Update the pre-commit configuration

The pre-commit is updated and improved in various ways:

 * Configuration is moved from tool specific configuration files to the
   standard `pyproject.toml`. This allows to remove `.style.yapf` and
   `pytest.ini`.
 * Update `yapf` requirement to `v0.31.0` which is necessary for the
   `pyproject.toml` support.
 * Add the `isort` hook to organize imports.
 * Add the `flynt` hook to automatically fix f-strings.

.pre-commit-config.yaml

@@ -9,36 +9,44 @@ repos:
     -   id: trailing-whitespace
 
 -   repo: https://github.com/ikamensh/flynt/
-    rev: '0.55'
+    rev: '0.66'
     hooks:
     -   id: flynt
         args: [
             '--line-length=120',
             '--fail-on-change',
         ]
 
+-   repo: https://github.com/pycqa/isort
+    rev: 5.9.3
+    hooks:
+    -   id: isort
+
 -   repo: https://github.com/pre-commit/mirrors-yapf
-    rev: v0.30.0
+    rev: v0.31.0
     hooks:
     -   id: yapf
         name: yapf
         types: [python]
         args: ['-i']
+        additional_dependencies: ['toml']
         exclude: &exclude_files >
             (?x)^(
                 docs/.*|
             )$
 
--   repo: https://github.com/PyCQA/pylint
-    rev: pylint-2.6.0
-    hooks:
-    -   id: pylint
-        language: system
-        exclude: *exclude_files
-
 -   repo: https://github.com/PyCQA/pydocstyle
     rev: 5.0.2
     hooks:
     -   id: pydocstyle
-        args: ['--ignore=D104,D203,D213']
+        additional_dependencies: ['toml']
+        exclude: *exclude_files
+
+-   repo: local
+    hooks:
+    -   id: pylint
+        name: pylint
+        entry: pylint
+        types: [python]
+        language: system
         exclude: *exclude_files

aiida_pseudo/cli/__init__.py

@@ -6,7 +6,7 @@
 # Activate the completion of parameter types provided by the click_completion package
 click_completion.init()
 
-from .root import cmd_root
 from .family import cmd_family
-from .install import cmd_install, cmd_install_family, cmd_install_sssp, cmd_install_pseudo_dojo
+from .install import cmd_install, cmd_install_family, cmd_install_pseudo_dojo, cmd_install_sssp
 from .list import cmd_list
+from .root import cmd_root

aiida_pseudo/cli/family.py

@@ -2,10 +2,9 @@
 """Commands to inspect or modify the contents of pseudo potential families."""
 import json
 
-import click
-
 from aiida.cmdline.params import options as options_core
 from aiida.cmdline.utils import decorators, echo
+import click
 
 from ..groups.mixins import RecommendedCutoffMixin
 from .params import arguments, options

aiida_pseudo/cli/install.py

@@ -4,15 +4,15 @@
 import pathlib
 import shutil
 import tempfile
-import yaml
 
+from aiida.cmdline.params import options as options_core
+from aiida.cmdline.utils import decorators, echo
 import click
 import requests
-
-from aiida.cmdline.utils import decorators, echo
-from aiida.cmdline.params import options as options_core
+import yaml
 
 from aiida_pseudo.groups.family import PseudoDojoConfiguration, SsspConfiguration
+
 from .params import options, types
 from .root import cmd_root
 
@@ -103,6 +103,7 @@ def download_sssp(
     :return: Latest patch version of the requested minor version
     """
     from aiida_pseudo.groups.family import SsspFamily
+
     from .utils import attempt
 
     url_template = 'https://archive.materialscloud.org/record/file?filename={filename}&parent_id=19'
@@ -156,6 +157,7 @@ def download_pseudo_dojo(
     :param traceback: boolean, if true, print the traceback when an exception occurs.
     """
     from aiida_pseudo.groups.family import PseudoDojoFamily
+
     from .utils import attempt
 
     label = PseudoDojoFamily.format_configuration_label(configuration)
@@ -196,6 +198,7 @@ def cmd_install_sssp(version, functional, protocol, download_only, traceback):
 
     from aiida_pseudo import __version__
     from aiida_pseudo.groups.family import SsspFamily
+
     from .utils import attempt, create_family_from_archive
 
     configuration = SsspConfiguration(version, functional, protocol)
@@ -274,8 +277,9 @@ def cmd_install_pseudo_dojo(
     # pylint: disable=too-many-locals,too-many-arguments,too-many-branches,too-many-statements
     from aiida.common.files import md5_file
     from aiida.orm import Group, QueryBuilder
+
     from aiida_pseudo import __version__
-    from aiida_pseudo.data.pseudo import JthXmlData, Psp8Data, PsmlData, UpfData
+    from aiida_pseudo.data.pseudo import JthXmlData, PsmlData, Psp8Data, UpfData
     from aiida_pseudo.groups.family import PseudoDojoFamily
 
     from .utils import attempt, create_family_from_archive

aiida_pseudo/cli/list.py

@@ -1,8 +1,8 @@
 # -*- coding: utf-8 -*-
 """Commands to list instances of `PseudoPotentialFamily`."""
-import click
 from aiida.cmdline.params import options as options_core
 from aiida.cmdline.utils import decorators, echo
+import click
 
 from .params import options
 from .root import cmd_root
@@ -17,6 +17,7 @@ def get_families_builder():
     :return: `QueryBuilder` instance
     """
     from aiida.orm import QueryBuilder
+
     from aiida_pseudo.groups.family import PseudoPotentialFamily
 
     builder = QueryBuilder().append(PseudoPotentialFamily)

aiida_pseudo/cli/params/arguments.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 """Reusable arguments for CLI commands."""
 from aiida.cmdline.params.arguments import OverridableArgument
+
 from .types import PseudoPotentialFamilyParam
 
 __all__ = ('PSEUDO_POTENTIAL_FAMILY',)

aiida_pseudo/cli/params/options.py

@@ -2,9 +2,9 @@
 """Reusable options for CLI commands."""
 import shutil
 
+from aiida.cmdline.params.options import OverridableOption
 import click
 
-from aiida.cmdline.params.options import OverridableOption
 from .types import PseudoPotentialFamilyTypeParam, PseudoPotentialTypeParam, UnitParamType
 
 __all__ = (

aiida_pseudo/cli/params/types.py

@@ -4,12 +4,12 @@
 import pathlib
 import typing
 
+from aiida.cmdline.params.types import GroupParamType
 import click
 import requests
 
-from aiida.cmdline.params.types import GroupParamType
-from ..utils import attempt
 from ...common.units import U
+from ..utils import attempt
 
 __all__ = ('PseudoPotentialFamilyTypeParam', 'PseudoPotentialFamilyParam', 'PseudoPotentialTypeParam')
 
@@ -28,6 +28,7 @@ def convert(self, value, _, __):
         """
         from aiida.common import exceptions
         from aiida.plugins import DataFactory
+
         from aiida_pseudo.data.pseudo import PseudoPotentialData
 
         try:
@@ -80,6 +81,7 @@ def convert(self, value, _, __):
         """
         from aiida.common import exceptions
         from aiida.plugins import GroupFactory
+
         from aiida_pseudo.groups.family import PseudoPotentialFamily
 
         try:

aiida_pseudo/cli/root.py

@@ -1,8 +1,7 @@
 # -*- coding: utf-8 -*-
 """Command line interface `aiida-pseudo`."""
-import click
-
 from aiida.cmdline.params import options, types
+import click
 
 
 @click.group('aiida-pseudo', context_settings={'help_option_names': ['-h', '--help']})

aiida_pseudo/data/pseudo/pseudo.py

@@ -4,8 +4,7 @@
 import pathlib
 import typing
 
-from aiida import orm
-from aiida import plugins
+from aiida import orm, plugins
 from aiida.common.constants import elements
 from aiida.common.exceptions import StoringNotAllowed
 from aiida.common.files import md5_from_filelike

aiida_pseudo/groups/family/pseudo.py

@@ -2,7 +2,7 @@
 """Subclass of ``Group`` that serves as a base class for representing pseudo potential families."""
 import os
 import re
-from typing import Union, List, Tuple, Mapping
+from typing import List, Mapping, Tuple, Union
 
 from aiida.common import exceptions
 from aiida.common.lang import classproperty, type_check

aiida_pseudo/groups/family/pseudo_dojo.py

@@ -3,14 +3,15 @@
 import json
 import os
 import re
+from pathlib import Path
+import re
 from typing import NamedTuple, Sequence
 import warnings
 
-from pathlib import Path
-
 from aiida.common.exceptions import ParsingError
 
-from aiida_pseudo.data.pseudo import UpfData, PsmlData, Psp8Data, JthXmlData
+from aiida_pseudo.data.pseudo import JthXmlData, PsmlData, Psp8Data, UpfData
+
 from ..mixins import RecommendedCutoffMixin
 from .pseudo import PseudoPotentialFamily
 

aiida_pseudo/groups/family/sssp.py

@@ -3,6 +3,7 @@
 from typing import NamedTuple, Optional, Sequence
 
 from aiida_pseudo.data.pseudo import UpfData
+
 from ..mixins import RecommendedCutoffMixin
 from .pseudo import PseudoPotentialFamily
 

aiida_pseudo/groups/mixins/cutoffs.py

@@ -1,8 +1,7 @@
 # -*- coding: utf-8 -*-
 """Mixin that adds support of recommended cutoffs to a ``Group`` subclass, using its extras."""
-import warnings
-
 from typing import Optional
+import warnings
 
 from aiida.common.lang import type_check
 from aiida.plugins import DataFactory

docs/source/conf.py

@@ -6,6 +6,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 from reentry import manager
+
 manager.scan()
 
 # -- Path setup --------------------------------------------------------------
@@ -16,6 +17,7 @@
 #
 import os
 import sys
+
 sys.path.insert(0, os.path.abspath('../../'))
 
 import aiida_pseudo

pyproject.toml

@@ -1,6 +1,22 @@
 [build-system]
-requires = ['setuptools>=40.8.0', 'wheel', 'reentry~=1.3', 'fastentrypoints~=0.12']
-build-backend = 'setuptools.build_meta:__legacy__'
+requires = ['setuptools>=40.8.0', 'wheel', 'fastentrypoints~=0.12']
+build-backend = 'setuptools.build_meta'
+
+[tool.isort]
+force_sort_within_sections = true
+include_trailing_comma = true
+line_length = 120
+multi_line_output = 3
+
+[tool.pydocstyle]
+ignore = [
+    'D104',
+    'D203',
+    'D213',
+]
+
+[tool.pylint.master]
+load-plugins = ['pylint_aiida']
 
 [tool.pylint.format]
 max-line-length = 120
@@ -12,3 +28,21 @@ disable = [
     'import-outside-toplevel',
     'too-many-arguments',
 ]
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    'ignore::DeprecationWarning:distutils:',
+    'ignore::DeprecationWarning:frozendict:',
+    'ignore::DeprecationWarning:sqlalchemy_utils:',
+    'ignore::DeprecationWarning:reentry:',
+    'ignore::DeprecationWarning:pkg_resources:',
+]
+
+[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

setup.json

@@ -46,7 +46,8 @@
     "extras_require": {
         "pre-commit": [
             "pre-commit~=2.2",
-            "pylint~=2.6.0"
+            "pylint~=2.6",
+            "pylint-aiida~=0.1"
         ],
         "tests": [
             "pgtest~=1.3",

setup.py

@@ -10,7 +10,8 @@
 def setup_package():
     """Install the `aiida-pseudo` package."""
     import json
-    from setuptools import setup, find_packages
+
+    from setuptools import find_packages, setup
 
     filename_setup_json = 'setup.json'
     filename_description = 'README.md'

tests/cli/test_family.py

@@ -3,13 +3,12 @@
 """Tests for the command `aiida-pseudo family`."""
 import json
 
+from aiida.orm import Group
 from numpy.testing import assert_almost_equal
 import pytest
 
-from aiida.orm import Group
-
 from aiida_pseudo.cli.family import cmd_family_cutoffs_set, cmd_family_show
-from aiida_pseudo.groups.family import PseudoPotentialFamily, CutoffsPseudoPotentialFamily
+from aiida_pseudo.groups.family import CutoffsPseudoPotentialFamily, PseudoPotentialFamily
 
 
 @pytest.mark.usefixtures('clear_db')

tests/cli/test_install.py

@@ -4,16 +4,14 @@
 import json
 import pathlib
 
-import pytest
-
 from aiida.orm import QueryBuilder
+import pytest
 
-from aiida_pseudo.cli import install
-from aiida_pseudo.cli import cmd_install_family, cmd_install_sssp, cmd_install_pseudo_dojo
+from aiida_pseudo.cli import cmd_install_family, cmd_install_pseudo_dojo, cmd_install_sssp, install
 from aiida_pseudo.data.pseudo.upf import UpfData
 from aiida_pseudo.groups.family import PseudoPotentialFamily
-from aiida_pseudo.groups.family.pseudo_dojo import PseudoDojoFamily, PseudoDojoConfiguration
-from aiida_pseudo.groups.family.sssp import SsspFamily, SsspConfiguration
+from aiida_pseudo.groups.family.pseudo_dojo import PseudoDojoConfiguration, PseudoDojoFamily
+from aiida_pseudo.groups.family.sssp import SsspConfiguration, SsspFamily
 
 
 @pytest.fixture