Remove editable annotations (#162)

* Fix typo * Remove spurious normalization * - Deactivate `EditQuantity` annotations - Remove more spurious normalizers * Apply ruff * Remove annotations * - Remove `ELNAnnotation` imports - Remove 2 extra editable annotations --------- Co-authored-by: ndaelman <[email protected]>
nomad-coe · Jan 28, 2025 · fe81d97 · fe81d97 · github-actions · Jan 28, 2025
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commit fe81d97
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Showing 16 changed files with 2 additions and 221 deletions.
diff --git a/docs/normalize.md b/docs/normalize.md
@@ -25,7 +25,7 @@ class Section1(ArchiveSection):
 class Section2(ArchiveSection):
     normalizer_level = 0
 
-    def normalize(self, achive, logger):
+    def normalize(self, archive, logger):
         super().normalize(archive, logger)
         # Some operations here or before `super().normalize(archive, logger)`
 
@@ -36,7 +36,7 @@ class ParentSection(ArchiveSection):
 
     sub_section_2 = SubSection(Section2.m_def, repeats=True)
 
-    def normalize(self, achive, logger):
+    def normalize(self, archive, logger):
         super().normalize(archive, logger)
         # Some operations here or before `super().normalize(archive, logger)`
 ```

diff --git a/src/nomad_simulations/schema_packages/atoms_state.py b/src/nomad_simulations/schema_packages/atoms_state.py
@@ -4,7 +4,6 @@
 import numpy as np
 import pint
 from nomad.datamodel.data import ArchiveSection
-from nomad.datamodel.metainfo.annotations import ELNAnnotation
 from nomad.datamodel.metainfo.basesections import Entity
 from nomad.metainfo import MEnum, Quantity, SubSection
 from nomad.units import ureg
@@ -308,7 +307,6 @@ class CoreHole(ArchiveSection):
         description="""
         Reference to the OrbitalsState section that is used as a basis to obtain the `CoreHole` section.
         """,
-        a_eln=ELNAnnotation(component='ReferenceEditQuantity'),
     )
 
     n_excited_electrons = Quantity(
@@ -411,7 +409,6 @@ class HubbardInteractions(ArchiveSection):
         description="""
         Value of the (intraorbital) Hubbard interaction
         """,
-        a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     j_hunds_coupling = Quantity(
@@ -420,7 +417,6 @@ class HubbardInteractions(ArchiveSection):
         description="""
         Value of the (interorbital) Hund's coupling.
         """,
-        a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     u_interorbital_interaction = Quantity(
@@ -430,7 +426,6 @@ class HubbardInteractions(ArchiveSection):
         Value of the (interorbital) Coulomb interaction. In rotational invariant systems,
         u_interorbital_interaction = u_interaction - 2 * j_hunds_coupling.
         """,
-        a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     j_local_exchange_interaction = Quantity(
@@ -439,7 +434,6 @@ class HubbardInteractions(ArchiveSection):
         description="""
         Value of the exchange interaction. In rotational invariant systems, j_local_exchange_interaction = j_hunds_coupling.
         """,
-        a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     u_effective = Quantity(
@@ -474,7 +468,6 @@ class HubbardInteractions(ArchiveSection):
         description="""
         Name of the double counting correction algorithm applied.
         """,
-        a_eln=ELNAnnotation(component='StringEditQuantity'),
     )
 
     def resolve_u_interactions(self, logger: 'BoundLogger') -> Optional[tuple]:
@@ -586,7 +579,6 @@ class AtomsState(Entity):
         Note: for `CoreHole` systems we do not consider the charge of the atom even if
         we do not store the final `OrbitalsState` where the electron was excited to.
         """,
-        a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     core_hole = SubSection(sub_section=CoreHole.m_def, repeats=False)

diff --git a/src/nomad_simulations/schema_packages/basis_set.py b/src/nomad_simulations/schema_packages/basis_set.py
@@ -12,7 +12,6 @@
 import pint
 from nomad import utils
 from nomad.datamodel.data import ArchiveSection
-from nomad.datamodel.metainfo.annotations import ELNAnnotation
 from nomad.metainfo import MEnum, Quantity, SubSection
 from nomad.units import ureg
 
@@ -57,7 +56,6 @@ class BasisSetComponent(ArchiveSection):
         description="""
         Reference to the section `AtomsState` specifying the localization of the basis set.
         """,
-        a_eln=ELNAnnotation(components='ReferenceEditQuantity'),
     )
 
     # TODO: add atom index-based instantiator for species if not present
@@ -69,7 +67,6 @@ class BasisSetComponent(ArchiveSection):
         Reference to the section `BaseModelMethod` containing the information
         of the Hamiltonian term to which the basis set applies.
         """,
-        a_eln=ELNAnnotation(components='ReferenceEditQuantity'),
     )
 
     # ? band_scope or orbital_scope: valence vs core
@@ -204,12 +201,6 @@ class AtomCenteredBasisSet(BasisSetComponent):
         sub_section=AtomCenteredFunction.m_def, repeats=True
     )  # TODO change name
 
-    def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
-        super().normalize(archive, logger)
-        # self.name = self.m_def.name
-        # TODO: set name based on basis functions
-        # ? use basis set names from Basis Set Exchange
-
 
 class APWBaseOrbital(ArchiveSection):
     """

diff --git a/src/nomad_simulations/schema_packages/general.py b/src/nomad_simulations/schema_packages/general.py
@@ -9,7 +9,6 @@
 import numpy as np
 from nomad.config import config
 from nomad.datamodel.data import Schema
-from nomad.datamodel.metainfo.annotations import ELNAnnotation
 from nomad.datamodel.metainfo.basesections import Activity, Entity
 from nomad.metainfo import Datetime, Quantity, SchemaPackage, Section, SubSection
 
@@ -70,23 +69,20 @@ class Program(Entity):
         description="""
         The name of the program.
         """,
-        a_eln=ELNAnnotation(component='StringEditQuantity'),
     )
 
     version = Quantity(
         type=str,
         description="""
         The version label of the program.
         """,
-        a_eln=ELNAnnotation(component='StringEditQuantity'),
     )
 
     link = Quantity(
         type=str,
         description="""
         Website link to the program in published information.
         """,
-        a_eln=ELNAnnotation(component='URLEditQuantity'),
     )
 
     version_internal = Quantity(
@@ -95,7 +91,6 @@ class Program(Entity):
         Specifies a program version tag used internally for development purposes.
         Any kind of tagging system is supported, including git commit hashes.
         """,
-        a_eln=ELNAnnotation(component='StringEditQuantity'),
     )
 
     subroutine_name_internal = Quantity(
@@ -106,20 +101,15 @@ class Program(Entity):
         so the naming is representative. This naming is mostly meant for users
         who are familiar with the program's structure.
         """,
-        a_eln=ELNAnnotation(component='StringEditQuantity'),
     )
 
     compilation_host = Quantity(
         type=str,
         description="""
         Specifies the host on which the program was compiled.
         """,
-        a_eln=ELNAnnotation(component='StringEditQuantity'),
     )
 
-    def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
-        pass
-
 
 class BaseSimulation(Activity):
     """
@@ -140,7 +130,6 @@ class BaseSimulation(Activity):
         description="""
         The date and time when this computation ended.
         """,
-        a_eln=ELNAnnotation(component='DateTimeEditQuantity'),
     )
 
     cpu1_start = Quantity(
@@ -149,7 +138,6 @@ class BaseSimulation(Activity):
         description="""
         The starting time of the computation on the (first) CPU 1.
         """,
-        a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     cpu1_end = Quantity(
@@ -158,7 +146,6 @@ class BaseSimulation(Activity):
         description="""
         The end time of the computation on the (first) CPU 1.
         """,
-        a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     wall_start = Quantity(
@@ -167,7 +154,6 @@ class BaseSimulation(Activity):
         description="""
         The internal wall-clock time from the starting of the computation.
         """,
-        a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     wall_end = Quantity(
@@ -176,14 +162,10 @@ class BaseSimulation(Activity):
         description="""
         The internal wall-clock time from the end of the computation.
         """,
-        a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     program = SubSection(sub_section=Program.m_def, repeats=False)
 
-    def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
-        pass
-
 
 class Simulation(BaseSimulation, Schema):
     """
File	Stmts	Miss	Cover	Missing
src/nomad_simulations
__init__.py	4	2	50%	3–4
_version.py	11	2	82%	5–6
src/nomad_simulations/schema_packages
__init__.py	15	2	87%	39–41
atoms_state.py	189	21	89%	12–14, 200–203, 227, 282–283, 350–351, 353, 530, 542–543, 603–607, 622–626, 633
basis_set.py	237	27	89%	8–9, 119–130, 169–182, 382–386, 408–409, 453–456, 575, 606, 608
general.py	84	6	93%	4–7, 277–278, 288
model_method.py	250	72	71%	9–11, 155–158, 161–168, 257–258, 278, 299–320, 336–362, 365–382, 567, 760, 771, 813–820
model_system.py	345	37	89%	44–50, 224, 243, 247, 250, 253, 279, 365–366, 440–441, 458–459, 671–674, 721–728, 902–903, 1122–1126, 1132–1133, 1141–1142, 1147, 1170
numerical_settings.py	255	60	76%	12–14, 214, 216–217, 220–223, 227–228, 235–238, 247–250, 254–257, 259–262, 267–270, 276–279, 466–493, 568, 603–606, 630, 633, 678, 680–683, 687, 691, 738, 742–763, 818–819
outputs.py	117	9	92%	8–9, 249–252, 292–295, 320, 322, 375
physical_property.py	101	7	93%	19–21, 201, 329–331
variables.py	86	12	86%	8–10, 98, 121, 145, 167, 189, 211, 233, 256, 276
src/nomad_simulations/schema_packages/properties
band_gap.py	51	5	90%	8–10, 135–136
band_structure.py	117	23	80%	9–11, 229–262, 275, 282, 318–319, 366–367
energies.py	30	3	90%	7–9
fermi_surface.py	17	4	76%	7–9, 40
forces.py	16	3	81%	7–9
greens_function.py	93	10	89%	7–9, 210–211, 232–233, 254–255, 391
hopping_matrix.py	25	3	88%	7–9
permittivity.py	48	8	83%	7–9, 97–105
spectral_profile.py	258	127	51%	9–11, 57–60, 95–98, 199–300, 356–368, 393–396, 416, 421–424, 466–502, 570–573, 589–590, 595–601
thermodynamics.py	45	12	73%	7–9, 142–144, 177–179, 212–214
src/nomad_simulations/schema_packages/utils
utils.py	79	16	80%	8–11, 65–74, 83–84, 89, 92, 169–170
TOTAL	2484	471	81%