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#4 Add code coverage & codacy badge

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Add code coverage configuration in codecov
Add some tests
This commit is contained in:
Ricardo Montañana Gómez
2020-06-06 03:04:18 +02:00
parent b4816b2995
commit b9f14aec05
14 changed files with 608 additions and 204 deletions
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14
.coveragerc Normal file
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@@ -0,0 +1,14 @@
[run]
branch = True
source = stree
[report]
exclude_lines =
if self.debug:
pragma: no cover
raise NotImplementedError
if __name__ == .__main__.:
ignore_errors = True
omit =
stree/tests/*
stree/__init__.py

1
.gitignore vendored
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@@ -130,3 +130,4 @@ dmypy.json
.idea .idea
.vscode .vscode
.pre-commit-config.yaml

9
.travis.yml
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@@ -3,6 +3,7 @@ os: linux
dist: xenial dist: xenial
install: install:
- pip install -r requirements.txt - pip install -r requirements.txt
- pip install --upgrade codecov coverage black flake8
notifications: notifications:
email: email:
recipients: recipients:
@@ -10,4 +11,10 @@ notifications:
on_success: never # default: change on_success: never # default: change
on_failure: always # default: always on_failure: always # default: always
# command to run tests # command to run tests
script: python -m unittest stree.tests script:
- black --check --diff stree
- flake8 --count --exclude __init__.py stree
- coverage run -m unittest -v stree.tests
after_success:
- codecov
- bash <(curl -Ls https://coverage.codacy.com/get.sh)

3
README.md
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@@ -1,5 +1,6 @@
[![Build Status](https://travis-ci.com/Doctorado-ML/STree.svg?branch=master)](https://travis-ci.com/Doctorado-ML/STree) [![Build Status](https://travis-ci.com/Doctorado-ML/STree.svg?branch=master)](https://travis-ci.com/Doctorado-ML/STree)
[![codecov](https://codecov.io/gh/doctorado-ml/stree/branch/master/graph/badge.svg)](https://codecov.io/gh/doctorado-ml/stree)
[![Codacy Badge](https://app.codacy.com/project/badge/Grade/35fa3dfd53a24a339344b33d9f9f2f3d)](https://www.codacy.com/gh/Doctorado-ML/STree?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=Doctorado-ML/STree&amp;utm_campaign=Badge_Grade)
# Stree # Stree
Oblique Tree classifier based on SVM nodes. The nodes are built and splitted with sklearn LinearSVC models.Stree is a sklearn estimator and can be integrated in pipelines, grid searches, etc. Oblique Tree classifier based on SVM nodes. The nodes are built and splitted with sklearn LinearSVC models.Stree is a sklearn estimator and can be integrated in pipelines, grid searches, etc.

15
codecov.yml Normal file
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@@ -0,0 +1,15 @@
overage:
status:
project:
default:
target: auto
patch:
default:
target: auto
comment:
layout: "reach, diff, flags, files"
behavior: default
require_changes: false
require_base: yes
require_head: yes
branches: null

55
main.py
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@@ -2,17 +2,29 @@ import time
from sklearn.model_selection import train_test_split from sklearn.model_selection import train_test_split
from stree import Stree from stree import Stree
random_state=1 random_state = 1
def load_creditcard(n_examples=0): def load_creditcard(n_examples=0):
import pandas as pd import pandas as pd
import numpy as np import numpy as np
import random import random
df = pd.read_csv('data/creditcard.csv')
print("Fraud: {0:.3f}% {1}".format(df.Class[df.Class == 1].count()*100/df.shape[0], df.Class[df.Class == 1].count())) df = pd.read_csv("data/creditcard.csv")
print("Valid: {0:.3f}% {1}".format(df.Class[df.Class == 0].count()*100/df.shape[0], df.Class[df.Class == 0].count())) print(
"Fraud: {0:.3f}% {1}".format(
df.Class[df.Class == 1].count() * 100 / df.shape[0],
df.Class[df.Class == 1].count(),
)
)
print(
"Valid: {0:.3f}% {1}".format(
df.Class[df.Class == 0].count() * 100 / df.shape[0],
df.Class[df.Class == 0].count(),
)
)
y = np.expand_dims(df.Class.values, axis=1) y = np.expand_dims(df.Class.values, axis=1)
X = df.drop(['Class', 'Time', 'Amount'], axis=1).values X = df.drop(["Class", "Time", "Amount"], axis=1).values
if n_examples > 0: if n_examples > 0:
# Take first n_examples samples # Take first n_examples samples
X = X[:n_examples, :] X = X[:n_examples, :]
@@ -26,11 +38,27 @@ def load_creditcard(n_examples=0):
X = np.append(Xt, X[indices], axis=0) X = np.append(Xt, X[indices], axis=0)
y = np.append(yt, y[indices], axis=0) y = np.append(yt, y[indices], axis=0)
print("X.shape", X.shape, " y.shape", y.shape) print("X.shape", X.shape, " y.shape", y.shape)
print("Fraud: {0:.3f}% {1}".format(len(y[y == 1])*100/X.shape[0], len(y[y == 1]))) print(
print("Valid: {0:.3f}% {1}".format(len(y[y == 0]) * 100 / X.shape[0], len(y[y == 0]))) "Fraud: {0:.3f}% {1}".format(
Xtrain, Xtest, ytrain, ytest = train_test_split(X, y, train_size=0.7, shuffle=True, random_state=random_state, stratify=y) len(y[y == 1]) * 100 / X.shape[0], len(y[y == 1])
)
)
print(
"Valid: {0:.3f}% {1}".format(
len(y[y == 0]) * 100 / X.shape[0], len(y[y == 0])
)
)
Xtrain, Xtest, ytrain, ytest = train_test_split(
X,
y,
train_size=0.7,
shuffle=True,
random_state=random_state,
stratify=y,
)
return Xtrain, Xtest, ytrain, ytest return Xtrain, Xtest, ytrain, ytest
# data = load_creditcard(-5000) # Take all true samples + 5000 of the others # data = load_creditcard(-5000) # Take all true samples + 5000 of the others
# data = load_creditcard(5000) # Take the first 5000 samples # data = load_creditcard(5000) # Take the first 5000 samples
data = load_creditcard() # Take all the samples data = load_creditcard() # Take all the samples
@@ -41,17 +69,20 @@ ytrain = data[2]
ytest = data[3] ytest = data[3]
now = time.time() now = time.time()
clf = Stree(C=.01, random_state=random_state) clf = Stree(C=0.01, random_state=random_state)
clf.fit(Xtrain, ytrain) clf.fit(Xtrain, ytrain)
print(f"Took {time.time() - now:.2f} seconds to train") print(f"Took {time.time() - now:.2f} seconds to train")
print(clf) print(clf)
print(f"Classifier's accuracy (train): {clf.score(Xtrain, ytrain):.4f}") print(f"Classifier's accuracy (train): {clf.score(Xtrain, ytrain):.4f}")
print(f"Classifier's accuracy (test) : {clf.score(Xtest, ytest):.4f}") print(f"Classifier's accuracy (test) : {clf.score(Xtest, ytest):.4f}")
proba = clf.predict_proba(Xtest) proba = clf.predict_proba(Xtest)
print("Checking that we have correct probabilities, these are probabilities of sample belonging to class 1") print(
"Checking that we have correct probabilities, these are probabilities of "
"sample belonging to class 1"
)
res0 = proba[proba[:, 0] == 0] res0 = proba[proba[:, 0] == 0]
res1 = proba[proba[:, 0] == 1] res1 = proba[proba[:, 0] == 1]
print("++++++++++res0 > .8++++++++++++") print("++++++++++res0 > .8++++++++++++")
print(res0[res0[:, 1] > .8]) print(res0[res0[:, 1] > 0.8])
print("**********res1 < .4************") print("**********res1 < .4************")
print(res1[res1[:, 1] < .4]) print(res1[res1[:, 1] < 0.4])

16
pyproject.toml Normal file
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@@ -0,0 +1,16 @@
[tool.black]
line-length = 79
include = '\.pyi?$'
exclude = '''
/(
\.git
| \.hg
| \.mypy_cache
| \.tox
| \.venv
| _build
| buck-out
| build
| dist
)/
'''

39
setup.py
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@@ -5,37 +5,32 @@ __author__ = "Ricardo Montañana Gómez"
def readme(): def readme():
with open('README.md') as f: with open("README.md") as f:
return f.read() return f.read()
setuptools.setup( setuptools.setup(
name='STree', name="STree",
version=__version__, version=__version__,
license='MIT License', license="MIT License",
description='Oblique decision tree with svm nodes', description="Oblique decision tree with svm nodes",
long_description=readme(), long_description=readme(),
long_description_content_type='text/markdown', long_description_content_type="text/markdown",
packages=setuptools.find_packages(), packages=setuptools.find_packages(),
url='https://github.com/doctorado-ml/stree', url="https://github.com/doctorado-ml/stree",
author=__author__, author=__author__,
author_email='ricardo.montanana@alu.uclm.es', author_email="ricardo.montanana@alu.uclm.es",
keywords='scikit-learn oblique-classifier oblique-decision-tree decision-\ keywords="scikit-learn oblique-classifier oblique-decision-tree decision-\
tree svm svc', tree svm svc",
classifiers=[ classifiers=[
'Development Status :: 4 - Beta', "Development Status :: 4 - Beta",
'License :: OSI Approved :: MIT License', "License :: OSI Approved :: MIT License",
'Programming Language :: Python :: 3.7', "Programming Language :: Python :: 3.7",
'Natural Language :: English', "Natural Language :: English",
'Topic :: Scientific/Engineering :: Artificial Intelligence', "Topic :: Scientific/Engineering :: Artificial Intelligence",
'Intended Audience :: Science/Research' "Intended Audience :: Science/Research",
],
install_requires=[
'scikit-learn>=0.23.0',
'numpy',
'matplotlib',
'ipympl'
], ],
install_requires=["scikit-learn>=0.23.0", "numpy", "matplotlib", "ipympl"],
test_suite="stree.tests", test_suite="stree.tests",
zip_safe=False zip_safe=False,
) )

133
stree/Strees.py
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@@ -1,11 +1,11 @@
''' """
__author__ = "Ricardo Montañana Gómez" __author__ = "Ricardo Montañana Gómez"
__copyright__ = "Copyright 2020, Ricardo Montañana Gómez" __copyright__ = "Copyright 2020, Ricardo Montañana Gómez"
__license__ = "MIT" __license__ = "MIT"
__version__ = "0.9" __version__ = "0.9"
Build an oblique tree classifier based on SVM Trees Build an oblique tree classifier based on SVM Trees
Uses LinearSVC Uses LinearSVC
''' """
import os import os
@@ -13,8 +13,12 @@ import numpy as np
from sklearn.base import BaseEstimator, ClassifierMixin from sklearn.base import BaseEstimator, ClassifierMixin
from sklearn.svm import LinearSVC from sklearn.svm import LinearSVC
from sklearn.utils.multiclass import check_classification_targets from sklearn.utils.multiclass import check_classification_targets
from sklearn.utils.validation import check_X_y, check_array, check_is_fitted, \ from sklearn.utils.validation import (
_check_sample_weight check_X_y,
check_array,
check_is_fitted,
_check_sample_weight,
)
class Snode: class Snode:
@@ -22,22 +26,23 @@ class Snode:
dataset assigned to it dataset assigned to it
""" """
def __init__(self, clf: LinearSVC, X: np.ndarray, y: np.ndarray, def __init__(
title: str): self, clf: LinearSVC, X: np.ndarray, y: np.ndarray, title: str
):
self._clf = clf self._clf = clf
self._vector = None if clf is None else clf.coef_ self._vector = None if clf is None else clf.coef_
self._interceptor = 0. if clf is None else clf.intercept_ self._interceptor = 0.0 if clf is None else clf.intercept_
self._title = title self._title = title
self._belief = 0. self._belief = 0.0
# Only store dataset in Testing # Only store dataset in Testing
self._X = X if os.environ.get('TESTING', 'NS') != 'NS' else None self._X = X if os.environ.get("TESTING", "NS") != "NS" else None
self._y = y self._y = y
self._down = None self._down = None
self._up = None self._up = None
self._class = None self._class = None
@classmethod @classmethod
def copy(cls, node: 'Snode') -> 'Snode': def copy(cls, node: "Snode") -> "Snode":
return cls(node._clf, node._X, node._y, node._title) return cls(node._clf, node._X, node._y, node._title)
def set_down(self, son): def set_down(self, son):
@@ -49,10 +54,10 @@ class Snode:
def is_leaf(self) -> bool: def is_leaf(self) -> bool:
return self._up is None and self._down is None return self._up is None and self._down is None
def get_down(self) -> 'Snode': def get_down(self) -> "Snode":
return self._down return self._down
def get_up(self) -> 'Snode': def get_up(self) -> "Snode":
return self._up return self._up
def make_predictor(self): def make_predictor(self):
@@ -68,7 +73,7 @@ class Snode:
try: try:
self._belief = max_card / (max_card + min_card) self._belief = max_card / (max_card + min_card)
except ZeroDivisionError: except ZeroDivisionError:
self._belief = 0. self._belief = 0.0
self._class = classes[card == max_card][0] self._class = classes[card == max_card][0]
else: else:
self._belief = 1 self._belief = 1
@@ -77,8 +82,10 @@ class Snode:
def __str__(self) -> str: def __str__(self) -> str:
if self.is_leaf(): if self.is_leaf():
count_values = np.unique(self._y, return_counts=True) count_values = np.unique(self._y, return_counts=True)
result = f"{self._title} - Leaf class={self._class} belief="\ result = (
f"{self._title} - Leaf class={self._class} belief="
f"{self._belief: .6f} counts={count_values}" f"{self._belief: .6f} counts={count_values}"
)
return result return result
else: else:
return f"{self._title}" return f"{self._title}"
@@ -116,9 +123,15 @@ class Stree(BaseEstimator, ClassifierMixin):
with "classifier" as value with "classifier" as value
""" """
def __init__(self, C: float = 1.0, max_iter: int = 1000, def __init__(
random_state: int = None, max_depth: int = None, self,
tol: float = 1e-4, use_predictions: bool = False): C: float = 1.0,
max_iter: int = 1000,
random_state: int = None,
max_depth: int = None,
tol: float = 1e-4,
use_predictions: bool = False,
):
self.max_iter = max_iter self.max_iter = max_iter
self.C = C self.C = C
self.random_state = random_state self.random_state = random_state
@@ -132,7 +145,7 @@ class Stree(BaseEstimator, ClassifierMixin):
:return: the tag required :return: the tag required
:rtype: dict :rtype: dict
""" """
return {'binary_only': True, 'requires_y': True} return {"binary_only": True, "requires_y": True}
def _linear_function(self, data: np.array, node: Snode) -> np.array: def _linear_function(self, data: np.array, node: Snode) -> np.array:
"""Compute the distance of set of samples to a hyperplane, in """Compute the distance of set of samples to a hyperplane, in
@@ -140,9 +153,9 @@ class Stree(BaseEstimator, ClassifierMixin):
hyperplane of each class hyperplane of each class
:param data: dataset of samples :param data: dataset of samples
:type data: np.array :type data: np.array shape(m, n)
:param node: the node that contains the hyperplance coefficients :param node: the node that contains the hyperplance coefficients
:type node: Snode :type node: Snode shape(1, n)
:return: array of distances of each sample to the hyperplane :return: array of distances of each sample to the hyperplane
:rtype: np.array :rtype: np.array
""" """
@@ -160,8 +173,10 @@ class Stree(BaseEstimator, ClassifierMixin):
:rtype: list :rtype: list
""" """
up = ~down up = ~down
return origin[up[:, 0]] if any(up) else None, \ return (
origin[down[:, 0]] if any(down) else None origin[up[:, 0]] if any(up) else None,
origin[down[:, 0]] if any(down) else None,
)
def _distances(self, node: Snode, data: np.ndarray) -> np.array: def _distances(self, node: Snode, data: np.ndarray) -> np.array:
"""Compute distances of the samples to the hyperplane of the node """Compute distances of the samples to the hyperplane of the node
@@ -194,8 +209,9 @@ class Stree(BaseEstimator, ClassifierMixin):
""" """
return data > 0 return data > 0
def fit(self, X: np.ndarray, y: np.ndarray, def fit(
sample_weight: np.array = None) -> 'Stree': self, X: np.ndarray, y: np.ndarray, sample_weight: np.array = None
) -> "Stree":
"""Build the tree based on the dataset of samples and its labels """Build the tree based on the dataset of samples and its labels
:raises ValueError: if parameters C or max_depth are out of bounds :raises ValueError: if parameters C or max_depth are out of bounds
@@ -203,17 +219,22 @@ class Stree(BaseEstimator, ClassifierMixin):
:rtype: Stree :rtype: Stree
""" """
# Check parameters are Ok. # Check parameters are Ok.
if type(y).__name__ == 'np.ndarray': if type(y).__name__ == "np.ndarray":
y = y.ravel() y = y.ravel()
if self.C < 0: if self.C < 0:
raise ValueError( raise ValueError(
f"Penalty term must be positive... got (C={self.C:f})") f"Penalty term must be positive... got (C={self.C:f})"
self.__max_depth = np.iinfo( )
np.int32).max if self.max_depth is None else self.max_depth self.__max_depth = (
np.iinfo(np.int32).max
if self.max_depth is None
else self.max_depth
)
if self.__max_depth < 1: if self.__max_depth < 1:
raise ValueError( raise ValueError(
f"Maximum depth has to be greater than 1... got (max_depth=\ f"Maximum depth has to be greater than 1... got (max_depth=\
{self.max_depth})") {self.max_depth})"
)
check_classification_targets(y) check_classification_targets(y)
X, y = check_X_y(X, y) X, y = check_X_y(X, y)
sample_weight = _check_sample_weight(sample_weight, X) sample_weight = _check_sample_weight(sample_weight, X)
@@ -223,13 +244,14 @@ class Stree(BaseEstimator, ClassifierMixin):
self.n_iter_ = self.max_iter self.n_iter_ = self.max_iter
self.depth_ = 0 self.depth_ = 0
self.n_features_in_ = X.shape[1] self.n_features_in_ = X.shape[1]
self.tree_ = self.train(X, y, sample_weight, 1, 'root') self.tree_ = self.train(X, y, sample_weight, 1, "root")
self._build_predictor() self._build_predictor()
return self return self
def _build_predictor(self): def _build_predictor(self):
"""Process the leaves to make them predictors """Process the leaves to make them predictors
""" """
def run_tree(node: Snode): def run_tree(node: Snode):
if node.is_leaf(): if node.is_leaf():
node.make_predictor() node.make_predictor()
@@ -239,8 +261,14 @@ class Stree(BaseEstimator, ClassifierMixin):
run_tree(self.tree_) run_tree(self.tree_)
def train(self, X: np.ndarray, y: np.ndarray, sample_weight: np.ndarray, def train(
depth: int, title: str) -> Snode: self,
X: np.ndarray,
y: np.ndarray,
sample_weight: np.ndarray,
depth: int,
title: str,
) -> Snode:
"""Recursive function to split the original dataset into predictor """Recursive function to split the original dataset into predictor
nodes (leaves) nodes (leaves)
@@ -261,10 +289,11 @@ class Stree(BaseEstimator, ClassifierMixin):
return None return None
if np.unique(y).shape[0] == 1: if np.unique(y).shape[0] == 1:
# only 1 class => pure dataset # only 1 class => pure dataset
return Snode(None, X, y, title + ', <pure>') return Snode(None, X, y, title + ", <pure>")
# Train the model # Train the model
clf = LinearSVC(max_iter=self.max_iter, random_state=self.random_state, clf = LinearSVC(
C=self.C) # , sample_weight=sample_weight) max_iter=self.max_iter, random_state=self.random_state, C=self.C
) # , sample_weight=sample_weight)
clf.fit(X, y, sample_weight=sample_weight) clf.fit(X, y, sample_weight=sample_weight)
tree = Snode(clf, X, y, title) tree = Snode(clf, X, y, title)
self.depth_ = max(depth, self.depth_) self.depth_ = max(depth, self.depth_)
@@ -274,9 +303,9 @@ class Stree(BaseEstimator, ClassifierMixin):
sw_u, sw_d = self._split_array(sample_weight, down) sw_u, sw_d = self._split_array(sample_weight, down)
if X_U is None or X_D is None: if X_U is None or X_D is None:
# didn't part anything # didn't part anything
return Snode(clf, X, y, title + ', <cgaf>') return Snode(clf, X, y, title + ", <cgaf>")
tree.set_up(self.train(X_U, y_u, sw_u, depth + 1, title + ' - Up')) tree.set_up(self.train(X_U, y_u, sw_u, depth + 1, title + " - Up"))
tree.set_down(self.train(X_D, y_d, sw_d, depth + 1, title + ' - Down')) tree.set_down(self.train(X_D, y_d, sw_d, depth + 1, title + " - Down"))
return tree return tree
def _reorder_results(self, y: np.array, indices: np.array) -> np.array: def _reorder_results(self, y: np.array, indices: np.array) -> np.array:
@@ -308,8 +337,10 @@ class Stree(BaseEstimator, ClassifierMixin):
:return: array of labels :return: array of labels
:rtype: np.array :rtype: np.array
""" """
def predict_class(xp: np.array, indices: np.array,
node: Snode) -> np.array: def predict_class(
xp: np.array, indices: np.array, node: Snode
) -> np.array:
if xp is None: if xp is None:
return [], [] return [], []
if node.is_leaf(): if node.is_leaf():
@@ -322,14 +353,18 @@ class Stree(BaseEstimator, ClassifierMixin):
prx_u, prin_u = predict_class(X_U, i_u, node.get_up()) prx_u, prin_u = predict_class(X_U, i_u, node.get_up())
prx_d, prin_d = predict_class(X_D, i_d, node.get_down()) prx_d, prin_d = predict_class(X_D, i_d, node.get_down())
return np.append(prx_u, prx_d), np.append(prin_u, prin_d) return np.append(prx_u, prx_d), np.append(prin_u, prin_d)
# sklearn check # sklearn check
check_is_fitted(self, ['tree_']) check_is_fitted(self, ["tree_"])
# Input validation # Input validation
X = check_array(X) X = check_array(X)
# setup prediction & make it happen # setup prediction & make it happen
indices = np.arange(X.shape[0]) indices = np.arange(X.shape[0])
result = self._reorder_results( result = (
*predict_class(X, indices, self.tree_)).astype(int).ravel() self._reorder_results(*predict_class(X, indices, self.tree_))
.astype(int)
.ravel()
)
return self.classes_[result] return self.classes_[result]
def predict_proba(self, X: np.array) -> np.array: def predict_proba(self, X: np.array) -> np.array:
@@ -341,8 +376,10 @@ class Stree(BaseEstimator, ClassifierMixin):
each class each class
:rtype: np.array :rtype: np.array
""" """
def predict_class(xp: np.array, indices: np.array, dist: np.array,
node: Snode) -> np.array: def predict_class(
xp: np.array, indices: np.array, dist: np.array, node: Snode
) -> np.array:
"""Run the tree to compute predictions """Run the tree to compute predictions
:param xp: subdataset of samples :param xp: subdataset of samples
@@ -375,7 +412,7 @@ class Stree(BaseEstimator, ClassifierMixin):
return np.append(prx_u, prx_d), np.append(prin_u, prin_d) return np.append(prx_u, prx_d), np.append(prin_u, prin_d)
# sklearn check # sklearn check
check_is_fitted(self, ['tree_']) check_is_fitted(self, ["tree_"])
# Input validation # Input validation
X = check_array(X) X = check_array(X)
# setup prediction & make it happen # setup prediction & make it happen
@@ -426,7 +463,7 @@ class Stree(BaseEstimator, ClassifierMixin):
:return: description of nodes in the tree in preorder :return: description of nodes in the tree in preorder
:rtype: str :rtype: str
""" """
output = '' output = ""
for i in self: for i in self:
output += str(i) + '\n' output += str(i) + "\n"
return output return output

76
stree/Strees_grapher.py
View File

@@ -1,10 +1,10 @@
''' """
__author__ = "Ricardo Montañana Gómez" __author__ = "Ricardo Montañana Gómez"
__copyright__ = "Copyright 2020, Ricardo Montañana Gómez" __copyright__ = "Copyright 2020, Ricardo Montañana Gómez"
__license__ = "MIT" __license__ = "MIT"
__version__ = "0.9" __version__ = "0.9"
Plot 3D views of nodes in Stree Plot 3D views of nodes in Stree
''' """
import os import os
@@ -17,7 +17,6 @@ from .Strees import Stree, Snode, Siterator
class Snode_graph(Snode): class Snode_graph(Snode):
def __init__(self, node: Stree): def __init__(self, node: Stree):
self._plot_size = (8, 8) self._plot_size = (8, 8)
self._xlimits = (None, None) self._xlimits = (None, None)
@@ -29,34 +28,36 @@ class Snode_graph(Snode):
def set_plot_size(self, size: tuple): def set_plot_size(self, size: tuple):
self._plot_size = size self._plot_size = size
def get_plot_size(self) -> tuple:
return self._plot_size
def _is_pure(self) -> bool: def _is_pure(self) -> bool:
"""is considered pure a leaf node with one label """is considered pure a leaf node with one label
""" """
if self.is_leaf(): if self.is_leaf():
return self._belief == 1. return self._belief == 1.0
return False return False
def set_axis_limits(self, limits: tuple): def set_axis_limits(self, limits: tuple):
self._xlimits = limits[0] self._xlimits, self._ylimits, self._zlimits = limits
self._ylimits = limits[1]
self._zlimits = limits[2]
def _set_graphics_axis(self, ax: Axes3D): def _set_graphics_axis(self, ax: Axes3D):
ax.set_xlim(self._xlimits) ax.set_xlim(self._xlimits)
ax.set_ylim(self._ylimits) ax.set_ylim(self._ylimits)
ax.set_zlim(self._zlimits) ax.set_zlim(self._zlimits)
def save_hyperplane(self, save_folder: str = './', save_prefix: str = '', def save_hyperplane(
save_seq: int = 1): self, save_folder: str = "./", save_prefix: str = "", save_seq: int = 1
):
_, fig = self.plot_hyperplane() _, fig = self.plot_hyperplane()
name = f"{save_folder}{save_prefix}STnode{save_seq}.png" name = f"{save_folder}{save_prefix}STnode{save_seq}.png"
fig.savefig(name, bbox_inches='tight') fig.savefig(name, bbox_inches="tight")
plt.close(fig) plt.close(fig)
def _get_cmap(self): def _get_cmap(self):
cmap = 'jet' cmap = "jet"
if self._is_pure() and self._class == 1: if self._is_pure() and self._class == 1:
cmap = 'jet_r' cmap = "jet_r"
return cmap return cmap
def _graph_title(self): def _graph_title(self):
@@ -65,22 +66,31 @@ class Snode_graph(Snode):
def plot_hyperplane(self, plot_distribution: bool = True): def plot_hyperplane(self, plot_distribution: bool = True):
fig = plt.figure(figsize=self._plot_size) fig = plt.figure(figsize=self._plot_size)
ax = fig.add_subplot(1, 1, 1, projection='3d') ax = fig.add_subplot(1, 1, 1, projection="3d")
if not self._is_pure(): if not self._is_pure():
# Can't plot hyperplane of leaves with one label because it hasn't # Can't plot hyperplane of leaves with one label because it hasn't
# classiffier # classiffier
# get the splitting hyperplane # get the splitting hyperplane
def hyperplane(x, y): return (-self._interceptor def hyperplane(x, y):
return (
-self._interceptor
- self._vector[0][0] * x - self._vector[0][0] * x
- self._vector[0][1] * y) \ - self._vector[0][1] * y
/ self._vector[0][2] ) / self._vector[0][2]
tmpx = np.linspace(self._X[:, 0].min(), self._X[:, 0].max()) tmpx = np.linspace(self._X[:, 0].min(), self._X[:, 0].max())
tmpy = np.linspace(self._X[:, 1].min(), self._X[:, 1].max()) tmpy = np.linspace(self._X[:, 1].min(), self._X[:, 1].max())
xx, yy = np.meshgrid(tmpx, tmpy) xx, yy = np.meshgrid(tmpx, tmpy)
ax.plot_surface(xx, yy, hyperplane(xx, yy), alpha=.5, ax.plot_surface(
antialiased=True, rstride=1, cstride=1, xx,
cmap='seismic') yy,
hyperplane(xx, yy),
alpha=0.5,
antialiased=True,
rstride=1,
cstride=1,
cmap="seismic",
)
self._set_graphics_axis(ax) self._set_graphics_axis(ax)
if plot_distribution: if plot_distribution:
self.plot_distribution(ax) self.plot_distribution(ax)
@@ -92,14 +102,15 @@ class Snode_graph(Snode):
def plot_distribution(self, ax: Axes3D = None): def plot_distribution(self, ax: Axes3D = None):
if ax is None: if ax is None:
fig = plt.figure(figsize=self._plot_size) fig = plt.figure(figsize=self._plot_size)
ax = fig.add_subplot(1, 1, 1, projection='3d') ax = fig.add_subplot(1, 1, 1, projection="3d")
plt.title(self._graph_title()) plt.title(self._graph_title())
cmap = self._get_cmap() cmap = self._get_cmap()
ax.scatter(self._X[:, 0], self._X[:, 1], ax.scatter(
self._X[:, 2], c=self._y, cmap=cmap) self._X[:, 0], self._X[:, 1], self._X[:, 2], c=self._y, cmap=cmap
ax.set_xlabel('X0') )
ax.set_ylabel('X1') ax.set_xlabel("X0")
ax.set_zlabel('X2') ax.set_ylabel("X1")
ax.set_zlabel("X2")
plt.show() plt.show()
@@ -112,17 +123,17 @@ class Stree_grapher(Stree):
self._plot_size = (8, 8) self._plot_size = (8, 8)
self._tree_gr = None self._tree_gr = None
# make Snode store X's # make Snode store X's
os.environ['TESTING'] = '1' os.environ["TESTING"] = "1"
self._fitted = False self._fitted = False
self._pca = None self._pca = None
super().__init__(**params) super().__init__(**params)
def __del__(self): def __del__(self):
try: try:
os.environ.pop('TESTING') os.environ.pop("TESTING")
except KeyError: except KeyError:
pass pass
plt.close('all') plt.close("all")
def _copy_tree(self, node: Snode) -> Snode_graph: def _copy_tree(self, node: Snode) -> Snode_graph:
mirror = Snode_graph(node) mirror = Snode_graph(node)
@@ -161,9 +172,9 @@ class Stree_grapher(Stree):
def _check_fitted(self): def _check_fitted(self):
if not self._fitted: if not self._fitted:
raise Exception('Have to fit the grapher first!') raise Exception("Have to fit the grapher first!")
def save_all(self, save_folder: str = './', save_prefix: str = ''): def save_all(self, save_folder: str = "./", save_prefix: str = ""):
"""Save all the node plots in png format, each with a sequence number """Save all the node plots in png format, each with a sequence number
:param save_folder: folder where the plots are saved, defaults to './' :param save_folder: folder where the plots are saved, defaults to './'
@@ -174,8 +185,9 @@ class Stree_grapher(Stree):
os.mkdir(save_folder) os.mkdir(save_folder)
seq = 1 seq = 1
for node in self: for node in self:
node.save_hyperplane(save_folder=save_folder, node.save_hyperplane(
save_prefix=save_prefix, save_seq=seq) save_folder=save_folder, save_prefix=save_prefix, save_seq=seq
)
seq += 1 seq += 1
def plot_all(self): def plot_all(self):

2
stree/__init__.py
View File

@@ -1,2 +1,4 @@
from .Strees import Stree, Snode, Siterator from .Strees import Stree, Snode, Siterator
from .Strees_grapher import Stree_grapher, Snode_graph from .Strees_grapher import Stree_grapher, Snode_graph
__all__ = ["Stree", "Snode", "Siterator", "Stree_grapher", "Snode_graph"]

211
stree/tests/Strees_grapher_test.py Normal file
View File

@@ -0,0 +1,211 @@
import os
import imghdr
import unittest
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import warnings
from sklearn.datasets import make_classification
from stree import Stree_grapher, Snode_graph
def get_dataset(random_state=0, n_features=3):
X, y = make_classification(
n_samples=1500,
n_features=n_features,
n_informative=3,
n_redundant=0,
n_repeated=0,
n_classes=2,
n_clusters_per_class=2,
class_sep=1.5,
flip_y=0,
weights=[0.5, 0.5],
random_state=random_state,
)
return X, y
class Stree_grapher_test(unittest.TestCase):
def __init__(self, *args, **kwargs):
os.environ["TESTING"] = "1"
self._random_state = 1
self._clf = Stree_grapher(
dict(random_state=self._random_state, use_predictions=False)
)
self._clf.fit(*get_dataset(self._random_state, n_features=4))
super().__init__(*args, **kwargs)
@classmethod
def tearDownClass(cls):
try:
os.environ.pop("TESTING")
except KeyError:
pass
def test_iterator(self):
"""Check preorder iterator
"""
expected = [
"root",
"root - Down",
"root - Down - Down, <cgaf> - Leaf class=1 belief= 0.976023 counts"
"=(array([0, 1]), array([ 17, 692]))",
"root - Down - Up",
"root - Down - Up - Down, <cgaf> - Leaf class=0 belief= 0.500000 "
"counts=(array([0, 1]), array([1, 1]))",
"root - Down - Up - Up, <cgaf> - Leaf class=0 belief= 0.888889 "
"counts=(array([0, 1]), array([8, 1]))",
"root - Up, <cgaf> - Leaf class=0 belief= 0.928205 counts=(array("
"[0, 1]), array([724, 56]))",
]
computed = []
for node in self._clf:
computed.append(str(node))
self.assertListEqual(expected, computed)
def test_score(self):
X, y = get_dataset(self._random_state)
accuracy_score = self._clf.score(X, y)
yp = self._clf.predict(X)
accuracy_computed = np.mean(yp == y)
self.assertEqual(accuracy_score, accuracy_computed)
self.assertGreater(accuracy_score, 0.86)
def test_save_all(self):
folder_name = "/tmp/"
file_names = [f"{folder_name}STnode{i}.png" for i in range(1, 8)]
with warnings.catch_warnings():
warnings.simplefilter("ignore")
matplotlib.use("Agg")
self._clf.save_all(save_folder=folder_name)
for file_name in file_names:
self.assertTrue(os.path.exists(file_name))
self.assertEqual("png", imghdr.what(file_name))
os.remove(file_name)
def test_plot_all(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
matplotlib.use("Agg")
num_figures_before = plt.gcf().number
self._clf.plot_all()
num_figures_after = plt.gcf().number
self.assertEqual(7, num_figures_after - num_figures_before)
def test_filt_4_dims_dataset(self):
self._clf.fit(*get_dataset(self._random_state, n_features=4))
class Snode_graph_test(unittest.TestCase):
def __init__(self, *args, **kwargs):
os.environ["TESTING"] = "1"
self._random_state = 1
self._clf = Stree_grapher(
dict(random_state=self._random_state, use_predictions=False)
)
self._clf.fit(*get_dataset(self._random_state))
super().__init__(*args, **kwargs)
@classmethod
def tearDownClass(cls):
"""Remove the testing environ variable
"""
try:
os.environ.pop("TESTING")
except KeyError:
pass
def test_plot_size(self):
default = self._clf._tree_gr.get_plot_size()
expected = (17, 3)
self._clf._tree_gr.set_plot_size(expected)
self.assertEqual(expected, self._clf._tree_gr.get_plot_size())
self._clf._tree_gr.set_plot_size(default)
self.assertEqual(default, self._clf._tree_gr.get_plot_size())
def test_attributes_in_leaves_graph(self):
"""Check if the attributes in leaves have correct values so they form a
predictor
"""
def check_leave(node: Snode_graph):
if not node.is_leaf():
check_leave(node.get_down())
check_leave(node.get_up())
return
# Check Belief in leave
classes, card = np.unique(node._y, return_counts=True)
max_card = max(card)
min_card = min(card)
if len(classes) > 1:
try:
belief = max_card / (max_card + min_card)
except ZeroDivisionError:
belief = 0.0
else:
belief = 1
self.assertEqual(belief, node._belief)
# Check Class
class_computed = classes[card == max_card]
self.assertEqual(class_computed, node._class)
check_leave(self._clf._tree_gr)
def test_nodes_graph_coefs(self):
"""Check if the nodes of the tree have the right attributes filled
"""
def run_tree(node: Snode_graph):
if node._belief < 1:
# only exclude pure leaves
self.assertIsNotNone(node._clf)
self.assertIsNotNone(node._clf.coef_)
self.assertIsNotNone(node._vector)
self.assertIsNotNone(node._interceptor)
if node.is_leaf():
return
run_tree(node.get_down())
run_tree(node.get_up())
run_tree(self._clf._tree_gr)
def test_save_hyperplane(self):
folder_name = "/tmp/"
file_name = f"{folder_name}STnode1.png"
with warnings.catch_warnings():
warnings.simplefilter("ignore")
matplotlib.use("Agg")
self._clf._tree_gr.save_hyperplane(folder_name)
self.assertTrue(os.path.exists(file_name))
self.assertEqual("png", imghdr.what(file_name))
os.remove(file_name)
def test_plot_hyperplane_with_distribution(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
matplotlib.use("Agg")
num_figures_before = plt.gcf().number
self._clf._tree_gr.plot_hyperplane(plot_distribution=True)
num_figures_after = plt.gcf().number
self.assertEqual(1, num_figures_after - num_figures_before)
def test_plot_hyperplane_without_distribution(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
matplotlib.use("Agg")
num_figures_before = plt.gcf().number
self._clf._tree_gr.plot_hyperplane(plot_distribution=False)
num_figures_after = plt.gcf().number
self.assertEqual(1, num_figures_after - num_figures_before)
def test_plot_distribution(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
matplotlib.use("Agg")
num_figures_before = plt.gcf().number
self._clf._tree_gr.plot_distribution()
num_figures_after = plt.gcf().number
self.assertEqual(1, num_figures_after - num_figures_before)

220
stree/tests/Strees_test.py
View File

@@ -7,30 +7,54 @@ from sklearn.datasets import make_classification
from stree import Stree, Snode from stree import Stree, Snode
class Stree_test(unittest.TestCase): def get_dataset(random_state=0):
X, y = make_classification(
n_samples=1500,
n_features=3,
n_informative=3,
n_redundant=0,
n_repeated=0,
n_classes=2,
n_clusters_per_class=2,
class_sep=1.5,
flip_y=0,
weights=[0.5, 0.5],
random_state=random_state,
)
return X, y
class Stree_test(unittest.TestCase):
def __init__(self, *args, **kwargs): def __init__(self, *args, **kwargs):
os.environ['TESTING'] = '1' os.environ["TESTING"] = "1"
self._random_state = 1 self._random_state = 1
self._clf = Stree(random_state=self._random_state, self._clf = Stree(
use_predictions=False) random_state=self._random_state, use_predictions=False
self._clf.fit(*self._get_Xy()) )
self._clf.fit(*get_dataset(self._random_state))
super().__init__(*args, **kwargs) super().__init__(*args, **kwargs)
@classmethod @classmethod
def tearDownClass(cls): def tearDownClass(cls):
try: try:
os.environ.pop('TESTING') os.environ.pop("TESTING")
except KeyError: except KeyError:
pass pass
def _get_Xy(self): def _get_Xy(self):
X, y = make_classification(n_samples=1500, n_features=3, X, y = make_classification(
n_informative=3, n_redundant=0, n_samples=1500,
n_repeated=0, n_classes=2, n_features=3,
n_clusters_per_class=2, class_sep=1.5, n_informative=3,
flip_y=0, weights=[0.5, 0.5], n_redundant=0,
random_state=self._random_state) n_repeated=0,
n_classes=2,
n_clusters_per_class=2,
class_sep=1.5,
flip_y=0,
weights=[0.5, 0.5],
random_state=self._random_state,
)
return X, y return X, y
def _check_tree(self, node: Snode): def _check_tree(self, node: Snode):
@@ -85,15 +109,16 @@ class Stree_test(unittest.TestCase):
Returns: Returns:
tuple -- tuple with samples, categories tuple -- tuple with samples, categories
""" """
data = np.genfromtxt(file_name, delimiter=',') data = np.genfromtxt(file_name, delimiter=",")
data = np.array(data) data = np.array(data)
column_y = data.shape[1] - 1 column_y = data.shape[1] - 1
fy = data[:, column_y] fy = data[:, column_y]
fx = np.delete(data, column_y, axis=1) fx = np.delete(data, column_y, axis=1)
return fx, fy return fx, fy
def _find_out(self, px: np.array, x_original: np.array, def _find_out(
y_original) -> list: self, px: np.array, x_original: np.array, y_original
) -> list:
"""Find the original values of y for a given array of samples """Find the original values of y for a given array of samples
Arguments: Arguments:
@@ -112,19 +137,19 @@ class Stree_test(unittest.TestCase):
return res return res
def test_single_prediction(self): def test_single_prediction(self):
X, y = self._get_Xy() X, y = get_dataset(self._random_state)
yp = self._clf.predict((X[0, :].reshape(-1, X.shape[1]))) yp = self._clf.predict((X[0, :].reshape(-1, X.shape[1])))
self.assertEqual(yp[0], y[0]) self.assertEqual(yp[0], y[0])
def test_multiple_prediction(self): def test_multiple_prediction(self):
# First 27 elements the predictions are the same as the truth # First 27 elements the predictions are the same as the truth
num = 27 num = 27
X, y = self._get_Xy() X, y = get_dataset(self._random_state)
yp = self._clf.predict(X[:num, :]) yp = self._clf.predict(X[:num, :])
self.assertListEqual(y[:num].tolist(), yp.tolist()) self.assertListEqual(y[:num].tolist(), yp.tolist())
def test_score(self): def test_score(self):
X, y = self._get_Xy() X, y = get_dataset(self._random_state)
accuracy_score = self._clf.score(X, y) accuracy_score = self._clf.score(X, y)
yp = self._clf.predict(X) yp = self._clf.predict(X)
accuracy_computed = np.mean(yp == y) accuracy_computed = np.mean(yp == y)
@@ -138,35 +163,55 @@ class Stree_test(unittest.TestCase):
# Element 28 has a different prediction than the truth # Element 28 has a different prediction than the truth
decimals = 5 decimals = 5
prob = 0.29026400766 prob = 0.29026400766
X, y = self._get_Xy() X, y = get_dataset(self._random_state)
yp = self._clf.predict_proba(X[28, :].reshape(-1, X.shape[1])) yp = self._clf.predict_proba(X[28, :].reshape(-1, X.shape[1]))
self.assertEqual(np.round(1 - prob, decimals), self.assertEqual(
np.round(yp[0:, 0], decimals)) np.round(1 - prob, decimals), np.round(yp[0:, 0], decimals)
)
self.assertEqual(1, y[28]) self.assertEqual(1, y[28])
self.assertAlmostEqual( self.assertAlmostEqual(
round(prob, decimals), round(prob, decimals), round(yp[0, 1], decimals), decimals
round(yp[0, 1], decimals),
decimals
) )
def test_multiple_predict_proba(self): def test_multiple_predict_proba(self):
# First 27 elements the predictions are the same as the truth # First 27 elements the predictions are the same as the truth
num = 27 num = 27
decimals = 5 decimals = 5
X, y = self._get_Xy() X, y = get_dataset(self._random_state)
yp = self._clf.predict_proba(X[:num, :]) yp = self._clf.predict_proba(X[:num, :])
self.assertListEqual( self.assertListEqual(
y[:num].tolist(), np.argmax(yp[:num], axis=1).tolist()) y[:num].tolist(), np.argmax(yp[:num], axis=1).tolist()
expected_proba = [0.88395641, 0.36746962, 0.84158767, 0.34106833, )
0.14269291, 0.85193236, expected_proba = [
0.29876058, 0.7282164, 0.85958616, 0.89517877, 0.88395641,
0.99745224, 0.18860349, 0.36746962,
0.30756427, 0.8318412, 0.18981198, 0.15564624, 0.84158767,
0.25740655, 0.22923355, 0.34106833,
0.87365959, 0.49928689, 0.95574351, 0.28761257, 0.14269291,
0.28906333, 0.32643692, 0.85193236,
0.29788483, 0.01657364, 0.81149083] 0.29876058,
0.7282164,
0.85958616,
0.89517877,
0.99745224,
0.18860349,
0.30756427,
0.8318412,
0.18981198,
0.15564624,
0.25740655,
0.22923355,
0.87365959,
0.49928689,
0.95574351,
0.28761257,
0.28906333,
0.32643692,
0.29788483,
0.01657364,
0.81149083,
]
expected = np.round(expected_proba, decimals=decimals).tolist() expected = np.round(expected_proba, decimals=decimals).tolist()
computed = np.round(yp[:, 1], decimals=decimals).tolist() computed = np.round(yp[:, 1], decimals=decimals).tolist()
for i in range(len(expected)): for i in range(len(expected)):
@@ -178,11 +223,13 @@ class Stree_test(unittest.TestCase):
use vector of coefficients to compute both predictions and splitted use vector of coefficients to compute both predictions and splitted
data data
""" """
model_clf = Stree(random_state=self._random_state, model_clf = Stree(
use_predictions=True) random_state=self._random_state, use_predictions=True
model_computed = Stree(random_state=self._random_state, )
use_predictions=False) model_computed = Stree(
X, y = self._get_Xy() random_state=self._random_state, use_predictions=False
)
X, y = get_dataset(self._random_state)
model_clf.fit(X, y) model_clf.fit(X, y)
model_computed.fit(X, y) model_computed.fit(X, y)
return model_clf, model_computed, X, y return model_clf, model_computed, X, y
@@ -194,74 +241,76 @@ class Stree_test(unittest.TestCase):
""" """
use_clf, use_math, X, _ = self.build_models() use_clf, use_math, X, _ = self.build_models()
self.assertListEqual( self.assertListEqual(
use_clf.predict(X).tolist(), use_clf.predict(X).tolist(), use_math.predict(X).tolist()
use_math.predict(X).tolist()
) )
def test_use_model_score(self): def test_use_model_score(self):
use_clf, use_math, X, y = self.build_models() use_clf, use_math, X, y = self.build_models()
b = use_math.score(X, y) b = use_math.score(X, y)
self.assertEqual( self.assertEqual(use_clf.score(X, y), b)
use_clf.score(X, y), self.assertGreater(b, 0.95)
b
)
self.assertGreater(b, .95)
def test_use_model_predict_proba(self): def test_use_model_predict_proba(self):
use_clf, use_math, X, _ = self.build_models() use_clf, use_math, X, _ = self.build_models()
self.assertListEqual( self.assertListEqual(
use_clf.predict_proba(X).tolist(), use_clf.predict_proba(X).tolist(),
use_math.predict_proba(X).tolist() use_math.predict_proba(X).tolist(),
) )
def test_single_vs_multiple_prediction(self): def test_single_vs_multiple_prediction(self):
"""Check if predicting sample by sample gives the same result as """Check if predicting sample by sample gives the same result as
predicting all samples at once predicting all samples at once
""" """
X, _ = self._get_Xy() X, _ = get_dataset(self._random_state)
# Compute prediction line by line # Compute prediction line by line
yp_line = np.array([], dtype=int) yp_line = np.array([], dtype=int)
for xp in X: for xp in X:
yp_line = np.append(yp_line, self._clf.predict( yp_line = np.append(
xp.reshape(-1, X.shape[1]))) yp_line, self._clf.predict(xp.reshape(-1, X.shape[1]))
)
# Compute prediction at once # Compute prediction at once
yp_once = self._clf.predict(X) yp_once = self._clf.predict(X)
# #
self.assertListEqual(yp_line.tolist(), yp_once.tolist()) self.assertListEqual(yp_line.tolist(), yp_once.tolist())
def test_iterator(self): def test_iterator_and_str(self):
"""Check preorder iterator """Check preorder iterator
""" """
expected = [ expected = [
'root', "root",
'root - Down', "root - Down",
'root - Down - Down, <cgaf> - Leaf class=1 belief= 0.975989 counts' "root - Down - Down, <cgaf> - Leaf class=1 belief= 0.975989 counts"
'=(array([0, 1]), array([ 17, 691]))', "=(array([0, 1]), array([ 17, 691]))",
'root - Down - Up', "root - Down - Up",
'root - Down - Up - Down, <cgaf> - Leaf class=1 belief= 0.750000 ' "root - Down - Up - Down, <cgaf> - Leaf class=1 belief= 0.750000 "
'counts=(array([0, 1]), array([1, 3]))', "counts=(array([0, 1]), array([1, 3]))",
'root - Down - Up - Up, <pure> - Leaf class=0 belief= 1.000000 ' "root - Down - Up - Up, <pure> - Leaf class=0 belief= 1.000000 "
'counts=(array([0]), array([7]))', "counts=(array([0]), array([7]))",
'root - Up, <cgaf> - Leaf class=0 belief= 0.928297 counts=(array(' "root - Up, <cgaf> - Leaf class=0 belief= 0.928297 counts=(array("
'[0, 1]), array([725, 56]))', "[0, 1]), array([725, 56]))",
] ]
computed = [] computed = []
expected_string = ""
for node in self._clf: for node in self._clf:
computed.append(str(node)) computed.append(str(node))
expected_string += str(node) + "\n"
self.assertListEqual(expected, computed) self.assertListEqual(expected, computed)
self.assertEqual(expected_string, str(self._clf))
def test_is_a_sklearn_classifier(self): def test_is_a_sklearn_classifier(self):
import warnings import warnings
from sklearn.exceptions import ConvergenceWarning from sklearn.exceptions import ConvergenceWarning
warnings.filterwarnings('ignore', category=ConvergenceWarning)
warnings.filterwarnings('ignore', category=RuntimeWarning) warnings.filterwarnings("ignore", category=ConvergenceWarning)
warnings.filterwarnings("ignore", category=RuntimeWarning)
from sklearn.utils.estimator_checks import check_estimator from sklearn.utils.estimator_checks import check_estimator
check_estimator(Stree()) check_estimator(Stree())
def test_exception_if_C_is_negative(self): def test_exception_if_C_is_negative(self):
tclf = Stree(C=-1) tclf = Stree(C=-1)
with self.assertRaises(ValueError): with self.assertRaises(ValueError):
tclf.fit(*self._get_Xy()) tclf.fit(*get_dataset(self._random_state))
def test_check_max_depth_is_positive_or_None(self): def test_check_max_depth_is_positive_or_None(self):
tcl = Stree() tcl = Stree()
@@ -270,12 +319,12 @@ class Stree_test(unittest.TestCase):
self.assertGreaterEqual(1, tcl.max_depth) self.assertGreaterEqual(1, tcl.max_depth)
with self.assertRaises(ValueError): with self.assertRaises(ValueError):
tcl = Stree(max_depth=-1) tcl = Stree(max_depth=-1)
tcl.fit(*self._get_Xy()) tcl.fit(*get_dataset(self._random_state))
def test_check_max_depth(self): def test_check_max_depth(self):
depth = 3 depth = 3
tcl = Stree(random_state=self._random_state, max_depth=depth) tcl = Stree(random_state=self._random_state, max_depth=depth)
tcl.fit(*self._get_Xy()) tcl.fit(*get_dataset(self._random_state))
self.assertEqual(depth, tcl.depth_) self.assertEqual(depth, tcl.depth_)
def test_unfitted_tree_is_iterable(self): def test_unfitted_tree_is_iterable(self):
@@ -284,13 +333,13 @@ class Stree_test(unittest.TestCase):
class Snode_test(unittest.TestCase): class Snode_test(unittest.TestCase):
def __init__(self, *args, **kwargs): def __init__(self, *args, **kwargs):
os.environ['TESTING'] = '1' os.environ["TESTING"] = "1"
self._random_state = 1 self._random_state = 1
self._clf = Stree(random_state=self._random_state, self._clf = Stree(
use_predictions=True) random_state=self._random_state, use_predictions=True
self._clf.fit(*self._get_Xy()) )
self._clf.fit(*get_dataset(self._random_state))
super().__init__(*args, **kwargs) super().__init__(*args, **kwargs)
@classmethod @classmethod
@@ -298,18 +347,10 @@ class Snode_test(unittest.TestCase):
"""[summary] """[summary]
""" """
try: try:
os.environ.pop('TESTING') os.environ.pop("TESTING")
except KeyError: except KeyError:
pass pass
def _get_Xy(self):
X, y = make_classification(n_samples=1500, n_features=3,
n_informative=3, n_redundant=0, n_classes=2,
n_repeated=0, n_clusters_per_class=2,
class_sep=1.5, flip_y=0, weights=[0.5, 0.5],
random_state=self._random_state)
return X, y
def test_attributes_in_leaves(self): def test_attributes_in_leaves(self):
"""Check if the attributes in leaves have correct values so they form a """Check if the attributes in leaves have correct values so they form a
predictor predictor
@@ -328,7 +369,7 @@ class Snode_test(unittest.TestCase):
try: try:
belief = max_card / (max_card + min_card) belief = max_card / (max_card + min_card)
except ZeroDivisionError: except ZeroDivisionError:
belief = 0. belief = 0.0
else: else:
belief = 1 belief = 1
self.assertEqual(belief, node._belief) self.assertEqual(belief, node._belief)
@@ -355,3 +396,16 @@ class Snode_test(unittest.TestCase):
run_tree(node.get_up()) run_tree(node.get_up())
run_tree(self._clf.tree_) run_tree(self._clf.tree_)
def test_make_predictor_on_leaf(self):
test = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], "test")
test.make_predictor()
self.assertEqual(1, test._class)
self.assertEqual(0.75, test._belief)
def test_make_predictor_on_not_leaf(self):
test = Snode(None, [1, 2, 3, 4], [1, 0, 1, 1], "test")
test.set_up(Snode(None, [1], [1], "another_test"))
test.make_predictor()
self.assertIsNone(test._class)
self.assertEqual(0, test._belief)

8
stree/tests/__init__.py
View File

@@ -1 +1,9 @@
from .Strees_test import Stree_test, Snode_test from .Strees_test import Stree_test, Snode_test
from .Strees_grapher_test import Stree_grapher_test, Snode_graph_test
__all__ = [
"Stree_test",
"Snode_test",
"Stree_grapher_test",
"Snode_graph_test",
]