generated with non-strict float parsing in python, updated generator to 7.7.0

Author: mfleisch

.updater/config/Python/config.json

@@ -1,5 +1,6 @@
 {
 	"packageName" : "PySirius",
 	"packageVersion" : "6.0.2",
-	"mapNumberTo" : "float"
+	"mapNumberTo" : "float",
+	"hideGenerationTimestamp": true
 }

.updater/config/R/config.json

@@ -2,5 +2,6 @@
 	"packageName" : "Rsirius",
 	"generateWrapper": true,
 	"library": "httr2",
-	"packageVersion": "6.0.2"
+	"packageVersion": "6.0.2",
+	"hideGenerationTimestamp": true
 }

.updater/openapi_generator/version

@@ -1 +1 @@
-7.6.0
+7.7.0

client-api_python/generated/.openapi-generator/FILES

@@ -229,109 +229,4 @@ setup.cfg
 setup.py
 test-requirements.txt
 test/__init__.py
-test/test_account_credentials.py
-test/test_account_info.py
-test/test_actuator_api.py
-test/test_aligned_feature.py
-test/test_aligned_feature_opt_field.py
-test/test_aligned_feature_quality.py
-test/test_annotated_ms_ms_data.py
-test/test_annotated_peak.py
-test/test_annotated_spectrum.py
-test/test_annotation.py
-test/test_axes.py
-test/test_background_computations_state_event.py
-test/test_basic_spectrum.py
-test/test_binary_fingerprint.py
-test/test_canopus.py
-test/test_canopus_prediction.py
-test/test_category.py
-test/test_compound.py
-test/test_compound_class.py
-test/test_compound_class_type.py
-test/test_compound_classes.py
-test/test_compound_import.py
-test/test_compound_opt_field.py
-test/test_compounds_api.py
-test/test_confidence_mode.py
-test/test_connection_check.py
-test/test_connection_error.py
-test/test_consensus_annotations_csi.py
-test/test_consensus_annotations_de_novo.py
-test/test_consensus_criterion_csi.py
-test/test_consensus_criterion_de_novo.py
-test/test_data_quality.py
-test/test_db_link.py
-test/test_deviation.py
-test/test_experimental_api.py
-test/test_feature_annotations.py
-test/test_feature_import.py
-test/test_features_api.py
-test/test_fingerprint_prediction.py
-test/test_formula_candidate.py
-test/test_formula_candidate_opt_field.py
-test/test_fragment_node.py
-test/test_fragmentation_tree.py
-test/test_gui_api.py
-test/test_gui_info.py
-test/test_import_result.py
-test/test_info.py
-test/test_info_api.py
-test/test_instrument_profile.py
-test/test_isotope_pattern_annotation.py
-test/test_item.py
-test/test_job.py
-test/test_job_opt_field.py
-test/test_job_progress.py
-test/test_job_submission.py
-test/test_jobs_api.py
-test/test_lcms_submission_parameters.py
-test/test_license_info.py
-test/test_lipid_annotation.py
-test/test_login_and_account_api.py
-test/test_loss_edge.py
-test/test_ms_data.py
-test/test_ms_novelist.py
-test/test_page_aligned_feature.py
-test/test_page_compound.py
-test/test_page_formula_candidate.py
-test/test_page_job.py
-test/test_page_spectral_library_match.py
-test/test_page_structure_candidate_formula.py
-test/test_page_structure_candidate_scored.py
-test/test_pageable_object.py
-test/test_parent_peak.py
-test/test_peak_annotation.py
-test/test_project_change_event.py
-test/test_project_info.py
-test/test_project_info_opt_field.py
-test/test_projects_api.py
-test/test_quantification_table.py
-test/test_searchable_database.py
-test/test_searchable_database_parameters.py
-test/test_searchable_databases_api.py
-test/test_simple_peak.py
-test/test_sirius.py
-test/test_sort_object.py
-test/test_spectral_library_match.py
-test/test_spectral_library_match_opt_field.py
-test/test_spectral_library_match_summary.py
-test/test_spectral_library_search.py
-test/test_spectral_matching_type.py
-test/test_spectrum_annotation.py
-test/test_structure_candidate.py
-test/test_structure_candidate_formula.py
-test/test_structure_candidate_opt_field.py
-test/test_structure_candidate_scored.py
-test/test_structure_db_search.py
-test/test_subscription.py
-test/test_subscription_consumables.py
-test/test_term.py
-test/test_timeout.py
-test/test_trace.py
-test/test_trace_set.py
-test/test_use_heuristic.py
-test/test_zodiac.py
-test/test_zodiac_edge_filter_thresholds.py
-test/test_zodiac_epochs.py
 tox.ini

client-api_python/generated/.openapi-generator/VERSION

@@ -1 +1 @@
-7.6.0
+7.7.0

client-api_python/generated/PySirius/api/features_api.py

@@ -16,8 +16,8 @@
 from typing import Any, Dict, List, Optional, Tuple, Union
 from typing_extensions import Annotated
 
-from pydantic import Field, StrictFloat, StrictInt, StrictStr, field_validator
-from typing import List, Optional, Union
+from pydantic import Field, StrictInt, StrictStr, field_validator
+from typing import List, Optional
 from typing_extensions import Annotated
 from PySirius.models.aligned_feature import AlignedFeature
 from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField
@@ -7237,7 +7237,7 @@ def get_spectral_library_matches(
         project_id: Annotated[StrictStr, Field(description="project-space to read from.")],
         aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")],
         min_shared_peaks: Optional[StrictInt] = None,
-        min_similarity: Optional[Union[StrictFloat, StrictInt]] = None,
+        min_similarity: Optional[float] = None,
         candidate_in_chi_key: Optional[StrictStr] = None,
         opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None,
         _request_timeout: Union[
@@ -7324,7 +7324,7 @@ def get_spectral_library_matches_with_http_info(
         project_id: Annotated[StrictStr, Field(description="project-space to read from.")],
         aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")],
         min_shared_peaks: Optional[StrictInt] = None,
-        min_similarity: Optional[Union[StrictFloat, StrictInt]] = None,
+        min_similarity: Optional[float] = None,
         candidate_in_chi_key: Optional[StrictStr] = None,
         opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None,
         _request_timeout: Union[
@@ -7411,7 +7411,7 @@ def get_spectral_library_matches_without_preload_content(
         project_id: Annotated[StrictStr, Field(description="project-space to read from.")],
         aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")],
         min_shared_peaks: Optional[StrictInt] = None,
-        min_similarity: Optional[Union[StrictFloat, StrictInt]] = None,
+        min_similarity: Optional[float] = None,
         candidate_in_chi_key: Optional[StrictStr] = None,
         opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None,
         _request_timeout: Union[
@@ -7581,7 +7581,7 @@ def get_spectral_library_matches_paged(
         size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None,
         sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None,
         min_shared_peaks: Optional[StrictInt] = None,
-        min_similarity: Optional[Union[StrictFloat, StrictInt]] = None,
+        min_similarity: Optional[float] = None,
         candidate_in_chi_key: Optional[StrictStr] = None,
         opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None,
         _request_timeout: Union[
@@ -7680,7 +7680,7 @@ def get_spectral_library_matches_paged_with_http_info(
         size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None,
         sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None,
         min_shared_peaks: Optional[StrictInt] = None,
-        min_similarity: Optional[Union[StrictFloat, StrictInt]] = None,
+        min_similarity: Optional[float] = None,
         candidate_in_chi_key: Optional[StrictStr] = None,
         opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None,
         _request_timeout: Union[
@@ -7779,7 +7779,7 @@ def get_spectral_library_matches_paged_without_preload_content(
         size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None,
         sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None,
         min_shared_peaks: Optional[StrictInt] = None,
-        min_similarity: Optional[Union[StrictFloat, StrictInt]] = None,
+        min_similarity: Optional[float] = None,
         candidate_in_chi_key: Optional[StrictStr] = None,
         opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None,
         _request_timeout: Union[
@@ -7971,7 +7971,7 @@ def get_spectral_library_matches_summary(
         project_id: Annotated[StrictStr, Field(description="project-space to read from.")],
         aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")],
         min_shared_peaks: Annotated[Optional[StrictInt], Field(description="min threshold of shared peaks.")] = None,
-        min_similarity: Annotated[Optional[Union[StrictFloat, StrictInt]], Field(description="min spectral similarity threshold.")] = None,
+        min_similarity: Annotated[Optional[float], Field(description="min spectral similarity threshold.")] = None,
         candidate_in_chi_key: Annotated[Optional[StrictStr], Field(description="inchi key of the database compound.")] = None,
         _request_timeout: Union[
             None,
@@ -8054,7 +8054,7 @@ def get_spectral_library_matches_summary_with_http_info(
         project_id: Annotated[StrictStr, Field(description="project-space to read from.")],
         aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")],
         min_shared_peaks: Annotated[Optional[StrictInt], Field(description="min threshold of shared peaks.")] = None,
-        min_similarity: Annotated[Optional[Union[StrictFloat, StrictInt]], Field(description="min spectral similarity threshold.")] = None,
+        min_similarity: Annotated[Optional[float], Field(description="min spectral similarity threshold.")] = None,
         candidate_in_chi_key: Annotated[Optional[StrictStr], Field(description="inchi key of the database compound.")] = None,
         _request_timeout: Union[
             None,
@@ -8137,7 +8137,7 @@ def get_spectral_library_matches_summary_without_preload_content(
         project_id: Annotated[StrictStr, Field(description="project-space to read from.")],
         aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")],
         min_shared_peaks: Annotated[Optional[StrictInt], Field(description="min threshold of shared peaks.")] = None,
-        min_similarity: Annotated[Optional[Union[StrictFloat, StrictInt]], Field(description="min spectral similarity threshold.")] = None,
+        min_similarity: Annotated[Optional[float], Field(description="min spectral similarity threshold.")] = None,
         candidate_in_chi_key: Annotated[Optional[StrictStr], Field(description="inchi key of the database compound.")] = None,
         _request_timeout: Union[
             None,

client-api_python/generated/PySirius/configuration.py

@@ -32,6 +32,9 @@ class Configuration:
     """This class contains various settings of the API client.
 
     :param host: Base url.
+    :param ignore_operation_servers
+      Boolean to ignore operation servers for the API client.
+      Config will use `host` as the base url regardless of the operation servers.
     :param api_key: Dict to store API key(s).
       Each entry in the dict specifies an API key.
       The dict key is the name of the security scheme in the OAS specification.
@@ -54,6 +57,7 @@ class Configuration:
       values before.
     :param ssl_ca_cert: str - the path to a file of concatenated CA certificates
       in PEM format.
+    :param retries: Number of retries for API requests.
 
     """
 
@@ -65,7 +69,11 @@ def __init__(self, host=None,
                  access_token=None,
                  server_index=None, server_variables=None,
                  server_operation_index=None, server_operation_variables=None,
+                 ignore_operation_servers=False,
                  ssl_ca_cert=None,
+                 retries=None,
+                 *,
+                 debug: Optional[bool] = None
                  ) -> None:
         """Constructor
         """
@@ -80,6 +88,9 @@ def __init__(self, host=None,
         self.server_operation_variables = server_operation_variables or {}
         """Default server variables
         """
+        self.ignore_operation_servers = ignore_operation_servers
+        """Ignore operation servers
+        """
         self.temp_folder_path = None
         """Temp file folder for downloading files
         """
@@ -123,7 +134,10 @@ def __init__(self, host=None,
         self.logger_file = None
         """Debug file location
         """
-        self.debug = False
+        if debug is not None:
+            self.debug = debug
+        else:
+            self.__debug = False
         """Debug switch
         """
 
@@ -166,7 +180,7 @@ def __init__(self, host=None,
         self.safe_chars_for_path_param = ''
         """Safe chars for path_param
         """
-        self.retries = None
+        self.retries = retries
         """Adding retries to override urllib3 default value 3
         """
         # Enable client side validation

client-api_python/generated/PySirius/models/aligned_feature.py

@@ -17,8 +17,8 @@
 import re  # noqa: F401
 import json
 
-from pydantic import BaseModel, ConfigDict, Field, StrictBool, StrictFloat, StrictInt, StrictStr
-from typing import Any, ClassVar, Dict, List, Optional, Union
+from pydantic import BaseModel, ConfigDict, Field, StrictBool, StrictInt, StrictStr
+from typing import Any, ClassVar, Dict, List, Optional
 from PySirius.models.data_quality import DataQuality
 from PySirius.models.feature_annotations import FeatureAnnotations
 from PySirius.models.ms_data import MsData
@@ -33,11 +33,11 @@ class AlignedFeature(BaseModel):
     compound_id: Optional[StrictStr] = Field(default=None, alias="compoundId")
     name: Optional[StrictStr] = None
     external_feature_id: Optional[StrictStr] = Field(default=None, description="Externally provided FeatureId (e.g. by some preprocessing tool).  This FeatureId is NOT used by SIRIUS but is stored to ease mapping information back to the source.", alias="externalFeatureId")
-    ion_mass: Optional[Union[StrictFloat, StrictInt]] = Field(default=None, alias="ionMass")
+    ion_mass: Optional[float] = Field(default=None, alias="ionMass")
     charge: StrictInt = Field(description="Ion mode (charge) this feature has been measured in.")
     detected_adducts: List[StrictStr] = Field(description="Adducts of this feature that have been detected during preprocessing.", alias="detectedAdducts")
-    rt_start_seconds: Optional[Union[StrictFloat, StrictInt]] = Field(default=None, alias="rtStartSeconds")
-    rt_end_seconds: Optional[Union[StrictFloat, StrictInt]] = Field(default=None, alias="rtEndSeconds")
+    rt_start_seconds: Optional[float] = Field(default=None, alias="rtStartSeconds")
+    rt_end_seconds: Optional[float] = Field(default=None, alias="rtEndSeconds")
     quality: Optional[DataQuality] = None
     has_ms1: Optional[StrictBool] = Field(default=None, description="If true, the feature has at lease one MS1 spectrum", alias="hasMs1")
     has_ms_ms: Optional[StrictBool] = Field(default=None, description="If true, the feature has at lease one MS/MS spectrum", alias="hasMsMs")

client-api_python/generated/PySirius/models/annotated_peak.py

@@ -17,8 +17,8 @@
 import re  # noqa: F401
 import json
 
-from pydantic import BaseModel, ConfigDict, Field, StrictFloat, StrictInt
-from typing import Any, ClassVar, Dict, List, Optional, Union
+from pydantic import BaseModel, ConfigDict, Field
+from typing import Any, ClassVar, Dict, List, Optional
 from PySirius.models.peak_annotation import PeakAnnotation
 from typing import Optional, Set
 from typing_extensions import Self
@@ -27,8 +27,8 @@ class AnnotatedPeak(BaseModel):
     """
     AnnotatedPeak
     """ # noqa: E501
-    mz: Optional[Union[StrictFloat, StrictInt]] = None
-    intensity: Optional[Union[StrictFloat, StrictInt]] = None
+    mz: Optional[float] = None
+    intensity: Optional[float] = None
     peak_annotation: Optional[PeakAnnotation] = Field(default=None, alias="peakAnnotation")
     __properties: ClassVar[List[str]] = ["mz", "intensity", "peakAnnotation"]
 

client-api_python/generated/PySirius/models/annotated_spectrum.py

@@ -17,8 +17,8 @@
 import re  # noqa: F401
 import json
 
-from pydantic import BaseModel, ConfigDict, Field, StrictFloat, StrictInt, StrictStr
-from typing import Any, ClassVar, Dict, List, Optional, Union
+from pydantic import BaseModel, ConfigDict, Field, StrictInt, StrictStr
+from typing import Any, ClassVar, Dict, List, Optional
 from PySirius.models.annotated_peak import AnnotatedPeak
 from PySirius.models.spectrum_annotation import SpectrumAnnotation
 from typing import Optional, Set
@@ -31,10 +31,10 @@ class AnnotatedSpectrum(BaseModel):
     name: Optional[StrictStr] = Field(default=None, description="Optional Displayable name of this spectrum.")
     ms_level: Optional[StrictInt] = Field(default=None, description="MS level of the measured spectrum.  Artificial spectra with no msLevel (e.g. Simulated Isotope patterns) use null or zero", alias="msLevel")
     collision_energy: Optional[StrictStr] = Field(default=None, description="Collision energy used for MS/MS spectra  Null for spectra where collision energy is not applicable", alias="collisionEnergy")
-    precursor_mz: Optional[Union[StrictFloat, StrictInt]] = Field(default=None, description="Precursor m/z of the MS/MS spectrum  Null for spectra where precursor m/z is not applicable", alias="precursorMz")
+    precursor_mz: Optional[float] = Field(default=None, description="Precursor m/z of the MS/MS spectrum  Null for spectra where precursor m/z is not applicable", alias="precursorMz")
     scan_number: Optional[StrictInt] = Field(default=None, description="Scan number of the spectrum.  Might be null for artificial spectra with no scan number (e.g. Simulated Isotope patterns or merged spectra)", alias="scanNumber")
     peaks: List[AnnotatedPeak] = Field(description="The peaks of this spectrum which might contain additional annotations such as molecular formulas.")
-    abs_intensity_factor: Optional[Union[StrictFloat, StrictInt]] = Field(default=None, description="Factor to convert relative intensities to absolute intensities.  Might be null or 1 for spectra where absolute intensities are not available (E.g. artificial or merged spectra)", alias="absIntensityFactor")
+    abs_intensity_factor: Optional[float] = Field(default=None, description="Factor to convert relative intensities to absolute intensities.  Might be null or 1 for spectra where absolute intensities are not available (E.g. artificial or merged spectra)", alias="absIntensityFactor")
     spectrum_annotation: Optional[SpectrumAnnotation] = Field(default=None, alias="spectrumAnnotation")
     __properties: ClassVar[List[str]] = ["name", "msLevel", "collisionEnergy", "precursorMz", "scanNumber", "peaks", "absIntensityFactor", "spectrumAnnotation"]
 

client-api_python/generated/PySirius/models/axes.py

@@ -17,8 +17,8 @@
 import re  # noqa: F401
 import json
 
-from pydantic import BaseModel, ConfigDict, Field, StrictFloat, StrictInt, StrictStr
-from typing import Any, ClassVar, Dict, List, Optional, Union
+from pydantic import BaseModel, ConfigDict, Field, StrictInt, StrictStr
+from typing import Any, ClassVar, Dict, List, Optional
 from typing import Optional, Set
 from typing_extensions import Self
 
@@ -28,7 +28,7 @@ class Axes(BaseModel):
     """ # noqa: E501
     scan_number: Optional[List[StrictInt]] = Field(default=None, alias="scanNumber")
     scan_ids: Optional[List[StrictStr]] = Field(default=None, alias="scanIds")
-    retention_time_in_seconds: Optional[List[Union[StrictFloat, StrictInt]]] = Field(default=None, alias="retentionTimeInSeconds")
+    retention_time_in_seconds: Optional[List[float]] = Field(default=None, alias="retentionTimeInSeconds")
     __properties: ClassVar[List[str]] = ["scanNumber", "scanIds", "retentionTimeInSeconds"]
 
     model_config = ConfigDict(