264 deprecate extends base section

electronicparsers/abacus/metainfo/abacus.py

@@ -187,7 +187,7 @@ class BasisSet(runschema.method.BasisSet):
     section for numerical atomic orbitals of ABACUS
     """
 
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abacus_basis_sets_delta_k = Quantity(
         type=np.float64,
@@ -232,7 +232,7 @@ class BasisSet(runschema.method.BasisSet):
 
 
 class Calculation(runschema.calculation.Calculation):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abacus_init_velocities = Quantity(
         type=bool,
@@ -321,7 +321,7 @@ class Calculation(runschema.calculation.Calculation):
 
 
 class Run(runschema.run.Run):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abacus_input_filename = Quantity(
         type=str,
@@ -396,7 +396,7 @@ class Run(runschema.run.Run):
 
 
 class Method(runschema.method.Method):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abacus_initial_magnetization_total = Quantity(
         type=np.float64,
@@ -613,7 +613,7 @@ class Method(runschema.method.Method):
 
 
 class System(runschema.system.System):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abacus_alat = Quantity(
         type=np.float64,
@@ -693,7 +693,7 @@ class System(runschema.system.System):
 
 
 class Symmetry(runschema.system.Symmetry):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abacus_ibrav = Quantity(
         type=np.int32,
@@ -737,7 +737,7 @@ class Symmetry(runschema.system.Symmetry):
 
 
 class AtomParameters(runschema.method.AtomParameters):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abacus_pp_type = Quantity(
         type=str,
@@ -781,7 +781,7 @@ class AtomParameters(runschema.method.AtomParameters):
 
 
 class ScfIteration(runschema.calculation.ScfIteration):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abacus_density_change_scf_iteration = Quantity(
         type=np.float64,
@@ -822,7 +822,7 @@ class ScfIteration(runschema.calculation.ScfIteration):
 
 
 class BandEnergies(runschema.calculation.BandEnergies):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abacus_eigenvalues_number_of_planewaves = Quantity(
         type=np.int32,

electronicparsers/abinit/metainfo/abinit.py

@@ -177,7 +177,7 @@ class x_abinit_section_var(MSection):
 
 
 class Run(runschema.run.Run):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abinit_parallel_compilation = Quantity(
         type=str,
@@ -265,7 +265,7 @@ class Run(runschema.run.Run):
 
 
 class Method(runschema.method.Method):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abinit_tolvrs = Quantity(
         type=np.float64,
@@ -310,7 +310,7 @@ class Method(runschema.method.Method):
 
 
 class System(runschema.system.System):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abinit_atom_xcart_final = Quantity(
         type=str,
@@ -553,7 +553,7 @@ class BandEnergies(runschema.calculation.BandEnergies):
     Could be depricated later on, since it runs counter to the regular way of working.
     """
 
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abinit_qp_band_gaps_params = SubSection(
         sub_section=x_abinit_qp_band_gaps_params.m_def, repeats=False
@@ -728,7 +728,7 @@ class x_abinit_gw_dataset(MSection):
 
 
 class Calculation(runschema.calculation.Calculation):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abinit_magnetisation = Quantity(
         type=np.float64,
@@ -848,7 +848,7 @@ class Calculation(runschema.calculation.Calculation):
 
 
 class x_abinit_section_dataset(abinit_autogenerated.x_abinit_section_dataset):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abinit_geometry_optimization_converged = Quantity(
         type=str,
@@ -869,3 +869,6 @@ class x_abinit_section_dataset(abinit_autogenerated.x_abinit_section_dataset):
     x_abinit_section_dataset_header = SubSection(
         sub_section=x_abinit_section_dataset_header.m_def, repeats=True
     )
+
+
+m_package.__init_metainfo__()

electronicparsers/abinit/metainfo/abinit_autogenerated.py

@@ -6787,8 +6787,11 @@ class x_abinit_section_dataset(MSection):
 
 
 class Run(runschema.run.Run):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_abinit_section_dataset = SubSection(
         sub_section=x_abinit_section_dataset.m_def, repeats=True
     )
+
+
+m_package.__init_metainfo__()

electronicparsers/ams/metainfo/ams.py

@@ -41,7 +41,7 @@
 
 
 class Program(runschema.run.Program):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_ams_name = Quantity(
         type=str,
@@ -59,7 +59,7 @@ class Program(runschema.run.Program):
 
 
 class BandEnergies(runschema.calculation.BandEnergies):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_ams_energy_min = Quantity(
         type=np.float64,
@@ -87,7 +87,7 @@ class BandEnergies(runschema.calculation.BandEnergies):
 
 
 class Energy(runschema.calculation.Energy):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_ams_dispersion = SubSection(sub_section=runschema.calculation.EnergyEntry)
 
@@ -161,7 +161,7 @@ class Energy(runschema.calculation.Energy):
 
 
 class Forces(runschema.calculation.Forces):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_ams_p_matrix = SubSection(sub_section=runschema.calculation.ForcesEntry)
 
@@ -181,7 +181,7 @@ class Forces(runschema.calculation.Forces):
 
 
 class GeometryOptimization(simulationworkflowschema.GeometryOptimization):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_ams_optimization_coordinates = Quantity(
         type=str,
@@ -284,7 +284,7 @@ class GeometryOptimization(simulationworkflowschema.GeometryOptimization):
 
 
 class Method(runschema.method.Method):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_ams_dftb_resources_dir = Quantity(
         type=str,
@@ -450,7 +450,7 @@ class Method(runschema.method.Method):
 
 
 class BasisSetAtomCentered(runschema.method.BasisSetAtomCentered):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_ams_basis_functions_confinement_radius = Quantity(
         type=np.float64,
@@ -468,7 +468,7 @@ class BasisSetAtomCentered(runschema.method.BasisSetAtomCentered):
 
 
 class AtomParameters(runschema.method.AtomParameters):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_ams_radial_points = Quantity(
         type=np.int32,
@@ -597,7 +597,7 @@ class AtomParameters(runschema.method.AtomParameters):
 
 
 class BandGapDeprecated(runschema.calculation.BandGapDeprecated):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_ams_n_valence_electrons = Quantity(
         type=np.int32,
@@ -636,7 +636,7 @@ class BandGapDeprecated(runschema.calculation.BandGapDeprecated):
 
 
 class Scf(runschema.method.Scf):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_ams_diis_settings_dirac = Quantity(
         type=JSON,
@@ -717,7 +717,7 @@ class Scf(runschema.method.Scf):
 
 
 class KMesh(runschema.method.KMesh):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_ams_general_integration_parameter = Quantity(
         type=np.int32,
@@ -767,3 +767,6 @@ class KMesh(runschema.method.KMesh):
         description="""
         """,
     )
+
+
+m_package.__init_metainfo__()

electronicparsers/atk/metainfo/atk.py

@@ -36,7 +36,7 @@
 
 
 class Method(method.Method):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_atk_density_convergence_criterion = Quantity(
         type=np.float64,
@@ -69,3 +69,6 @@ class Method(method.Method):
         Monkhorstpack grid sampling
         """,
     )
+
+
+m_package.__init_metainfo__()

electronicparsers/castep/metainfo/castep.py

@@ -1754,7 +1754,7 @@ class x_castep_section_van_der_Waals_parameters(MSection):
 
 
 class Run(runschema.run.Run):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_castep_atom_forces = Quantity(
         type=np.float64,
@@ -2017,7 +2017,7 @@ class Run(runschema.run.Run):
 
 
 class System(runschema.system.System):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_castep_net_charge = Quantity(
         type=np.float64,
@@ -2165,7 +2165,7 @@ class System(runschema.system.System):
 
 
 class BasisSet(runschema.method.BasisSet):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_castep_size_std_grid = Quantity(
         type=np.float64,
@@ -2185,7 +2185,7 @@ class BasisSet(runschema.method.BasisSet):
 
 
 class Calculation(runschema.calculation.Calculation):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_castep_enthalpy = Quantity(
         type=np.float64,
@@ -2299,7 +2299,7 @@ class Calculation(runschema.calculation.Calculation):
 
 
 class Method(runschema.method.Method):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_castep_functional_and_weight = Quantity(
         type=str,
@@ -2323,7 +2323,7 @@ class Method(runschema.method.Method):
 
 
 class MolecularDynamicsMethod(simulationworkflowschema.MolecularDynamicsMethod):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_castep_thermostat_target_temperature = Quantity(
         type=np.float64,
@@ -2413,7 +2413,7 @@ class MolecularDynamicsMethod(simulationworkflowschema.MolecularDynamicsMethod):
 
 
 class GeometryOptimizationMethod(simulationworkflowschema.GeometryOptimizationMethod):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_castep_geometry_stress_com_tolerance = Quantity(
         type=np.float64,
@@ -2434,7 +2434,7 @@ class GeometryOptimizationMethod(simulationworkflowschema.GeometryOptimizationMe
 
 
 class BandStructure(runschema.calculation.BandStructure):
-    m_def = Section(validate=False, extends_base_section=True)
+    m_def = Section(validate=False)
 
     x_castep_k_path = Quantity(
         type=np.float64,
@@ -2479,3 +2479,6 @@ class BandStructure(runschema.calculation.BandStructure):
     x_castep_section_k_points = SubSection(
         sub_section=SectionProxy('x_castep_section_k_points'), repeats=True
     )
+
+
+m_package.__init_metainfo__()