Doctorado-ML/mufs
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Change module name to MUFS

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This commit is contained in:
Ricardo Montañana Gómez
2021-08-02 17:44:51 +02:00
parent bd709131e4
commit d8299766c9
14 changed files with 77 additions and 76 deletions
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4
.coveragerc
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@@ -1,6 +1,6 @@
[run] [run]
branch = True branch = True
source = mfs source = mufs
[report] [report]
exclude_lines = exclude_lines =
@@ -10,4 +10,4 @@ exclude_lines =
if __name__ == .__main__.: if __name__ == .__main__.:
ignore_errors = True ignore_errors = True
omit = omit =
mfs/__init__.py mufs/__init__.py

6
.github/workflows/main.yml vendored
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@@ -30,9 +30,9 @@ jobs:
pip install -q --upgrade codecov coverage black flake8 codacy-coverage pip install -q --upgrade codecov coverage black flake8 codacy-coverage
- name: Lint - name: Lint
run: | run: |
black --check --diff mfs black --check --diff mufs
flake8 --count mfs flake8 --count mufs
- name: Tests & coverage - name: Tests & coverage
run: | run: |
coverage run -m unittest -v mfs.tests coverage run -m unittest -v mufs.tests
coverage report -m --fail-under=100 coverage report -m --fail-under=100

14
Makefile
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@@ -4,28 +4,26 @@ SHELL := /bin/bash
coverage: ## Run tests with coverage coverage: ## Run tests with coverage
coverage erase coverage erase
coverage run -m unittest -v mfs.tests coverage run -m unittest -v mufs.tests
coverage report -m coverage report -m
deps: ## Install dependencies deps: ## Install dependencies
pip install -r requirements.txt pip install -r requirements.txt
lint: ## Lint and static-check lint: ## Lint and static-check
black mfs black mufs
flake8 mfs flake8 mufs
mypy mfs mypy mufs
push: ## Push code with tags push: ## Push code with tags
git push && git push --tags git push && git push --tags
test: ## Run tests test: ## Run tests
python -m unittest -v mfs.tests python -m unittest -v mufs.tests
doc: ## Update documentation
make -C docs --makefile=Makefile html
build: ## Build package build: ## Build package
rm -fr dist/* rm -fr dist/*
rm -fr build/*
python setup.py sdist bdist_wheel python setup.py sdist bdist_wheel
doc-clean: ## Update documentation doc-clean: ## Update documentation

8
README.md
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@@ -1,8 +1,8 @@
![CI](https://github.com/Doctorado-ML/mfs/workflows/CI/badge.svg) ![CI](https://github.com/Doctorado-ML/mufs/workflows/CI/badge.svg)
[![Codacy Badge](https://app.codacy.com/project/badge/Grade/66ad727eb13e4c7a8816db1e44d994a7)](https://www.codacy.com/gh/Doctorado-ML/mfs/dashboard?utm_source=github.com&utm_medium=referral&utm_content=Doctorado-ML/mfs&utm_campaign=Badge_Grade) [![Codacy Badge](https://app.codacy.com/project/badge/Grade/66ad727eb13e4c7a8816db1e44d994a7)](https://www.codacy.com/gh/Doctorado-ML/mufs/dashboard?utm_source=github.com&utm_medium=referral&utm_content=Doctorado-ML/mufs&utm_campaign=Badge_Grade)
[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/Doctorado-ML/mfs.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/Doctorado-ML/mfs/context:python) [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/Doctorado-ML/mufs.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/Doctorado-ML/mufs/context:python)
# MFS # MUFS
## Multi Feature Selection ## Multi Feature Selection

4
mfs/tests/__init__.py
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@@ -1,4 +0,0 @@
from .MFS_test import MFS_test
from .Metrics_test import Metrics_test
__all__ = ["MFS_test", "Metrics_test"]

0
mfs/Metrics.py → mufs/Metrics.py
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2
mfs/Selection.py → mufs/Selection.py
View File

@@ -5,7 +5,7 @@ import numpy as np
from .Metrics import Metrics from .Metrics import Metrics
class MFS: class MUFS:
"""Compute Fast Fast Correlation Based Filter """Compute Fast Fast Correlation Based Filter
Yu, L. and Liu, H.; Feature Selection for High-Dimensional Data: A Fast Yu, L. and Liu, H.; Feature Selection for High-Dimensional Data: A Fast
Correlation Based Filter Solution,Proc. 20th Intl. Conf. Mach. Learn. Correlation Based Filter Solution,Proc. 20th Intl. Conf. Mach. Learn.

6
mfs/__init__.py → mufs/__init__.py
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@@ -1,9 +1,9 @@
from .Selection import MFS from .Selection import MUFS
__version__ = "0.1" __version__ = "0.1.1"
__author__ = "Ricardo Montañana Gómez" __author__ = "Ricardo Montañana Gómez"
__author_email__ = "Ricardo.Montanana@alu.uclm.es" __author_email__ = "Ricardo.Montanana@alu.uclm.es"
__copyright__ = "Copyright 2021, Ricardo Montañana Gómez" __copyright__ = "Copyright 2021, Ricardo Montañana Gómez"
__license__ = "MIT License" __license__ = "MIT License"
__all__ = ["MFS"] __all__ = ["MUFS"]

82
mfs/tests/MFS_test.py → mufs/tests/MUFS_test.py
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@@ -2,10 +2,10 @@ import unittest
from mdlp import MDLP from mdlp import MDLP
from sklearn.datasets import load_wine, load_iris from sklearn.datasets import load_wine, load_iris
from ..Selection import MFS from ..Selection import MUFS
class MFS_test(unittest.TestCase): class MUFS_test(unittest.TestCase):
def __init__(self, *args, **kwargs): def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs) super().__init__(*args, **kwargs)
mdlp = MDLP(random_state=1) mdlp = MDLP(random_state=1)
@@ -21,19 +21,19 @@ class MFS_test(unittest.TestCase):
self.assertAlmostEqual(a, b, tol) self.assertAlmostEqual(a, b, tol)
def test_initialize(self): def test_initialize(self):
mfs = MFS() mufs = MUFS()
mfs.fcbf(self.X_w, self.y_w, 0.05) mufs.fcbf(self.X_w, self.y_w, 0.05)
mfs._initialize(self.X_w, self.y_w) mufs._initialize(self.X_w, self.y_w)
self.assertIsNone(mfs.get_results()) self.assertIsNone(mufs.get_results())
self.assertListEqual([], mfs.get_scores()) self.assertListEqual([], mufs.get_scores())
self.assertDictEqual({}, mfs._su_features) self.assertDictEqual({}, mufs._su_features)
self.assertIsNone(mfs._su_labels) self.assertIsNone(mufs._su_labels)
def test_csf_wine(self): def test_csf_wine(self):
mfs = MFS() mufs = MUFS()
expected = [6, 12, 9, 4, 10, 0] expected = [6, 12, 9, 4, 10, 0]
self.assertListAlmostEqual( self.assertListAlmostEqual(
expected, mfs.cfs(self.X_w, self.y_w).get_results() expected, mufs.cfs(self.X_w, self.y_w).get_results()
) )
expected = [ expected = [
0.5218299405215557, 0.5218299405215557,
@@ -43,13 +43,13 @@ class MFS_test(unittest.TestCase):
0.28795671854246285, 0.28795671854246285,
0.2309165735173175, 0.2309165735173175,
] ]
self.assertListAlmostEqual(expected, mfs.get_scores()) self.assertListAlmostEqual(expected, mufs.get_scores())
def test_csf_wine_cont(self): def test_csf_wine_cont(self):
mfs = MFS(discrete=False) mufs = MUFS(discrete=False)
expected = [10, 6, 0, 2, 11, 9] expected = [10, 6, 0, 2, 11, 9]
self.assertListEqual( self.assertListEqual(
expected, mfs.cfs(self.X_wc, self.y_w).get_results() expected, mufs.cfs(self.X_wc, self.y_w).get_results()
) )
expected = [ expected = [
0.735264150416997, 0.735264150416997,
@@ -59,25 +59,25 @@ class MFS_test(unittest.TestCase):
0.513637402071709, 0.513637402071709,
0.41596400981378984, 0.41596400981378984,
] ]
self.assertListAlmostEqual(expected, mfs.get_scores()) self.assertListAlmostEqual(expected, mufs.get_scores())
def test_csf_max_features(self): def test_csf_max_features(self):
mfs = MFS(max_features=3) mufs = MUFS(max_features=3)
expected = [6, 12, 9] expected = [6, 12, 9]
self.assertListAlmostEqual( self.assertListAlmostEqual(
expected, mfs.cfs(self.X_w, self.y_w).get_results() expected, mufs.cfs(self.X_w, self.y_w).get_results()
) )
expected = [ expected = [
0.5218299405215557, 0.5218299405215557,
0.602513857132804, 0.602513857132804,
0.4877384978817362, 0.4877384978817362,
] ]
self.assertListAlmostEqual(expected, mfs.get_scores()) self.assertListAlmostEqual(expected, mufs.get_scores())
def test_csf_iris(self): def test_csf_iris(self):
mfs = MFS() mufs = MUFS()
expected = [3, 2, 0, 1] expected = [3, 2, 0, 1]
computed = mfs.cfs(self.X_i, self.y_i).get_results() computed = mufs.cfs(self.X_i, self.y_i).get_results()
self.assertListAlmostEqual(expected, computed) self.assertListAlmostEqual(expected, computed)
expected = [ expected = [
0.870521418179061, 0.870521418179061,
@@ -85,11 +85,11 @@ class MFS_test(unittest.TestCase):
0.5908278453318913, 0.5908278453318913,
0.40371971570693366, 0.40371971570693366,
] ]
self.assertListAlmostEqual(expected, mfs.get_scores()) self.assertListAlmostEqual(expected, mufs.get_scores())
def test_fcbf_wine(self): def test_fcbf_wine(self):
mfs = MFS() mufs = MUFS()
computed = mfs.fcbf(self.X_w, self.y_w, threshold=0.05).get_results() computed = mufs.fcbf(self.X_w, self.y_w, threshold=0.05).get_results()
expected = [6, 9, 12, 0, 11, 4] expected = [6, 9, 12, 0, 11, 4]
self.assertListAlmostEqual(expected, computed) self.assertListAlmostEqual(expected, computed)
expected = [ expected = [
@@ -100,11 +100,11 @@ class MFS_test(unittest.TestCase):
0.3790082191220976, 0.3790082191220976,
0.24972405134844652, 0.24972405134844652,
] ]
self.assertListAlmostEqual(expected, mfs.get_scores()) self.assertListAlmostEqual(expected, mufs.get_scores())
def test_fcbf_max_features(self): def test_fcbf_max_features(self):
mfs = MFS(max_features=3) mufs = MUFS(max_features=3)
computed = mfs.fcbf(self.X_w, self.y_w, threshold=0.05).get_results() computed = mufs.fcbf(self.X_w, self.y_w, threshold=0.05).get_results()
expected = [6, 9, 12] expected = [6, 9, 12]
self.assertListAlmostEqual(expected, computed) self.assertListAlmostEqual(expected, computed)
expected = [ expected = [
@@ -112,32 +112,34 @@ class MFS_test(unittest.TestCase):
0.46224298637417455, 0.46224298637417455,
0.44518278979085646, 0.44518278979085646,
] ]
self.assertListAlmostEqual(expected, mfs.get_scores()) self.assertListAlmostEqual(expected, mufs.get_scores())
def test_fcbf_iris(self): def test_fcbf_iris(self):
mfs = MFS() mufs = MUFS()
computed = mfs.fcbf(self.X_i, self.y_i, threshold=0.05).get_results() computed = mufs.fcbf(self.X_i, self.y_i, threshold=0.05).get_results()
expected = [3, 2] expected = [3, 2]
self.assertListAlmostEqual(expected, computed) self.assertListAlmostEqual(expected, computed)
expected = [0.870521418179061, 0.810724587460511] expected = [0.870521418179061, 0.810724587460511]
self.assertListAlmostEqual(expected, mfs.get_scores()) self.assertListAlmostEqual(expected, mufs.get_scores())
def test_compute_su_labels(self): def test_compute_su_labels(self):
mfs = MFS() mufs = MUFS()
mfs.fcbf(self.X_i, self.y_i, threshold=0.05) mufs.fcbf(self.X_i, self.y_i, threshold=0.05)
expected = [0.0, 0.0, 0.810724587460511, 0.870521418179061] expected = [0.0, 0.0, 0.810724587460511, 0.870521418179061]
self.assertListAlmostEqual(expected, mfs._compute_su_labels().tolist()) self.assertListAlmostEqual(
mfs._su_labels = [1, 2, 3, 4] expected, mufs._compute_su_labels().tolist()
self.assertListAlmostEqual([1, 2, 3, 4], mfs._compute_su_labels()) )
mufs._su_labels = [1, 2, 3, 4]
self.assertListAlmostEqual([1, 2, 3, 4], mufs._compute_su_labels())
def test_invalid_threshold(self): def test_invalid_threshold(self):
mfs = MFS() mufs = MUFS()
with self.assertRaises(ValueError): with self.assertRaises(ValueError):
mfs.fcbf(self.X_i, self.y_i, threshold=1e-15) mufs.fcbf(self.X_i, self.y_i, threshold=1e-15)
def test_fcbf_exit_threshold(self): def test_fcbf_exit_threshold(self):
mfs = MFS() mufs = MUFS()
computed = mfs.fcbf(self.X_w, self.y_w, threshold=0.4).get_results() computed = mufs.fcbf(self.X_w, self.y_w, threshold=0.4).get_results()
expected = [6, 9, 12] expected = [6, 9, 12]
self.assertListAlmostEqual(expected, computed) self.assertListAlmostEqual(expected, computed)
expected = [ expected = [
@@ -145,4 +147,4 @@ class MFS_test(unittest.TestCase):
0.46224298637417455, 0.46224298637417455,
0.44518278979085646, 0.44518278979085646,
] ]
self.assertListAlmostEqual(expected, mfs.get_scores()) self.assertListAlmostEqual(expected, mufs.get_scores())

0
mfs/tests/Metrics_test.py → mufs/tests/Metrics_test.py
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4
mufs/tests/__init__.py Normal file
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@@ -0,0 +1,4 @@
from .MUFS_test import MUFS_test
from .Metrics_test import Metrics_test
__all__ = ["MUFS_test", "Metrics_test"]

1
requirements.txt
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@@ -1 +1,2 @@
scikit-learn>0.24 scikit-learn>0.24
mdlp

10
sample.py
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@@ -1,11 +1,11 @@
import warnings import warnings
from mfs import MFS from mufs import MUFS
from mfs.Metrics import Metrics from mufs.Metrics import Metrics
from stree import Stree from stree import Stree
import numpy as np import numpy as np
from scipy.io import arff from scipy.io import arff
mfsc = MFS(discrete=False) mufsc = MUFS(discrete=False)
filename = "conn-bench-sonar-mines-rocks.arff" filename = "conn-bench-sonar-mines-rocks.arff"
data, meta = arff.loadarff(filename) data, meta = arff.loadarff(filename)
@@ -26,10 +26,10 @@ for i in range(n):
# Classification # Classification
warnings.filterwarnings("ignore") warnings.filterwarnings("ignore")
print("CFS") print("CFS")
cfs_f = mfsc.cfs(X, y).get_results() cfs_f = mufsc.cfs(X, y).get_results()
print(cfs_f) print(cfs_f)
print("FCBF") print("FCBF")
fcfb_f = mfsc.fcbf(X, y, 5e-2).get_results() fcfb_f = mufsc.fcbf(X, y, 5e-2).get_results()
print(fcfb_f, len(fcfb_f)) print(fcfb_f, len(fcfb_f))
print("X.shape=", X.shape) print("X.shape=", X.shape)
clf = Stree(random_state=0) clf = Stree(random_state=0)

10
setup.py
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@@ -8,7 +8,7 @@ def readme():
def get_data(field: str): def get_data(field: str):
item = "" item = ""
with open("mfs/__init__.py") as f: with open("mufs/__init__.py") as f:
for line in f.readlines(): for line in f.readlines():
if line.startswith(f"__{field}__"): if line.startswith(f"__{field}__"):
delim = '"' if '"' in line else "'" delim = '"' if '"' in line else "'"
@@ -20,16 +20,16 @@ def get_data(field: str):
setuptools.setup( setuptools.setup(
name="MFS", name="MUFS",
version=get_data("version"), version=get_data("version"),
license=get_data("license"), license=get_data("license"),
description="Multi Feature Selection", description="Multi Feature Selection",
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/mfs#mfs", url="https://github.com/Doctorado-ML/mufs#mufs",
project_urls={ project_urls={
"Code": "https://github.com/Doctorado-ML/mfs", "Code": "https://github.com/Doctorado-ML/mufs",
}, },
author=get_data("author"), author=get_data("author"),
author_email=get_data("author_email"), author_email=get_data("author_email"),
@@ -43,6 +43,6 @@ setuptools.setup(
"Intended Audience :: Science/Research", "Intended Audience :: Science/Research",
], ],
install_requires=["scikit-learn"], install_requires=["scikit-learn"],
test_suite="mfs.tests", test_suite="mufs.tests",
zip_safe=False, zip_safe=False,
) )