Fix #21

.github/workflows/build.yml

@@ -1,36 +1,34 @@
-
 name: Build and Test
 
 on: [push]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.9, '3.10']
+        python-version: ['3.7', '3.8', 3.9', '3.10']
 
     steps:
-    - name: Checkout
-      uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python3 -m pip install --upgrade pip
-        pip3 install python-copasi
-        pip3 install -e .[test]
-    - name: Test with pytest
-      run: |
-        python3 -m pytest
-    - name: Lint with flake8
-      run: |
-        pip install flake8
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=13 --max-line-length=127 --statistics
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          pip3 install python-copasi
+          pip3 install -e .[test]
+      - name: Test with pytest
+        run: |
+          python3 -m pytest
+      - name: Lint with flake8
+        run: |
+          pip install flake8
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=13 --max-line-length=127 --statistics

pyenzyme/enzymeml/core/__init__.py

@@ -1,25 +1,25 @@
-'''
-File: __init__.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Tuesday June 15th 2021 7:32:36 pm
-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
-from pyenzyme.enzymeml.core.protein import Protein
-from pyenzyme.enzymeml.core.complex import Complex
-from pyenzyme.enzymeml.core.reactant import Reactant
-from pyenzyme.enzymeml.core.replicate import Replicate
-from pyenzyme.enzymeml.core.unitdef import UnitDef
-from pyenzyme.enzymeml.core.vessel import Vessel
-from pyenzyme.enzymeml.core.enzymereaction import EnzymeReaction
-from pyenzyme.enzymeml.core.enzymemlbase import EnzymeMLBase
-from pyenzyme.enzymeml.core.measurementData import MeasurementData
-from pyenzyme.enzymeml.core.measurement import Measurement
-from pyenzyme.enzymeml.core.ontology import SBOTerm, DataTypes
+'''
+File: __init__.py
+Project: core
+Author: Jan Range
+License: BSD-2 clause
+-----
+Last Modified: Tuesday June 15th 2021 7:32:36 pm
+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
+from pyenzyme.enzymeml.core.protein import Protein
+from pyenzyme.enzymeml.core.complex import Complex
+from pyenzyme.enzymeml.core.reactant import Reactant
+from pyenzyme.enzymeml.core.replicate import Replicate
+from pyenzyme.enzymeml.core.unitdef import UnitDef
+from pyenzyme.enzymeml.core.vessel import Vessel
+from pyenzyme.enzymeml.core.enzymereaction import EnzymeReaction
+from pyenzyme.enzymeml.core.enzymemlbase import EnzymeMLBase
+from pyenzyme.enzymeml.core.measurementData import MeasurementData
+from pyenzyme.enzymeml.core.measurement import Measurement
+from pyenzyme.enzymeml.core.ontology import SBOTerm, DataTypes

pyenzyme/enzymeml/core/complex.py

@@ -13,7 +13,7 @@
 import re
 
 from pydantic import validator, Field
-from typing import Optional, TYPE_CHECKING
+from typing import List, Optional, TYPE_CHECKING
 from dataclasses import dataclass
 
 from pyenzyme.enzymeml.core.enzymemlbase import EnzymeMLBase
@@ -38,7 +38,7 @@ class Complex(EnzymeMLBase, AbstractSpecies):
         description="Name of the complex",
     )
 
-    participants: list[str] = Field(
+    participants: List[str] = Field(
         default_factory=list,
         description="Array of IDs the complex contains",
     )
@@ -108,7 +108,7 @@ def set_meta_id(cls, id: Optional[str], values: dict):
         return id
 
     @validator("participants")
-    def check_reactant_ids(cls, ids: list[str]):
+    def check_reactant_ids(cls, ids: List[str]):
         """Checks ID consistency for reactants"""
 
         for id in ids:

pyenzyme/enzymeml/core/creator.py

@@ -1,81 +1,81 @@
-'''
-File: creator.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Tuesday June 15th 2021 6:28:16 pm
-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
-)
-
-if TYPE_CHECKING:  # pragma: no cover
-    static_check_init_args = dataclass
-else:
-    static_check_init_args = type_checking
-
-
-@static_check_init_args
-class Creator(EnzymeMLBase):
-
-    given_name: str = Field(
-        ...,
-        description='Given name of the author or contributor.',
-    )
-
-    family_name: str = Field(
-        ...,
-        description='Family name of the author or contributor.',
-    )
-
-    mail: str = Field(
-        ...,
-        description='Email address of the author or contributor.',
-    )
-
-    id: Optional[str] = Field(
-        None,
-        description="Unique identifier of the protein.",
-        regex=r"a[\d]+"
-    )
-
-    @validator("given_name", "family_name", "mail", pre=True)
-    def check_empty_strings(cls, value):
-        if not value:
-            raise ValueError(
-                "An empty string has been provided. Please make sure to provide a valid string."
-            )
-
-        return value
-
-    @validator("mail")
-    def check_mail_consistency(cls, mail):
-        if len(mail.split("@")) != 2:
-            raise ValueError(
-                f"{mail} is not a valid mail adress."
-            )
-
-        return mail
-
-    @deprecated_getter("family_name")
-    def getFname(self) -> str:
-        return self.family_name
-
-    @deprecated_getter("given_name")
-    def getGname(self) -> str:
-        return self.given_name
-
-    @deprecated_getter("mail")
-    def getMail(self) -> str:
-        return self.mail
+'''
+File: creator.py
+Project: core
+Author: Jan Range
+License: BSD-2 clause
+-----
+Last Modified: Tuesday June 15th 2021 6:28:16 pm
+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
+)
+
+if TYPE_CHECKING:  # pragma: no cover
+    static_check_init_args = dataclass
+else:
+    static_check_init_args = type_checking
+
+
+@static_check_init_args
+class Creator(EnzymeMLBase):
+
+    given_name: str = Field(
+        ...,
+        description='Given name of the author or contributor.',
+    )
+
+    family_name: str = Field(
+        ...,
+        description='Family name of the author or contributor.',
+    )
+
+    mail: str = Field(
+        ...,
+        description='Email address of the author or contributor.',
+    )
+
+    id: Optional[str] = Field(
+        None,
+        description="Unique identifier of the protein.",
+        regex=r"a[\d]+"
+    )
+
+    @validator("given_name", "family_name", "mail", pre=True)
+    def check_empty_strings(cls, value):
+        if not value:
+            raise ValueError(
+                "An empty string has been provided. Please make sure to provide a valid string."
+            )
+
+        return value
+
+    @validator("mail")
+    def check_mail_consistency(cls, mail):
+        if len(mail.split("@")) != 2:
+            raise ValueError(
+                f"{mail} is not a valid mail adress."
+            )
+
+        return mail
+
+    @deprecated_getter("family_name")
+    def getFname(self) -> str:
+        return self.family_name
+
+    @deprecated_getter("given_name")
+    def getGname(self) -> str:
+        return self.given_name
+
+    @deprecated_getter("mail")
+    def getMail(self) -> str:
+        return self.mail