ms2pip - npm Package Compare versions

Comparing version 4.0.0.dev11 to 4.0.0.dev12

ms2pip.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: ms2pip
-Version: 4.0.0.dev11
+Version: 4.0.0.dev12
 Summary: MS2PIP: Accurate and versatile peptide fragmentation spectrum prediction.
@@ -236,5 +236,5 @@ Author: Ana Sílvia C. Silva
 Requires-Dist: rich>=13
-Requires-Dist: pydantic<2,>=1.10
+Requires-Dist: pydantic>=2
 Requires-Dist: werkzeug>=2
-Requires-Dist: psm_utils>=0.8.0
+Requires-Dist: psm_utils>=0.9
 Requires-Dist: ms2rescore-rs
@@ -241,0 +241,0 @@ Provides-Extra: plotting

ms2pip.egg-info/requires.txt

@@ -11,5 +11,5 @@ numpy<2,>=1.16
 rich>=13
-pydantic<2,>=1.10
+pydantic>=2
 werkzeug>=2
-psm_utils>=0.8.0
+psm_utils>=0.9
 ms2rescore-rs
@@ -16,0 +16,0 @@

ms2pip/__init__.py

 # isort: skip_file
 """MS2PIP: Accurate and versatile peptide fragmentation spectrum prediction."""
 
-__version__ = "4.0.0-dev11"
+__version__ = "4.0.0-dev12"
 
@@ -6,0 +6,0 @@ from warnings import filterwarnings

ms2pip/result.py

@@ -9,3 +9,3 @@ """Definition and handling of MS²PIP results."""
 from psm_utils import PSM
-from pydantic import BaseModel
+from pydantic import ConfigDict, BaseModel
 
@@ -32,6 +32,4 @@ try:
     feature_vectors: Optional[np.ndarray] = None
+    model_config = ConfigDict(arbitrary_types_allowed=True)
 
-    class Config:
-        arbitrary_types_allowed = True
-
     def __init__(__pydantic_self__, **data: Any) -> None:
@@ -38,0 +36,0 @@ """Result of processing a single PSM."""

ms2pip/spectrum.py

@@ -10,3 +10,3 @@ """MS2 spectrum handling."""
 from psm_utils import Peptidoform
-from pydantic import BaseModel, root_validator, validator
+from pydantic import model_validator, field_validator, ConfigDict, BaseModel
 try:
@@ -34,4 +34,3 @@ import spectrum_utils.spectrum as sus
 
-    class Config:
-        arbitrary_types_allowed = True
+    model_config = ConfigDict(arbitrary_types_allowed=True)
 
@@ -75,22 +74,21 @@ def __init__(__pydantic_self__, **data: Any) -> None:
 
-    @root_validator()
-    def check_array_lengths(cls, values):
-        if len(values["mz"]) != len(values["intensity"]):
+    @model_validator(mode="after")
+    @classmethod
+    def check_array_lengths(cls, data: dict):
+        if len(data["mz"]) != len(data["intensity"]):
             raise ValueError("Array lengths do not match.")
-        if values["annotations"] is not None:
-            if len(values["annotations"]) != len(values["intensity"]):
+        if data["annotations"] is not None:
+            if len(data["annotations"]) != len(data["intensity"]):
                 raise ValueError("Array lengths do not match.")
-        return values
+        return data
 
-    @validator("peptidoform")
-    def check_peptidoform(cls, value, values):
-        if not value:
-            pass
+    @field_validator("peptidoform")
+    @classmethod
+    def check_peptidoform(cls, value):
+        if not value or isinstance(value, Peptidoform):
+            return value
         elif isinstance(value, str):
-            value = Peptidoform(value)
-        elif isinstance(value, Peptidoform):
-            pass
+            return Peptidoform(value)
         else:
             raise ValueError("Peptidoform must be a string, a Peptidoform object, or None.")
-        return value
 
@@ -97,0 +95,0 @@ @property

PKG-INFO

 Metadata-Version: 2.1
 Name: ms2pip
-Version: 4.0.0.dev11
+Version: 4.0.0.dev12
 Summary: MS2PIP: Accurate and versatile peptide fragmentation spectrum prediction.
@@ -236,5 +236,5 @@ Author: Ana Sílvia C. Silva
 Requires-Dist: rich>=13
-Requires-Dist: pydantic<2,>=1.10
+Requires-Dist: pydantic>=2
 Requires-Dist: werkzeug>=2
-Requires-Dist: psm_utils>=0.8.0
+Requires-Dist: psm_utils>=0.9
 Requires-Dist: ms2rescore-rs
@@ -241,0 +241,0 @@ Provides-Extra: plotting

pyproject.toml

@@ -46,5 +46,5 @@ [project]
     "rich>=13",
-    "pydantic>=1.10,<2",
+    "pydantic>=2",
     "werkzeug>=2",
-    "psm_utils>=0.8.0",
+    "psm_utils>=0.9",
     "ms2rescore-rs",
@@ -94,3 +94,3 @@ ]
 [tool.cibuildwheel]
-build = "cp3*-manylinux_x86_64 cp3*-win_amd64 cp3*-macosx_x86_64"
+build = "cp3*-manylinux_x86_64 cp3*-win_amd64 cp3*-macosx_x86_64 cp3*-macosx_arm64"
 skip = "cp36-* cp37-* cp312-*"                                    # EOL / no Numpy wheels available yet for Python 3.12
@@ -97,0 +97,0 @@ manylinux-x86_64-image = "manylinux2014"

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Lines of code

3380

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