fix format issue

.github/workflows/main.yml

@@ -12,13 +12,11 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest]
+        os: [macos-latest, ubuntu-latest]
-        python: ["3.10"]
+        python: [3.8]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v2
-        with:
-          fetch-depth: 0
       - name: Set up Python ${{ matrix.python }}
         uses: actions/setup-python@v2
         with:
@@ -28,37 +26,14 @@ jobs:
           pip install -q --upgrade pip
           pip install -q cython
           pip install -q numpy
-          pip install -q git+https://github.com/doctorado-ml/mdlp
+          pip install -q git+git://github.com/doctorado-ml/mdlp
           pip install -q -r requirements/dev.txt
-          pip install -q --upgrade codecov coverage black flake8 codacy-coverage unittest-xml-reporting
+          pip install -q --upgrade codecov coverage black flake8 codacy-coverage
       - name: Lint
         run: |
           black --check --diff mufs
           flake8 --count mufs
       - name: Tests & coverage
         run: |
-          mkdir .report
+          coverage run -m unittest -v mufs.tests
-          coverage run -m xmlrunner -v mufs.tests -o .report
-          coverage xml -i -o .report/coverage.xml
           coverage report -m --fail-under=100
-      - name: Get project version
-        run: echo "project_version=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV
-      - name: Override Coverage Source Path for Sonar
-        run: sed -i 's/\/home\/runner\/work\/mufs\/mufs\//\/github\/workspace\//g' .report/coverage.xml
-      - name: SonarQube scanner
-        uses: sonarsource/sonarqube-scan-action@master
-        env:
-          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-          SONAR_HOST_URL: ${{ secrets.SONAR_HOST_URL }}
-        with:
-          args: >
-            -Dsonar.projectVersion=${{ env.project_version }}
-            -Dsonar.python.coverage.reportPaths=.report/coverage.xml
-            -Dsonar.python.xunit.reportPath=.report/TEST*
-        # If you wish to fail your job when the Quality Gate is red, uncomment the
-        # following lines. This would typically be used to fail a deployment.
-      - name: Quality Gate
-        uses: sonarsource/sonarqube-quality-gate-action@master
-        timeout-minutes: 5
-        env:
-          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

.pre-commit-config.yaml

@@ -1,12 +1,12 @@
 repos:
   - repo: https://github.com/ambv/black
-    rev: 22.3.0
+    rev: 22.1.0
     hooks:
       - id: black
         exclude: ".virtual_documents"
         language_version: python3.8
   - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.9.2
+    rev: 3.8.4
     hooks:
       - id: flake8
         exclude: ".virtual_documents"
@@ -16,7 +16,7 @@ repos:
   #     - id: mypy
   #       # args: [--strict, --ignore-missing-imports]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v3.4.0
     hooks:
       - id: trailing-whitespace
       - id: check-case-conflict

Makefile

@@ -1,6 +1,6 @@
 SHELL := /bin/bash
 .DEFAULT_GOAL := help
-.PHONY: coverage deps help lint push test build
+.PHONY: coverage deps help lint push test doc build
 
 coverage:  ## Run tests with coverage
 	coverage erase
@@ -26,6 +26,9 @@ build:  ## Build package
 	rm -fr build/*
 	python setup.py sdist bdist_wheel
 
+doc-clean:  ## Update documentation
+	make -C docs --makefile=Makefile clean
+
 help: ## Show help message
 	@IFS=$$'\n' ; \
 	help_lines=(`fgrep -h "##" $(MAKEFILE_LIST) | fgrep -v fgrep | sed -e 's/\\$$//' | sed -e 's/##/:/'`); \

README.md

@@ -2,8 +2,6 @@
 [![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/mufs.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/Doctorado-ML/mufs/context:python)
 [![PyPI version](https://badge.fury.io/py/MUFS.svg)](https://badge.fury.io/py/MUFS)
-[![Technical Debt](https://haystack.rmontanana.es:25000/api/project_badges/measure?project=mufs&metric=sqale_index&token=1119a3bfd4025d50ef3009a44c600c16670ee31a)](https://haystack.rmontanana.es:25000/dashboard?id=mufs)
-[![Quality Gate Status](https://haystack.rmontanana.es:25000/api/project_badges/measure?project=mufs&metric=alert_status&token=1119a3bfd4025d50ef3009a44c600c16670ee31a)](https://haystack.rmontanana.es:25000/dashboard?id=mufs)
 ![https://img.shields.io/badge/python-3.8%2B-blue](https://img.shields.io/badge/python-3.8%2B-brightgreen)
 
 # MUFS

mufs/Selection.py

@@ -3,7 +3,6 @@ from sys import float_info
 from itertools import combinations
 import numpy as np
 from .Metrics import Metrics
-from ._version import __version__
 
 
 class MUFS:
@@ -41,11 +40,6 @@ class MUFS:
         )
         self._fitted = False
 
-    @staticmethod
-    def version() -> str:
-        """Return the version of the package."""
-        return __version__
-
     def _initialize(self, X, y):
         """Initialize the attributes so support multiple calls using same
         object
@@ -134,7 +128,7 @@ class MUFS:
         k = len(features)
         for pair in list(combinations(features, 2)):
             rff += self._compute_su_features(*pair)
-        return rcf / sqrt(k + (k**2 - k) * rff)
+        return k * rcf / sqrt(k + (k**2 - k) * rff)
 
     def cfs(self, X, y):
         """Correlation-based Feature Selection
@@ -172,10 +166,6 @@ class MUFS:
                     id_selected = idx
                     merit = merit_new
                 candidates.pop()
-            if id_selected is None:
-                # No more features to add all merits are nan because of
-                # constant features
-                break
             candidates.append(feature_order[id_selected])
             self._scores.append(merit)
             del feature_order[id_selected]

mufs/__init__.py

@@ -1,8 +1,9 @@
 from .Selection import MUFS
 
+__version__ = "0.1.2"
 __author__ = "Ricardo Montañana Gómez"
 __author_email__ = "Ricardo.Montanana@alu.uclm.es"
-__copyright__ = "Copyright 2021-2022, Ricardo Montañana Gómez"
+__copyright__ = "Copyright 2021, Ricardo Montañana Gómez"
 __license__ = "MIT License"
 
 __all__ = ["MUFS"]

mufs/_version.py

@@ -1 +0,0 @@
-__version__ = "0.1.3"

mufs/tests/MUFS_test.py

@@ -4,8 +4,8 @@ import pandas as pd
 import numpy as np
 from mdlp import MDLP
 from sklearn.datasets import load_wine, load_iris
+
 from ..Selection import MUFS
-from .._version import __version__
 
 
 class MUFSTest(unittest.TestCase):
@@ -18,11 +18,6 @@ class MUFSTest(unittest.TestCase):
         mdlp = MDLP(random_state=1)
         self.X_i = mdlp.fit_transform(self.X_ic, self.y_i).astype("int64")
 
-    def test_version(self):
-        """Check package version."""
-        mufs = MUFS()
-        self.assertEqual(__version__, mufs.version())
-
     def assertListAlmostEqual(self, list1, list2, tol=7):
         self.assertEqual(len(list1), len(list2))
         for a, b in zip(list1, list2):
@@ -39,33 +34,38 @@ class MUFSTest(unittest.TestCase):
 
     def test_csf_wine(self):
         mufs = MUFS()
-        expected = [6, 12, 9, 4, 10, 0]
+        expected = [6, 12, 9, 4, 10, 0, 7, 8]
         self.assertListEqual(
             expected, mufs.cfs(self.X_w, self.y_w).get_results()
         )
         expected = [
             0.5218299405215557,
-            0.602513857132804,
+            1.205027714265608,
-            0.4877384978817362,
+            1.4632154936452084,
-            0.3743688234383051,
+            1.4974752937532203,
-            0.28795671854246285,
+            1.4397835927123144,
-            0.2309165735173175,
+            1.385499441103905,
+            1.340618857006277,
+            1.2989177695790775,
         ]
         self.assertListAlmostEqual(expected, mufs.get_scores())
 
     def test_csf_wine_cont(self):
         mufs = MUFS(discrete=False)
-        expected = [10, 6, 0, 2, 11, 9]
+        expected = [10, 6, 0, 2, 11, 9, 8, 1, 5]
         self.assertListEqual(
             expected, mufs.cfs(self.X_wc, self.y_w).get_results()
         )
         expected = [
             0.735264150416997,
-            0.8321684551546848,
+            1.6643369103093697,
-            0.7439915858469107,
+            2.231974757540732,
-            0.6238883340158233,
+            2.4955533360632933,
-            0.513637402071709,
+            2.568187010358545,
-            0.41596400981378984,
+            2.495784058882739,
+            2.4409992149141915,
+            2.3665143407182456,
+            2.280111788845658,
         ]
         self.assertListAlmostEqual(expected, mufs.get_scores())
 
@@ -75,11 +75,7 @@ class MUFSTest(unittest.TestCase):
         self.assertListAlmostEqual(
             expected, mufs.cfs(self.X_w, self.y_w).get_results()
         )
-        expected = [
+        expected = [0.5218299405215557, 1.205027714265608, 1.4632154936452084]
-            0.5218299405215557,
-            0.602513857132804,
-            0.4877384978817362,
-        ]
         self.assertListAlmostEqual(expected, mufs.get_scores())
 
     def test_csf_iris(self):
@@ -89,9 +85,9 @@ class MUFSTest(unittest.TestCase):
         self.assertListEqual(expected, computed)
         expected = [
             0.870521418179061,
-            0.8968651482682227,
+            1.7937302965364454,
-            0.5908278453318913,
+            1.7724835359956739,
-            0.40371971570693366,
+            1.6148788628277346,
         ]
         self.assertListAlmostEqual(expected, mufs.get_scores())
 
@@ -159,11 +155,19 @@ class MUFSTest(unittest.TestCase):
 
     def test_iwss_wine(self):
         mufs = MUFS()
-        expected = [6, 9, 12]
+        expected = [6, 9, 12, 0, 11, 10, 5]
         self.assertListEqual(
             expected, mufs.iwss(self.X_w, self.y_w, 0.2).get_results()
         )
-        expected = [0.5218299405215557, 0.5947822876110085, 0.4877384978817362]
+        expected = [
+            0.5218299405215557,
+            1.189564575222017,
+            1.4632154936452084,
+            1.428626297656075,
+            1.3384248731269246,
+            1.2869213430115078,
+            1.1949414936926785,
+        ]
         self.assertListAlmostEqual(expected, mufs.get_scores())
 
     def test_iwss_wine_max_features(self):
@@ -172,7 +176,7 @@ class MUFSTest(unittest.TestCase):
         self.assertListEqual(
             expected, mufs.iwss(self.X_w, self.y_w, 0.4).get_results()
         )
-        expected = [0.5218299405215557, 0.5947822876110085, 0.4877384978817362]
+        expected = [0.5218299405215557, 1.189564575222017, 1.4632154936452084]
         self.assertListAlmostEqual(expected, mufs.get_scores())
 
     def test_iwss_exception(self):

requirements/dev.txt

@@ -1,3 +1,3 @@
 -r production.txt
 mdlp
-pandas
+pandas

setup.py

@@ -1,4 +1,3 @@
-import os
 import setuptools
 
 
@@ -7,10 +6,9 @@ def readme():
         return f.read()
 
 
-def get_data(field):
+def get_data(field: str):
     item = ""
-    file_name = "_version.py" if field == "version" else "__init__.py"
+    with open("mufs/__init__.py") as f:
-    with open(os.path.join("mufs", file_name)) as f:
         for line in f.readlines():
             if line.startswith(f"__{field}__"):
                 delim = '"' if '"' in line else "'"
@@ -21,11 +19,6 @@ def get_data(field):
     return item
 
 
-def get_requirements():
-    with open("requirements/production.txt") as f:
-        return f.read().splitlines()
-
-
 setuptools.setup(
     name="MUFS",
     version=get_data("version"),
@@ -45,13 +38,11 @@ setuptools.setup(
         "Development Status :: 4 - Beta",
         "License :: OSI Approved :: " + get_data("license"),
         "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
         "Natural Language :: English",
         "Topic :: Scientific/Engineering :: Artificial Intelligence",
         "Intended Audience :: Science/Research",
     ],
-    install_requires=get_requirements(),
+    install_requires=["scikit-learn"],
     test_suite="mufs.tests",
     zip_safe=False,
 )

sonar-project.properties

@@ -1,4 +0,0 @@
-sonar.projectKey=mufs
-sonar.sourceEncoding=UTF-8
-sonar.sources=.
-sonar.python.version=3.8, 3.9, 3.10