Merge branch 'main' into feature/add-upfdata-input

aiida_cp2k/calculations/__init__.py

@@ -23,9 +23,9 @@
     write_pseudos,
 )
 
-BandsData = DataFactory("core.array.bands")  # pylint: disable=invalid-name
-StructureData = DataFactory("core.structure")  # pylint: disable=invalid-name
-KpointsData = DataFactory("core.array.kpoints")  # pylint: disable=invalid-name
+BandsData = DataFactory("core.array.bands")
+StructureData = DataFactory("core.structure")
+KpointsData = DataFactory("core.array.kpoints")
 UpfData = DataFactory("pseudo.upf")
 
 
@@ -224,8 +224,6 @@ def prepare_for_submission(self, folder):
         :return: `aiida.common.datastructures.CalcInfo` instance
         """
 
-        # pylint: disable=too-many-statements,too-many-branches
-
         # Create cp2k input file.
         inp = Cp2kInput(self.inputs.parameters.get_dict())
         inp.add_keyword("GLOBAL/PROJECT", self._DEFAULT_PROJECT_NAME)

aiida_cp2k/parsers/__init__.py

@@ -18,8 +18,8 @@
 
 # -
 
-StructureData = DataFactory("core.structure")  # pylint: disable=invalid-name
-BandsData = DataFactory("core.array.bands")  # pylint: disable=invalid-name
+StructureData = DataFactory("core.structure")
+BandsData = DataFactory("core.array.bands")
 
 
 class Cp2kBaseParser(Parser):
@@ -71,9 +71,7 @@ def _parse_trajectory(self):
 
         from ase import Atoms
 
-        fname = (
-            self.node.process_class._DEFAULT_RESTART_FILE_NAME
-        )  # pylint: disable=protected-access
+        fname = self.node.process_class._DEFAULT_RESTART_FILE_NAME
 
         # Check if the restart file is present.
         if fname not in self.retrieved.base.repository.list_object_names():

aiida_cp2k/utils/datatype_helpers.py

@@ -136,7 +136,6 @@ def validate_basissets(inp, basissets, structure):
     listed in a KIND section, or none of them are, at which point they're
     verified against the symbols in the structure.
     """
-    # pylint: disable=too-many-branches,too-many-statements
 
     # convert a structure
     #   {
@@ -294,8 +293,6 @@ def validate_pseudos_namespace(pseudos, _):
 def validate_pseudos(inp, pseudos, structure):
     """Verify that all referenced pseudos are present in the input"""
 
-    # pylint: disable=too-many-branches,too-many-statements
-
     pseudos_specified = {pseudo for _, pseudo in _unpack(pseudos)}
     pseudos_used = set()
     explicit_kinds = []  # list of kinds with explicitly specified kind sections

aiida_cp2k/utils/parser.py

@@ -28,7 +28,7 @@ def parse_cp2k_output(fstring):
 
 def parse_cp2k_output_advanced(
     fstring,
-):  # pylint: disable=too-many-locals, too-many-statements, too-many-branches
+):
     """Parse CP2K output into a dictionary (ADVANCED: more info parsed @ PRINT_LEVEL MEDIUM)."""
     lines = fstring.splitlines()
 
@@ -380,8 +380,7 @@ def parse_cp2k_trajectory(content):
 
     import numpy as np
 
-    # pylint: disable=protected-access
-    # parse coordinate section
+    # Parse coordinate section
     match = re.search(r"\n\s*&COORD\n(.*?)\n\s*&END COORD\n", content, re.DOTALL)
     coord_lines = [line.strip().split() for line in match.group(1).splitlines()]
 

aiida_cp2k/utils/workchains.py

@@ -10,7 +10,7 @@
 from aiida.orm import Dict
 from aiida.plugins import DataFactory
 
-StructureData = DataFactory("core.structure")  # pylint: disable=invalid-name
+StructureData = DataFactory("core.structure")
 
 HARTREE2EV = 27.211399
 HARTREE2KJMOL = 2625.500
@@ -36,7 +36,7 @@ def merge_dict(dct, merge_dct):
 
 
 @calcfunction
-def merge_Dict(d1, d2):  # pylint: disable=invalid-name
+def merge_Dict(d1, d2):
     """Make all the data in the second Dict overwrite the corrisponding data in the first Dict"""
     d1_dict = d1.get_dict()
     d2_dict = d2.get_dict()
@@ -86,9 +86,7 @@ def ot_has_small_bandgap(cp2k_input, cp2k_output, bandgap_thr_ev):
     list_true = [True, "T", "t", ".TRUE.", "True", "true"]  # add more?
     try:
         ot_settings = cp2k_input["FORCE_EVAL"]["DFT"]["SCF"]["OT"]
-        if (
-            "_" not in ot_settings.keys() or ot_settings["_"] in list_true
-        ):  # pylint: disable=simplifiable-if-statement
+        if "_" not in ot_settings.keys() or ot_settings["_"] in list_true:
             using_ot = True
         else:
             using_ot = False
@@ -103,7 +101,7 @@ def ot_has_small_bandgap(cp2k_input, cp2k_output, bandgap_thr_ev):
 
 
 @calcfunction
-def check_resize_unit_cell(struct, threshold):  # pylint: disable=too-many-locals
+def check_resize_unit_cell(struct, threshold):
     """Returns the multiplication factors for the cell vectors to respect, in every direction:
     min(perpendicular_width) > threshold.
     """

aiida_cp2k/workchains/base.py

@@ -12,7 +12,7 @@
 
 from ..utils import add_ext_restart_section, add_wfn_restart_section
 
-Cp2kCalculation = CalculationFactory('cp2k')  # pylint: disable=invalid-name
+Cp2kCalculation = CalculationFactory('cp2k')
 
 
 class Cp2kBaseWorkChain(BaseRestartWorkChain):
@@ -81,7 +81,7 @@ def restart_incomplete_calculation(self, calc):
                         "Sending a signal to stop the Base work chain.")
 
             # Signaling to the base work chain that the problem could not be recovered.
-            return ProcessHandlerReport(True, self.exit_codes.NO_RESTART_DATA)  # pylint: disable=no-member
+            return ProcessHandlerReport(True, self.exit_codes.NO_RESTART_DATA)
 
         self.ctx.inputs.parent_calc_folder = calc.outputs.remote_folder
         params = self.ctx.inputs.parameters

conftest.py

@@ -1,13 +1,11 @@
-"""
-For pytest initialise a test database and profile
-"""
+"""For pytest initialise a test database and profile."""
 import pytest
 
-pytest_plugins = ["aiida.manage.tests.pytest_fixtures"]  # pylint: disable=invalid-name
+pytest_plugins = ["aiida.manage.tests.pytest_fixtures"]
 
 
 @pytest.fixture(scope="function")
-def cp2k_code(aiida_local_code_factory):  # pylint: disable=unused-argument
+def cp2k_code(aiida_local_code_factory):
     return aiida_local_code_factory("cp2k", "cp2k")
 
 
@@ -18,13 +16,13 @@ def clear_database(aiida_profile_clean):
 
 # from https://stackoverflow.com/a/25188424
 # required for examples for optional features to show appropriate error messages
-def pytest_configure(config):  # pylint: disable=unused-argument
+def pytest_configure(config):
     import sys
 
-    sys._called_from_test = True  # pylint: disable=protected-access
+    sys._called_from_test = True
 
 
-def pytest_unconfigure(config):  # pylint: disable=unused-argument
+def pytest_unconfigure(config):
     import sys
 
-    del sys._called_from_test  # pylint: disable=protected-access
+    del sys._called_from_test

docs/source/conf.py

@@ -10,8 +10,6 @@
 serve to show the default.
 """
 
-# pylint: disable=invalid-name,ungrouped-imports
-
 import os
 import sys
 import time
@@ -32,7 +30,7 @@
     html_theme = "sphinx_rtd_theme"
     html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
-import aiida_cp2k  # pylint: disable=wrong-import-position
+import aiida_cp2k
 
 # -- General configuration ------------------------------------------------
 
@@ -80,7 +78,6 @@
     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

examples/gaussian_datatypes/example_automatic.py

@@ -1,4 +1,3 @@
-# pylint: disable=import-outside-toplevel
 ###############################################################################
 # Copyright (c), The AiiDA-CP2K authors.                                      #
 # SPDX-License-Identifier: MIT                                                #
@@ -18,7 +17,7 @@
 from aiida.plugins import DataFactory
 from gdt_data import load_data
 
-StructureData = DataFactory("core.structure")  # pylint: disable=invalid-name
+StructureData = DataFactory("core.structure")
 
 
 def example_gdt(cp2k_code):
@@ -95,4 +94,4 @@ def cli(codelabel):
 
 
 if __name__ == "__main__":
-    cli()  # pylint: disable=no-value-for-parameter
+    cli()

examples/gaussian_datatypes/example_explicit.py

@@ -1,4 +1,3 @@
-# pylint: disable=import-outside-toplevel
 ###############################################################################
 # Copyright (c), The AiiDA-CP2K authors.                                      #
 # SPDX-License-Identifier: MIT                                                #
@@ -18,7 +17,7 @@
 from aiida.plugins import DataFactory
 from gdt_data import load_data
 
-StructureData = DataFactory("core.structure")  # pylint: disable=invalid-name
+StructureData = DataFactory("core.structure")
 
 
 def example_gdt(cp2k_code):
@@ -113,4 +112,4 @@ def cli(codelabel):
 
 
 if __name__ == "__main__":
-    cli()  # pylint: disable=no-value-for-parameter
+    cli()

examples/gaussian_datatypes/gdt_data.py

@@ -1,4 +1,3 @@
-# pylint: disable=import-outside-toplevel
 ###############################################################################
 # Copyright (c), The AiiDA-CP2K authors.                                      #
 # SPDX-License-Identifier: MIT                                                #
@@ -59,8 +58,8 @@ def load_data(prefix="MY-"):
          0.25682890    0
     """
 
-    BasisSet = DataFactory("gaussian.basisset")  # pylint: disable=invalid-name
-    Pseudo = DataFactory("gaussian.pseudo")  # pylint: disable=invalid-name
+    BasisSet = DataFactory("gaussian.basisset")
+    Pseudo = DataFactory("gaussian.pseudo")
 
     fhandle_bset = StringIO(bset_input)
     fhandle_pseudo = StringIO(pseudo_input)

examples/single_calculations/example_bands.py

@@ -1,4 +1,3 @@
-# pylint: disable=invalid-name
 ###############################################################################
 # Copyright (c), The AiiDA-CP2K authors.                                      #
 # SPDX-License-Identifier: MIT                                                #
@@ -18,8 +17,8 @@
 from aiida.plugins import DataFactory
 from ase.atoms import Atoms
 
-StructureData = DataFactory("core.structure")  # pylint: disable=invalid-name
-KpointsData = DataFactory("core.array.kpoints")  # pylint: disable=invalid-name
+StructureData = DataFactory("core.structure")
+KpointsData = DataFactory("core.array.kpoints")
 
 
 def example_bands(cp2k_code):
@@ -241,4 +240,4 @@ def cli(codelabel):
 
 
 if __name__ == "__main__":
-    cli()  # pylint: disable=no-value-for-parameter
+    cli()

examples/single_calculations/example_dft.py

@@ -1,4 +1,3 @@
-# pylint: disable=invalid-name
 ###############################################################################
 # Copyright (c), The AiiDA-CP2K authors.                                      #
 # SPDX-License-Identifier: MIT                                                #
@@ -17,7 +16,7 @@
 from aiida.orm import Dict, SinglefileData, load_code
 from aiida.plugins import DataFactory
 
-StructureData = DataFactory("core.structure")  # pylint: disable=invalid-name
+StructureData = DataFactory("core.structure")
 
 
 def example_dft(cp2k_code):
@@ -120,4 +119,4 @@ def cli(codelabel):
 
 
 if __name__ == "__main__":
-    cli()  # pylint: disable=no-value-for-parameter
+    cli()

examples/single_calculations/example_dft_atomic_kinds.py

@@ -1,4 +1,3 @@
-# pylint: disable=invalid-name
 ###############################################################################
 # Copyright (c), The AiiDA-CP2K authors.                                      #
 # SPDX-License-Identifier: MIT                                                #
@@ -17,7 +16,7 @@
 from aiida.orm import Dict, SinglefileData, load_code
 from aiida.plugins import DataFactory
 
-StructureData = DataFactory("core.structure")  # pylint: disable=invalid-name
+StructureData = DataFactory("core.structure")
 
 
 def example_dft_atomic_kinds(cp2k_code):
@@ -141,4 +140,4 @@ def cli(codelabel):
 
 
 if __name__ == "__main__":
-    cli()  # pylint: disable=no-value-for-parameter
+    cli()

examples/single_calculations/example_failure.py

@@ -1,4 +1,3 @@
-# pylint: disable=invalid-name
 ###############################################################################
 # Copyright (c), The AiiDA-CP2K authors.                                      #
 # SPDX-License-Identifier: MIT                                                #
@@ -58,4 +57,4 @@ def cli(codelabel):
 
 
 if __name__ == "__main__":
-    cli()  # pylint: disable=no-value-for-parameter
+    cli()

examples/single_calculations/example_geopt.py

@@ -1,4 +1,3 @@
-# pylint: disable=invalid-name
 ###############################################################################
 # Copyright (c), The AiiDA-CP2K authors.                                      #
 # SPDX-License-Identifier: MIT                                                #
@@ -17,7 +16,7 @@
 from aiida.orm import Dict, SinglefileData, load_code
 from aiida.plugins import DataFactory
 
-StructureData = DataFactory("core.structure")  # pylint: disable=invalid-name
+StructureData = DataFactory("core.structure")
 
 
 def example_geopt(cp2k_code):
@@ -147,4 +146,4 @@ def cli(codelabel):
 
 
 if __name__ == "__main__":
-    cli()  # pylint: disable=no-value-for-parameter
+    cli()

examples/single_calculations/example_max_error.py

@@ -1,4 +1,3 @@
-# pylint: disable=invalid-name
 ###############################################################################
 # Copyright (c), The AiiDA-CP2K authors.                                      #
 # SPDX-License-Identifier: MIT                                                #
@@ -17,7 +16,7 @@
 from aiida.orm import Dict, SinglefileData, load_code
 from aiida.plugins import CalculationFactory, DataFactory
 
-StructureData = DataFactory("core.structure")  # pylint: disable=invalid-name
+StructureData = DataFactory("core.structure")
 Cp2kCalculation = CalculationFactory("cp2k")
 
 
@@ -134,4 +133,4 @@ def cli(codelabel):
 
 
 if __name__ == "__main__":
-    cli()  # pylint: disable=no-value-for-parameter
+    cli()

examples/single_calculations/example_mm.py

@@ -1,4 +1,3 @@
-# pylint: disable=invalid-name
 ###############################################################################
 # Copyright (c), The AiiDA-CP2K authors.                                      #
 # SPDX-License-Identifier: MIT                                                #
@@ -45,9 +44,7 @@ def example_mm(cp2k_code):
     END"""
         )
 
-    water_pot = SinglefileData(
-        file=os.path.join("/tmp", "water.pot")
-    )  # pylint: disable=no-value-for-parameter
+    water_pot = SinglefileData(file=os.path.join("/tmp", "water.pot"))
 
     thisdir = os.path.dirname(os.path.realpath(__file__))
 
@@ -148,4 +145,4 @@ def cli(codelabel):
 
 
 if __name__ == "__main__":
-    cli()  # pylint: disable=no-value-for-parameter
+    cli()