasks.py" = ["D"]
-"tests/*" = ["D"]
+"tasks.py" = ["ANN", "D", "T203"]
+"tests/*" = ["D", "INP001", "N802", "N803", "S101"]
 
 [tool.pytest.ini_options]
 addopts = "--durations=30 --quiet -rXs --color=yes -p no:warnings"

tasks.py

@@ -67,8 +67,6 @@ def make_docs(ctx):
         ctx.run("cp ../README.md index.md", warn=True)
         ctx.run("rm matcalc.*.rst", warn=True)
         ctx.run("sphinx-apidoc -P -M -d 6 -o . -f ../matcalc")
-        # ctx.run("rm matcalc*.html", warn=True)
-        # ctx.run("sphinx-build -b html . ../docs")  # HTML building.
         ctx.run("cp modules.rst index.rst")
         ctx.run("sphinx-build -M markdown . .")
         ctx.run("rm *.rst", warn=True)
@@ -110,7 +108,7 @@ def publish(ctx):
 
 
 @task
-def release_github(ctx):
+def release_github(ctx):  # noqa: ARG001
     desc = get_changelog()
     payload = {
         "tag_name": "v" + NEW_VER,
@@ -124,16 +122,16 @@ def release_github(ctx):
         "https://api.github.com/repos/materialsvirtuallab/matcalc/releases",
         data=json.dumps(payload),
         headers={"Authorization": "token " + os.environ["GITHUB_RELEASES_TOKEN"]},
+        timeout=10,
     )
     pprint(response.json())
 
 
 @task
-def release(ctx, notest=False):
+def release(ctx, notest: bool = False) -> None:
     ctx.run("rm -r dist build matcalc.egg-info", warn=True)
     if not notest:
         ctx.run("pytest tests")
-    # publish(ctx)
     release_github(ctx)
 
 
@@ -145,6 +143,6 @@ def get_changelog():
 
 
 @task
-def view_docs(ctx):
+def view_docs(ctx) -> None:
     with cd("docs"):
         ctx.run("bundle exec jekyll serve")

tests/conftest.py

@@ -10,30 +10,35 @@
 """
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import matgl
 import pytest
 from matgl.ext.ase import M3GNetCalculator
 from pymatgen.util.testing import PymatgenTest
 
+if TYPE_CHECKING:
+    from pymatgen.core import Structure
+
 matgl.clear_cache(confirm=False)
 
 
 @pytest.fixture(scope="session")
-def LiFePO4():
+def LiFePO4() -> Structure:
     """LiFePO4 structure as session-scoped fixture (don't modify in-place,
     will affect other tests).
     """
     return PymatgenTest.get_structure("LiFePO4")
 
 
 @pytest.fixture(scope="session")
-def Li2O():
+def Li2O() -> Structure:
     """Li2O structure as session-scoped fixture."""
     return PymatgenTest.get_structure("Li2O")
 
 
 @pytest.fixture(scope="session")
-def M3GNetCalc():
+def M3GNetCalc() -> M3GNetCalculator:
     """M3GNet calculator as session-scoped fixture."""
     potential = matgl.load_model("M3GNet-MP-2021.2.8-PES")
     return M3GNetCalculator(potential=potential, stress_weight=0.01)

tests/test_elasticity.py

@@ -59,12 +59,13 @@ def test_elastic_calc(Li2O: Structure, M3GNetCalc: M3GNetCalculator) -> None:
     assert results["bulk_modulus_vrh"] == pytest.approx(0.6631894154825593, rel=1e-3)
 
 
-def test_elastic_calc_invalid_states(M3GNetCalc: M3GNetCalculator):
-    with pytest.raises(ValueError, match="shear_strains must be nonempty"):
+def test_elastic_calc_invalid_states(M3GNetCalc: M3GNetCalculator) -> None:
+    with pytest.raises(ValueError, match="shear_strains is empty"):
         ElasticityCalc(M3GNetCalc, shear_strains=[])
-    with pytest.raises(ValueError, match="norm_strains must be nonempty"):
+    with pytest.raises(ValueError, match="norm_strains is empty"):
         ElasticityCalc(M3GNetCalc, norm_strains=[])
-    with pytest.raises(ValueError, match="Strains must be nonzero"):
+
+    with pytest.raises(ValueError, match="strains must be non-zero"):
         ElasticityCalc(M3GNetCalc, norm_strains=[0.0, 0.1])
-    with pytest.raises(ValueError, match="Strains must be nonzero"):
+    with pytest.raises(ValueError, match="strains must be non-zero"):
         ElasticityCalc(M3GNetCalc, shear_strains=[0.0, 0.1])

tests/test_neb.py

@@ -19,12 +19,11 @@ def test_neb_calc(LiFePO4: Structure, M3GNetCalc: M3GNetCalculator, tmp_path: Pa
     image_start.remove_sites([2])
     image_end = LiFePO4.copy()
     image_end.remove_sites([3])
-    NEBcalc = NEBCalc.from_end_images(image_start, image_end, M3GNetCalc, n_images=5, traj_folder=tmp_path)
-    barriers = NEBcalc.calc(fmax=0.5)
-    print(barriers)
-    assert len(NEBcalc.neb.images) == 7
+    neb_calc = NEBCalc.from_end_images(image_start, image_end, M3GNetCalc, n_images=5, traj_folder=tmp_path)
+    barriers = neb_calc.calc(fmax=0.5)
+    assert len(neb_calc.neb.images) == 7
     assert barriers[0] == pytest.approx(0.0184783935546875, rel=0.002)
     assert barriers[1] == pytest.approx(0.0018920898, rel=0.002)
 
     with pytest.raises(ValueError, match="Unknown optimizer='invalid', must be one of "):
-        NEBcalc.from_end_images(image_start, image_end, M3GNetCalc, optimizer="invalid")
+        neb_calc.from_end_images(image_start, image_end, M3GNetCalc, optimizer="invalid")