.

.github/workflows/generate_api.yaml

@@ -1,6 +1,6 @@
 name: Generate API
 
-on: push
+on: pull_request
 
 
 jobs:

chromatopy/core/chromatogram.py

@@ -1,178 +1,105 @@
-import sdRDM
-import validators
+from __future__ import annotations
+
+from datetime import datetime as Datetime
+from typing import TYPE_CHECKING, Dict, List, Optional
+from uuid import uuid4
+
 import numpy as np
 import pandas as pd
 import plotly.graph_objects as go
-from typing import Optional, Union, List, Dict, Set, TYPE_CHECKING
-from uuid import uuid4
-from pydantic import PrivateAttr, Field, field_validator, model_validator
-from pydantic_xml import attr, element, wrapped
+import sdRDM
+from hplc.quant import Chromatogram as hplcChromatogram
 from lxml.etree import _Element
-from sdRDM.base.listplus import ListPlus
-from sdRDM.base.utils import forge_signature
+from pydantic import PrivateAttr, model_validator
+from pydantic_xml import attr, element
+from rich import print
 from sdRDM.base.datatypes import Unit
+from sdRDM.base.listplus import ListPlus
 from sdRDM.tools.utils import elem2dict
-from datetime import datetime as Datetime
-from .signaltype import SignalType
+
 from .peak import Peak
-from __future__ import annotations
-from hplc.quant import Chromatogram as hplcChromatogram
-from rich import print
-from chromatopy.tools.species import Species
+from .signaltype import SignalType
 
 if TYPE_CHECKING:
+    from chromatopy.tools.species import Species
 
 
-class Chromatogram(sdRDM.DataModel,
-
-                search_mode="unordered",
-                ):
-
-
+class Chromatogram(
+    sdRDM.DataModel,
+    search_mode="unordered",
+):
     """"""
 
-
     id: Optional[str] = attr(
-            name="id",
-            alias="@id",
-            description="Unique identifier of the given object.",
-            default_factory=lambda: str(uuid4()),
+        name="id",
+        alias="@id",
+        description="Unique identifier of the given object.",
+        default_factory=lambda: str(uuid4()),
     )
-
 
-
     peaks: List[Peak] = element(
-
-    description="Peaks in the signal",
-
-    default_factory=ListPlus,
-    tag="peaks",
-    json_schema_extra=dict(
-
-
-
-
-
-
-        multiple=True,
-
-
-    ),
+        description="Peaks in the signal",
+        default_factory=ListPlus,
+        tag="peaks",
+        json_schema_extra=dict(
+            multiple=True,
+        ),
     )
 
-
     signals: List[float] = element(
-
-    description="Signal values",
-
-    default_factory=ListPlus,
-    tag="signals",
-    json_schema_extra=dict(
-
-
-
-
-
-
-        multiple=True,
-
-
-    ),
+        description="Signal values",
+        default_factory=ListPlus,
+        tag="signals",
+        json_schema_extra=dict(
+            multiple=True,
+        ),
     )
 
-
     times: List[float] = element(
-
-    description="Time values of the signal",
-
-    default_factory=ListPlus,
-    tag="times",
-    json_schema_extra=dict(
-
-
-
-
-
-
-        multiple=True,
-
-
-    ),
+        description="Time values of the signal",
+        default_factory=ListPlus,
+        tag="times",
+        json_schema_extra=dict(
+            multiple=True,
+        ),
     )
 
-
     time_unit: Optional[Unit] = element(
-
-    description="Unit of time",
-    default=None,
-
-    tag="time_unit",
-    json_schema_extra=dict(
-
-
-
-
-
-    ),
+        description="Unit of time",
+        default=None,
+        tag="time_unit",
+        json_schema_extra=dict(),
     )
 
-
     processed_signal: List[float] = element(
-
-    description="Processed signal values after baseline correction and deconvolution",
-
-    default_factory=ListPlus,
-    tag="processed_signal",
-    json_schema_extra=dict(
-
-
-
-
-
-
-        multiple=True,
-
-
-    ),
+        description="Processed signal values after baseline correction and deconvolution",
+        default_factory=ListPlus,
+        tag="processed_signal",
+        json_schema_extra=dict(
+            multiple=True,
+        ),
     )
 
-
     wavelength: Optional[float] = element(
-
-    description="Wavelength of the signal in nm",
-    default=None,
-
-    tag="wavelength",
-    json_schema_extra=dict(
-
-
-
-
-
-    ),
+        description="Wavelength of the signal in nm",
+        default=None,
+        tag="wavelength",
+        json_schema_extra=dict(),
     )
 
-
     type: Optional[SignalType] = element(
-
-    description="Type of signal",
-    default=None,
-
-    tag="type",
-    json_schema_extra=dict(
-
-
-
-
-
-    ),
+        description="Type of signal",
+        default=None,
+        tag="type",
+        json_schema_extra=dict(),
     )
 
-
-
-    _repo: Optional[str] = PrivateAttr(default="https://github.com/FAIRChemistry/chromatopy")
-    _commit: Optional[str] = PrivateAttr(default="7f6ad248fce5c9df91bc6e91c0d0b2126d8dcee8")
-
+    _repo: Optional[str] = PrivateAttr(
+        default="https://github.com/FAIRChemistry/chromatopy"
+    )
+    _commit: Optional[str] = PrivateAttr(
+        default="7f6ad248fce5c9df91bc6e91c0d0b2126d8dcee8"
+    )
 
     _raw_xml_data: Dict = PrivateAttr(default_factory=dict)
 
@@ -187,24 +114,25 @@ def _parse_raw_xml_data(self):
                 self._raw_xml_data[attr] = elem2dict(value)
 
         return self
+
     def add_to_peaks(
         self,
-        analyte_id: Optional[str] = None ,
-        retention_time: Optional[float] = None ,
-        timestamp: Optional[Datetime] = None ,
-        retention_time_unit: Optional[Unit] = None ,
-        type: Optional[str] = None ,
-        peak_start: Optional[float] = None ,
-        peak_end: Optional[float] = None ,
-        width: Optional[float] = None ,
-        width_unit: Optional[Unit] = None ,
-        area: Optional[float] = None ,
-        area_unit: Optional[Unit] = None ,
-        height: Optional[float] = None ,
-        height_unit: Optional[Unit] = None ,
-        percent_area: Optional[float] = None ,
-        tailing_factor: Optional[float] = None ,
-        separation_factor: Optional[float] = None ,
+        analyte_id: Optional[str] = None,
+        retention_time: Optional[float] = None,
+        timestamp: Optional[Datetime] = None,
+        retention_time_unit: Optional[Unit] = None,
+        type: Optional[str] = None,
+        peak_start: Optional[float] = None,
+        peak_end: Optional[float] = None,
+        width: Optional[float] = None,
+        width_unit: Optional[Unit] = None,
+        area: Optional[float] = None,
+        area_unit: Optional[Unit] = None,
+        height: Optional[float] = None,
+        height_unit: Optional[Unit] = None,
+        percent_area: Optional[float] = None,
+        tailing_factor: Optional[float] = None,
+        separation_factor: Optional[float] = None,
         id: Optional[str] = None,
         **kwargs,
     ) -> Peak:
@@ -259,7 +187,6 @@ def add_to_peaks(
 
         return self.peaks[-1]
 
-
     @classmethod
     def from_csv(cls, path: str, time_unit: Unit) -> "Chromatogram":
         """