nomad-material-processing 0.0.7__tar.gz → 0.0.9__tar.gz

nomad_material_processing-0.0.9/.vscode/settings.json

@@ -0,0 +1,19 @@
+{
+    "python.defaultInterpreterPath": ".pyenv/bin/python",
+    "python.terminal.activateEnvInCurrentTerminal": true,
+    "editor.rulers": [
+        90
+    ],
+    "editor.renderWhitespace": "all",
+    "editor.tabSize": 4,
+    "files.trimTrailingWhitespace": true,
+    "files.watcherExclude": {
+      "${workspaceFolder}/.pyenv/**": true,
+    },
+    "python.testing.unittestEnabled": false,
+    "editor.defaultFormatter": "charliermarsh.ruff",
+    "editor.formatOnSave": true,
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff"
+    },
+}

{nomad-material-processing-0.0.7 → nomad_material_processing-0.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nomad-material-processing
-Version: 0.0.7
+Version: 0.0.9
 Summary: A plugin for NOMAD containing base sections for material processing.
 Author-email: Hampus Näsström <hampus.naesstroem@physik.hu-berlin.de>, Andrea Albino <andrea.albino@physik.hu-berlin.de>, Sebastian Brückner <sebastian.brueckner@ikz-berlin.de>
 License:                                  Apache License

{nomad-material-processing-0.0.7 → nomad_material_processing-0.0.9}/pyproject.toml

@@ -38,6 +38,48 @@ file = "LICENSE"
 "Homepage" = "https://github.com/FAIRmat-NFDI/nomad-material-processing"
 "Bug Tracker" = "https://github.com/FAIRmat-NFDI/nomad-material-processing/issues"
 
+[tool.ruff]
+include = ["src/*.py", "tests/*.py"]
+select = [
+    "E", # pycodestyle
+    "W", # pycodestyle
+    "PL", # pylint
+]
+ignore = [
+    "E501", # Line too long ({width} > {limit} characters)
+    "E701", # Multiple statements on one line (colon)
+    "E731", # Do not assign a lambda expression, use a def
+    "E402",  # Module level import not at top of file
+    "PLR0911", # Too many return statements
+    "PLR0912", # Too many branches
+    "PLR0913", # Too many arguments in function definition
+    "PLR0915", # Too many statements
+    "PLR2004", # Magic value used instead of constant
+    "PLW0603", # Using the global statement
+    "PLW2901", # redefined-loop-name
+    "PLR1714", # consider-using-in
+    "PLR5501", # else-if-used
+]
+fixable = ["ALL"]
+exclude = ["dependencies"]
+
+# Same as Black.
+line-length = 88
+indent-width = 4
+
+[tool.ruff.format]
+# use single quotes for strings.
+quote-style = "single"
+
+# indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
 [tool.setuptools.packages.find]
 where = [
     "src",

{nomad-material-processing-0.0.7 → nomad_material_processing-0.0.9}/src/nomad_material_processing/__init__.py

@@ -51,7 +51,7 @@ if TYPE_CHECKING:
         BoundLogger,
     )
 
-m_package = Package(name="Material Processing")
+m_package = Package(name='Material Processing')
 
 
 class Geometry(ArchiveSection):
@@ -63,11 +63,11 @@ class Geometry(ArchiveSection):
     m_def = Section()
     volume = Quantity(
         type=float,
-        description="The measure of the amount of space occupied in 3D space.",
+        description='The measure of the amount of space occupied in 3D space.',
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.NumberEditQuantity,
         ),
-        unit="meter ** 3",
+        unit='meter ** 3',
     )
 
 
@@ -80,33 +80,33 @@ class Parallelepiped(Geometry):
     m_def = Section()
     height = Quantity(
         type=float,
-        description="The z dimension of the parallelepiped.",
+        description='The z dimension of the parallelepiped.',
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.NumberEditQuantity,
-            defaultDisplayUnit="millimeter",
-            label="Height (z)",
+            defaultDisplayUnit='millimeter',
+            label='Height (z)',
         ),
-        unit="meter",
+        unit='meter',
     )
     width = Quantity(
         type=float,
-        description="The x dimension of the parallelepiped.",
+        description='The x dimension of the parallelepiped.',
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.NumberEditQuantity,
-            defaultDisplayUnit="millimeter",
-            label="Width (x)",
+            defaultDisplayUnit='millimeter',
+            label='Width (x)',
         ),
-        unit="meter",
+        unit='meter',
     )
     length = Quantity(
         type=float,
-        description="The y dimension of the parallelepiped.",
+        description='The y dimension of the parallelepiped.',
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.NumberEditQuantity,
-            defaultDisplayUnit="millimeter",
-            label="Length (y)",
+            defaultDisplayUnit='millimeter',
+            label='Length (y)',
         ),
-        unit="meter",
+        unit='meter',
     )
     surface_area = Quantity(
         type=float,
@@ -116,10 +116,10 @@ class Parallelepiped(Geometry):
         """,
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.NumberEditQuantity,
-            defaultDisplayUnit="millimeter ** 2",
-            label="Surface Area (x*y)",
+            defaultDisplayUnit='millimeter ** 2',
+            label='Surface Area (x*y)',
         ),
-        unit="meter ** 2",
+        unit='meter ** 2',
     )
 
 
@@ -137,27 +137,27 @@ class Miscut(ArchiveSection):
         """,
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.NumberEditQuantity,
-            defaultDisplayUnit="deg",
-            label="Miscut Angle",
+            defaultDisplayUnit='deg',
+            label='Miscut Angle',
         ),
-        unit="deg",
+        unit='deg',
     )
     angle_deviation = Quantity(
         type=float,
-        description="The ± uncertainty in the angular displacement.",
+        description='The ± uncertainty in the angular displacement.',
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.NumberEditQuantity,
-            defaultDisplayUnit="deg",
-            label="± Miscut Angle Deviation",
+            defaultDisplayUnit='deg',
+            label='± Miscut Angle Deviation',
         ),
-        unit="deg",
+        unit='deg',
     )
     orientation = Quantity(
         type=str,
-        description="The direction of the miscut in Miller index, [hkl].",
+        description='The direction of the miscut in Miller index, [hkl].',
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.StringEditQuantity,
-            label="Miscut Orientation [hkl]",
+            label='Miscut Orientation [hkl]',
         ),
     )
 
@@ -170,12 +170,12 @@ class Dopant(ElementalComposition):
 
     doping_level = Quantity(
         type=float,
-        description="The chemical doping level.",
+        description='The chemical doping level.',
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.NumberEditQuantity,
-            defaultDisplayUnit="1 / cm ** 3",
+            defaultDisplayUnit='1 / cm ** 3',
         ),
-        unit="1 / m ** 3",
+        unit='1 / m ** 3',
     )
 
 
@@ -200,7 +200,7 @@ class SubstrateCrystalProperties(CrystalProperties):
         """,
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.StringEditQuantity,
-            label="Substrate Orientation (hkl)",
+            label='Substrate Orientation (hkl)',
         ),
     )
     miscut = SubSection(
@@ -221,25 +221,25 @@ class Substrate(CompositeSystem):
     m_def = Section()
     supplier = Quantity(
         type=str,
-        description="The supplier of the current substrate specimen.",
+        description='The supplier of the current substrate specimen.',
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.StringEditQuantity,
-            label="Name of Supplier",
+            label='Name of Supplier',
         ),
     )
     supplier_id = Quantity(
         type=str,
-        description="An ID string that is unique from the supplier.",
+        description='An ID string that is unique from the supplier.',
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.StringEditQuantity,
-            label="Supplier ID",
+            label='Supplier ID',
         ),
     )
     lab_id = Quantity(
         type=str,
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.StringEditQuantity,
-            label="Substrate ID",
+            label='Substrate ID',
         ),
     )
 
@@ -253,11 +253,11 @@ class CrystallineSubstrate(Substrate):
     m_def = Section()
     geometry = SubSection(
         section_def=Geometry,
-        description="Section containing the geometry of the substrate.",
+        description='Section containing the geometry of the substrate.',
     )
     crystal_properties = SubSection(
         section_def=SubstrateCrystalProperties,
-        description="Section containing the crystal properties of the substrate.",
+        description='Section containing the crystal properties of the substrate.',
     )
     dopants = SubSection(
         section_def=Dopant,
@@ -277,7 +277,7 @@ class ThinFilm(CompositeSystem):
 
     geometry = SubSection(
         section_def=Geometry,
-        description="Section containing the geometry of the thin film.",
+        description='Section containing the geometry of the thin film.',
     )
 
 
@@ -290,14 +290,14 @@ class ThinFilmReference(CompositeSystemReference):
         type=str,
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.StringEditQuantity,
-            label="Thin Film ID",
+            label='Thin Film ID',
         ),
     )
     reference = Quantity(
         type=ThinFilm,
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.ReferenceEditQuantity,
-            label="Thin Film",
+            label='Thin Film',
         ),
     )
 
@@ -311,14 +311,14 @@ class SubstrateReference(CompositeSystemReference):
         type=str,
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.StringEditQuantity,
-            label="Substrate ID",
+            label='Substrate ID',
         ),
     )
     reference = Quantity(
         type=Substrate,
         a_eln=ELNAnnotation(
             component=ELNComponentEnum.ReferenceEditQuantity,
-            label="Substrate",
+            label='Substrate',
         ),
     )
 
@@ -331,7 +331,7 @@ class ThinFilmStack(CompositeSystem):
     m_def = Section(
         a_eln=ELNAnnotation(
             hide=[
-                "components",
+                'components',
             ],
         ),
     )
@@ -351,7 +351,7 @@ class ThinFilmStack(CompositeSystem):
         section_def=SubstrateReference,
     )
 
-    def normalize(self, archive: "EntryArchive", logger: "BoundLogger") -> None:
+    def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
         """
         The normalizer for the `ThinFilmStack` class.
 
@@ -363,7 +363,9 @@ class ThinFilmStack(CompositeSystem):
         self.components = []
         if self.layers:
             self.components = [
-                SystemComponent(system=layer.reference) for layer in self.layers if layer.reference
+                SystemComponent(system=layer.reference)
+                for layer in self.layers
+                if layer.reference
             ]
         if self.substrate.reference:
             self.components.append(SystemComponent(system=self.substrate.reference))
@@ -401,7 +403,7 @@ class SampleDeposition(SynthesisMethod):
     """
 
     m_def = Section(
-        links=["http://purl.obolibrary.org/obo/CHMO_0001310"],
+        links=['http://purl.obolibrary.org/obo/CHMO_0001310'],
     )
 
     def is_serial(self) -> bool:
@@ -418,7 +420,7 @@ class SampleDeposition(SynthesisMethod):
             if step.start_time is None or step.duration is None:
                 return False
             start_times.append(step.start_time.timestamp())
-            durations.append(step.duration.to("s").magnitude)
+            durations.append(step.duration.to('s').magnitude)
         start_times = np.array(start_times)
         durations = np.array(durations)
         end_times = start_times + durations
@@ -427,7 +429,7 @@ class SampleDeposition(SynthesisMethod):
             return False
         return True
 
-    def normalize(self, archive: "EntryArchive", logger: "BoundLogger") -> None:
+    def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
         """
         The normalizer for the `SampleDeposition` class.
 
@@ -450,4 +452,69 @@ class SampleDeposition(SynthesisMethod):
             archive.workflow2.tasks = tasks
 
 
+class TimeSeries(ArchiveSection):
+    """
+    A time series of data during a process step.
+    This is an abstract class and should not be used directly.
+    Instead, it should be derived and the the units of the `value` and `set_value` should
+    be specified.
+
+    For example, a derived class could be `Temperature` with `value` in Kelvin:
+    ```python
+    class Temperature(TimeSeries):
+        value = TimeSeries.value.m_copy()
+        value.unit = "kelvin"
+        set_value = TimeSeries.set_value.m_copy()
+        set_value.unit = "kelvin"
+        set_value.a_eln.defaultDisplayUnit = "celsius"
+    ```
+    """
+
+    m_def = Section(
+        a_plot=dict(
+            # x=['time', 'set_time'],
+            # y=['value', 'set_value'],
+            x='time',
+            y='value',
+        ),
+    )
+    set_value = Quantity(
+        type=float,
+        description='The set value(s) (i.e. the intended values) set.',
+        shape=['*'],
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.NumberEditQuantity,
+            label='Set value',
+        ),
+    )
+    set_time = Quantity(
+        type=float,
+        unit='s',
+        description="""
+        The process time when each of the set values were set.
+        If this is empty and only one set value is present, it is assumed that the value
+        was set at the start of the process step.
+        If two set values are present, it is assumed that a linear ramp between the two
+        values was set.
+        """,
+        shape=['*'],
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.NumberEditQuantity,
+            defaultDisplayUnit='s',
+            label='Set time',
+        ),
+    )
+    value = Quantity(
+        type=float,
+        description='The observed value as a function of time.',
+        shape=['*'],
+    )
+    time = Quantity(
+        type=float,
+        unit='s',
+        description='The process time when each of the values were recorded.',
+        shape=['*'],
+    )
+
+
 m_package.__init_metainfo__()