Pre-commit: Migrate to ruff

This replaces the `pylint`, `isort`, `yapf` and `pydocstyle` tools.

.github/workflows/validate_release_tag.py

@@ -17,8 +17,11 @@ def get_version_from_module(content: str) -> str:
 
     try:
         return next(
-            ast.literal_eval(statement.value) for statement in module.body if isinstance(statement, ast.Assign)
-            for target in statement.targets if isinstance(target, ast.Name) and target.id == '__version__'
+            ast.literal_eval(statement.value)
+            for statement in module.body
+            if isinstance(statement, ast.Assign)
+            for target in statement.targets
+            if isinstance(target, ast.Name) and target.id == '__version__'
         )
     except StopIteration as exception:
         raise IOError('Unable to find the `__version__` attribute in the module.') from exception

.pre-commit-config.yaml

@@ -13,25 +13,12 @@ repos:
     hooks:
     -   id: flynt
 
--   repo: https://github.com/pycqa/isort
-    rev: '5.12.0'
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: 'v0.1.6'
     hooks:
-    -   id: isort
-
--   repo: https://github.com/pre-commit/mirrors-yapf
-    rev: 'v0.32.0'
-    hooks:
-    -   id: yapf
-        name: yapf
-        types: [python]
-        args: ['-i']
-        additional_dependencies: ['toml']
-
--   repo: https://github.com/PyCQA/pydocstyle
-    rev: '6.1.1'
-    hooks:
-    -   id: pydocstyle
-        additional_dependencies: ['toml']
+    -   id: ruff-format
+    -   id: ruff
+        args: [--fix, --exit-non-zero-on-fix, --show-fixes]
 
 -   repo: local
     hooks:
@@ -47,9 +34,3 @@ repos:
             (?x)^(
                 src/.*py|
             )$
-
-    -   id: pylint
-        name: pylint
-        entry: pylint
-        types: [python]
-        language: system

pyproject.toml

@@ -51,8 +51,6 @@ Source = 'https://github.com/microsoft/aiida-pyscf'
 pre-commit = [
     'mypy==1.3.0',
     'pre-commit~=2.17',
-    'pylint~=2.16.0',
-    'pylint-aiida~=0.1.1',
 ]
 tests = [
     'packaging',
@@ -75,11 +73,29 @@ exclude = [
 line-length = 120
 fail-on-change = true
 
-[tool.isort]
-force_sort_within_sections = true
-include_trailing_comma = true
-line_length = 120
-multi_line_output = 3
+[tool.ruff]
+line-length = 120
+select = [
+    'E',    # pydocstyle
+    'W',    # pydocstyle
+    'F',    # pyflakes
+    'I',    # isort
+    'N',    # pep8-naming
+    'D',    # pydocstyle
+    'PLC',  # pylint-convention
+    'PLE',  # pylint-error
+    'PLR',  # pylint-refactor
+    'PLW',  # pylint-warning
+    'RUF',  # ruff
+]
+ignore = [
+    'D203',  # Incompatible with D211 `no-blank-line-before-class`
+    'D213',  # Incompatible with D212 `multi-line-summary-second-line`
+    'PLR2004',  # Magic value used in comparison
+]
+
+[tool.ruff.format]
+quote-style = 'single'
 
 [tool.mypy]
 show_error_codes = true
@@ -105,37 +121,7 @@ module = [
 ]
 ignore_missing_imports = true
 
-[tool.pydocstyle]
-ignore = [
-    'D104',
-    'D203',
-    'D213'
-]
-
-[tool.pylint.master]
-load-plugins = ['pylint_aiida']
-
-[tool.pylint.format]
-max-line-length = 120
-
-[tool.pylint.messages_control]
-disable = [
-    'duplicate-code',
-    'import-outside-toplevel',
-    'inconsistent-return-statements',
-    'too-many-ancestors',
-]
-
 [tool.pytest.ini_options]
 filterwarnings = [
     'ignore:Creating AiiDA configuration folder.*:UserWarning'
 ]
-
-[tool.yapf]
-align_closing_bracket_with_visual_indent = true
-based_on_style = 'google'
-coalesce_brackets = true
-column_limit = 120
-dedent_closing_brackets = true
-indent_dictionary_value = false
-split_arguments_when_comma_terminated = true

src/aiida_pyscf/calculations/base.py

@@ -8,14 +8,14 @@
 import pathlib
 import typing as t
 
+import numpy as np
 from aiida.common.datastructures import CalcInfo, CodeInfo
 from aiida.common.folders import Folder
 from aiida.engine import CalcJob, CalcJobProcessSpec
 from aiida.orm import ArrayData, Dict, SinglefileData, StructureData, TrajectoryData
 from aiida_shell.data import PickledData
 from ase.io.xyz import write_xyz
 from jinja2 import Environment, PackageLoader, PrefixLoader
-import numpy as np
 from plumpy.utils import AttributesFrozendict
 
 __all__ = ('PyscfCalculation',)
@@ -69,7 +69,7 @@ def define(cls, spec: CalcJobProcessSpec):  # type: ignore[override]
             'parameters',
             valid_type=Dict,
             required=False,
-            help='Various computed properties parsed from the `FILENAME_RESULTS` output file.'
+            help='Various computed properties parsed from the `FILENAME_RESULTS` output file.',
         )
         spec.output(
             'structure',
@@ -106,7 +106,7 @@ def define(cls, spec: CalcJobProcessSpec):  # type: ignore[override]
             'cubegen.mep',
             valid_type=SinglefileData,
             required=False,
-            help='The molecular electrostatic potential (MEP) in `.cube` format.'
+            help='The molecular electrostatic potential (MEP) in `.cube` format.',
         )
         spec.output(
             'hessian',
@@ -120,16 +120,16 @@ def define(cls, spec: CalcJobProcessSpec):  # type: ignore[override]
         spec.exit_code(
             410,
             'ERROR_ELECTRONIC_CONVERGENCE_NOT_REACHED',
-            message='The electronic minimization cycle did not reach self-consistency.'
+            message='The electronic minimization cycle did not reach self-consistency.',
         )
         spec.exit_code(
             500,
             'ERROR_IONIC_CONVERGENCE_NOT_REACHED',
-            message='The ionic minimization cycle did not converge for the given thresholds.'
+            message='The ionic minimization cycle did not converge for the given thresholds.',
         )
 
     @classmethod
-    def validate_parameters(cls, value: Dict | None, _) -> str | None:  # pylint: disable=too-many-return-statements,too-many-branches,too-many-locals
+    def validate_parameters(cls, value: Dict | None, _) -> str | None:  # noqa: PLR0911, PLR0912
         """Validate the parameters input."""
         if not value:
             return None

src/aiida_pyscf/parsers/__init__.py

@@ -0,0 +1,2 @@
+# -*- coding: utf-8 -*-
+"""Module for :mod:`aiida_pyscf.parsers`."""

src/aiida_pyscf/parsers/base.py

@@ -5,13 +5,13 @@
 import json
 import pathlib
 
+import dill
+import numpy
 from aiida.engine import ExitCode
 from aiida.orm import ArrayData, Dict, SinglefileData, TrajectoryData
 from aiida.parsers.parser import Parser
 from aiida_shell.data import PickledData
 from ase.io.extxyz import read_extxyz
-import dill
-import numpy
 from pint import UnitRegistry
 
 from aiida_pyscf.calculations.base import PyscfCalculation
@@ -27,7 +27,7 @@ def __init__(self, *args, **kwargs):
         self.dirpath_temporary: pathlib.Path | None = None
         super().__init__(*args, **kwargs)
 
-    def parse(self, retrieved_temporary_folder: str | None = None, **kwargs):  # pylint: disable=arguments-differ,too-many-locals,too-many-branches,too-many-statements
+    def parse(self, retrieved_temporary_folder: str | None = None, **kwargs):  # noqa: PLR0912, PLR0915
         """Parse the contents of the output files stored in the ``retrieved`` output node.
 
         :returns: An exit code if the job failed.
@@ -41,7 +41,7 @@ def parse(self, retrieved_temporary_folder: str | None = None, **kwargs):  # pyl
 
         try:
             with self.retrieved.base.repository.open(PyscfCalculation.FILENAME_STDOUT, 'r') as handle:
-                stdout = handle.read()  # pylint: disable=unused-variable
+                handle.read()
         except FileNotFoundError:
             return self.handle_failure('ERROR_OUTPUT_STDOUT_MISSING')
 
@@ -133,7 +133,7 @@ def build_output_trajectory(self, filepath_trajectory: pathlib.Path) -> Trajecto
 
         def batch(iterable, batch_size):
             """Split an iterable into a list of elements which size ``batch_size."""
-            return [iterable[i:i + batch_size] for i in range(0, len(iterable), batch_size)]
+            return [iterable[i : i + batch_size] for i in range(0, len(iterable), batch_size)]
 
         with filepath_trajectory.open() as handle:
             for atoms in read_extxyz(handle, index=slice(None, None)):
@@ -155,8 +155,8 @@ def batch(iterable, batch_size):
             symbols=[site.kind_name for site in self.node.inputs.structure.sites],
             positions=numpy.array(positions),
         )
-        energies = (numpy.array(energies) * ureg.hartree).to(ureg.electron_volt).magnitude  # type: ignore[attr-defined]
-        trajectory.set_array('energies', energies)
+        energies = (numpy.array(energies) * ureg.hartree).to(ureg.electron_volt).magnitude
+        trajectory.set_array('energies', energies)  # type: ignore[arg-type]
 
         return trajectory
 

src/aiida_pyscf/workflows/__init__.py

@@ -0,0 +1,2 @@
+# -*- coding: utf-8 -*-
+"""Module for :mod:`aiida_pyscf.workflows`."""

src/aiida_pyscf/workflows/base.py

@@ -32,7 +32,7 @@ def define(cls, spec):
         spec.exit_code(
             310,
             'ERROR_NO_CHECKPOINT_TO_RESTART',
-            message='The calculation failed and did not retrieve a checkpoint file from which can be restarted.'
+            message='The calculation failed and did not retrieve a checkpoint file from which can be restarted.',
         )
 
     def setup(self):
@@ -68,7 +68,7 @@ def handle_unrecoverable_failure(self, node):
         priority=500,
         exit_codes=[
             PyscfCalculation.exit_codes.ERROR_IONIC_CONVERGENCE_NOT_REACHED,  # type: ignore[union-attr]
-        ]
+        ],
     )
     def handle_ionic_convergence_not_reached(self, node):
         """Handle ``ERROR_IONIC_CONVERGENCE_NOT_REACHED`` error.
@@ -95,7 +95,7 @@ def handle_ionic_convergence_not_reached(self, node):
         priority=410,
         exit_codes=[
             PyscfCalculation.exit_codes.ERROR_ELECTRONIC_CONVERGENCE_NOT_REACHED,  # type: ignore[union-attr]
-        ]
+        ],
     )
     def handle_electronic_convergence_not_reached(self, node):
         """Handle ``ERROR_ELECTRONIC_CONVERGENCE_NOT_REACHED`` error.
@@ -110,7 +110,7 @@ def handle_electronic_convergence_not_reached(self, node):
         priority=110,
         exit_codes=[
             PyscfCalculation.exit_codes.ERROR_SCHEDULER_NODE_FAILURE,  # type: ignore[union-attr]
-        ]
+        ],
     )
     def handle_scheduler_node_failure(self, node):
         """Handle ``ERROR_SCHEDULER_NODE_FAILURE`` error.
@@ -128,7 +128,7 @@ def handle_scheduler_node_failure(self, node):
         priority=100,
         exit_codes=[
             PyscfCalculation.exit_codes.ERROR_SCHEDULER_OUT_OF_WALLTIME,  # type: ignore[union-attr]
-        ]
+        ],
     )
     def handle_out_of_walltime(self, node):
         """Handle ``ERROR_SCHEDULER_OUT_OF_WALLTIME`` error.

tests/calculations/__init__.py

@@ -0,0 +1,2 @@
+# -*- coding: utf-8 -*-
+"""Tests for :mod:`aiida_pyscf.calculations`."""

tests/calculations/test_base.py

@@ -1,15 +1,13 @@
 # -*- coding: utf-8 -*-
 """Tests for the :mod:`aiida_pyscf.calculations.base` module."""
-# pylint: disable=redefined-outer-name
 import io
 import textwrap
 
+import pytest
 from aiida.manage.tests.pytest_fixtures import recursive_merge
 from aiida.orm import Dict, SinglefileData
-from jinja2 import BaseLoader, Environment
-import pytest
-
 from aiida_pyscf.calculations.base import PyscfCalculation
+from jinja2 import BaseLoader, Environment
 
 
 @pytest.fixture
@@ -24,13 +22,7 @@ def factory(**kwargs):
             'code': aiida_local_code_factory('pyscf.base', 'python'),
             'structure': generate_structure(),
             'parameters': Dict(parameters),
-            'metadata': {
-                'options': {
-                    'resources': {
-                        'num_machines': 1
-                    }
-                }
-            },
+            'metadata': {'options': {'resources': {'num_machines': 1}}},
         }
         inputs.update(**kwargs)
         return inputs
@@ -43,15 +35,19 @@ def test_default(generate_calc_job, generate_inputs_pyscf, file_regression):
     inputs = generate_inputs_pyscf()
     tmp_path, calc_info = generate_calc_job(PyscfCalculation, inputs=inputs)
 
-    assert sorted(calc_info.retrieve_list) == sorted([
-        PyscfCalculation.FILENAME_RESULTS,
-        PyscfCalculation.FILENAME_MODEL,
-        PyscfCalculation.FILENAME_STDOUT,
-    ])
+    assert sorted(calc_info.retrieve_list) == sorted(
+        [
+            PyscfCalculation.FILENAME_RESULTS,
+            PyscfCalculation.FILENAME_MODEL,
+            PyscfCalculation.FILENAME_STDOUT,
+        ]
+    )
 
-    assert sorted(calc_info.retrieve_temporary_list) == sorted([
-        PyscfCalculation.FILENAME_CHECKPOINT,
-    ])
+    assert sorted(calc_info.retrieve_temporary_list) == sorted(
+        [
+            PyscfCalculation.FILENAME_CHECKPOINT,
+        ]
+    )
 
     content_input_file = (tmp_path / PyscfCalculation.FILENAME_SCRIPT).read_text()
     file_regression.check(content_input_file, encoding='utf-8', extension='.pyr')
@@ -61,10 +57,7 @@ def test_parameters_structure(generate_calc_job, generate_inputs_pyscf, file_reg
     """Test the ``structure`` key of the ``parameters`` input."""
     parameters = {
         'structure': {
-            'basis': {
-                'O': 'sto-3g',
-                'H': 'cc-pvdz'
-            },
+            'basis': {'O': 'sto-3g', 'H': 'cc-pvdz'},
             'cart': True,
             'charge': 1,
             'spin': 2,
@@ -83,9 +76,7 @@ def test_parameters_mean_field(generate_calc_job, generate_inputs_pyscf, file_re
         'mean_field': {
             'diis_start_cycle': 2,
             'method': 'RHF',
-            'grids': {
-                'level': 3
-            },
+            'grids': {'level': 3},
             'xc': 'PBE',
         },
     }