Drop Python 2 support

The following commands were executed to clean all source files:

    sed -i '/from __future__.*$/d' {} +
    sed -i 's/(object):/:/g' {} +
    sed -i 's/super([^)]*,[^)]*)/super()/g' {} +
    sed -i '/\(import six\|from six\).*$/d' {} +
    sed -i '/\(six\.add_metaclass\).*$/d' {} +
    sed -i 's/six.integer_types/int/g' {} +
    sed -i 's/six.string_types/str/g' {} +
    sed -i 's/six.text_type/str/g' {} +
    sed -i 's/six.binary_type/bytes/g' {} +
    sed -i 's/six.moves.StringIO/io.StringIO/g' {} +
    sed -i 's/six.StringIO/io.StringIO/g' {} +
    sed -i 's/six.moves.BytesIO/io.BytesIO/g' {} +
    sed -i 's/six.BytesIO/io.BytesIO/g' {} +
    sed -i 's/six.moves.range/range/g' {} +
    sed -i 's|six.iterkeys(\([^)]*\))|\1.keys()|' {} +
    sed -i 's|six.iteritems(\([^)]*\))|\1.items()|' {} +
    sed -i 's|six.itervalues(\([^)]*\))|\1.values()|' {} +

The operations were applied to all files using `find -exec`:

    find . -type f -not -path './.git*' -exec

Note the exclusion of the `.git` folder which is very important.

.github/workflows/ci.yml

@@ -70,7 +70,7 @@ jobs:
 
         strategy:
             matrix:
-                python-version: [2.7, 3.5, 3.6, 3.7, 3.8]
+                python-version: [3.5, 3.6, 3.7, 3.8]
 
         services:
             postgres:
@@ -111,7 +111,6 @@ jobs:
         -   name: Install python dependencies
             run: |
                 pip install --upgrade setuptools
-                pip install numpy==1.16.4
                 pip install -e .[dev]
                 reentry scan
 

.pre-commit-config.yaml

@@ -61,16 +61,3 @@ repos:
         ./utils/validate_version_number.py|
       )$
     pass_filenames: false
-
-- repo: https://github.com/python-modernize/python-modernize.git
-  rev: a234ce4e185cf77a55632888f1811d83b4ad9ef2
-  hooks:
-  - id: python-modernize
-    exclude: >
-      (?x)^(
-        docs/.*|
-        examples/.*
-      )$
-    args:
-      - --write
-      - --nobackups

CHANGELOG.md

@@ -1,6 +1,4 @@
-## v3.0.0:
-
-**TODO**
+## v4.0.0:
 
 ## v2.1.0:
 Minor release adding a new feature, fixing a critical bug in `PwParser` and reducing the size of the package

aiida_quantumespresso/calculations/__init__.py

@@ -1,11 +1,7 @@
 # -*- coding: utf-8 -*-
 """Base `CalcJob` for implementations for pw.x and cp.x of Quantum ESPRESSO."""
-from __future__ import absolute_import
-
 import abc
 import os
-import six
-from six.moves import zip
 
 from aiida import orm
 from aiida.common import datastructures, exceptions
@@ -68,9 +64,9 @@ def xml_filepaths(cls):  # pylint: disable=no-self-argument
     @classmethod
     def define(cls, spec):
         # yapf: disable
-        super(BasePwCpInputGenerator, cls).define(spec)
-        spec.input('metadata.options.input_filename', valid_type=six.string_types, default=cls._DEFAULT_INPUT_FILE)
-        spec.input('metadata.options.output_filename', valid_type=six.string_types, default=cls._DEFAULT_OUTPUT_FILE)
+        super().define(spec)
+        spec.input('metadata.options.input_filename', valid_type=str, default=cls._DEFAULT_INPUT_FILE)
+        spec.input('metadata.options.output_filename', valid_type=str, default=cls._DEFAULT_OUTPUT_FILE)
         spec.input('metadata.options.withmpi', valid_type=bool, default=True)  # Override default withmpi=False
         spec.input('structure', valid_type=orm.StructureData,
             help='The input structure.')
@@ -183,7 +179,7 @@ def prepare_for_submission(self, folder):
 
             with folder.open(self._ENVIRON_INPUT_FILE_NAME, 'w') as handle:
                 handle.write('&ENVIRON\n')
-                for key, value in sorted(six.iteritems(environ_namelist)):
+                for key, value in sorted(environ_namelist.items()):
                     handle.write(convert_input_to_namelist_entry(key, value, mapping=mapping_species))
                 handle.write('/\n')
 
@@ -255,7 +251,7 @@ def _generate_PWCPinputdata(cls, parameters, settings, pseudos, structure, kpoin
         # and the second-level keys as lowercase
         # (deeper levels are unchanged)
         input_params = _uppercase_dict(parameters.get_dict(), dict_name='parameters')
-        input_params = {k: _lowercase_dict(v, dict_name=k) for k, v in six.iteritems(input_params)}
+        input_params = {k: _lowercase_dict(v, dict_name=k) for k, v in input_params.items()}
 
         # I remove unwanted elements (for the moment, instead, I stop; to change when we setup a reasonable logging)
         for blocked in cls._blocked_keywords:
@@ -559,14 +555,14 @@ def _generate_PWCPinputdata(cls, parameters, settings, pseudos, structure, kpoin
                                            "namelists using the NAMELISTS inside the 'settings' input "
                                            'node'.format(calculation_type))
 
-        inputfile = u''
+        inputfile = ''
         for namelist_name in namelists_toprint:
-            inputfile += u'&{0}\n'.format(namelist_name)
+            inputfile += '&{0}\n'.format(namelist_name)
             # namelist content; set to {} if not present, so that we leave an empty namelist
             namelist = input_params.pop(namelist_name, {})
             for key, value in sorted(namelist.items()):
                 inputfile += convert_input_to_namelist_entry(key, value, mapping=mapping_species)
-            inputfile += u'/\n'
+            inputfile += '/\n'
 
         # Write cards now
         inputfile += atomic_species_card
@@ -608,7 +604,7 @@ def _case_transform_dict(dictionary, dict_name, func_name, transform):
 
     if not isinstance(dictionary, dict):
         raise TypeError('{} accepts only dictionaries as argument, got {}'.format(func_name, type(dictionary)))
-    new_dict = dict((transform(str(k)), v) for k, v in six.iteritems(dictionary))
+    new_dict = dict((transform(str(k)), v) for k, v in dictionary.items())
     if len(new_dict) != len(dictionary):
         num_items = Counter(transform(str(k)) for k in dictionary.keys())
         double_keys = ','.join([k for k, v in num_items if v > 1])

aiida_quantumespresso/calculations/base.py

@@ -4,8 +4,6 @@
 The custom `CalcJob` base class automatically sets the `invalidates_cache` attribute of exit codes based on the status
 integer. All `CalcJob` implementations in `aiida-quantumespresso` must use this base class, not `aiida.engine.CalcJob`.
 """
-from __future__ import absolute_import
-
 from aiida.engine import CalcJob as _BaseCalcJob
 from aiida.engine.processes.process_spec import CalcJobProcessSpec as _BaseCalcJobProcessSpec
 
@@ -37,7 +35,7 @@ def exit_code(self, status, label, message, invalidates_cache=None):
             super(CalcJobProcessSpec,
                   self).exit_code(status=status, label=label, message=message, invalidates_cache=invalidates_cache)
         except TypeError:  # For AiiDA version <1.1
-            super(CalcJobProcessSpec, self).exit_code(status=status, message=message, label=label)
+            super().exit_code(status=status, message=message, label=label)
 
 
 class CalcJob(_BaseCalcJob):  # pylint: disable=abstract-method
@@ -48,5 +46,5 @@ class CalcJob(_BaseCalcJob):  # pylint: disable=abstract-method
     @classmethod
     def define(cls, spec):
         # yapf: disable
-        super(CalcJob, cls).define(spec)
+        super().define(spec)
         spec.inputs['metadata']['options']['resources'].default = lambda: {'num_machines': 1}

aiida_quantumespresso/calculations/cp.py

@@ -14,11 +14,8 @@
       for development when new cards are needed
 TODO: all a lot of logger.debug stuff
 """
-from __future__ import absolute_import
-
 import os
 
-import six
 from aiida import orm
 from aiida.common.lang import classproperty
 
@@ -129,8 +126,8 @@ def xml_filepaths(cls):
     @classmethod
     def define(cls, spec):
         # yapf: disable
-        super(CpCalculation, cls).define(spec)
-        spec.input('metadata.options.parser_name', valid_type=six.string_types, default='quantumespresso.cp')
+        super().define(spec)
+        spec.input('metadata.options.parser_name', valid_type=str, default='quantumespresso.cp')
         spec.output('output_trajectory', valid_type=orm.TrajectoryData)
         spec.output('output_parameters', valid_type=orm.Dict)
         spec.default_output_node = 'output_parameters'

aiida_quantumespresso/calculations/dos.py

@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
 """`CalcJob` implementation for the dos.x code of Quantum ESPRESSO."""
-from __future__ import absolute_import
-
 from aiida import orm
 from aiida_quantumespresso.calculations.namelists import NamelistsCalculation
 
@@ -22,7 +20,7 @@ class DosCalculation(NamelistsCalculation):
     @classmethod
     def define(cls, spec):
         # yapf: disable
-        super(DosCalculation, cls).define(spec)
+        super().define(spec)
         spec.input('parent_folder', valid_type=(orm.RemoteData, orm.FolderData), required=True)
         spec.output('output_parameters', valid_type=orm.Dict)
         spec.output('output_dos', valid_type=orm.XyData)

aiida_quantumespresso/calculations/epw.py

@@ -1,12 +1,7 @@
 # -*- coding: utf-8 -*-
 """Plugin to create a Quantum Espresso epw.x input file."""
-from __future__ import absolute_import
-
-from __future__ import print_function
 import os
 import numpy as np
-import six
-from six.moves import range
 
 from aiida import orm
 from aiida.common import datastructures, exceptions
@@ -43,9 +38,9 @@ class EpwCalculation(CalcJob):
     @classmethod
     def define(cls, spec):
         # yapf: disable
-        super(EpwCalculation, cls).define(spec)
-        spec.input('metadata.options.input_filename', valid_type=six.string_types, default=cls._DEFAULT_INPUT_FILE)
-        spec.input('metadata.options.output_filename', valid_type=six.string_types, default=cls._DEFAULT_OUTPUT_FILE)
+        super().define(spec)
+        spec.input('metadata.options.input_filename', valid_type=str, default=cls._DEFAULT_INPUT_FILE)
+        spec.input('metadata.options.output_filename', valid_type=str, default=cls._DEFAULT_OUTPUT_FILE)
         spec.input('metadata.options.withmpi', valid_type=bool, default=True)
         spec.input('kpoints', valid_type=orm.KpointsData, help='coarse kpoint mesh')
         spec.input('qpoints', valid_type=orm.KpointsData, help='coarse qpoint mesh')
@@ -109,7 +104,7 @@ def test_offset(offset):
 
         # I put the first-level keys as uppercase (i.e., namelist and card names) and the second-level keys as lowercase
         parameters = _uppercase_dict(self.inputs.parameters.get_dict(), dict_name='parameters')
-        parameters = {k: _lowercase_dict(v, dict_name=k) for k, v in six.iteritems(parameters)}
+        parameters = {k: _lowercase_dict(v, dict_name=k) for k, v in parameters.items()}
 
         if 'INPUTEPW' not in parameters:
             raise exceptions.InputValidationError('required namelist INPUTEPW not specified')
@@ -188,18 +183,18 @@ def test_offset(offset):
 
         # add here the list of point coordinates
         if len(list_of_points) > 1:
-            postpend_text = u'{} cartesian\n'.format(len(list_of_points))
+            postpend_text = '{} cartesian\n'.format(len(list_of_points))
             for points in list_of_points:
-                postpend_text += u'{0:18.10f} {1:18.10f} {2:18.10f} \n'.format(*points)
+                postpend_text += '{0:18.10f} {1:18.10f} {2:18.10f} \n'.format(*points)
 
         with folder.open(self.metadata.options.input_filename, 'w') as infile:
             for namelist_name in namelists_toprint:
-                infile.write(u'&{0}\n'.format(namelist_name))
+                infile.write('&{0}\n'.format(namelist_name))
                 # namelist content; set to {} if not present, so that we leave an empty namelist
                 namelist = parameters.pop(namelist_name, {})
-                for key, value in sorted(six.iteritems(namelist)):
+                for key, value in sorted(namelist.items()):
                     infile.write(convert_input_to_namelist_entry(key, value))
-                infile.write(u'/\n')
+                infile.write('/\n')
 
             # add list of qpoints if required
             if postpend_text is not None:

aiida_quantumespresso/calculations/helpers/__init__.py

@@ -1,14 +1,10 @@
 # -*- coding: utf-8 -*-
 """Utilities to automatically format, convert and validate data structures from python to fortran."""
-from __future__ import absolute_import
-from __future__ import print_function
-
 import copy
 import difflib
 import os
 import xml.dom.minidom
 from packaging.version import Version
-import six
 
 from aiida.common import InputValidationError, InternalError
 
@@ -34,19 +30,19 @@ def _check_and_convert(keyword, val, expected_type):
         else:
             raise TypeError('Expected a boolean for keyword {}, found {} instead'.format(keyword, type(val)))
     elif expected_type.upper() == 'REAL':
-        if isinstance(val, six.integer_types):
+        if isinstance(val, int):
             outval = float(val)
         elif isinstance(val, float):
             outval = val
         else:
             raise TypeError('Expected a float for keyword {}, found {} instead'.format(keyword, type(val)))
     elif expected_type.upper() == 'INTEGER':
-        if isinstance(val, six.integer_types):
+        if isinstance(val, int):
             outval = val
         else:
             raise TypeError('Expected an integer for keyword {}, found {} instead'.format(keyword, type(val)))
     elif expected_type.upper() == 'CHARACTER':
-        if isinstance(val, six.string_types):
+        if isinstance(val, str):
             outval = val
         else:
             raise TypeError('Expected a string for keyword {}, found {} instead'.format(keyword, type(val)))
@@ -139,13 +135,13 @@ def pw_input_helper(input_params, structure, stop_at_first_error=False, flat_mod
         input_params_internal = {}
         input_original_namelists = {}
         all_input_namelists = set()
-        for namelist, content in six.iteritems(input_params):
+        for namelist, content in input_params.items():
             if not isinstance(content, dict):
                 raise QEInputValidationError(
                     "The content associated to the namelist '{}' must be a dictionary".format(namelist)
                 )
             all_input_namelists.add(namelist)
-            for key, value in six.iteritems(content):
+            for key, value in content.items():
                 input_params_internal[key] = copy.deepcopy(value)
                 if key in input_original_namelists:
                     err_str = "The keyword '{}' was specified both in the namelist {} and {}.".format(
@@ -382,7 +378,7 @@ def pw_input_helper(input_params, structure, stop_at_first_error=False, flat_mod
     # the compulsory ones at the end
     inserted_kws = []
     # I parse each element of the input dictionary
-    for keyword, value in six.iteritems(input_params_internal):
+    for keyword, value in input_params_internal.items():
         keyword = keyword.lower()
 
         if keyword in valid_kws:
@@ -449,7 +445,7 @@ def pw_input_helper(input_params, structure, stop_at_first_error=False, flat_mod
                         continue
 
                 outdict = {}
-                for kindname, found_item in six.iteritems(value):
+                for kindname, found_item in value.items():
                     if kindname not in atomic_species_list:
                         err_str = "Error, '{}' is not a valid kind name.".format(kindname)
                         if stop_at_first_error:

aiida_quantumespresso/calculations/matdyn.py

@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
 """`CalcJob` implementation for the matdyn.x code of Quantum ESPRESSO."""
-from __future__ import absolute_import
-
 from aiida import orm
 from aiida_quantumespresso.calculations.namelists import NamelistsCalculation
 from aiida_quantumespresso.data.force_constants import ForceConstantsData
@@ -28,7 +26,7 @@ class MatdynCalculation(NamelistsCalculation):
     @classmethod
     def define(cls, spec):
         # yapf: disable
-        super(MatdynCalculation, cls).define(spec)
+        super().define(spec)
         spec.input('force_constants', valid_type=ForceConstantsData, required=True)
         spec.input('kpoints', valid_type=orm.KpointsData, help='Kpoints on which to calculate the phonon frequencies.')
         spec.inputs.pop('parent_folder')
@@ -55,9 +53,9 @@ def _get_following_text(self):
         except AttributeError:
             kpoints = self.inputs.kpoints.get_kpoints_mesh(print_list=True)
 
-        kpoints_string = [u'{}'.format(len(kpoints))]
+        kpoints_string = ['{}'.format(len(kpoints))]
         for kpoint in kpoints:
-            kpoints_string.append(u'{:18.10f} {:18.10f} {:18.10f}'.format(*kpoint))
+            kpoints_string.append('{:18.10f} {:18.10f} {:18.10f}'.format(*kpoint))
 
         return '\n'.join(kpoints_string) + '\n'
 
@@ -70,7 +68,7 @@ def prepare_for_submission(self, folder):
         force_constants = self.inputs.force_constants
         self._blocked_keywords.append(('INPUT', 'flfrc', force_constants.filename))
 
-        calcinfo = super(MatdynCalculation, self).prepare_for_submission(folder)
+        calcinfo = super().prepare_for_submission(folder)
         calcinfo.local_copy_list.append((force_constants.uuid, force_constants.filename, force_constants.filename))
 
         return calcinfo