Merge pull request jorgecasas#2 from jorgecasas/master

Master

.editorconfig

@@ -0,0 +1,9 @@
+root = true
+
+[*]
+end_of_line = lf
+charset = utf-8
+max_line_length = 80
+indent_style = space
+indent_size = 4
+insert_final_newline = true

.gitattributes

@@ -0,0 +1,14 @@
+* text=auto
+
+/docs export-ignore
+/tests export-ignore
+/.gitattributes export-ignore
+/.gitignore export-ignore
+/.travis.yml export-ignore
+/ecs.yml export-ignore
+/CHANGELOG.md export-ignore
+/CONTRIBUTING.md export-ignore
+/mkdocs.yml export-ignore
+/phpbench.json export-ignore
+/phpstan.neon export-ignore
+/phpunit.xml export-ignore

.gitignore

@@ -1,3 +1,5 @@
 /vendor/
-humbuglog.*
-/bin/phpunit
+/build
+/tests/Performance/Data/*.csv
+.php_cs.cache
+.phpunit.result.cache

.travis.yml

@@ -1,5 +1,38 @@
 language: php
-php:
-  - '7.0'
-before_script: composer install
-script: bin/phpunit
+
+matrix:
+  fast_finish: true
+
+  include:
+    - os: linux
+      php: '7.2'
+      env: PHPUNIT_FLAGS="--coverage-clover build/logs/clover.xml" DISABLE_XDEBUG="true" STATIC_ANALYSIS="true"
+
+    - os: linux
+      php: '7.3'
+
+    - os: linux
+      php: '7.4'
+
+cache:
+  directories:
+    - $HOME/.composer/cache
+
+before_install:
+  - if [[ $DISABLE_XDEBUG == "true" ]]; then phpenv config-rm xdebug.ini; fi
+
+install:
+  - curl -s http://getcomposer.org/installer | php
+  - php composer.phar install --no-interaction --ignore-platform-reqs
+
+script:
+  - vendor/bin/phpunit $PHPUNIT_FLAGS
+  - if [[ $STATIC_ANALYSIS != "" ]]; then composer check-cs; fi
+  - if [[ $STATIC_ANALYSIS != "" ]]; then composer phpstan; fi
+
+after_success:
+  - |
+    if [[ $PHPUNIT_FLAGS != "" ]]; then
+      wget https://github.com/php-coveralls/php-coveralls/releases/download/v2.0.0/php-coveralls.phar
+      php php-coveralls.phar --verbose;
+    fi

CHANGELOG.md

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+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.9.0] - Unreleased
+### Added
+- [Preprocessing] Implement LabelEncoder
+- [Preprocessing] Implement ColumnFilter
+- [Preprocessing] Implement LambdaTransformer
+- [Preprocessing] Implement NumberConverter
+- [Preprocessing] Implement OneHotEncoder
+- [Workflow] Implement FeatureUnion
+- [Metric] Add Regression metrics: meanSquaredError, meanSquaredLogarithmicError, meanAbsoluteError, medianAbsoluteError, r2Score, maxError
+- [Regression] Implement DecisionTreeRegressor 
+
+## [0.8.0] - 2019-03-20
+### Added
+- [Tokenization] Added NGramTokenizer (#350)
+- editorconfig file (#355)
+### Fixed
+- [Dataset] FilesDataset read samples without additional array (#363)
+- [Tokenization] fixed error with numeric token values (#363)
+### Changed
+- [Math] improved performance with pow and sqrt replacement (#350) 
+- [Math] reduce duplicated code in distance metrics (#348)
+- update phpunit to 7.5.1 (#335)
+- code style fixes (#334)
+
+## [0.7.0] - 2018-11-07
+### Added
+- [Clustering] added KMeans associative clustering (#262)
+- [Dataset] added removeColumns function to ArrayDataset (#249)
+- [Dataset] added a SvmDataset class for SVM-Light (or LibSVM) format files (#237)
+- [Dataset] added Mnist Dataset for MNIST file format (#326)
+- [Internal] Add performance test for LeastSquares (#263)
+
+### Changed
+- [Internal] implement Keep a Changelog format
+- [Classification] changed the default kernel type in SVC to Kernel::RBF (#267)
+- [Optimizer] removed $initialTheta property and renamed setInitialTheta method to setTheta (#252)
+- [Imputer] Throw exception when trying to transform without train data (#314)
+- [Math] Micro optimization for matrix multiplication (#255)
+- [Internal] Throw proper exception (#259, #251)
+- [MLPClassifier] return labels in output (#315)
+- [Internal] Update phpstan to 0.10.5 (#320)
+
+### Fixed
+- [SVM] ensure DataTransformer::testSet samples array is not empty (#204)
+- [Optimizer] optimizer initial theta randomization (#239) 
+- [Internal] travis build on osx (#281)
+- [SVM] SVM locale (non-locale aware) (#288)
+- [Internal] typo, tests, code styles and documentation fixes (#265, #261, #254, #253, #251, #250, #248, #245, #243, #317, #328)
+- [Classification] Check if feature exist when predict target in NaiveBayes (#327)
+
+## [0.6.2] - 2018-02-22
+### Fixed
+- Fix Apriori array keys (#238)
+
+## [0.6.1] - 2018-02-18
+### Fixed
+- Fix KMeans and EigenvalueDecomposition (#235)
+
+## [0.6.0] - 2018-02-16
+- feature [FeatureSelection] implement SelectKBest with scoring functions (#232)
+- feature [FeatureSelection] implement VarianceThreshold - simple baseline approach to feature selection.  (#228)
+- feature [Classification] support probability estimation in SVC (#218)
+- feature [NeuralNetwork] configure an Activation Function per hidden layer (#208)
+- feature [NeuralNetwork] Ability to update learningRate in MLP (#160)
+- feature [Metric] Choose averaging method in classification report (#205)
+- enhancement Add phpstan strict rules (#233)
+- enhancement Flatten directory structure (#220)
+- enhancement Update phpunit/phpunit (#219)
+- enhancement Cache dependencies installed with composer on Travis (#215)
+- enhancement Add support for coveralls.io (#153)
+- enhancement Add phpstan and easy coding standards (#156, #168)
+- enhancement Throw exception when libsvm command fails to run (#200, #202)
+- enhancement Normalize composer.json and sort packages (#214, #210)
+- enhancement Rewrite DBSCAN (#185)
+- fix phpunit include tests path (#230)
+- fix support of a rule in Apriori (#229)
+- fix apriori generates an empty array as a part of the frequent item sets (#224)
+- fix backpropagation random error (#157)
+- fix logistic regression implementation (#169)
+- fix activation functions support (#163)
+- fix string representation of integer labels issue in NaiveBayes (#206)
+- fix the implementation of conjugate gradient method (#184)
+- typo, tests and documentation fixes (#234, #221, #181, #183, #155, #159, #165, #187, #154, #191, #203, #209, #213, #212, #211)
+
+## [0.5.0] - 2017-11-14
+- general [php] Upgrade to PHP 7.1 (#150)
+- general [coding standard] fix imports order and drop unused docs typehints
+- feature [NeuralNetwork] Add PReLU activation function (#128)
+- feature [NeuralNetwork] Add ThresholdedReLU activation function (#129)
+- feature [Dataset] Support CSV with long lines (#119)
+- feature [NeuralNetwork] Neural networks partial training and persistency (#91)
+- feature Add french stopwords (#92)
+- feature New methods: setBinPath, setVarPath in SupportVectorMachine (#73)
+- feature Linear Discrimant Analysis (LDA) (#82)
+- feature Linear algebra operations, Dimensionality reduction and some other minor changes (#81)
+- feature Partial training base (#78)
+- feature Add delimiter option for CsvDataset (#66)
+- feature LogisticRegression classifier & Optimization methods (#63)
+- feature Additional training for SVR (#59)
+- optimization Comparison - replace eval (#130)
+- optimization Use C-style casts (#124)
+- optimization Speed up DataTransformer (#122)
+- bug DBSCAN fix for associative keys and array_merge performance optimization (#139)
+- bug Ensure user-provided SupportVectorMachine paths are valid (#126)
+- bug [DecisionTree] Fix string cast #120 (#121)
+- bug fix invalid typehint for subs method (#110)
+- bug Fix samples transformation in Pipeline training (#94)
+- bug Fix division by 0 error during normalization (#83)
+- bug Fix wrong docs references (#79)
+
+## [0.4.0] - 2017-02-23
+- feature [Classification] - Ensemble Classifiers : Bagging and RandomForest by Mustafa Karabulut
+- feature [Classification] - RandomForest::getFeatureImportances() method by Mustafa Karabulut
+- feature [Classification] - Linear classifiers: Perceptron, Adaline, DecisionStump by Mustafa Karabulut
+- feature [Classification] - AdaBoost algorithm by Mustafa Karabulut
+- bug [Math] - Check if matrix is singular doing inverse by Povilas Susinskas
+- optimization - Euclidean optimization by Mustafa Karabulut
+
+## [0.3.0] - 2017-02-04
+- feature [Persistency] - ModelManager - save and restore trained models by David Monllaó
+- feature [Classification] - DecisionTree implementation by Mustafa Karabulut
+- feature [Clustering] - Fuzzy C Means implementation by Mustafa Karabulut
+- other small fixes and code styles refactors
+
+## [0.2.1] - 2016-11-20
+- feature [Association] - Apriori algorithm implementation
+- bug [Metric] - division by zero
+
+## [0.2.0] - 2016-08-14
+- feature [NeuralNetwork] - MultilayerPerceptron and Backpropagation training
+
+## [0.1.2] - 2016-07-24
+- feature [Dataset] - FilesDataset - load dataset from files (folder names as targets)
+- feature [Metric] - ClassificationReport - report about trained classifier
+- bug [Feature Extraction] - fix problem with token count vectorizer array order
+- tests [General] - add more tests for specific conditions
+
+## [0.1.1] - 2016-07-12
+- feature [Cross Validation] Stratified Random Split - equal distribution for targets in split
+- feature [General] Documentation - add missing pages (Pipeline, ConfusionMatrix and TfIdfTransformer) and fix links
+
+## [0.1.0] - 2016-07-08
+- first develop release
+- base tools for Machine Learning: Algorithms, Cross Validation, Preprocessing, Feature Extraction
+- bug [General] #7 - PHP-ML doesn't work on Mac

CONTRIBUTING.md

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+# Contributing to PHP-ML
+
+PHP-ML is an open source project. If you'd like to contribute, please read the following text. Before I can merge your 
+Pull-Request here are some guidelines that you need to follow. These guidelines exist not to annoy you, but to keep the 
+code base clean, unified and future proof.
+
+## Branch
+
+You should only open pull requests against the `master` branch.
+
+## Unit Tests
+
+Please try to add a test for your pull-request. You can run the unit-tests by calling:
+
+```bash
+vendor/bin/phpunit
+```
+
+## Performance Tests
+
+Before first run bootstrap script will download all necessary datasets from public repository `php-ai/php-ml-datasets`.
+
+Time performance tests:
+
+```bash
+vendor/bin/phpbench run --report=time
+```
+
+Memory performance tests:
+
+```bash
+vendor/bin/phpbench run --report=memory
+```
+
+## Travis
+
+GitHub automatically run your pull request through Travis CI.
+If you break the tests, I cannot merge your code, so please make sure that your code is working before opening up a Pull-Request.
+
+## Merge
+
+Please give me time to review your pull requests. I will give my best to review everything as fast as possible, but cannot always live up to my own expectations.
+
+## Coding Standards & Static Analysis
+
+When contributing code to PHP-ML, you must follow its coding standards. To do that, just run:
+
+```bash
+composer fix-cs
+```
+[More about EasyCodingStandard](https://github.com/Symplify/EasyCodingStandard)
+
+Code has to also pass static analysis by [PHPStan](https://github.com/phpstan/phpstan):
+
+```bash
+composer phpstan
+```
+
+
+## Documentation
+
+Please update the documentation pages if necessary. You can find them in docs/.
+
+---
+
+Thank you very much again for your contribution!

LICENSE

@@ -1,6 +1,7 @@
 The MIT License (MIT)
 
-Copyright (c) 2016 Arkadiusz Kondas <arkadiusz.kondas[at]gmail>
+Copyright (c) 2016-2019 Arkadiusz Kondas <arkadiusz.kondas[at]gmail>
+Copyright (c) 2018 Andrew DalPino
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal