Reformatting according to Black

Changed from Autopep to Black :-)
EnzymeML · Mar 3, 2022 · ae2c946 · ae2c946
1 parent 1965b70
commit ae2c946
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Showing 28 changed files with 912 additions and 1,265 deletions.
diff --git a/pyenzyme/__init__.py b/pyenzyme/__init__.py
@@ -1,4 +1,4 @@
-'''
+"""
 File: __init__.py
 Project: pyenzyme
 Author: Jan Range
@@ -8,7 +8,7 @@
 Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
 -----
 Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-'''
+"""
 
 from pyenzyme.enzymeml.core import EnzymeMLDocument
 from pyenzyme.enzymeml.core import Vessel

diff --git a/pyenzyme/enzymeml/core/__init__.py b/pyenzyme/enzymeml/core/__init__.py
@@ -1,4 +1,4 @@
-'''
+"""
 File: __init__.py
 Project: core
 Author: Jan Range
@@ -8,7 +8,7 @@
 Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
 -----
 Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-'''
+"""
 
 from pyenzyme.enzymeml.core.creator import Creator
 from pyenzyme.enzymeml.core.enzymemldocument import EnzymeMLDocument

diff --git a/pyenzyme/enzymeml/core/abstract_classes.py b/pyenzyme/enzymeml/core/abstract_classes.py
@@ -1,4 +1,4 @@
-'''
+"""
 File: creator.py
 Project: core
 Author: Jan Range
@@ -8,7 +8,7 @@
 Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
 -----
 Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-'''
+"""
 
 from pydantic import BaseModel, PrivateAttr, validator
 from typing import Optional
@@ -58,7 +58,5 @@ class AbstractSpeciesFactory(ABC):
     enzymeml_part: str
 
     @abstractmethod
-    def get_species(
-        self, **kwargs
-    ) -> AbstractSpecies:
+    def get_species(self, **kwargs) -> AbstractSpecies:
         """Return a new species object"""
diff --git a/pyenzyme/enzymeml/core/complex.py b/pyenzyme/enzymeml/core/complex.py
@@ -1,4 +1,4 @@
-'''
+"""
 File: complex.py
 Project: core
 Author: Jan Range
@@ -8,7 +8,7 @@
 Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
 -----
 Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-'''
+"""
 
 import re
 
@@ -46,13 +46,11 @@ class Complex(EnzymeMLBase, AbstractSpecies):
     vessel_id: str = Field(
         ...,
         description="Identifier of the vessel in which the protein was stored.",
-        regex=r"v[\d]+"
+        regex=r"v[\d]+",
     )
 
     init_conc: Optional[float] = Field(
-        None,
-        description="Initial concentration of the protein.",
-        inclusiveMinimum=0.0
+        None, description="Initial concentration of the protein.", inclusiveMinimum=0.0
     )
 
     unit: Optional[str] = Field(
@@ -71,9 +69,7 @@ class Complex(EnzymeMLBase, AbstractSpecies):
     )
 
     id: Optional[str] = Field(
-        None,
-        description="Unique identifier of the protein.",
-        regex=r"c[\d]+"
+        None, description="Unique identifier of the protein.", regex=r"c[\d]+"
     )
 
     boundary: bool = Field(

diff --git a/pyenzyme/enzymeml/core/creator.py b/pyenzyme/enzymeml/core/creator.py
@@ -1,4 +1,4 @@
-'''
+"""
 File: creator.py
 Project: core
 Author: Jan Range
@@ -8,17 +8,14 @@
 Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
 -----
 Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-'''
+"""
 
 from pydantic import Field, validator, ValidationError
 from typing import TYPE_CHECKING, Optional
 from dataclasses import dataclass
 
 from pyenzyme.enzymeml.core.enzymemlbase import EnzymeMLBase
-from pyenzyme.enzymeml.core.utils import (
-    type_checking,
-    deprecated_getter
-)
+from pyenzyme.enzymeml.core.utils import type_checking, deprecated_getter
 
 if TYPE_CHECKING:  # pragma: no cover
     static_check_init_args = dataclass
@@ -31,23 +28,21 @@ class Creator(EnzymeMLBase):
 
     given_name: str = Field(
         ...,
-        description='Given name of the author or contributor.',
+        description="Given name of the author or contributor.",
     )
 
     family_name: str = Field(
         ...,
-        description='Family name of the author or contributor.',
+        description="Family name of the author or contributor.",
     )
 
     mail: str = Field(
         ...,
-        description='Email address of the author or contributor.',
+        description="Email address of the author or contributor.",
     )
 
     id: Optional[str] = Field(
-        None,
-        description="Unique identifier of the protein.",
-        regex=r"a[\d]+"
+        None, description="Unique identifier of the protein.", regex=r"a[\d]+"
     )
 
     @validator("given_name", "family_name", "mail", pre=True)
@@ -62,9 +57,7 @@ def check_empty_strings(cls, value):
     @validator("mail")
     def check_mail_consistency(cls, mail):
         if len(mail.split("@")) != 2:
-            raise ValueError(
-                f"{mail} is not a valid mail adress."
-            )
+            raise ValueError(f"{mail} is not a valid mail adress.")
 
         return mail
 

diff --git a/pyenzyme/enzymeml/core/enzymemlbase.py b/pyenzyme/enzymeml/core/enzymemlbase.py
@@ -1,4 +1,4 @@
-'''
+"""
 File: baseclass.py
 Project: core
 Author: Jan Range
@@ -8,7 +8,7 @@
 Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
 -----
 Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-'''
+"""
 
 import json
 import logging
@@ -32,39 +32,47 @@ def json(self, indent: int = 2, **kwargs):
                 "log": ...,
                 "unit_dict": ...,
                 "file_dict": ...,
-                "protein_dict":
-                    {
-                        "Protein": {"__all__": {"_unit_id"}}
-                    }
+                "protein_dict": {"Protein": {"__all__": {"_unit_id"}}},
             },
             by_alias=True,
             **kwargs
         )
 
     @classmethod
     def fromJSON(cls, json_string):
-        return cls.parse_obj(
-            json.loads(json_string)
-        )
+        return cls.parse_obj(json.loads(json_string))
 
     def __setattr__(self, name, value):
         """Modified attribute setter to document changes in the EnzymeML document"""
         old_value = getattr(self, name)
 
-        if isinstance(old_value, list) is False and name.startswith("_") is False and name != "id" and old_value:
+        if (
+            isinstance(old_value, list) is False
+            and name.startswith("_") is False
+            and name != "id"
+            and old_value
+        ):
 
             if type(self).__name__ != "EnzymeMLDocument":
 
                 try:
                     log_change(
-                        logger, type(self).__name__, getattr(self, 'id'),
-                        name, old_value, value
+                        logger,
+                        type(self).__name__,
+                        getattr(self, "id"),
+                        name,
+                        old_value,
+                        value,
                     )
 
                 except AttributeError:
                     log_change(
-                        logger, type(self).__name__, self.get_id(),
-                        name, old_value, value
+                        logger,
+                        type(self).__name__,
+                        self.get_id(),
+                        name,
+                        old_value,
+                        value,
                     )
 
         super().__setattr__(name, value)