Devops: Update the pre-commit hooks

* Add `check-merge-conflict`
* Add `check-yaml`
* Add `--fix=lf` to `mixed-line-ending`
  This is more explicit and prevents ambiguity
* Add `--remove` to `fix-encoding-pragma`
  This pragma was really only necessary during the Python 2 to 3
  transition.

Author: sphuber

.github/workflows/validate_release_tag.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Validate that the version in the tag label matches the version of the package."""
 import argparse
 import ast

.pre-commit-config.yaml

@@ -2,10 +2,14 @@ repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
     hooks:
+    -   id: check-merge-conflict
+    -   id: check-yaml
     -   id: double-quote-string-fixer
     -   id: end-of-file-fixer
     -   id: fix-encoding-pragma
+        args: [--remove]
     -   id: mixed-line-ending
+        args: [--fix=lf]
     -   id: trailing-whitespace
 
 -   repo: https://github.com/ikamensh/flynt/

docs/source/conf.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 # Configuration file for the Sphinx documentation builder.
 #
 # This file only contains a selection of the most common options. For a full

src/aiida_common_workflows/__init__.py

@@ -1,3 +1,2 @@
-# -*- coding: utf-8 -*-
 """Package that defines common interfaces for workflows that are implemented in AiiDA for various quantum engines."""
 __version__ = '1.0.1'

src/aiida_common_workflows/cli/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module for the command line interface."""
 import click_completion
 

src/aiida_common_workflows/cli/launch.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Commands to launch common workflows."""
 import functools
 

src/aiida_common_workflows/cli/options.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Module with pre-defined options and defaults for CLI command parameters."""
 import json
 import pathlib

src/aiida_common_workflows/cli/plot.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Commands to plot results from a workflow."""
 import click
 from aiida.cmdline.params import arguments

src/aiida_common_workflows/cli/root.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Command line interface ``acwf``."""
 import click
 from aiida.cmdline.groups import VerdiCommandGroup

src/aiida_common_workflows/cli/utils.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Module with utitlies for the CLI."""
 import sys
 

src/aiida_common_workflows/common/__init__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Module for resources common to the entire `aiida-common-workflows` package."""
 from .types import ElectronicType, RelaxType, SpinType
 

src/aiida_common_workflows/common/types.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Module with basic type definitions."""
 from enum import Enum
 

src/aiida_common_workflows/common/visualization/dissociation.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Utilities to visualize a dissociation curve based on set of distances and energies."""
 import typing
 

src/aiida_common_workflows/common/visualization/eos.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Utilities to fit and visualize a Equation of States based on set of volumes and energies."""
 import typing
 

src/aiida_common_workflows/generators/__init__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Module with resources for input generators for workflows."""
 from .generator import InputGenerator
 from .ports import ChoiceType, CodeType, InputGeneratorPort

src/aiida_common_workflows/generators/generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Base class for an input generator for a common workflow."""
 import abc
 import copy

src/aiida_common_workflows/generators/ports.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Modules with resources to define specific port types for input generator specifications."""
 from __future__ import annotations
 

src/aiida_common_workflows/generators/spec.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Class to define the specification of an input generator."""
 from __future__ import annotations
 

src/aiida_common_workflows/plugins/__init__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Module with utilities for working with the plugins provided by this plugin package."""
 from .entry_point import get_entry_point_name_from_class, get_workflow_entry_point_names, load_workflow_entry_point
 

src/aiida_common_workflows/plugins/entry_point.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Module with utilities for working with the plugins provided by this plugin package."""
 import typing
 

src/aiida_common_workflows/protocol/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with utilities to define and implement workchain protocols."""
 from .registry import ProtocolRegistry
 

src/aiida_common_workflows/protocol/registry.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with base protocol registry."""
 import copy
 import typing

src/aiida_common_workflows/utils/sphinx_extension/__init__.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Module with Spinx extension to facilitate the automatic documentation of common workflows."""
 
 

src/aiida_common_workflows/utils/sphinx_extension/input_generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Define a Restructured Text directive to auto-document :class:`aiida_common_workflows.generators.InputGenerator`."""
 import inspect
 import typing as t

src/aiida_common_workflows/workflows/bands/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with the base classes for the common bands workchains."""
 from .generator import *
 

src/aiida_common_workflows/workflows/bands/generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Module with base input generator for the common bands workchains."""
 import abc
 

src/aiida_common_workflows/workflows/bands/siesta/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with the implementations of the common bands workchain for Siesta."""
 from .generator import *
 from .workchain import *

src/aiida_common_workflows/workflows/bands/siesta/generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.bands.generator.CommonBandsInputGenerator` for SIESTA."""
 from aiida import engine, orm
 

src/aiida_common_workflows/workflows/bands/siesta/workchain.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.workchain.CommonRelaxWorkChain` for SIESTA."""
 from aiida.engine import calcfunction
 from aiida.orm import Float

src/aiida_common_workflows/workflows/bands/workchain.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Module with base wrapper workchain for bands workchains."""
 from abc import ABCMeta, abstractmethod
 

src/aiida_common_workflows/workflows/dissociation.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """
 Workflow calculating the dissociation curve of diatomic molecules.
 It can use any code plugin implementing the common relax workflow.

src/aiida_common_workflows/workflows/eos.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Equation of state workflow that can use any code plugin implementing the common relax workflow."""
 import inspect
 

src/aiida_common_workflows/workflows/relax/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with the base classes for the common structure relaxation workchains."""
 from .generator import *
 

src/aiida_common_workflows/workflows/relax/abinit/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with the implementations of the common structure relaxation workchain for Abinit."""
 from .generator import *
 from .workchain import *

src/aiida_common_workflows/workflows/relax/abinit/extractors.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """
 Collects some functions to postprocess a `CommonWorkflowAbinitWorkChain`.
 """

src/aiida_common_workflows/workflows/relax/abinit/generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.generator.CommonRelaxInputGenerator` for ABINIT."""
 import collections
 import copy

src/aiida_common_workflows/workflows/relax/abinit/workchain.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.workchain.CommonRelaxWorkChain` for Abinit."""
 import numpy as np
 from aiida import orm

src/aiida_common_workflows/workflows/relax/bigdft/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with the implementations of the common structure relaxation workchain for BigDFT."""
 from .generator import *
 from .workchain import *

src/aiida_common_workflows/workflows/relax/bigdft/generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.generator.CommonRelaxInputGenerator` for BigDFT."""
 import typing as t
 

src/aiida_common_workflows/workflows/relax/bigdft/workchain.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.workchain.CommonRelaxWorkChain` for BigDFT"""
 from aiida.plugins import WorkflowFactory
 

src/aiida_common_workflows/workflows/relax/castep/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with the implementations of the common structure relaxation workchain for CASTEP"""
 from .generator import *
 from .workchain import *

src/aiida_common_workflows/workflows/relax/castep/extractors.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """
 Collects some functions to postprocess a `CastepCommonRelaxWorkChain`.
 """

src/aiida_common_workflows/workflows/relax/castep/generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.generator.CommonRelaxInputGenerator` for CASTEP"""
 import collections
 import copy

src/aiida_common_workflows/workflows/relax/castep/workchain.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.workchain.CommonRelaxWorkChain` for CASTEP"""
 from aiida import orm
 from aiida.engine import calcfunction

src/aiida_common_workflows/workflows/relax/cp2k/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with the implementations of the common structure relaxation workchain for CP2K."""
 from .generator import *
 from .workchain import *

src/aiida_common_workflows/workflows/relax/cp2k/generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.generator.CommonRelaxInputGenerator` for CP2K."""
 import collections
 import pathlib

src/aiida_common_workflows/workflows/relax/cp2k/workchain.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.workchain.CommonRelaxWorkChain` for CP2K."""
 import re
 

src/aiida_common_workflows/workflows/relax/fleur/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with the implementations of the common structure relaxation workchain for FLEUR."""
 from .generator import *
 from .workchain import *

src/aiida_common_workflows/workflows/relax/fleur/extractors.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """
 Collects some functions to postprocess a `FleurCommonRelaxWorkChain`.
 """

src/aiida_common_workflows/workflows/relax/fleur/generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.generator.CommonRelaxInputGenerator` for FLEUR."""
 import collections
 import pathlib

src/aiida_common_workflows/workflows/relax/fleur/workchain.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.workchain.CommonRelaxWorkChain` for FLEUR (www.flapw.de)."""
 from aiida import orm
 from aiida.engine import calcfunction

src/aiida_common_workflows/workflows/relax/gaussian/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with the implementations of the common structure relaxation workchain for Gaussian."""
 from .generator import *
 from .workchain import *

src/aiida_common_workflows/workflows/relax/gaussian/generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.generator.CommonRelaxInputGenerator` for Gaussian."""
 import copy
 import typing as t

src/aiida_common_workflows/workflows/relax/gaussian/workchain.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.workchain.CommonRelaxWorkChain` for Gaussian."""
 import numpy as np
 from aiida import orm

src/aiida_common_workflows/workflows/relax/generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Module with base input generator for the common structure relax workchains."""
 import abc
 

src/aiida_common_workflows/workflows/relax/gpaw/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with the implementations of the common structure relaxation workchain for GPAW."""
 from .generator import *
 from .workchain import *

src/aiida_common_workflows/workflows/relax/gpaw/generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.generator.CommonRelaxInputGenerator` for GPAW."""
 from __future__ import annotations
 

src/aiida_common_workflows/workflows/relax/gpaw/workchain.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.workchain.CommonRelaxWorkChain` for GPAW."""
 from aiida import orm
 from aiida.engine import calcfunction

src/aiida_common_workflows/workflows/relax/nwchem/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with the implementations of the common structure relaxation workchain for NWChem."""
 from .generator import *
 from .workchain import *

src/aiida_common_workflows/workflows/relax/nwchem/generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.generator.CommonRelaxInputGenerator` for NWChem."""
 import pathlib
 import warnings

src/aiida_common_workflows/workflows/relax/nwchem/workchain.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.workchain.CommonRelaxWorkChain` for NWChem."""
 import numpy as np
 from aiida import orm

src/aiida_common_workflows/workflows/relax/orca/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with the implementations of the common structure relaxation workchain for Orca."""
 from .generator import *
 from .workchain import *

src/aiida_common_workflows/workflows/relax/orca/generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.generator.CommonRelaxInputGenerator` for Orca."""
 import os
 import warnings

src/aiida_common_workflows/workflows/relax/orca/workchain.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.workchain.CommonRelaxWorkChain` for Orca."""
 import numpy as np
 from aiida.engine import calcfunction

src/aiida_common_workflows/workflows/relax/quantum_espresso/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with the implementations of the common structure relaxation workchain for Quantum ESPRESSO."""
 from .generator import *
 from .workchain import *

src/aiida_common_workflows/workflows/relax/quantum_espresso/extractors.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """
 Post-processing extractor functions for the ``QuantumEspressoCommonRelaxWorkChain``.
 """

src/aiida_common_workflows/workflows/relax/quantum_espresso/generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.generator.CommonRelaxInputGenerator` for Quantum ESPRESSO."""
 from importlib import resources
 

src/aiida_common_workflows/workflows/relax/quantum_espresso/workchain.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.workchain.CommonRelaxWorkChain` for Quantum ESPRESSO."""
 import pint
 from aiida import orm

src/aiida_common_workflows/workflows/relax/siesta/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with the implementations of the common structure relaxation workchain for Siesta."""
 from .generator import *
 from .workchain import *

src/aiida_common_workflows/workflows/relax/siesta/extractors.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """
 Collects some functions to postprocess a `CommonWorkflowSiestaWorkChain`.
 """

src/aiida_common_workflows/workflows/relax/siesta/generator.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.generator.CommonRelaxInputGenerator` for SIESTA."""
 import os
 

src/aiida_common_workflows/workflows/relax/siesta/workchain.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Implementation of `aiida_common_workflows.common.relax.workchain.CommonRelaxWorkChain` for SIESTA."""
 from aiida import orm
 from aiida.engine import calcfunction

src/aiida_common_workflows/workflows/relax/vasp/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Module with the implementations of the common structure relaxation workchain for VASP."""
 from .generator import *
 from .workchain import *

src/aiida_common_workflows/workflows/relax/vasp/extractors.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """
 Collects some functions to postprocess a `VaspCommonRelaxWorkChain`.
 """