Various bug fixes, delete template schema and parser

pyproject.toml

@@ -112,10 +112,9 @@ package-dir = { "" = "src" }
 where = ["src"]
 
 [project.entry-points.'nomad.plugin']
-myparser = "nomad_uibk_plugin.parsers:myparser"
-mypackage = "nomad_uibk_plugin.schema_packages:mypackage"
-microcellschema = "nomad_uibk_plugin.schema_packages:microcellschema"
+# schema
 xrfschema = "nomad_uibk_plugin.schema_packages:xrfschema"
-xrfparser = "nomad_uibk_plugin.parsers:xrfparser"
 sputtering = "nomad_uibk_plugin.schema_packages:sputtering"
 sample = "nomad_uibk_plugin.schema_packages:sample"
+# parser
+xrfparser = "nomad_uibk_plugin.parsers:xrfparser"

src/nomad_uibk_plugin/parsers/__init__.py

@@ -1,21 +1,4 @@
 from nomad.config.models.plugins import ParserEntryPoint
-from pydantic import Field
-
-
-class MyParserEntryPoint(ParserEntryPoint):
-    parameter: int = Field(0, description='Custom configuration parameter')
-
-    def load(self):
-        from nomad_uibk_plugin.parsers.myparser import MyParser
-
-        return MyParser(**self.dict())
-
-
-myparser = MyParserEntryPoint(
-    name='MyParser',
-    description='Parser defined using the new plugin mechanism.',
-    mainfile_name_re='.*\.myparser',
-)
 
 
 class XRFParserEntryPoint(ParserEntryPoint):
@@ -33,6 +16,6 @@ def load(self):
 xrfparser = XRFParserEntryPoint(
     name='XRFParser',
     description='XRF Parser for UIBK .txt files.',
-    mainfile_name_re='.*\.txt',
-    mainfile_content_re='PositionType\s+Application\s+Sample\s+name\s+Date\s+\n[A-Z0-9-]+\s+Quant\s+analysis',
+    mainfile_name_re=r'.*\.txt',
+    mainfile_content_re=r'PositionType\s+Application\s+Sample\s+name\s+Date\s+\n[A-Z0-9-]+\s+Quant\s+analysis',
 )

src/nomad_uibk_plugin/schema_packages/XRFreader.py

@@ -30,12 +30,12 @@
 
 
 def group_composition_into_layers(
-        layers: dict = {},
-        names: list = [],
-        values: list = [],
-        units: list = [],
-        logger: 'BoundLogger' = None,
-    ) -> dict:
+    layers: dict = {},
+    names: list = [],
+    values: list = [],
+    units: list = [],
+    logger: 'BoundLogger' = None,
+) -> dict:
     """
     Function for grouping the composition data into layers.
 
@@ -69,16 +69,15 @@ def group_composition_into_layers(
             if unit == 'mass%':
                 layers[current_layer]['elements'][name] = dict(mass_fraction=value)
             elif unit == 'at%':
-                layers[current_layer]['elements'][name] = dict(
-                    atomic_fraction=value
-                )
+                layers[current_layer]['elements'][name] = dict(atomic_fraction=value)
             elif logger is not None:
                 logger.warn(
                     'read_UIBK_txt found unknown unit "{unit}" '
                     'in file: "{file_path}"'
                 )
     return layers
 
+
 def sort_intensity_values_into_layers(  # noqa: PLR0913
     layers: dict = {},
     int_peak_elements: list = [],
@@ -133,6 +132,7 @@ def sort_intensity_values_into_layers(  # noqa: PLR0913
 
     return layers
 
+
 def read_xrf_txt(file_path: str, logger: 'BoundLogger' = None) -> dict[str, Any]:  # noqa: PLR0915, PLR0912
     """
     Function for reading the X-ray fluorescence data in a UIBK `.txt` file.
@@ -156,9 +156,11 @@ def read_xrf_txt(file_path: str, logger: 'BoundLogger' = None) -> dict[str, Any]
         if len(measurement) > 100:  # noqa: PLR2004
             # Try to match meta information
             meta_match = re.search(
-                (r'PositionType\s+Application\s+Sample name\s+Date\s+(\S+)\s+'
-                 r'Quant analysis\s+(\S+(?:\s\S+)*)\s+(\S+)\s+'
-                 r'(\d{4}-\s*\d{1,2}-\s*\d{1,2}\s+\d{1,2}:\d{2})'),
+                (
+                    r'PositionType\s+Application\s+Sample name\s+Date\s+(\S+)\s+'
+                    r'Quant analysis\s+(\S+(?:\s\S+)*)\s+(\S+)\s+'
+                    r'(\d{4}-\s*\d{1,2}-\s*\d{1,2}\s+\d{1,2}:\d{2})'
+                ),
                 measurement,
             )
 

src/nomad_uibk_plugin/schema_packages/__init__.py

@@ -12,21 +12,6 @@ class UIBKCategory(EntryDataCategory):
     m_def = Category(label='UIBK', categories=[EntryDataCategory])
 
 
-class MySchemaPackageEntryPoint(SchemaPackageEntryPoint):
-    parameter: int = Field(0, description='Custom configuration parameter')
-
-    def load(self):
-        from nomad_uibk_plugin.schema_packages.mypackage import m_package
-
-        return m_package
-
-
-mypackage = MySchemaPackageEntryPoint(
-    name='MyPackage',
-    description='Schema package defined using the new plugin mechanism.',
-)
-
-
 class XRFSchemaPackageEntryPoint(SchemaPackageEntryPoint):
     parameter: int = Field(0, description='Custom configuration parameter')
 
@@ -55,17 +40,17 @@ def load(self):
 )
 
 
-class MicroCellSchemaPackageEntryPoint(SchemaPackageEntryPoint):
-    def load(self):
-        from nomad_uibk_plugin.schema_packages.microcellschema import m_package
+# class MicroCellSchemaPackageEntryPoint(SchemaPackageEntryPoint):
+#     def load(self):
+#         from nomad_uibk_plugin.schema_packages.microcellschema import m_package
 
-        return m_package
+#         return m_package
 
 
-microcellschema = MicroCellSchemaPackageEntryPoint(
-    name='MicroCellSchema',
-    description='MicroCell Schema package defined using the new plugin mechanism.',
-)
+# microcellschema = MicroCellSchemaPackageEntryPoint(
+#     name='MicroCellSchema',
+#     description='MicroCell Schema package defined using the new plugin mechanism.',
+# )
 
 
 class SampleSchemaPackageEntryPoint(SchemaPackageEntryPoint):

src/nomad_uibk_plugin/schema_packages/sample.py

@@ -9,13 +9,14 @@
     CompositeSystem,  # CompositeSystemReference
 )
 from nomad.datamodel.metainfo.plot import PlotlyFigure, PlotSection
-from nomad.metainfo import Quantity, Section, SubSection
+from nomad.metainfo import Quantity, SchemaPackage, Section, SubSection
 
 if TYPE_CHECKING:
     from nomad.datamodel.datamodel import EntryArchive
     from structlog.stdlib import BoundLogger
 
-from itertools import product
+
+m_package = SchemaPackage(name='nomad_uibk_sample')
 
 
 class MicroCell(CompositeSystem):
@@ -130,3 +131,6 @@ def normalize(self, archive, logger):
         super().normalize(archive, logger)
         self.figures = []
         self.plot(archive, logger)
+
+
+m_package.__init_metainfo__()

src/nomad_uibk_plugin/schema_packages/sputtering.py

@@ -14,18 +14,21 @@
     #  MEnum,
     Datetime,
     Quantity,
+    #  SectionProxy,
+    SchemaPackage,
     #  Package,
     Section,
     # MSection,
     SubSection,
-    #  SectionProxy,
 )
 from nomad_material_processing.vapor_deposition.pvd.general import PVDSource
 from nomad_material_processing.vapor_deposition.pvd.sputtering import SputterDeposition
 
 from nomad_uibk_plugin.schema_packages import UIBKCategory
 from nomad_uibk_plugin.schema_packages.sample import UIBKSample
 
+m_package = SchemaPackage(name='nomad_uibk_sputtering')
+
 
 class Target(PVDSource, EntryData):
     """
@@ -70,7 +73,9 @@ class Target(PVDSource, EntryData):
     )
     internal_name = Quantity(
         type=str,
-        description='Common name of the target. Usually the (simplified) elements and ID',
+        description=(
+            'Common name of the target. ' 'Usually the (simplified) elements and ID'
+        ),
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.StringEditQuantity,
         ),
@@ -103,7 +108,7 @@ class Target(PVDSource, EntryData):
     composition = Quantity(
         type=ElementalComposition,
         description='Composition of the target as stated by the manufacturer',
-        #a_eln=ELNAnnotation(component=ELNComponentEnum.element),
+        # a_eln=ELNAnnotation(component=ELNComponentEnum.element),
         repeatable=True,
     )
     thickness_total = Quantity(
@@ -316,4 +321,7 @@ class UIBKSputterDeposition(SputterDeposition, EntryData):
 
     target = SubSection(section_def=TargetReference, repeats=True)
 
-    parameter = SubSection()
+    # parameter = SubSection()
+
+
+m_package.__init_metainfo__()