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- Deactivate EditQuantity annotations
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- Remove more spurious normalizers
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ndaelman committed Jan 24, 2025
1 parent b11f5f9 commit 55cc292
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Showing 6 changed files with 58 additions and 91 deletions.
14 changes: 7 additions & 7 deletions src/nomad_simulations/schema_packages/atoms_state.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -308,7 +308,7 @@ 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'),
# a_eln=ELNAnnotation(component='ReferenceEditQuantity'),
)

n_excited_electrons = Quantity(
Expand Down Expand Up @@ -411,7 +411,7 @@ class HubbardInteractions(ArchiveSection):
description="""
Value of the (intraorbital) Hubbard interaction
""",
a_eln=ELNAnnotation(component='NumberEditQuantity'),
# a_eln=ELNAnnotation(component='NumberEditQuantity'),
)

j_hunds_coupling = Quantity(
Expand All @@ -420,7 +420,7 @@ class HubbardInteractions(ArchiveSection):
description="""
Value of the (interorbital) Hund's coupling.
""",
a_eln=ELNAnnotation(component='NumberEditQuantity'),
# a_eln=ELNAnnotation(component='NumberEditQuantity'),
)

u_interorbital_interaction = Quantity(
Expand All @@ -430,7 +430,7 @@ 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'),
# a_eln=ELNAnnotation(component='NumberEditQuantity'),
)

j_local_exchange_interaction = Quantity(
Expand All @@ -439,7 +439,7 @@ 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'),
# a_eln=ELNAnnotation(component='NumberEditQuantity'),
)

u_effective = Quantity(
Expand Down Expand Up @@ -474,7 +474,7 @@ class HubbardInteractions(ArchiveSection):
description="""
Name of the double counting correction algorithm applied.
""",
a_eln=ELNAnnotation(component='StringEditQuantity'),
# a_eln=ELNAnnotation(component='StringEditQuantity'),
)

def resolve_u_interactions(self, logger: 'BoundLogger') -> Optional[tuple]:
Expand Down Expand Up @@ -586,7 +586,7 @@ 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'),
# a_eln=ELNAnnotation(component='NumberEditQuantity'),
)

core_hole = SubSection(sub_section=CoreHole.m_def, repeats=False)
Expand Down
4 changes: 2 additions & 2 deletions src/nomad_simulations/schema_packages/basis_set.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ class BasisSetComponent(ArchiveSection):
description="""
Reference to the section `AtomsState` specifying the localization of the basis set.
""",
a_eln=ELNAnnotation(components='ReferenceEditQuantity'),
# a_eln=ELNAnnotation(components='ReferenceEditQuantity'),
)

# TODO: add atom index-based instantiator for species if not present
Expand All @@ -69,7 +69,7 @@ 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'),
# a_eln=ELNAnnotation(components='ReferenceEditQuantity'),
)

# ? band_scope or orbital_scope: valence vs core
Expand Down
28 changes: 11 additions & 17 deletions src/nomad_simulations/schema_packages/general.py
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Original file line number Diff line number Diff line change
Expand Up @@ -70,23 +70,23 @@ class Program(Entity):
description="""
The name of the program.
""",
a_eln=ELNAnnotation(component='StringEditQuantity'),
# a_eln=ELNAnnotation(component='StringEditQuantity'),
)

version = Quantity(
type=str,
description="""
The version label of the program.
""",
a_eln=ELNAnnotation(component='StringEditQuantity'),
# a_eln=ELNAnnotation(component='StringEditQuantity'),
)

link = Quantity(
type=str,
description="""
Website link to the program in published information.
""",
a_eln=ELNAnnotation(component='URLEditQuantity'),
# a_eln=ELNAnnotation(component='URLEditQuantity'),
)

version_internal = Quantity(
Expand All @@ -95,7 +95,7 @@ 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'),
# a_eln=ELNAnnotation(component='StringEditQuantity'),
)

subroutine_name_internal = Quantity(
Expand All @@ -106,20 +106,17 @@ 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'),
# 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'),
# a_eln=ELNAnnotation(component='StringEditQuantity'),
)

def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
pass


class BaseSimulation(Activity):
"""
Expand All @@ -140,7 +137,7 @@ class BaseSimulation(Activity):
description="""
The date and time when this computation ended.
""",
a_eln=ELNAnnotation(component='DateTimeEditQuantity'),
# a_eln=ELNAnnotation(component='DateTimeEditQuantity'),
)

cpu1_start = Quantity(
Expand All @@ -149,7 +146,7 @@ class BaseSimulation(Activity):
description="""
The starting time of the computation on the (first) CPU 1.
""",
a_eln=ELNAnnotation(component='NumberEditQuantity'),
# a_eln=ELNAnnotation(component='NumberEditQuantity'),
)

cpu1_end = Quantity(
Expand All @@ -158,7 +155,7 @@ class BaseSimulation(Activity):
description="""
The end time of the computation on the (first) CPU 1.
""",
a_eln=ELNAnnotation(component='NumberEditQuantity'),
# a_eln=ELNAnnotation(component='NumberEditQuantity'),
)

wall_start = Quantity(
Expand All @@ -167,7 +164,7 @@ class BaseSimulation(Activity):
description="""
The internal wall-clock time from the starting of the computation.
""",
a_eln=ELNAnnotation(component='NumberEditQuantity'),
# a_eln=ELNAnnotation(component='NumberEditQuantity'),
)

wall_end = Quantity(
Expand All @@ -176,14 +173,11 @@ class BaseSimulation(Activity):
description="""
The internal wall-clock time from the end of the computation.
""",
a_eln=ELNAnnotation(component='NumberEditQuantity'),
# 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):
"""
Expand Down
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Coverage

Coverage Report
FileStmtsMissCoverMissing
src/nomad_simulations
   __init__.py4250%3–4
   _version.py11282%5–6
src/nomad_simulations/schema_packages
   __init__.py15287%39–41
   atoms_state.py1902189%13–15, 201–204, 228, 283–284, 352–353, 355, 537, 549–550, 611–615, 630–634, 641
   basis_set.py2382789%8–9, 122–133, 172–185, 384–388, 410–411, 455–458, 577, 608, 610
   general.py85693%4–7, 289–290, 300
   model_method.py2517271%10–12, 162–165, 168–175, 267–268, 288, 309–330, 346–372, 375–392, 578, 771, 782, 824–831
   model_system.py3463789%45–51, 235, 254, 258, 261, 264, 290, 376–377, 451–452, 469–470, 683–686, 733–740, 914–915, 1137–1141, 1147–1148, 1156–1157, 1162, 1185
   numerical_settings.py2556076%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.py118992%9–10, 252–255, 295–298, 323, 325, 378
   physical_property.py102793%20–22, 202, 331–333
   variables.py861286%8–10, 98, 121, 145, 167, 189, 211, 233, 256, 276
src/nomad_simulations/schema_packages/properties
   band_gap.py51590%8–10, 135–136
   band_structure.py1172380%9–11, 229–262, 275, 282, 318–319, 366–367
   energies.py30390%7–9
   fermi_surface.py17476%7–9, 40
   forces.py16381%7–9
   greens_function.py931089%7–9, 210–211, 232–233, 254–255, 391
   hopping_matrix.py25388%7–9
   permittivity.py48883%7–9, 97–105
   spectral_profile.py25812751%9–11, 57–60, 95–98, 199–300, 356–368, 393–396, 416, 421–424, 466–502, 570–573, 589–590, 595–601
   thermodynamics.py451273%7–9, 142–144, 177–179, 212–214
src/nomad_simulations/schema_packages/utils
   utils.py791680%8–11, 65–74, 83–84, 89, 92, 169–170
TOTAL249147181% 

Tests Skipped Failures Errors Time
402 0 💤 0 ❌ 0 🔥 6.558s ⏱️

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