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 <ndaelman@physik.hu-berlin.de>

Author: ndaelman-hu

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)`
 ```

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)

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):
     """

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):
     """