From 91102b05d3b1fa2e2cd7f5999120cd3c2608d974 Mon Sep 17 00:00:00 2001
From: Borja Esteban <boressan@outlook.com>
Date: Tue, 15 Nov 2022 10:41:18 +0000
Subject: [PATCH 01/14] add first src file __init__

---
 src/gevopy/__init__.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 src/gevopy/__init__.py

diff --git a/src/gevopy/__init__.py b/src/gevopy/__init__.py
new file mode 100644
index 0000000..e69de29

From 978bca2992da38d2be33d5194fefd1fecb4b4f15 Mon Sep 17 00:00:00 2001
From: Borja Esteban <boressan@outlook.com>
Date: Tue, 15 Nov 2022 11:20:29 +0000
Subject: [PATCH 02/14] add README file

---
 README.md | 136 +++++++++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 134 insertions(+), 2 deletions(-)
 mode change 100644 => 100755 README.md

diff --git a/README.md b/README.md
old mode 100644
new mode 100755
index bdc3a0a..b5b64b4
--- a/README.md
+++ b/README.md
@@ -1,2 +1,134 @@
-# gevopy
-Genetics for Evolutionary Algorithms in Python
+# gevopy
+![qc.sec](https://github.com/BorjaEst/gevopy/actions/workflows/qc-sec.yml/badge.svg)
+![qc.sty](https://github.com/BorjaEst/gevopy/actions/workflows/qc-sty.yml/badge.svg)
+![qc.uni](https://github.com/BorjaEst/gevopy/actions/workflows/qc-uni.yml/badge.svg)
+
+Awesome Genetics for Evolutionary Algorithms library created by Borja Esteban.
+
+## Install it from PyPI
+```bash
+pip install gevopy
+```
+
+## Usage
+This package is designed in order to create your own evolution scripts based on the following concepts:
+ - **Chromosomes**: Genetic instructions for phenotypes.
+ - **Genotype**: Genetic design to instantiate phenotypes.
+ - **Phenotypes**: Genotype instances which perform a task.
+ - **Fitness**: Provide the methods to evaluate phenotypes.
+ - **Algorithm**: Evolution procedure for phenotypes.
+ - **Experiment**: Evolution session with phenotypes.
+
+Now the following sections will introduce a fast initialization to the package.
+Do not hesitate to extend your knowledge by using all the additional provided
+examples at the folder [examples](./examples).
+
+### Genotypes
+Define your Genotypes following the `dataclass` principles from `pydantic` by
+using the base model `GenotypeModel`. All dataclass attributes are accepted in 
+addition to an special type `Chromosome` provided in the module `genetics`.
+To start use the already defined chromosome subclasses such `Haploid` and
+`Diploid` depending on the complexity of your genetic model.
+```py
+from gevopy import genetics, random
+
+class Genotype(genetics.GenotypeModel):
+    chromosome_1: genetics.Haploid = Field(default_factory=lambda: random.haploid(12))
+    chromosome_2: genetics.Haploid = Field(default_factory=lambda: random.haploid(10))
+    simple_attribute: float = 1.0
+
+phenotypes = [Genotype() for _ in range(20)]
+```
+> Note Genotype attrubutes *id*, *experiment*, *created*, *parents*,
+*generation*, *score* and *clone* are attributes used by the library.
+Overwriting of this attributes might lead to unexpected behaviors.
+
+### Fitness
+Create your fitness using the parent class `fitness.FitnessModel` and defining
+the class method `score`. The fitness to use on the experiment will be an 
+instance of the defined class. You can use the init arguments `cache` and
+`parallel` to optimize how the evaluation flow is executed.
+
+```py
+from genopy import fitness
+
+class MyFitness1(fitness.FitnessModel):
+    def score(self, phenotype):
+        return phenotype.chromosome.count(1)
+
+fx = MyFitness1(cache=True, parallel=True)
+```
+> You can additionally define `setUp` as method to execute once at the begining
+of each generation before phenotypes are evaluated.
+
+### Algorithm
+The algorithm is the core of your experiment. It defines the rules of the
+evolution process. You can create your own algorithm or use the already
+existing templates. Algorithms are generally composed by 4 components:
+ - **Selection**: Callable which provides the first list of candidates.
+ - **Mating**: Callable which provides the second list of candidates.
+ - **Crossover**: Callable to generate offspring from candidates.
+ - **Mutation**: Callable to mutate phenotype's chromosomes.
+
+Additionally, each algorithm template might contain additional arguments such a
+`survival_rate` or `similarity`. Make sure you read and understand each of the 
+arguments and steps.
+
+```py
+from gevopy.tools import crossover, mutation, selection
+from gevopy import algorithms
+
+my_algorithm=algorithms.Survival(
+    selection=selection.Tournaments(tournsize=3),
+    mating=selection.Best(),
+    crossover=crossover.TwoPoint(indpb=0.8),
+    mutation=mutation.SinglePoint(indpb=0.5, mutpb=0.2),
+    survival_rate=0.40,
+)
+```
+> The modules `tools.crossover`, `tools.mutation` and `tools.selection` contain
+templates and utilities to simplify your algorithm definition.
+
+### Experiment
+The experiment is the final expression of your evolutionary algorithm.
+it provides the methods to evolve and store phenotypes. Once an experiment
+is instantiated, use the method `run` to force the evolution of the population
+until a desired state.
+
+The results of the experiment can be collected from the method output, calling
+`best` method or adding a [Neo4j]() connection as `database` input when
+instantiating the experiment to store all phenotypes during the execution.
+
+```py
+import gevopy
+
+experiment = gevopy.SimpleEvolution(
+    population=[Genotype() for _ in range(20)],
+    fitness=MyFitness1(cache=True, parallel=True),
+)
+
+experiment.run(
+    algorithm=my_algorithm,
+    max_generations=20,
+    max_score=12.0,
+)
+
+best_phenotype = experiment.best()
+```
+>The method `run` forces the evolution of the experiment which is updated on
+each cycle. After the method is completed, you can force again te evolution
+process using higher inputs for `max_generations` or `max_score`.
+
+
+## Development
+Fork the repository, pick one of the issues at the [issues](https://github.com/BorjaEst/gevopy/issues)
+and create a [Pull request](https://github.com/BorjaEst/gevopy/pulls).
+
+
+## FAQ and Notes
+
+### Why Graph Database?
+Storing relationships at the record level makes sense in genotype 
+relationships as it provides index-free adjacency.
+Graph traversal operations such 'genealogy tree' or certain matches can
+be performed with no index lookups leading to much better performance.

From 990c439a183e035d10b8d3b1873c6d37de53b036 Mon Sep 17 00:00:00 2001
From: Borja Esteban <boressan@outlook.com>
Date: Tue, 15 Nov 2022 11:42:27 +0000
Subject: [PATCH 03/14] add pyproyect.toml

---
 pyproyect.toml | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 pyproyect.toml

diff --git a/pyproyect.toml b/pyproyect.toml
new file mode 100644
index 0000000..79bbf5c
--- /dev/null
+++ b/pyproyect.toml
@@ -0,0 +1,30 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "gevopy"
+description = "Genetics for Evolutionary Algorithms in Python."
+readme = "README.md"
+requires-python = ">=3.10"
+license = {text = "GNU General Public License v3 (GPLv3)"}
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Operating System :: OS Independent",
+]
+dynamic = ["version", "dependencies"]
+
+[project.urls]
+"Homepage" = "https://github.com/BorjaEst/gevopy/"
+"Bug Tracker" = "https://github.com/BorjaEst/gevopy/issues"
+
+[tool.setuptools.dynamic]
+version = {file = "src/gevopy/VERSION"}
+dependencies = {file = ["requirements.txt"]}
+
+[tool.pytest.ini_options]
+addopts = ["--import-mode=importlib"]
+
+[tool.pylint.'MESSAGES CONTROL']
+extension-pkg-whitelist = "pydantic"

From 15a6a9cb2e60c42bf09c31b34454e1c320332e2d Mon Sep 17 00:00:00 2001
From: Borja Esteban <boressan@outlook.com>
Date: Tue, 15 Nov 2022 15:43:40 +0000
Subject: [PATCH 04/14] first version for genetics

---
 src/gevopy/VERSION     |   1 +
 src/gevopy/__init__.py |   6 ++
 src/gevopy/genetics.py | 224 +++++++++++++++++++++++++++++++++++++++++
 src/gevopy/random.py   |  31 ++++++
 4 files changed, 262 insertions(+)
 create mode 100755 src/gevopy/VERSION
 create mode 100755 src/gevopy/genetics.py
 create mode 100755 src/gevopy/random.py

diff --git a/src/gevopy/VERSION b/src/gevopy/VERSION
new file mode 100755
index 0000000..6c6aa7c
--- /dev/null
+++ b/src/gevopy/VERSION
@@ -0,0 +1 @@
+0.1.0
\ No newline at end of file
diff --git a/src/gevopy/__init__.py b/src/gevopy/__init__.py
index e69de29..70b4217 100644
--- a/src/gevopy/__init__.py
+++ b/src/gevopy/__init__.py
@@ -0,0 +1,6 @@
+"""Evolution algorithms with python."""
+
+import logging
+
+# Application logger
+module_logger = logging.getLogger(__name__)
diff --git a/src/gevopy/genetics.py b/src/gevopy/genetics.py
new file mode 100755
index 0000000..4d62e86
--- /dev/null
+++ b/src/gevopy/genetics.py
@@ -0,0 +1,224 @@
+"""The :mod:`genetics` module is intended to contain generic and specific
+classes to design your Genotype models.
+
+Define your Genotypes following the `dataclass` principles from `pydantic` by
+using the base model `GenotypeModel`. All dataclass attributes are accepted in
+addition to an special type `Chromosome` provided in the module. To start
+use the already defined chromosome subclasses such `Haploid` and `Diploid`
+depending on the complexity of your genetic model.
+"""
+
+import copy
+import uuid
+from datetime import datetime
+from typing import List, MutableSequence
+
+import numpy as np
+from pydantic import BaseModel, Field, PositiveInt
+
+from gevopy import random as ea_random
+
+
+class Chromosome(np.ndarray, MutableSequence):
+    """A chromosome is a long DNA molecule with part or all of the genetic
+    material of an organism. In the case of Evolutionary Algorithms it
+    contains the information required to evaluate a phenotype.
+
+    This library bases chromosomes on numpy.ndarray to and therefore when
+    creating one, the steps defined at `subclassing ndarray` must be followed.
+    Additionally it subclasses from `collections.abc.MutableSequence` to
+    provide additional and standard python methods such as `count`.
+
+    In order to suport serialization/deserialization the new method must
+    accept only the first input parameter for the function np.array.
+    """
+
+    def __new__(cls, data):
+        """Standard python method required to subclass np.ndarray.
+        :param cls: Chromosome ndarray subclass type
+        :param data: Any object exposing the array interface or sequence
+        :param pairs: Number of pairs the chromosome represents
+        :return: A new generated Chromosome instance
+        """
+        return np.array(data, dtype="uint8").view(cls)
+
+    def __array_finalize__(self, obj):
+        """Mechanism that numpy provides to allow subclasses to handle
+        the various ways that new instances get created.
+        :param obj: New instance provided for slicing and `view`
+        """
+        if obj is None:
+            return
+
+    def __mutate__(self):
+        """Performs the chromosome mutation operation.
+        :return: Chromosome with mutated values
+        """
+        raise NotImplementedError
+
+    def __eq__(self, other):
+        """Standard python method to compares 2 chromosomes.
+        :param other: Chromosome to compare with
+        :return: Boolean, True if are equal, otherwise False
+        """
+        return np.array_equal(self, other)
+
+    def __cross__(self, other):
+        """Magic method to compare a chromosome bitwise.
+        :param other: Chromosome to compare with
+        :return: List of chromosome bits where equal
+        """
+        return super().__eq__(other)
+
+    @classmethod
+    def __get_validators__(cls):
+        """Pydantic magic method for custom validation and deserialization.
+        :yield: Validation method for construction
+        """
+        yield cls.validate_type
+
+    @classmethod
+    def validate_type(cls, val):
+        """Validation method for construction and deserialization.
+        :param val: Value to pass to __new__ data
+        :return: Deserialized chromosome
+        """
+        return cls(data=val)
+
+
+class Haploid(Chromosome):
+    """The word haploid describes a condition, a cell, or an organism that
+    contains half of the set of homologous chromosomes present in the somatic
+    cell. Homologous chromosomes are two chromosomes that pair up by having
+    the same gene sequence, loci, chromosomal length, and centromere location.
+
+    Half of the homologous pairs are maternal (coming from the mother) whereas
+    the other half, paternal (coming from the father). Thus, in other words,
+    a haploid is when a cell, for instance, contains half of the total
+    homologous chromosomes, i.e. a single set of chromosomes that are unpaired.
+    """
+
+    @classmethod
+    @property
+    def states(cls):
+        """Returns the number of possible chromosome states.
+        :return: Chromosome with inverted values
+        """
+        return 2
+
+    def __invert__(self):
+        """Computes and returns the bit-wise inversion of the chromosome.
+        :return: Chromosome with inverted values
+        """
+        return np.logical_not(self).view("uint8")
+
+    def __mutate__(self):
+        """Computes and returns the bit-wise mutation of the chromosome.
+        :return: Chromosome with mutated values
+        """
+        return ea_random.haploid(self.size)
+
+
+class Diploid(Chromosome):
+    """In genetics and biology, the term diploid refers to the cell containing
+    two sets of homologous chromosomes wherein each chromosome in a set is
+    obtained from each of the two-parent cells.
+
+    As example, the fusion of two haploid sex cells results in the formation
+    of a diploid cell called a zygote.
+    """
+
+    @classmethod
+    @property
+    def states(cls):
+        """Returns the number of possible chromosome states.
+        :return: Chromosome with inverted values
+        """
+        return 4
+
+    def __invert__(self):
+        """Computes and returns the bit-wise inversion of the chromosome.
+        :return: Chromosome with inverted values
+        """
+        return np.bitwise_and(super().__invert__(), 3)
+
+    def __mutate__(self):
+        """Computes and returns the bit-wise mutation of the chromosome.
+        :return: Chromosome with mutated values
+        """
+        return ea_random.diploid(self.size)
+
+
+class Triploid(Chromosome):
+    """Similar to haploid and diploid, cells can contain three sets of
+    homologous chromosomes, increasing the amount of combinations for each
+    bit (trinary) position.
+
+    In biology triploidy is a rare chromosomal abnormality.
+    """
+
+    @classmethod
+    @property
+    def states(cls):
+        """Returns the number of possible chromosome states.
+        :return: Chromosome with inverted values
+        """
+        return 8
+
+    def __invert__(self):
+        """Computes and returns the bit-wise inversion of the chromosome.
+        :return: Chromosome with inverted values
+        """
+        return np.bitwise_and(super().__invert__(), 7)
+
+    def __mutate__(self):
+        """Computes and returns the bit-wise mutation of the chromosome.
+        :return: Chromosome with mutated values
+        """
+        return ea_random.triploid(self.size)
+
+
+class GenotypeModel(BaseModel):
+    """Evolution Genotype is the most basic but flexible form of genetics.
+    It is a chromosomes container with an unique identifier. Different
+    organisms might have different numbers of chromosomes.
+
+    When subclassing a genotype note the following attributes are reserved:
+     - id: A unique identifier for the phenotype
+     - experiment: Name of the experiment the phenotype belongs, can be None
+     - created: Datetime when the phenotype was instantiated
+     - parents: List of phenotype ids used to generate the phenotype
+     - generation: Positive integer indicating the evolution generations
+     - score: Float indicating the phenotype score (None, when not evaluated)
+     - clone: Method to produce a genotype deep copy with different id
+    """
+
+    id: uuid.UUID = Field(default_factory=uuid.uuid4)
+    experiment: str = None
+    created: datetime = Field(default_factory=datetime.utcnow)
+    parents: List[uuid.UUID] = []
+    generation: PositiveInt = Field(default=1)
+    score: float = None
+
+    class Config:
+        json_encoders = {Chromosome: lambda x: x.astype("uint8").tolist()}
+
+    def clone(self):
+        """Clones the phenotype producing a copy with different id and
+        an empty score.
+        :return: Phenotype copy
+        """
+        clone = copy.deepcopy(self)
+        clone.id = uuid.uuid4()  # Generate new id
+        clone.score = None  # Reset the clone score
+        return clone
+
+    def __repr__(self):
+        """Representation method for phenotype. It displays the class name
+        together with the phenotype id.
+        :return: String representing the genotype instance (phenotype)
+        """
+        return "{name} {id}".format(
+            name=self.__class__.__name__,
+            id=self.id,
+        )
diff --git a/src/gevopy/random.py b/src/gevopy/random.py
new file mode 100755
index 0000000..21d6322
--- /dev/null
+++ b/src/gevopy/random.py
@@ -0,0 +1,31 @@
+"""Evolution algorithm module to generate random units, for example random
+chromosomes.
+"""
+
+import numpy as np
+
+from gevopy import genetics
+
+
+def haploid(size):
+    """Returns a random standard Haploid chromosome.
+    :param size: Integer with chromosome size
+    """
+    data = np.random.randint(2 ** 1, size=size, dtype="uint8")
+    return genetics.Haploid(data)
+
+
+def diploid(size):
+    """Returns a random standard Diploid chromosome.
+    :param size: Integer with chromosome size
+    """
+    data = np.random.randint(2 ** 2, size=size, dtype="uint8")
+    return genetics.Diploid(data)
+
+
+def triploid(size):
+    """Returns a random standard Triploid chromosome.
+    :param size: Integer with chromosome size
+    """
+    data = np.random.randint(2 ** 3, size=size, dtype="uint8")
+    return genetics.Triploid(data)

From d1a6bd3bb579223a0e483db1722b33600a205b78 Mon Sep 17 00:00:00 2001
From: Borja Esteban <boressan@outlook.com>
Date: Tue, 15 Nov 2022 15:44:04 +0000
Subject: [PATCH 05/14] add temp pylintrc

---
 .pylintrc      | 5 +++++
 pyproyect.toml | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)
 create mode 100644 .pylintrc

diff --git a/.pylintrc b/.pylintrc
new file mode 100644
index 0000000..0c9b5cc
--- /dev/null
+++ b/.pylintrc
@@ -0,0 +1,5 @@
+# Temporary file to delete once vscode supports pyproyect.toml
+# See: https://github.com/pydantic/pydantic/issues/1961
+
+[MASTER]
+extension-pkg-whitelist=pydantic
diff --git a/pyproyect.toml b/pyproyect.toml
index 79bbf5c..8f45a62 100644
--- a/pyproyect.toml
+++ b/pyproyect.toml
@@ -26,5 +26,5 @@ dependencies = {file = ["requirements.txt"]}
 [tool.pytest.ini_options]
 addopts = ["--import-mode=importlib"]
 
-[tool.pylint.'MESSAGES CONTROL']
+[tool.pylint.messages_control]
 extension-pkg-whitelist = "pydantic"

From 1862bf55e5d03add16696966a16631d3e60690b5 Mon Sep 17 00:00:00 2001
From: Borja Esteban <boressan@outlook.com>
Date: Tue, 15 Nov 2022 15:46:29 +0000
Subject: [PATCH 06/14] add project requirements

---
 requirements-test.txt | 7 +++++++
 requirements.txt      | 2 ++
 2 files changed, 9 insertions(+)
 create mode 100755 requirements-test.txt
 create mode 100755 requirements.txt

diff --git a/requirements-test.txt b/requirements-test.txt
new file mode 100755
index 0000000..35f3198
--- /dev/null
+++ b/requirements-test.txt
@@ -0,0 +1,7 @@
+# This requirements are for development and testing only, not for production.
+-r requirements.txt
+pytest
+pytest-xdist
+pytest-cov
+flake8
+black
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
new file mode 100755
index 0000000..eee8de2
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,2 @@
+numpy~=1.23.4
+pydantic~=1.10.2
\ No newline at end of file

From 2075b2a156da498eec76b24b010e69eba72fd215 Mon Sep 17 00:00:00 2001
From: Borja Esteban <boressan@outlook.com>
Date: Tue, 15 Nov 2022 15:52:34 +0000
Subject: [PATCH 07/14] Fix misspell of pyproject.toml

---
 .pylintrc                        | 5 -----
 pyproyect.toml => pyproject.toml | 0
 2 files changed, 5 deletions(-)
 delete mode 100644 .pylintrc
 rename pyproyect.toml => pyproject.toml (100%)

diff --git a/.pylintrc b/.pylintrc
deleted file mode 100644
index 0c9b5cc..0000000
--- a/.pylintrc
+++ /dev/null
@@ -1,5 +0,0 @@
-# Temporary file to delete once vscode supports pyproyect.toml
-# See: https://github.com/pydantic/pydantic/issues/1961
-
-[MASTER]
-extension-pkg-whitelist=pydantic
diff --git a/pyproyect.toml b/pyproject.toml
similarity index 100%
rename from pyproyect.toml
rename to pyproject.toml

From 579b92e5ba352e0bc9f8a8712edc740c5ce649d6 Mon Sep 17 00:00:00 2001
From: Borja Esteban <boressan@outlook.com>
Date: Tue, 15 Nov 2022 18:08:44 +0000
Subject: [PATCH 08/14] add first test files for genotype requirements

---
 tests/conftest.py                         | 26 +++++++
 tests/genotypes.py                        | 16 +++++
 tests/test_requirements/test_genotypes.py | 87 +++++++++++++++++++++++
 3 files changed, 129 insertions(+)
 create mode 100755 tests/conftest.py
 create mode 100644 tests/genotypes.py
 create mode 100755 tests/test_requirements/test_genotypes.py

diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100755
index 0000000..05b2580
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,26 @@
+"""Module for evolution requirements fixtures"""
+# pylint: disable=redefined-outer-name
+
+import random
+
+from pytest import fixture
+
+from tests import genotypes
+
+
+@fixture(scope="function", autouse=True)
+def set_random_seed():
+    """Fix the random seed for repeatable testing"""
+    random.seed(1)
+
+
+@fixture(scope="package", params=["OneHaploid", "OneDiploid"])
+def genotype(request):
+    """Fixture to return the phenotype generator"""
+    return genotypes.__dict__[request.param]
+
+
+@fixture(scope="package")
+def phenotype(phenotype_gen):
+    """Fixture to return a phenotype instance"""
+    return phenotype_gen()
diff --git a/tests/genotypes.py b/tests/genotypes.py
new file mode 100644
index 0000000..f9a48a0
--- /dev/null
+++ b/tests/genotypes.py
@@ -0,0 +1,16 @@
+"""Module for test genotypes"""
+from gevopy import genetics, random
+
+
+class OneHaploid(genetics.GenotypeModel):
+    """Simple and most basic haploid genotype"""
+    chromosome: genetics.Haploid = genetics.Field(
+        default_factory=lambda: random.haploid(size=12)
+    )
+
+
+class OneDiploid(genetics.GenotypeModel):
+    """Simple and most basic diploid genotype"""
+    chromosome: genetics.Diploid = genetics.Field(
+        default_factory=lambda: random.diploid(size=12)
+    )
diff --git a/tests/test_requirements/test_genotypes.py b/tests/test_requirements/test_genotypes.py
new file mode 100755
index 0000000..6a4843c
--- /dev/null
+++ b/tests/test_requirements/test_genotypes.py
@@ -0,0 +1,87 @@
+"""Module to test genotype requirements"""
+# pylint: disable=redefined-outer-name
+
+import uuid
+from collections.abc import MutableSequence
+from datetime import datetime
+
+from pytest import fixture
+
+from gevopy import genetics
+
+
+# Module fixtures ---------------------------------------------------
+@fixture(scope="class")
+def clone(phenotype):
+    """Returns a phenotype clone"""
+    return phenotype.clone()
+
+
+# Requirements ------------------------------------------------------
+class AttrRequirements:
+    """Tests group for Genotype instances attributes"""
+
+    def test_attr_chromosome(self, phenotype):
+        """Test phenotype has a correct 'chromosome' attribute"""
+        assert hasattr(phenotype, "chromosome")
+        assert isinstance(phenotype.chromosome, MutableSequence)
+
+    def test_attr_id(self, phenotype):
+        """Test phenotype has a correct 'id' attribute"""
+        assert hasattr(phenotype, "id")
+        assert isinstance(phenotype.id, uuid.UUID)
+
+    def test_attr_created(self, phenotype):
+        """Test phenotype has a correct 'created' attribute"""
+        assert hasattr(phenotype, "created")
+        assert isinstance(phenotype.created, datetime)
+
+    def test_attr_parents(self, phenotype):
+        """Test phenotype has a correct 'parents' attribute"""
+        assert hasattr(phenotype, "parents")
+        assert isinstance(phenotype.parents, list)
+
+    def test_attr_generation(self, phenotype):
+        """Test phenotype has a correct 'generation' attribute"""
+        assert hasattr(phenotype, "generation")
+        assert isinstance(phenotype.generation, int)
+        assert phenotype.generation > 0
+
+    def test_attr_score(self, phenotype):
+        """Test phenotype has a correct 'score' attribute"""
+        assert hasattr(phenotype, "score")
+        assert isinstance(phenotype.score, type(None))
+
+    def test_is_instance_genotype(self, phenotype):
+        """Test phenotype is instance of GenotypeModel"""
+        assert isinstance(phenotype, genetics.GenotypeModel)
+
+
+class CloneRequirements:
+    """Tests group for phenotype clone function"""
+
+    def test_clone_id(self, phenotype, clone):
+        """Test clone 'id' is different from phenotype"""
+        assert clone.id != phenotype.id
+
+    def test_clone_chromosome(self, phenotype, clone):
+        """Test clone 'chromosome' is equal to phenotype"""
+        assert clone.chromosome == phenotype.chromosome
+
+    def test_clone_parents(self, phenotype, clone):
+        """Test clone 'parents' are equal to phenotype"""
+        assert clone.parents == phenotype.parents
+
+    def test_clone_generation(self, phenotype, clone):
+        """Test clone 'generation' is equal to phenotype"""
+        assert clone.generation == phenotype.generation
+
+
+# Parametrization ---------------------------------------------------
+class TestGenotype(AttrRequirements, CloneRequirements):
+    """Parametrization for testing Genotypes"""
+
+    @fixture(scope="class")
+    def phenotype(self, genotype):
+        """Fixture to return a genotype instance"""
+        return genotype()

From 8261241da07ce75a75cb972a47af8898aef75a7a Mon Sep 17 00:00:00 2001
From: Borja Esteban <boressan@outlook.com>
Date: Tue, 15 Nov 2022 18:08:54 +0000
Subject: [PATCH 09/14] add tox file

---
 tox.ini | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 tox.ini

diff --git a/tox.ini b/tox.ini
new file mode 100644
index 0000000..c60fcc7
--- /dev/null
+++ b/tox.ini
@@ -0,0 +1,21 @@
+[tox]
+minversion = 3.25.0
+isolated_build = True
+envlist = qc.sty, qc.uni, qc.sec
+
+[testenv]
+deps = -r{toxinidir}/requirements-test.txt
+install_command = pip install -U {opts} {packages}
+commands = python -m pytest --numprocesses='auto' {posargs}
+
+[testenv:qc.sty]
+deps = -r{toxinidir}/requirements-test.txt
+commands = python -m flake8 --format=pylint --output-file=flake8.log
+
+[testenv:qc.uni]
+deps = -r{toxinidir}/requirements-test.txt
+commands = python -m pytest --cov=ndautomata --cov-report=html -n=auto tests
+
+[testenv:qc.sec]
+deps = -r{toxinidir}/requirements-test.txt
+commands = python -m bandit -r ndautomata -x tests 

From c3e1d03b440e85d82c3b9eb76acb270022116047 Mon Sep 17 00:00:00 2001
From: Borja Esteban <boressan@outlook.com>
Date: Tue, 15 Nov 2022 18:09:19 +0000
Subject: [PATCH 10/14] add vscode settings

---
 .vscode/settings.json | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 .vscode/settings.json

diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000..e685004
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,8 @@
+{
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true,
+    "python.envFile": "${workspaceFolder}/.env"
+}
\ No newline at end of file

From d41c1060d2a5525fd3bf4c85080c592a858a4161 Mon Sep 17 00:00:00 2001
From: Borja Esteban <boressan@outlook.com>
Date: Tue, 15 Nov 2022 18:09:28 +0000
Subject: [PATCH 11/14] add vscode first launch file

---
 .vscode/launch.json | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 .vscode/launch.json

diff --git a/.vscode/launch.json b/.vscode/launch.json
new file mode 100644
index 0000000..cfb2b6b
--- /dev/null
+++ b/.vscode/launch.json
@@ -0,0 +1,16 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Python: Current File",
+            "type": "python",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal",
+            "justMyCode": true
+        },
+    ]
+}
\ No newline at end of file

From 3dedadc68c4ab370e4b73465eeb59c1d830cb854 Mon Sep 17 00:00:00 2001
From: Borja Esteban <boressan@outlook.com>
Date: Tue, 15 Nov 2022 18:11:24 +0000
Subject: [PATCH 12/14] Fix tox file

---
 tox.ini | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tox.ini b/tox.ini
index c60fcc7..af8601e 100644
--- a/tox.ini
+++ b/tox.ini
@@ -14,8 +14,8 @@ commands = python -m flake8 --format=pylint --output-file=flake8.log
 
 [testenv:qc.uni]
 deps = -r{toxinidir}/requirements-test.txt
-commands = python -m pytest --cov=ndautomata --cov-report=html -n=auto tests
+commands = python -m pytest --cov=gevopy --cov-report=html -n=auto tests
 
 [testenv:qc.sec]
 deps = -r{toxinidir}/requirements-test.txt
-commands = python -m bandit -r ndautomata -x tests 
+commands = python -m bandit -r gevopy -x tests 

From 0458f08c513d7b14695ea05de78b7e0a60ce3815 Mon Sep 17 00:00:00 2001
From: Borja Esteban <boressan@outlook.com>
Date: Tue, 15 Nov 2022 18:19:59 +0000
Subject: [PATCH 13/14] add bandit to requirements-test

---
 requirements-test.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/requirements-test.txt b/requirements-test.txt
index 35f3198..10cec12 100755
--- a/requirements-test.txt
+++ b/requirements-test.txt
@@ -4,4 +4,5 @@ pytest
 pytest-xdist
 pytest-cov
 flake8
-black
\ No newline at end of file
+black
+bandit
\ No newline at end of file

From 5486c5fe830a9eb98c1280060b0f58254e65a1b6 Mon Sep 17 00:00:00 2001
From: Borja Esteban <boressan@outlook.com>
Date: Tue, 15 Nov 2022 18:25:17 +0000
Subject: [PATCH 14/14] add github workflows for quality

---
 .github/workflows/qc-sec.yml | 30 ++++++++++++++++++++++++++++++
 .github/workflows/qc-sty.yml | 30 ++++++++++++++++++++++++++++++
 .github/workflows/qc-uni.yml | 30 ++++++++++++++++++++++++++++++
 3 files changed, 90 insertions(+)
 create mode 100644 .github/workflows/qc-sec.yml
 create mode 100644 .github/workflows/qc-sty.yml
 create mode 100644 .github/workflows/qc-uni.yml

diff --git a/.github/workflows/qc-sec.yml b/.github/workflows/qc-sec.yml
new file mode 100644
index 0000000..4200c84
--- /dev/null
+++ b/.github/workflows/qc-sec.yml
@@ -0,0 +1,30 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: qc.sec
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  qc-sec:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install tox
+      run: python -m pip install --upgrade tox
+    - name: Run Quality Check for Security
+      run: tox -e qc.sec
diff --git a/.github/workflows/qc-sty.yml b/.github/workflows/qc-sty.yml
new file mode 100644
index 0000000..ec41510
--- /dev/null
+++ b/.github/workflows/qc-sty.yml
@@ -0,0 +1,30 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: qc.sty
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  qc-sty:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install tox
+      run: python -m pip install --upgrade tox
+    - name: Run Quality Check for Style
+      run: tox -e qc.sty
diff --git a/.github/workflows/qc-uni.yml b/.github/workflows/qc-uni.yml
new file mode 100644
index 0000000..fbed5d0
--- /dev/null
+++ b/.github/workflows/qc-uni.yml
@@ -0,0 +1,30 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: qc.uni
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  qc-uni:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install tox
+      run: python -m pip install --upgrade tox
+    - name: Run Quality Check for Unittest
+      run: tox -e qc.uni