Update to latest tools

.coveragerc

@@ -9,4 +9,5 @@ exclude_lines =
     raise NotImplementedError
     if __name__ == .__main__.:
 ignore_errors = True
-omit =
+omit =
+    odte/__init__.py

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,56 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ master ]
+  schedule:
+    - cron: '16 17 * * 3'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
+        # Learn more:
+        # https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.github/workflows/main.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-latest, ubuntu-latest]
+        os: [macos-latest, ubuntu-latest, windows-latest]
         python: [3.8]
 
     steps:

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: black
         exclude: ".virtual_documents"
-        language_version: python3.8
+        language_version: python3.9
   - repo: https://gitlab.com/pycqa/flake8
     rev: 3.8.4
     hooks:

Makefile

@@ -0,0 +1,50 @@
+SHELL := /bin/bash
+.DEFAULT_GOAL := help
+.PHONY: coverage deps help lint push test doc build
+
+coverage:  ## Run tests with coverage
+	coverage erase
+	coverage run -m unittest -v odte.tests
+	coverage report -m
+
+deps:  ## Install dependencies
+	pip install -r requirements.txt
+
+lint:  ## Lint and static-check
+	black stree
+	flake8 stree
+	mypy stree
+
+push:  ## Push code with tags
+	git push && git push --tags
+
+test:  ## Run tests
+	python -m unittest -v odte.tests
+
+doc:  ## Update documentation
+	make -C docs --makefile=Makefile html
+
+build:  ## Build package
+	rm -fr dist/*
+	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/##/:/'`); \
+	printf "%s\n\n" "Usage: make [task]"; \
+	printf "%-20s %s\n" "task" "help" ; \
+	printf "%-20s %s\n" "------" "----" ; \
+	for help_line in $${help_lines[@]}; do \
+		IFS=$$':' ; \
+		help_split=($$help_line) ; \
+		help_command=`echo $${help_split[0]} | sed -e 's/^ *//' -e 's/ *$$//'` ; \
+		help_info=`echo $${help_split[2]} | sed -e 's/^ *//' -e 's/ *$$//'` ; \
+		printf '\033[36m'; \
+		printf "%-20s %s" $$help_command ; \
+		printf '\033[0m'; \
+		printf "%s\n" $$help_info; \
+	done

README.md

@@ -1,6 +1,9 @@
 ![CI](https://github.com/Doctorado-ML/Odte/workflows/CI/badge.svg)
 [![codecov](https://codecov.io/gh/Doctorado-ML/odte/branch/master/graph/badge.svg)](https://codecov.io/gh/Doctorado-ML/odte)
-[![Codacy Badge](https://app.codacy.com/project/badge/Grade/c85f935ac6a0482ab67d3ebed4611459)](https://www.codacy.com/gh/Doctorado-ML/Odte?utm_source=github.com&utm_medium=referral&utm_content=Doctorado-ML/Odte&utm_campaign=Badge_Grade)
+[![Codacy Badge](https://app.codacy.com/project/badge/Grade/f4b5ef87584b4095b6e49aefbe594c82)](https://www.codacy.com/gh/Doctorado-ML/Odte/dashboard?utm_source=github.com&utm_medium=referral&utm_content=Doctorado-ML/Odte&utm_campaign=Badge_Grade)
+[![PyPI version](https://badge.fury.io/py/Odte.svg)](https://badge.fury.io/py/Odte)
+![https://img.shields.io/badge/python-3.8%2B-blue](https://img.shields.io/badge/python-3.8%2B-brightgreen)
+doi
 
 # Odte
 

codecov.yml

@@ -1,12 +1,12 @@
-overage:
+coverage:
   status:
     project:
       default:
-        target: 90%
+        target: 100%
 comment:
   layout: "reach, diff, flags, files"
   behavior: default
-  require_changes: false  
+  require_changes: false
   require_base: yes
-  require_head: yes       
+  require_head: yes
-  branches: null
+  branches: null

odte/__init__.py

@@ -1,3 +1,10 @@
 from .Odte import Odte
 
+__version__ = "0.3.0"
+
+__author__ = "Ricardo Montañana Gómez"
+__copyright__ = "Copyright 2020-2021, Ricardo Montañana Gómez"
+__license__ = "MIT License"
+__author_email__ = "ricardo.montanana@alu.uclm.es"
+
 __all__ = ["Odte"]

odte/tests/Odte_tests.py

@@ -31,13 +31,13 @@ class Odte_test(unittest.TestCase):
 
     def test_initialize_max_feature(self):
         expected_values = [
-            [6, 7, 8, 15],
+            [4, 7, 12, 14],
-            [3, 4, 5, 6, 10, 13],
+            [2, 4, 6, 7, 12, 14],
             [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
             [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
-            [6, 7, 8, 15],
+            [4, 7, 12, 14],
-            [6, 7, 8, 15],
+            [4, 7, 12, 14],
-            [6, 7, 8, 15],
+            [4, 7, 12, 14],
         ]
         X, y = load_dataset(
             random_state=self._random_state, n_features=16, n_samples=10
@@ -122,7 +122,7 @@ class Odte_test(unittest.TestCase):
 
     def test_score(self):
         X, y = load_dataset(self._random_state)
-        expected = 0.9526666666666667
+        expected = 0.9513333333333334
         tclf = Odte(
             random_state=self._random_state,
             max_features=None,
@@ -132,24 +132,40 @@ class Odte_test(unittest.TestCase):
         self.assertAlmostEqual(expected, computed)
 
     def test_score_splitter_max_features(self):
-        X, y = load_dataset(self._random_state, n_features=12, n_samples=150)
+        X, y = load_dataset(self._random_state, n_features=16, n_samples=500)
         results = [
-            0.86,
+            0.948,
-            0.8933333333333333,
+            0.924,
-            0.9933333333333333,
+            0.926,
-            0.9933333333333333,
+            0.94,
+            0.932,
+            0.936,
+            0.962,
+            0.962,
+            0.962,
+            0.962,
+            0.962,
+            0.962,
+            0.962,
         ]
         random.seed(self._random_state)
         for max_features in ["auto", None]:
-            for splitter in ["best", "random"]:
+            for splitter in [
+                "best",
+                "random",
+                "trandom",
+                "mutual",
+                "iwss",
+                "cfs",
+            ]:
                 tclf = Odte(
                     base_estimator=Stree(),
                     random_state=self._random_state,
-                    max_features=max_features,
+                    n_estimators=3,
-                    n_estimators=10,
                 )
                 tclf.set_params(
                     **dict(
+                        base_estimator__max_features=max_features,
                         base_estimator__splitter=splitter,
                         base_estimator__random_state=self._random_state,
                     )

requirements.txt

@@ -1,5 +1 @@
-numpy
+stree
-scikit-learn
-pandas
-ipympl
-git+https://github.com/doctorado-ml/stree

setup.py

@@ -1,25 +1,35 @@
 import setuptools
 
-__version__ = "0.2.0"
-__author__ = "Ricardo Montañana Gómez"
-
 
 def readme():
     with open("README.md") as f:
         return f.read()
 
 
+def get_data(field):
+    item = ""
+    with open("stree/__init__.py") as f:
+        for line in f.readlines():
+            if line.startswith(f"__{field}__"):
+                delim = '"' if '"' in line else "'"
+                item = line.split(delim)[1]
+                break
+        else:
+            raise RuntimeError(f"Unable to find {field} string.")
+    return item
+
+
 setuptools.setup(
     name="Odte",
-    version=__version__,
+    version=get_data("version"),
-    license="MIT License",
+    license=get_data("license"),
     description="Oblique decision tree Ensemble",
     long_description=readme(),
     long_description_content_type="text/markdown",
     packages=setuptools.find_packages(),
-    url="https://github.com/doctorado-ml/stree",
+    url="https://github.com/doctorado-ml/odte",
-    author=__author__,
+    author=get_data("author"),
-    author_email="ricardo.montanana@alu.uclm.es",
+    author_email=get_data("author_email"),
     keywords="scikit-learn oblique-classifier oblique-decision-tree decision-\
     tree ensemble svm svc",
     classifiers=[
@@ -30,7 +40,7 @@ setuptools.setup(
         "Topic :: Scientific/Engineering :: Artificial Intelligence",
         "Intended Audience :: Science/Research",
     ],
-    install_requires=["scikit-learn", "numpy", "ipympl", "stree"],
+    install_requires=["stree"],
     test_suite="odte.tests",
     zip_safe=False,
 )