Update pre-commit to use ruff (#161)

* Update pre-commit

* Apply ruff format

* Apply safe ruff check fixes

* Apply unsafe ruff check fixes

* Update ruff exclude

* Apply manual ruff check fixes

* Ignore ruff lowercase error

* Lower ruff requirement to match janus

* Update docs

* Remove pylint references

.pre-commit-config.yaml

@@ -9,36 +9,15 @@ repos:
     - id: trailing-whitespace
     - id: check-json
 
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.5.7
   hooks:
-  - id: pyupgrade
-    args: ["--py39-plus"]
-
-- repo: https://github.com/PyCQA/isort
-  rev: 5.13.2
-  hooks:
-    - id: isort
-      args: ["--profile=black"]
-
-- repo: https://github.com/psf/black
-  rev: 24.1.1
-  hooks:
-    - id: black
-      args: [--line-length=88]
-
-- repo: local
-  hooks:
-  - id: pylint
-    language: system
-    types: [file, python]
-    name: pylint
-    description: "This hook runs the pylint static code analyzer"
-    exclude: &exclude_files >
-      (?x)^(
-          docs/.*|
-      )$
-    entry: pylint
+    # Run the linter.
+    - id: ruff
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
 
 - repo: https://github.com/numpy/numpydoc
   rev: v1.6.0

aiida_mlip/__init__.py

@@ -1,5 +1,3 @@
-"""
-Machine learning interatomic potentials aiida plugin.
-"""
+"""Machine learning interatomic potentials aiida plugin."""
 
 __version__ = "0.2.1"

aiida_mlip/calculations/__init__.py

@@ -1,3 +1 @@
-"""
-Calculations using MLIPs.
-"""
+"""Calculations using MLIPs."""

aiida_mlip/calculations/base.py

@@ -2,13 +2,12 @@
 
 import shutil
 
-from ase.io import read, write
-
 from aiida.common import InputValidationError, datastructures
 import aiida.common.folders
 from aiida.engine import CalcJob, CalcJobProcessSpec
 import aiida.engine.processes
 from aiida.orm import SinglefileData, Str, StructureData
+from ase.io import read, write
 
 from aiida_mlip.data.config import JanusConfigfile
 from aiida_mlip.data.model import ModelData
@@ -186,7 +185,6 @@ def define(cls, spec: CalcJobProcessSpec) -> None:
             message="Some output files missing or cannot be read",
         )
 
-    # pylint: disable=too-many-locals
     def prepare_for_submission(
         self, folder: aiida.common.folders.Folder
     ) -> datastructures.CalcInfo:
@@ -203,7 +201,6 @@ def prepare_for_submission(
         aiida.common.datastructures.CalcInfo
             An instance of `aiida.common.datastructures.CalcInfo`.
         """
-
         if "struct" in self.inputs:
             structure = self.inputs.struct
         elif "config" in self.inputs and "struct" in self.inputs.config.as_dictionary:

aiida_mlip/calculations/geomopt.py

@@ -107,7 +107,6 @@ def prepare_for_submission(
         aiida.common.datastructures.CalcInfo
             An instance of `aiida.common.datastructures.CalcInfo`.
         """
-
         # Call the parent class method to prepare common inputs
         calcinfo = super().prepare_for_submission(folder)
         codeinfo = calcinfo.codes_info[0]

aiida_mlip/calculations/md.py

@@ -90,7 +90,6 @@ def prepare_for_submission(
         aiida.common.datastructures.CalcInfo
             An instance of `aiida.common.datastructures.CalcInfo`.
         """
-
         # Call the parent class method to prepare common inputs
         calcinfo = super().prepare_for_submission(folder)
         codeinfo = calcinfo.codes_info[0]

aiida_mlip/calculations/singlepoint.py

@@ -72,7 +72,6 @@ def define(cls, spec: CalcJobProcessSpec) -> None:
         print("defining outputnode")
         spec.default_output_node = "results_dict"
 
-    # pylint: disable=too-many-locals
     def prepare_for_submission(
         self, folder: aiida.common.folders.Folder
     ) -> datastructures.CalcInfo:

aiida_mlip/calculations/train.py

@@ -145,7 +145,6 @@ def define(cls, spec: CalcJobProcessSpec) -> None:
             message="Some output files missing or cannot be read",
         )
 
-    # pylint: disable=too-many-locals
     def prepare_for_submission(
         self, folder: aiida.common.folders.Folder
     ) -> datastructures.CalcInfo:

aiida_mlip/data/__init__.py

@@ -1,3 +1 @@
-"""
-Data types for MLIPs calculations.
-"""
+"""Data types for MLIPs calculations."""

aiida_mlip/data/config.py

@@ -3,9 +3,8 @@
 from pathlib import Path
 from typing import Any, Optional, Union
 
-import yaml
-
 from aiida.orm import Data, SinglefileData
+import yaml
 
 from aiida_mlip.helpers.converters import convert_to_nodes
 

aiida_mlip/data/model.py

@@ -65,8 +65,7 @@ def _calculate_hash(file: Union[str, Path]) -> str:
             # calculating sha in chunks rather than 1 large pass
             while data := f.read(buf_size):
                 sha256.update(data)
-        file_hash = sha256.hexdigest()
-        return file_hash
+        return sha256.hexdigest()
 
     def __init__(
         self,
@@ -153,7 +152,6 @@ def from_local(
         return cls(file=file_path, architecture=architecture, filename=filename)
 
     @classmethod
-    # pylint: disable=too-many-arguments
     def from_uri(
         cls,
         uri: str,

aiida_mlip/helpers/converters.py

@@ -1,21 +1,18 @@
-"""
-Some helpers to convert between different formats.
-"""
+"""Some helpers to convert between different formats."""
 
 from pathlib import Path
 from typing import Union
 
+from aiida.orm import Bool, Dict, Str, StructureData, TrajectoryData, load_code
 from ase.io import read
 import numpy as np
 
-from aiida.orm import Bool, Dict, Str, StructureData, TrajectoryData, load_code
-
 from aiida_mlip.helpers.help_load import load_model, load_structure
 
 
 def convert_numpy(dictionary: dict) -> dict:
     """
-    A function to convert numpy ndarrays in dictionary into lists.
+    Convert numpy ndarrays in dictionary into lists.
 
     Parameters
     ----------
@@ -35,10 +32,10 @@ def convert_numpy(dictionary: dict) -> dict:
 
 
 def xyz_to_aiida_traj(
-    traj_file: Union[str, Path]
+    traj_file: Union[str, Path],
 ) -> tuple[StructureData, TrajectoryData]:
     """
-    A function to convert xyz trajectory file to `TrajectoryData` data type.
+    Convert xyz trajectory file to `TrajectoryData` data type.
 
     Parameters
     ----------

aiida_mlip/helpers/help_load.py

@@ -1,16 +1,13 @@
-"""
-Helper functions for automatically loading models and strucutres as data nodes.
-"""
+"""Helper functions for automatically loading models and strucutres as data nodes."""
 
 from pathlib import Path
 from typing import Optional, Union
 
+from aiida.orm import StructureData, load_node
 from ase.build import bulk
 import ase.io
 import click
 
-from aiida.orm import StructureData, load_node
-
 from aiida_mlip.data.model import ModelData
 
 
@@ -43,7 +40,7 @@ def load_model(
     """
     if model is None:
         loaded_model = ModelData.from_uri(
-            "https://github.com/stfc/janus-core/raw/main/tests/models/mace_mp_small.model",  # pylint: disable=line-too-long
+            "https://github.com/stfc/janus-core/raw/main/tests/models/mace_mp_small.model",
             architecture,
             cache_dir=cache_dir,
         )

aiida_mlip/parsers/__init__.py

@@ -1,3 +1 @@
-"""
-Parsers for calculations.
-"""
+"""Parsers for calculations."""

aiida_mlip/parsers/base_parser.py

@@ -1,6 +1,4 @@
-"""
-Parsers provided by aiida_mlip.
-"""
+"""Parsers provided by aiida_mlip."""
 
 from aiida.engine import ExitCode
 from aiida.orm import SinglefileData

aiida_mlip/parsers/md_parser.py

@@ -1,16 +1,13 @@
-"""
-MD parser.
-"""
+"""MD parser."""
 
 from pathlib import Path
 
-import yaml
-
 from aiida.common import exceptions
 from aiida.engine import ExitCode
 from aiida.orm import Dict, SinglefileData
 from aiida.orm.nodes.process.process import ProcessNode
 from aiida.plugins import CalculationFactory
+import yaml
 
 from aiida_mlip.calculations.md import MD
 from aiida_mlip.helpers.converters import xyz_to_aiida_traj

aiida_mlip/parsers/opt_parser.py

@@ -1,6 +1,4 @@
-"""
-Geom optimisation parser.
-"""
+"""Geom optimisation parser."""
 
 from pathlib import Path
 
@@ -13,7 +11,7 @@
 from aiida_mlip.helpers.converters import xyz_to_aiida_traj
 from aiida_mlip.parsers.sp_parser import SPParser
 
-geomoptCalculation = CalculationFactory("mlip.opt")
+GeomoptCalc = CalculationFactory("mlip.opt")
 
 
 class GeomOptParser(SPParser):
@@ -54,7 +52,7 @@ def __init__(self, node: ProcessNode):
         """
         super().__init__(node)
 
-        if not issubclass(node.process_class, geomoptCalculation):
+        if not issubclass(node.process_class, GeomoptCalc):
             raise exceptions.ParsingError("Can only parse `GeomOpt` calculations")
 
     def parse(self, **kwargs) -> ExitCode:

aiida_mlip/parsers/sp_parser.py

@@ -1,21 +1,18 @@
-"""
-Parsers provided by aiida_mlip.
-"""
+"""Parsers provided by aiida_mlip."""
 
 from pathlib import Path
 
-from ase.io import read
-
 from aiida.common import exceptions
 from aiida.engine import ExitCode
 from aiida.orm import Dict, SinglefileData
 from aiida.orm.nodes.process.process import ProcessNode
 from aiida.plugins import CalculationFactory
+from ase.io import read
 
 from aiida_mlip.helpers.converters import convert_numpy
 from aiida_mlip.parsers.base_parser import BaseParser
 
-singlePointCalculation = CalculationFactory("mlip.sp")
+SinglepointCalc = CalculationFactory("mlip.sp")
 
 
 class SPParser(BaseParser):
@@ -43,7 +40,7 @@ class SPParser(BaseParser):
     Raises
     ------
     exceptions.ParsingError
-        If the ProcessNode being passed was not produced by a singlePointCalculation.
+        If the ProcessNode being passed was not produced by a SinglepointCalc.
     """
 
     def __init__(self, node: ProcessNode):
@@ -57,7 +54,7 @@ def __init__(self, node: ProcessNode):
         """
         super().__init__(node)
 
-        if not issubclass(node.process_class, singlePointCalculation):
+        if not issubclass(node.process_class, SinglepointCalc):
             raise exceptions.ParsingError("Can only parse `Singlepoint` calculations")
 
     def parse(self, **kwargs) -> int:
@@ -74,7 +71,6 @@ def parse(self, **kwargs) -> int:
         int
             An exit code.
         """
-
         exit_code = super().parse(**kwargs)
 
         if exit_code != ExitCode(0):

aiida_mlip/parsers/train_parser.py

@@ -1,6 +1,4 @@
-"""
-Parser for mlip train.
-"""
+"""Parser for mlip train."""
 
 import json
 from pathlib import Path

docs/source/conf.py

@@ -80,7 +80,6 @@
     if current_year == copyright_first_year
     else f"{copyright_first_year}-{current_year}"
 )
-# pylint: disable=redefined-builtin
 copyright = f"{copyright_year_string}, {copyright_owners}. All rights reserved"
 
 # The version info for the project you're documenting, acts as replacement for