Added Python module isolation-forest-onnx which can convert an isolation forest model to ONNX format.

.gitignore

@@ -1,10 +1,60 @@
-.gradle
+# Gradle and Build directories
+.gradle/
 build/
+
+# macOS system files
 .DS_Store
-.idea
-spark-warehouse
+
+# IDE configurations
+.idea/
 *.ipr
 *.iml
 *.iws
+.vscode/
+.sublime-*
+
+# Python artifacts and caches
+*.egg
+*.egg-info/
+*.pyc
+*.pyo
+__pycache__/
+.cache/
+.tox*
+.venv*
+.env
+.envrc
+.direnv/
+.mypy_cache/
+pinned.txt
+/*/*pinned.txt
+
+# Test-related files
+.coverage
+TEST-*.xml
+coverage.xml
+/htmlcov/
+
+# Python build artifacts
+dist/
+/build/
+/*/dist/
+/*/build/
+/MANIFEST
+/*/MANIFEST
+/*/activate
+
+# Configuration files
+product-spec.json
+/*/product-spec.json
+config/
+/config/external/
+/*/config
+
+# Miscellaneous project files
+spark-warehouse
+version.txt
 
+# Project-specific paths
 isolation-forest/bin
+isolation-forest-onnx/venv

LICENSE

@@ -44,8 +44,8 @@ Outlier Detection Datasets (ODDS)
 This project includes datasets from the Outlier Detection Datasets (ODDS)
 repository (http://odds.cs.stonybrook.edu/).
 
-- Dataset at isolation-forest/src/test/resources/mammography.csv
-- Dataset at isolation-forest/src/test/resources/shuttle.csv
+- Dataset at isolation-forest/src/test/resources/mammography.csv and isolation-forest-onnx/test/resources/mammography.csv
+- Dataset at isolation-forest/src/test/resources/shuttle.csv and isolation-forest-onnx/test/resources/shuttle.csv
 
 Your use of these datasets is subject to the citation requirements
 outlined here: http://odds.cs.stonybrook.edu/about-odds/

NOTICE

@@ -30,22 +30,22 @@ terms than as set forth above. In addition, such third party code may also
 depend on and load multiple tiers of dependencies.
 
 ========================================================================
-Dataset at isolation-forest/src/test/resources/mammography.csv
+Dataset at isolation-forest/src/test/resources/mammography.csv and isolation-forest-onnx/test/resources/mammography.csv
 ========================================================================
 Shebuti Rayana (2016). ODDS Library [http://odds.cs.stonybrook.edu].
 Stony Brook, NY: Stony Brook University, Department of Computer Science.
-Dataset from http://odds.cs.stonybrook.edu/mammography-dataset/
+Dataset from https://odds.cs.stonybrook.edu/mammography-dataset/
 
 The original Mammography (Woods et al., 1993) data set was made available by the courtesy of
 Aleksandar Lazarevic. This dataset is publicly available in openML (https://www.openml.org/d/310)
 under Public Domain Mark 1.0.
 
 ========================================================================
-Dataset at isolation-forest/src/test/resources/shuttle.csv
+Dataset at isolation-forest/src/test/resources/shuttle.csv and isolation-forest-onnx/test/resources/shuttle.csv
 ========================================================================
 Shebuti Rayana (2016). ODDS Library [http://odds.cs.stonybrook.edu].
 Stony Brook, NY: Stony Brook University, Department of Computer Science.
-Dataset from http://odds.cs.stonybrook.edu/shuttle-dataset/
+Dataset from https://odds.cs.stonybrook.edu/shuttle-dataset/
 
 Dua, D. and Graff, C. (2019). UCI Machine Learning Repository [http://archive.ics.uci.edu/ml].
 Irvine, CA: University of California, School of Information and Computer Science.

build.gradle

@@ -1,6 +1,5 @@
 buildscript {
     repositories {
-        jcenter()
         maven {
             url "https://plugins.gradle.org/m2/"
         }
@@ -24,11 +23,6 @@ allprojects {
     group = "com.linkedin.isolation-forest"
 
     repositories {
-        jcenter()
         mavenCentral()
     }
 }
-
-task clean(type: Delete) {
-    delete "build"
-}

gradlew

@@ -7,7 +7,7 @@
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
 #
-#      http://www.apache.org/licenses/LICENSE-2.0
+#      https://www.apache.org/licenses/LICENSE-2.0
 #
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
@@ -82,6 +82,7 @@ esac
 
 CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 
+
 # Determine the Java command to use to start the JVM.
 if [ -n "$JAVA_HOME" ] ; then
     if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
@@ -125,10 +126,11 @@ if $darwin; then
     GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
 fi
 
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin ; then
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
     APP_HOME=`cygpath --path --mixed "$APP_HOME"`
     CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+
     JAVACMD=`cygpath --unix "$JAVACMD"`
 
     # We build the pattern for arguments to be converted via cygpath
@@ -154,19 +156,19 @@ if $cygwin ; then
         else
             eval `echo args$i`="\"$arg\""
         fi
-        i=$((i+1))
+        i=`expr $i + 1`
     done
     case $i in
-        (0) set -- ;;
-        (1) set -- "$args0" ;;
-        (2) set -- "$args0" "$args1" ;;
-        (3) set -- "$args0" "$args1" "$args2" ;;
-        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
-        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
-        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
-        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
-        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
-        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+        0) set -- ;;
+        1) set -- "$args0" ;;
+        2) set -- "$args0" "$args1" ;;
+        3) set -- "$args0" "$args1" "$args2" ;;
+        4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
     esac
 fi
 
@@ -175,14 +177,9 @@ save () {
     for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
     echo " "
 }
-APP_ARGS=$(save "$@")
+APP_ARGS=`save "$@"`
 
 # Collect all arguments for the java command, following the shell quoting and substitution rules
 eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
 
-# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
-if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
-  cd "$(dirname "$0")"
-fi
-
 exec "$JAVACMD" "$@"

gradlew.bat

@@ -5,7 +5,7 @@
 @rem you may not use this file except in compliance with the License.
 @rem You may obtain a copy of the License at
 @rem
-@rem      http://www.apache.org/licenses/LICENSE-2.0
+@rem      https://www.apache.org/licenses/LICENSE-2.0
 @rem
 @rem Unless required by applicable law or agreed to in writing, software
 @rem distributed under the License is distributed on an "AS IS" BASIS,
@@ -29,6 +29,9 @@ if "%DIRNAME%" == "" set DIRNAME=.
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
 @rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
 set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
 
@@ -37,7 +40,7 @@ if defined JAVA_HOME goto findJavaFromJavaHome
 
 set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto init
+if "%ERRORLEVEL%" == "0" goto execute
 
 echo.
 echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
@@ -51,7 +54,7 @@ goto fail
 set JAVA_HOME=%JAVA_HOME:"=%
 set JAVA_EXE=%JAVA_HOME%/bin/java.exe
 
-if exist "%JAVA_EXE%" goto init
+if exist "%JAVA_EXE%" goto execute
 
 echo.
 echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
@@ -61,28 +64,14 @@ echo location of your Java installation.
 
 goto fail
 
-:init
-@rem Get command-line arguments, handling Windows variants
-
-if not "%OS%" == "Windows_NT" goto win9xME_args
-
-:win9xME_args
-@rem Slurp the command line arguments.
-set CMD_LINE_ARGS=
-set _SKIP=2
-
-:win9xME_args_slurp
-if "x%~1" == "x" goto execute
-
-set CMD_LINE_ARGS=%*
-
 :execute
 @rem Setup the command line
 
 set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
 
+
 @rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
 
 :end
 @rem End local scope for the variables with windows NT shell

isolation-forest-onnx/MANIFEST.in

@@ -0,0 +1 @@
+include version.txt

isolation-forest-onnx/build.gradle

@@ -0,0 +1,124 @@
+plugins {
+    id 'base'
+}
+
+def venvDir = file('venv')  // Directory for the virtual environment
+
+task createVersionFile {
+    description = 'Create version.txt file for package version used in setup.py'
+    doLast {
+        def versionFile = file("${projectDir}/version.txt")
+        versionFile.parentFile.mkdirs()
+        versionFile.text = project.version
+    }
+}
+
+task createVenv(type: Exec) {
+    description = 'Create a Python virtual environment'
+    commandLine 'python3', '-m', 'venv', venvDir
+}
+
+task installDependencies(type: Exec) {
+    description = 'Install Python dependencies into the virtual environment'
+    dependsOn createVenv
+    commandLine "${venvDir}/bin/pip", 'install', '-r', 'requirements-dev.txt'
+}
+
+task buildPythonPackage(type: Exec) {
+    description = 'Build the Python source distribution and wheel'
+    dependsOn installDependencies, createVersionFile
+    commandLine "${venvDir}/bin/python", 'setup.py', 'sdist', 'bdist_wheel'
+}
+
+// Task to publish the Python package to PyPI
+task publishPythonPackage(type: Exec) {
+    description = 'Upload the Python package to PyPI'
+    group = 'upload'
+
+    dependsOn buildPythonPackage
+    environment 'TWINE_USERNAME', '__token__'
+    environment 'TWINE_PASSWORD', System.getenv('PYPI_TOKEN')
+    commandLine "${venvDir}/bin/twine", 'upload', 'dist/*'
+}
+
+task publishPythonPackageToTestPyPI(type: Exec) {
+    description = 'Upload the Python package to Test PyPI'
+    group = 'upload'
+
+    dependsOn buildPythonPackage
+    environment 'TWINE_USERNAME', '__token__'
+    environment 'TWINE_PASSWORD', System.getenv('TEST_PYPI_TOKEN')
+    commandLine "${venvDir}/bin/twine", 'upload', '--repository-url', 'https://test.pypi.org/legacy/', 'dist/*'
+}
+
+task test(type: Exec) {
+    description = 'Run Python tests using pytest'
+    group = 'verification'
+
+    dependsOn installDependencies
+    environment 'PYTHONPATH', "${projectDir}/src"
+    commandLine "${venvDir}/bin/python", '-m', 'pytest', 'test', '--junitxml=build/reports/tests/TEST-pytest.xml'
+    inputs.dir file("src")
+    inputs.dir file("test")
+    outputs.dir file("build/reports/tests")
+}
+
+task runCoverage(type: Exec) {
+    description = 'Run tests with coverage'
+    group = 'verification'
+
+    dependsOn installDependencies
+    environment 'PYTHONPATH', "${projectDir}/src"
+
+    // Define the coverage report directory
+    def coverageReportDir = file("${buildDir}/reports/coverage")
+    def coverageFile = file("${coverageReportDir}/.coverage")
+    def coverageReportFile = file("${coverageReportDir}/coverage_report.txt")
+
+    // Create the directory if it doesn't exist
+    doFirst {
+        if (!coverageReportDir.exists()) {
+            coverageReportDir.mkdirs()
+        }
+    }
+
+    commandLine 'bash', '-c', ". ${venvDir}/bin/activate && coverage run --data-file=${coverageFile} -m pytest"
+    doLast {
+        // Generate the coverage report and output it to the specified file
+        exec {
+            commandLine 'bash', '-c', ". ${venvDir}/bin/activate && coverage report --data-file=${coverageFile} > ${coverageReportFile}"
+        }
+        // Generate HTML coverage report
+        exec {
+            commandLine 'bash', '-c', ". ${venvDir}/bin/activate && coverage html -d ${coverageReportDir}/html_report --data-file=${coverageFile}"
+        }
+    }
+}
+
+task runFlake8(type: Exec) {
+    description = 'Run flake8 linting'
+    group = 'verification'
+
+    dependsOn installDependencies
+    commandLine 'bash', '-c', ". ${venvDir}/bin/activate && flake8"
+}
+
+task runMypy(type: Exec) {
+    description = 'Run mypy type checks'
+    group = 'verification'
+
+    dependsOn installDependencies
+    commandLine 'bash', '-c', ". ${venvDir}/bin/activate && mypy src"
+    inputs.dir file("src")
+    outputs.dir file("build/reports/mypy")
+}
+
+clean {
+    delete 'venv'  // Virtual environment for Python
+    delete 'dist'  // Python distribution directory
+    delete 'version.txt'  // Version file used for setup.py
+}
+
+// Define task dependencies
+check.dependsOn test, runFlake8, runCoverage, runMypy
+build.dependsOn buildPythonPackage