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b136511
Order quantities; revert modification of basesection quantities
ka-sarthak May 30, 2024
b2e3ff8
Modify description of quantities
ka-sarthak May 30, 2024
dbb8e9c
Populate elements and components based on chemical_composition
ka-sarthak May 30, 2024
0c8f116
Add overwrite_quantity in merge_sections
ka-sarthak May 30, 2024
fe05373
Include merge section capability to allow GUI interaction in `compone…
ka-sarthak May 30, 2024
9e50ae3
Restrict component class to `PureSubstanceComponent`
ka-sarthak May 30, 2024
932f738
Move material system as sub-section in TransmissionSample
ka-sarthak Jul 2, 2024
ebf1c06
Add module for material_system and classes for Solid Solution
ka-sarthak Jul 2, 2024
5c83255
Create TransmissionSampleReference class and use it in samples subsec…
ka-sarthak Jul 2, 2024
7acdaf0
Make SolidSolution as an entry class; reference it in TransmissionSample
ka-sarthak Jul 2, 2024
69b8408
Bugfix: logic of adjusting composition
ka-sarthak Jul 2, 2024
f432cd1
Rearrange imports
ka-sarthak Jul 3, 2024
45d29cc
Add physical properties classes
ka-sarthak Jul 3, 2024
b3a5f78
Refactor Transmission sample to be a section containing reference and…
ka-sarthak Jul 3, 2024
b21f99f
Fixing rebase
ka-sarthak Aug 28, 2024
c977b10
Changing warn to warning
ka-sarthak Aug 28, 2024
c6ddb2e
Move Physical properties to schema
ka-sarthak Aug 29, 2024
71617fc
Rename section names; add docstring for naming convention
ka-sarthak Aug 29, 2024
2ffba2f
Add crystal, polycrystal, mixed crystal, mixed polycrystal sections
ka-sarthak Aug 29, 2024
0d3dba3
Ruff
ka-sarthak Aug 29, 2024
550739f
Add material system entry point; rename dopant as impurity
ka-sarthak Aug 30, 2024
a1e7f7e
Refine the ELN properties of sample related schemas
ka-sarthak Sep 3, 2024
a4d3af1
Refine ELN properties for material system; make atomic percentage in …
ka-sarthak Sep 3, 2024
ca31aba
Remove materials_system: they will be moved to nomad-material-processing
ka-sarthak Sep 3, 2024
40afb79
Align TransmissionSampleReference with CompositeSystemReference
ka-sarthak Sep 9, 2024
8e11830
Compose a Sample class based on composite system
ka-sarthak Sep 9, 2024
c5f85f2
Refactor extinction coefficient calc and plot
ka-sarthak Sep 9, 2024
14f8202
Temporary bugfix for extinction coeff calc; minor changes in schema
ka-sarthak Sep 10, 2024
fa015fd
Update nomad
ka-sarthak Sep 10, 2024
ab6d39d
Bugfix schema import; ignore search when in client context
ka-sarthak Sep 10, 2024
0727e60
Add caplog conftest
ka-sarthak Sep 10, 2024
99cdb6c
Bugfix: updating schema in search_quantities
ka-sarthak Sep 10, 2024
d0b91b8
Add aliases
ka-sarthak Sep 10, 2024
f660591
Add previous archives to test for backward compatibility
ka-sarthak Sep 10, 2024
cd3b517
Add test for backward compatibility
ka-sarthak Sep 10, 2024
d877d54
Add fixes for backward compatibility
ka-sarthak Sep 10, 2024
4b6a549
Move RawFileTransmissionData to schema
ka-sarthak Sep 10, 2024
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Original file line number Diff line number Diff line change
Expand Up @@ -19,13 +19,15 @@ classifiers = [
"License :: OSI Approved :: Apache Software License",
]
dependencies = [
"nomad-lab>=1.2.2dev578",
"nomad-lab>=1.3.4dev",
"nomad-material-processing"
]
[project.optional-dependencies]
dev = [
"ruff",
"pytest",
"structlog",
"nomad-lab[infrastructure]>=1.3.4dev",
]

[project.license]
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@ def load(self):
description='Schema for data from Transmission Spectrophotometry.',
)


parser = TransmissionParserEntryPoint(
name='Transmission Parser',
description='Parser for data from Transmission Spectrophotometry.',
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Original file line number Diff line number Diff line change
Expand Up @@ -17,18 +17,9 @@
#
from typing import TYPE_CHECKING

from nomad.datamodel.data import (
EntryData,
)
from nomad.datamodel.metainfo.annotations import (
ELNAnnotation,
)
from nomad.metainfo import (
Quantity,
)
from nomad.parsing import MatchingParser

from transmission.schema import ELNUVVisTransmission
from transmission.schema import ELNUVVisNirTransmission, RawFileTransmissionData
from transmission.utils import create_archive

if TYPE_CHECKING:
Expand All @@ -37,19 +28,6 @@
)


class RawFileTransmissionData(EntryData):
"""
Section for a Transmission Spectrophotometry data file.
"""

measurement = Quantity(
type=ELNUVVisTransmission,
a_eln=ELNAnnotation(
component='ReferenceEditQuantity',
),
)


class TransmissionParser(MatchingParser):
"""
Parser for matching files from Transmission Spectrophotometry and
Expand All @@ -60,7 +38,9 @@ def parse(
self, mainfile: str, archive: 'EntryArchive', logger=None, child_archives=None
) -> None:
data_file = mainfile.split('/')[-1]
entry = ELNUVVisTransmission.m_from_dict(ELNUVVisTransmission.m_def.a_template)
entry = ELNUVVisNirTransmission.m_from_dict(
ELNUVVisNirTransmission.m_def.a_template
)
entry.data_file = data_file
file_name = f'{".".join(data_file.split(".")[:-1])}.archive.json'
archive.data = RawFileTransmissionData(
Expand Down
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