From 2233f348c75b379b91d759990be72e6f5060cc76 Mon Sep 17 00:00:00 2001
From: JosePizarro3 <jose.pizarro@physik.hu-berlin.de>
Date: Tue, 27 Aug 2024 10:39:41 +0200
Subject: [PATCH] Fix ruff

---
 pyproject.toml                                |  3 +-
 .../properties/greens_function.py             | 48 ++++++++++++++++---
 tests/conftest.py                             |  1 -
 tests/test_atoms_state.py                     |  1 -
 tests/test_band_gap.py                        |  1 -
 tests/test_band_structure.py                  |  1 -
 tests/test_fermi_surface.py                   |  1 -
 tests/test_general.py                         |  1 -
 tests/test_greens_function.py                 | 28 ++++++++---
 tests/test_hopping_matrix.py                  |  1 -
 tests/test_model_method.py                    |  1 -
 tests/test_model_system.py                    |  1 -
 tests/test_numerical_settings.py              |  1 -
 tests/test_outputs.py                         |  1 -
 tests/test_permittivity.py                    |  1 -
 tests/test_physical_properties.py             |  1 -
 tests/test_spectral_profile.py                |  1 -
 tests/test_utils.py                           |  1 -
 tests/test_variables.py                       |  1 -
 19 files changed, 64 insertions(+), 31 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 117c62f6..da497aba 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -84,7 +84,6 @@ indent-width = 4
 [tool.ruff.lint]
 select = [
     "E", # pycodestyle
-    "W", # pycodestyle
     "PL", # pylint
     "F", # Pyflakes
     "UP", # pyupgrade
@@ -92,11 +91,11 @@ select = [
 ]
 
 ignore = [
+    "F401", # Module imported but unused
     "E501", # Line too long ({width} > {limit} characters)
     "E701", # Multiple statements on one line (colon)
     "E731", # Do not assign a lambda expression, use a def
     "E402",  # Module level import not at top of file
-    "F401",
     "PLR0911", # Too many return statements
     "PLR0912", # Too many branches
     "PLR0913", # Too many arguments in function definition
diff --git a/src/nomad_simulations/schema_packages/properties/greens_function.py b/src/nomad_simulations/schema_packages/properties/greens_function.py
index c4788c7e..51928a84 100644
--- a/src/nomad_simulations/schema_packages/properties/greens_function.py
+++ b/src/nomad_simulations/schema_packages/properties/greens_function.py
@@ -54,6 +54,7 @@ class BaseGreensFunction(PhysicalProperty):
 
     Further information in M. Wallerberger et al., Comput. Phys. Commun. 235, 2 (2019).
     """
+
     # ! we use `atoms_state_ref` and `orbitals_state_ref` to enforce order in the matrices
 
     n_atoms = Quantity(
@@ -108,7 +109,22 @@ class BaseGreensFunction(PhysicalProperty):
     )
 
     space_id = Quantity(
-        type=MEnum('r', 'rt', 'rw', 'rit', 'riw', 'k', 'kt', 'kw', 'kit', 'kiw', 't', 'it', 'w', 'iw'),
+        type=MEnum(
+            'r',
+            'rt',
+            'rw',
+            'rit',
+            'riw',
+            'k',
+            'kt',
+            'kw',
+            'kit',
+            'kiw',
+            't',
+            'it',
+            'w',
+            'iw',
+        ),
         description="""
         String used to identify the space in which the Green's function property is represented. The spaces are:
 
@@ -136,7 +152,10 @@ def __init__(
     ) -> None:
         super().__init__(m_def, m_context, **kwargs)
         # ! n_orbitals need to be set up during initialization of the class
-        self.rank = [int(kwargs.get('n_atoms')), int(kwargs.get('n_correlated_orbitals'))]
+        self.rank = [
+            int(kwargs.get('n_atoms')),
+            int(kwargs.get('n_correlated_orbitals')),
+        ]
 
     def resolve_space_id(self) -> str:
         """
@@ -167,7 +186,9 @@ def find_space_id(space_map: dict) -> str:
                 str: _description_
             """
             for space_id, variable_cls in space_map.items():
-                space_variable = get_variables(variables=self.variables, variable_cls=variable_cls)
+                space_variable = get_variables(
+                    variables=self.variables, variable_cls=variable_cls
+                )
                 if len(space_variable) > 0:
                     return space_id
             return ''
@@ -179,12 +200,13 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
         super().normalize(archive, logger)
 
         space_id = self.resolve_space_id()
-        if (self.space_id is not None and self.space_id != space_id):
+        if self.space_id is not None and self.space_id != space_id:
             logger.warning(
                 f'The stored `space_id`, {self.space_id}, does not coincide with the resolved one, {space_id}. We will update it.'
             )
         self.space_id = space_id
 
+
 class ElectronicGreensFunction(BaseGreensFunction):
     """
     Charge-charge correlation functions.
@@ -271,12 +293,18 @@ class QuasiparticleWeight(PhysicalProperty):
     electron-electron interactions and takes values between 0 and 1, with Z = 1 representing a non-correlated
     system, and Z = 0 the Mott state.
     """
+
     # ! we use `atoms_state_ref` and `orbitals_state_ref` to enforce order in the matrices
 
     iri = 'http://fairmat-nfdi.eu/taxonomy/HybridizationFunction'
 
     system_correlation_strengths = Quantity(
-        type=MEnum('non-correlated metal', 'strongly-correlated metal', 'OSMI', 'Mott insulator'),
+        type=MEnum(
+            'non-correlated metal',
+            'strongly-correlated metal',
+            'OSMI',
+            'Mott insulator',
+        ),
         description="""
         String used to identify the type of system based on the strength of the electron-electron interactions.
 
@@ -338,7 +366,10 @@ def __init__(
     ) -> None:
         super().__init__(m_def, m_context, **kwargs)
         # ! n_orbitals need to be set up during initialization of the class
-        self.rank = [int(kwargs.get('n_atoms')), int(kwargs.get('n_correlated_orbitals'))]
+        self.rank = [
+            int(kwargs.get('n_atoms')),
+            int(kwargs.get('n_correlated_orbitals')),
+        ]
         self.name = self.m_def.name
 
     def is_valid_quasiparticle_weight(self) -> bool:
@@ -380,7 +411,10 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
             return
 
         system_correlation_strengths = self.resolve_system_correlation_strengths()
-        if (self.system_correlation_strengths is not None and self.system_correlation_strengths != system_correlation_strengths):
+        if (
+            self.system_correlation_strengths is not None
+            and self.system_correlation_strengths != system_correlation_strengths
+        ):
             logger.warning(
                 f'The stored `system_correlation_strengths`, {self.system_correlation_strengths}, does not coincide with the resolved one, {system_correlation_strengths}. We will update it.'
             )
diff --git a/tests/conftest.py b/tests/conftest.py
index 097298c2..c4a5a798 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -23,7 +23,6 @@
 import pytest
 from nomad.datamodel import EntryArchive
 from nomad.units import ureg
-
 from nomad_simulations.schema_packages.atoms_state import AtomsState, OrbitalsState
 from nomad_simulations.schema_packages.general import Simulation
 from nomad_simulations.schema_packages.model_method import ModelMethod
diff --git a/tests/test_atoms_state.py b/tests/test_atoms_state.py
index dd2aa70c..65a1e3d0 100644
--- a/tests/test_atoms_state.py
+++ b/tests/test_atoms_state.py
@@ -22,7 +22,6 @@
 import pytest
 from nomad.datamodel import EntryArchive
 from nomad.units import ureg
-
 from nomad_simulations.schema_packages.atoms_state import (
     AtomsState,
     CoreHole,
diff --git a/tests/test_band_gap.py b/tests/test_band_gap.py
index 8d8a6b53..b47abe1b 100644
--- a/tests/test_band_gap.py
+++ b/tests/test_band_gap.py
@@ -22,7 +22,6 @@
 import pytest
 from nomad.datamodel import EntryArchive
 from nomad.units import ureg
-
 from nomad_simulations.schema_packages.properties import ElectronicBandGap
 from nomad_simulations.schema_packages.variables import Temperature
 
diff --git a/tests/test_band_structure.py b/tests/test_band_structure.py
index 1e81aab5..4dd72ecd 100644
--- a/tests/test_band_structure.py
+++ b/tests/test_band_structure.py
@@ -21,7 +21,6 @@
 import numpy as np
 import pytest
 from nomad.datamodel import EntryArchive
-
 from nomad_simulations.schema_packages.properties import ElectronicEigenvalues
 
 from . import logger
diff --git a/tests/test_fermi_surface.py b/tests/test_fermi_surface.py
index 05c7206b..dde4ce1f 100644
--- a/tests/test_fermi_surface.py
+++ b/tests/test_fermi_surface.py
@@ -19,7 +19,6 @@
 from typing import Optional
 
 import pytest
-
 from nomad_simulations.schema_packages.properties import FermiSurface
 
 
diff --git a/tests/test_general.py b/tests/test_general.py
index 06a360c9..e722e03e 100644
--- a/tests/test_general.py
+++ b/tests/test_general.py
@@ -19,7 +19,6 @@
 import numpy as np
 import pytest
 from nomad.datamodel import EntryArchive
-
 from nomad_simulations.schema_packages.general import Simulation
 from nomad_simulations.schema_packages.model_system import (
     AtomicCell,
diff --git a/tests/test_greens_function.py b/tests/test_greens_function.py
index 3dae739b..e7b90f00 100644
--- a/tests/test_greens_function.py
+++ b/tests/test_greens_function.py
@@ -20,7 +20,6 @@
 
 import pytest
 from nomad.datamodel import EntryArchive
-
 from nomad_simulations.schema_packages.properties import (
     QuasiparticleWeight,
 )
@@ -64,7 +63,15 @@ class TestBaseGreensFunction:
             ([KMesh(), MatsubaraFrequency()], 'kiw'),
         ],
     )
-    def test_resolve_space_id(self, variables: list[Union[WignerSeitz, KMesh, Time, ImaginaryTime, Frequency, MatsubaraFrequency]], result: str):
+    def test_resolve_space_id(
+        self,
+        variables: list[
+            Union[
+                WignerSeitz, KMesh, Time, ImaginaryTime, Frequency, MatsubaraFrequency
+            ]
+        ],
+        result: str,
+    ):
         """
         Test the `resolve_space_id` method of the `BaseGreensFunction` class.
         """
@@ -94,7 +101,16 @@ def test_resolve_space_id(self, variables: list[Union[WignerSeitz, KMesh, Time,
             ('', [KMesh(), MatsubaraFrequency()], 'kiw'),
         ],
     )
-    def test_normalize(self, space_id: str, variables: list[Union[WignerSeitz, KMesh, Time, ImaginaryTime, Frequency, MatsubaraFrequency]], result: Optional[str]):
+    def test_normalize(
+        self,
+        space_id: str,
+        variables: list[
+            Union[
+                WignerSeitz, KMesh, Time, ImaginaryTime, Frequency, MatsubaraFrequency
+            ]
+        ],
+        result: Optional[str],
+    ):
         """
         Test the `normalize` method of the `BaseGreensFunction` class.
         """
@@ -105,7 +121,6 @@ def test_normalize(self, space_id: str, variables: list[Union[WignerSeitz, KMesh
         assert gfs.space_id == result
 
 
-
 class TestQuasiparticleWeight:
     """
     Test the `QuasiparticleWeight` class defined in `properties/greens_function.py`.
@@ -127,7 +142,6 @@ def test_is_valid_quasiparticle_weight(self, value: list[float], result: bool):
         quasiparticle_weight.value = value
         assert quasiparticle_weight.is_valid_quasiparticle_weight() == result
 
-
     @pytest.mark.parametrize(
         'value, result',
         [
@@ -138,7 +152,9 @@ def test_is_valid_quasiparticle_weight(self, value: list[float], result: bool):
             ([[1.0, 0.8, 0.2]], None),
         ],
     )
-    def test_resolve_system_correlation_strengths(self, value: list[float], result: Optional[str]):
+    def test_resolve_system_correlation_strengths(
+        self, value: list[float], result: Optional[str]
+    ):
         """
         Test the `resolve_system_correlation_strengths` method of the `QuasiparticleWeight` class.
         """
diff --git a/tests/test_hopping_matrix.py b/tests/test_hopping_matrix.py
index b7cf43d7..cfe6ada2 100644
--- a/tests/test_hopping_matrix.py
+++ b/tests/test_hopping_matrix.py
@@ -19,7 +19,6 @@
 from typing import Optional
 
 import pytest
-
 from nomad_simulations.schema_packages.properties import (
     CrystalFieldSplitting,
     HoppingMatrix,
diff --git a/tests/test_model_method.py b/tests/test_model_method.py
index 7e51e22d..b66c5e25 100644
--- a/tests/test_model_method.py
+++ b/tests/test_model_method.py
@@ -20,7 +20,6 @@
 
 import pytest
 from nomad.datamodel import EntryArchive
-
 from nomad_simulations.schema_packages.atoms_state import AtomsState, OrbitalsState
 from nomad_simulations.schema_packages.general import Simulation
 from nomad_simulations.schema_packages.model_method import (
diff --git a/tests/test_model_system.py b/tests/test_model_system.py
index 6ead47e8..ecb67a76 100644
--- a/tests/test_model_system.py
+++ b/tests/test_model_system.py
@@ -21,7 +21,6 @@
 import numpy as np
 import pytest
 from nomad.datamodel import EntryArchive
-
 from nomad_simulations.schema_packages.model_system import (
     ChemicalFormula,
     ModelSystem,
diff --git a/tests/test_numerical_settings.py b/tests/test_numerical_settings.py
index 70ab30da..aab071ce 100644
--- a/tests/test_numerical_settings.py
+++ b/tests/test_numerical_settings.py
@@ -22,7 +22,6 @@
 import pytest
 from nomad.datamodel import EntryArchive
 from nomad.units import ureg
-
 from nomad_simulations.schema_packages.numerical_settings import (
     KLinePath,
     KMesh,
diff --git a/tests/test_outputs.py b/tests/test_outputs.py
index a63a1f23..b3e81d48 100644
--- a/tests/test_outputs.py
+++ b/tests/test_outputs.py
@@ -20,7 +20,6 @@
 
 import pytest
 from nomad.datamodel import EntryArchive
-
 from nomad_simulations.schema_packages.model_method import ModelMethod
 from nomad_simulations.schema_packages.model_system import ModelSystem
 from nomad_simulations.schema_packages.numerical_settings import SelfConsistency
diff --git a/tests/test_permittivity.py b/tests/test_permittivity.py
index f6955f97..9cb58fbc 100644
--- a/tests/test_permittivity.py
+++ b/tests/test_permittivity.py
@@ -20,7 +20,6 @@
 
 import numpy as np
 import pytest
-
 from nomad_simulations.schema_packages.properties import Permittivity
 from nomad_simulations.schema_packages.variables import Frequency, KMesh, Variables
 
diff --git a/tests/test_physical_properties.py b/tests/test_physical_properties.py
index b9e9e1bf..12191221 100644
--- a/tests/test_physical_properties.py
+++ b/tests/test_physical_properties.py
@@ -23,7 +23,6 @@
 from nomad.datamodel import EntryArchive
 from nomad.metainfo import Quantity
 from nomad.units import ureg
-
 from nomad_simulations.schema_packages.physical_property import (
     PhysicalProperty,
     validate_quantity_wrt_value,
diff --git a/tests/test_spectral_profile.py b/tests/test_spectral_profile.py
index 4184bbb7..003bd029 100644
--- a/tests/test_spectral_profile.py
+++ b/tests/test_spectral_profile.py
@@ -22,7 +22,6 @@
 import pytest
 from nomad.datamodel import EntryArchive
 from nomad.units import ureg
-
 from nomad_simulations.schema_packages.atoms_state import AtomsState
 from nomad_simulations.schema_packages.general import Simulation
 from nomad_simulations.schema_packages.model_system import AtomicCell, ModelSystem
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 3d3e69cf..8cf7512a 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -17,7 +17,6 @@
 #
 
 import pytest
-
 from nomad_simulations.schema_packages.model_system import (
     AtomicCell,
     ModelSystem,
diff --git a/tests/test_variables.py b/tests/test_variables.py
index c64faf91..2fd63a00 100644
--- a/tests/test_variables.py
+++ b/tests/test_variables.py
@@ -18,7 +18,6 @@
 
 import pytest
 from nomad.datamodel import EntryArchive
-
 from nomad_simulations.schema_packages.variables import Variables
 
 from . import logger