Remove annotations

nomad-coe · Jan 24, 2025 · f885f1e · f885f1e · github-actions · Jan 24, 2025
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diff --git a/src/nomad_simulations/schema_packages/atoms_state.py b/src/nomad_simulations/schema_packages/atoms_state.py
@@ -308,7 +308,6 @@ 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 +410,6 @@ class HubbardInteractions(ArchiveSection):
         description="""
         Value of the (intraorbital) Hubbard interaction
         """,
-        # a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     j_hunds_coupling = Quantity(
@@ -420,7 +418,6 @@ class HubbardInteractions(ArchiveSection):
         description="""
         Value of the (interorbital) Hund's coupling.
         """,
-        # a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     u_interorbital_interaction = Quantity(
@@ -430,7 +427,6 @@ 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 +435,6 @@ 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 +469,6 @@ 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 +580,6 @@ 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
@@ -57,7 +57,6 @@ 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 +68,6 @@ 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

diff --git a/src/nomad_simulations/schema_packages/general.py b/src/nomad_simulations/schema_packages/general.py
@@ -70,23 +70,20 @@ 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 +92,6 @@ 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(
@@ -106,15 +102,13 @@ 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'),
     )
 
 
@@ -137,7 +131,6 @@ class BaseSimulation(Activity):
         description="""
         The date and time when this computation ended.
         """,
-        # a_eln=ELNAnnotation(component='DateTimeEditQuantity'),
     )
 
     cpu1_start = Quantity(
@@ -146,7 +139,6 @@ class BaseSimulation(Activity):
         description="""
         The starting time of the computation on the (first) CPU 1.
         """,
-        # a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     cpu1_end = Quantity(
@@ -155,7 +147,6 @@ class BaseSimulation(Activity):
         description="""
         The end time of the computation on the (first) CPU 1.
         """,
-        # a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     wall_start = Quantity(
@@ -164,7 +155,6 @@ class BaseSimulation(Activity):
         description="""
         The internal wall-clock time from the starting of the computation.
         """,
-        # a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     wall_end = Quantity(
@@ -173,7 +163,6 @@ 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)

diff --git a/src/nomad_simulations/schema_packages/model_method.py b/src/nomad_simulations/schema_packages/model_method.py
@@ -46,7 +46,6 @@ class BaseModelMethod(ArchiveSection):
         Name of the mathematical model. This is typically used to identify the model Hamiltonian used in the
         simulation. Typical standard names: 'DFT', 'TB', 'GW', 'BSE', 'DMFT', 'NMR', 'kMC'.
         """,
-        # a_eln=ELNAnnotation(component='StringEditQuantity'),
     )
 
     type = Quantity(
@@ -56,15 +55,13 @@ class BaseModelMethod(ArchiveSection):
         model can be 'Wannier', 'DFTB', 'xTB' or 'Slater-Koster'. This quantity should be
         rewritten to a MEnum when inheriting from this class.
         """,
-        # a_eln=ELNAnnotation(component='StringEditQuantity'),
     )
 
     external_reference = Quantity(
         type=URL,
         description="""
         External reference to the model e.g. DOI, URL.
         """,
-        # a_eln=ELNAnnotation(component='URLEditQuantity'),
     )
 
     numerical_settings = SubSection(sub_section=NumericalSettings.m_def, repeats=True)
@@ -112,7 +109,6 @@ class ModelMethodElectronic(ModelMethod):
         Describes the relativistic treatment used for the calculation of the final energy
         and related quantities. If `None`, no relativistic treatment is applied.
         """,
-        # a_eln=ELNAnnotation(component='EnumEditQuantity'),
     )
 
 
@@ -127,7 +123,6 @@ class XCFunctional(ArchiveSection):
         Provides the name of one of the exchange or correlation (XC) functional following the libxc
         convention. For the code base containing the conventions, see https://gitlab.com/libxc/libxc.
         """,  # TODO: step away from the libxc naming convention
-        # a_eln=ELNAnnotation(component='StringEditQuantity'),
     )
 
     name = Quantity(
@@ -144,7 +139,6 @@ class XCFunctional(ArchiveSection):
         Weight of the functional. This quantity is relevant when defining linear combinations of the
         different functionals. If not specified, its value is 1.
         """,
-        # a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     # ? add method to extract `name` from `libxc_name`
@@ -211,7 +205,6 @@ class DFT(ModelMethodElectronic):
         description="""
         Amount of exact exchange mixed in with the XC functional (value range = [0, 1]).
         """,
-        # a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     # ! MEnum this
@@ -243,7 +236,6 @@ class DFT(ModelMethodElectronic):
         | `"SIC_MAURI_US"`          | A (scaled) correction proposed by Mauri and co-
         workers on the spin density / doublet unpaired orbital |
         """,
-        # a_eln=ELNAnnotation(component='StringEditQuantity'),
     )
 
     van_der_waals_correction = Quantity(
@@ -260,7 +252,6 @@ class DFT(ModelMethodElectronic):
         | `"MDB"` | http://dx.doi.org/10.1103/PhysRevLett.108.236402 and http://dx.doi.org/10.1063/1.4865104 |
         | `"XC"` | The method to calculate the VdW energy uses a non-local functional |
         """,
-        # a_eln=ELNAnnotation(component='EnumEditQuantity'),
     )
 
     def __init__(self, m_def: 'Section' = None, m_context: 'Context' = None, **kwargs):
@@ -417,7 +408,6 @@ class TB(ModelMethodElectronic):
         | `'SlaterKoster'` | https://journals.aps.org/pr/abstract/10.1103/PhysRev.94.1498 |
         | `'unavailable'` | - |
         """,
-        # a_eln=ELNAnnotation(component='EnumEditQuantity'),
     )
 
     # ? these 4 quantities will change when `BasisSet` is defined
@@ -845,15 +835,13 @@ class ExcitedStateMethodology(ModelMethodElectronic):
         description="""
         Number of states used to calculate the excitations.
         """,
-        # a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     n_empty_states = Quantity(
         type=np.int32,
         description="""
         Number of empty states used to calculate the excitations. This quantity is complementary to `n_states`.
         """,
-        # a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
     broadening = Quantity(
@@ -862,7 +850,6 @@ class ExcitedStateMethodology(ModelMethodElectronic):
         description="""
         Lifetime broadening applied to the spectra in full-width at half maximum for excited-state calculations.
         """,
-        # a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
 
@@ -878,7 +865,6 @@ class Screening(ExcitedStateMethodology):
         Value of the static dielectric constant at infinite q. For metals, this is infinite
         (or a very large value), while for insulators is finite.
         """,
-        # a_eln=ELNAnnotation(component='NumberEditQuantity'),
     )
 
 
@@ -912,7 +898,6 @@ class GW(ExcitedStateMethodology):
         | `'qp-scGW0'`  | quasiparticle self-consistent G with fixed W0 | https://journals.aps.org/prb/abstract/10.1103/PhysRevB.76.115109 |
         | `'qp-scGW'`  | quasiparticle self-consistent G and W | https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.96.226402 |
         """,
-        # a_eln=ELNAnnotation(component='EnumEditQuantity'),
     )
 
     analytical_continuation = Quantity(
@@ -938,7 +923,6 @@ class GW(ExcitedStateMethodology):
         | `'ppm_FaridEngel'` | Farid and Engel plasmon-pole model  | https://journals.aps.org/prb/abstract/10.1103/PhysRevB.47.15931 |
         | `'multi_pole'` | Multi-pole fitting  | https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.74.1827 |
         """,
-        # a_eln=ELNAnnotation(component='EnumEditQuantity'),
     )
 
     # TODO improve description
@@ -955,7 +939,6 @@ class GW(ExcitedStateMethodology):
         description="""
         Reference to the `Screening` section that the GW calculation used to obtain the screened Coulomb interactions.
         """,
-        # a_eln=ELNAnnotation(component='ReferenceEditQuantity'),
     )
 
 
@@ -985,7 +968,6 @@ class BSE(ExcitedStateMethodology):
         | `'IP'` | Independent-particle approach |
         | `'RPA'` | Random Phase Approximation |
         """,
-        # a_eln=ELNAnnotation(component='EnumEditQuantity'),
     )
 
     solver = Quantity(
@@ -1001,15 +983,13 @@ class BSE(ExcitedStateMethodology):
         | `'SLEPc'` | Scalable Library for Eigenvalue Problem Computations | https://slepc.upv.es/ |
         | `'TDA'` | Tamm-Dancoff approximation | https://doi.org/10.1016/S0009-2614(99)01149-5 |
         """,
-        # a_eln=ELNAnnotation(component='EnumEditQuantity'),
     )
 
     screening_ref = Quantity(
         type=Screening,
         description="""
         Reference to the `Screening` section that the BSE calculation used to obtain the screened Coulomb interactions.
         """,
-        # a_eln=ELNAnnotation(component='ReferenceEditQuantity'),
     )
 
 
@@ -1036,7 +1016,6 @@ class CoreHoleSpectra(ModelMethodElectronic):
         description="""
         Type of the CoreHole excitation spectra calculated, either "absorption" or "emission".
         """,
-        # a_eln=ELNAnnotation(component='EnumEditQuantity'),
     )
 
     edge = Quantity(
@@ -1071,15 +1050,13 @@ class CoreHoleSpectra(ModelMethodElectronic):
         description="""
         Reference to the `CoreHole` section that contains the information of the edge of the excited core-hole.
         """,
-        # a_eln=ELNAnnotation(component='ReferenceEditQuantity'),
     )
 
     excited_state_method_ref = Quantity(
         type=ModelMethodElectronic,
         description="""
         Reference to the `ModelMethodElectronic` section (e.g., `DFT` or `BSE`) that was used to obtain the core-hole spectra.
         """,
-        # a_eln=ELNAnnotation(component='ReferenceEditQuantity'),
     )
 
     # TODO add normalization to obtain `edge`
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	190	21	89%	13–15, 201–204, 228, 283–284, 351–352, 354, 531, 543–544, 604–608, 623–627, 634
basis_set.py	238	27	89%	8–9, 120–131, 170–183, 383–387, 409–410, 454–457, 576, 607, 609
general.py	85	6	93%	4–7, 278–279, 289
model_method.py	251	72	71%	10–12, 156–159, 162–169, 258–259, 279, 300–321, 337–363, 366–383, 568, 761, 772, 814–821
model_system.py	346	37	89%	45–51, 225, 244, 248, 251, 254, 280, 366–367, 441–442, 459–460, 672–675, 722–729, 903–904, 1123–1127, 1133–1134, 1142–1143, 1148, 1171
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	118	9	92%	9–10, 252–255, 295–298, 323, 325, 378
physical_property.py	102	7	93%	20–22, 202, 330–332
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	2491	471	81%