Add constant features treatment

.github/workflows/main.yml

@@ -12,11 +12,13 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-latest, ubuntu-latest]
+        os: [ubuntu-latest]
-        python: [3.8]
+        python: ["3.10"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - name: Set up Python ${{ matrix.python }}
         uses: actions/setup-python@v2
         with:
@@ -26,14 +28,37 @@ jobs:
           pip install -q --upgrade pip
           pip install -q cython
           pip install -q numpy
-          pip install -q git+git://github.com/doctorado-ml/mdlp
+          pip install -q git+https://github.com/doctorado-ml/mdlp
           pip install -q -r requirements/dev.txt
-          pip install -q --upgrade codecov coverage black flake8 codacy-coverage
+          pip install -q --upgrade codecov coverage black flake8 codacy-coverage unittest-xml-reporting
       - name: Lint
         run: |
           black --check --diff mufs
           flake8 --count mufs
       - name: Tests & coverage
         run: |
-          coverage run -m unittest -v mufs.tests
+          mkdir .report
+          coverage run -m xmlrunner -v mufs.tests -o .report
+          coverage xml -i -o .report/coverage.xml
           coverage report -m --fail-under=100
+      - name: Get project version
+        run: echo "project_version=$(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: 20.8b1
+    rev: 22.3.0
     hooks:
       - id: black
         exclude: ".virtual_documents"
         language_version: python3.8
   - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.8.4
+    rev: 3.9.2
     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: v3.4.0
+    rev: v4.2.0
     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 doc build
+.PHONY: coverage deps help lint push test build
 
 coverage:  ## Run tests with coverage
 	coverage erase
@@ -26,9 +26,6 @@ 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

@@ -2,6 +2,8 @@
 [![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

@@ -3,6 +3,7 @@ from sys import float_info
 from itertools import combinations
 import numpy as np
 from .Metrics import Metrics
+from ._version import __version__
 
 
 class MUFS:
@@ -40,6 +41,11 @@ 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
@@ -128,7 +134,7 @@ 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 rcf / sqrt(k + (k**2 - k) * rff)
 
     def cfs(self, X, y):
         """Correlation-based Feature Selection
@@ -166,6 +172,10 @@ 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

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

mufs/_version.py

@@ -0,0 +1 @@
+__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):
@@ -18,6 +18,11 @@ 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):

setup.py

@@ -1,3 +1,4 @@
+import os
 import setuptools
 
 
@@ -6,9 +7,10 @@ def readme():
         return f.read()
 
 
-def get_data(field: str):
+def get_data(field):
     item = ""
-    with open("mufs/__init__.py") as f:
+    file_name = "_version.py" if field == "version" else "__init__.py"
+    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 "'"
@@ -19,6 +21,11 @@ def get_data(field: str):
     return item
 
 
+def get_requirements():
+    with open("requirements/production.txt") as f:
+        return f.read().splitlines()
+
+
 setuptools.setup(
     name="MUFS",
     version=get_data("version"),
@@ -38,11 +45,13 @@ 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=["scikit-learn"],
+    install_requires=get_requirements(),
     test_suite="mufs.tests",
     zip_safe=False,
 )

sonar-project.properties

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