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Annotating classes of util package #1

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Annotating classes of util package #1

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adde8f7
annotating
Kakarot-SSJ4 Jul 12, 2019
a1e270d
MultidimesnionalCounter
Kakarot-SSJ4 Jul 12, 2019
f0c7f44
pom.xml
Kakarot-SSJ4 Jul 12, 2019
91e7996
unnecessary changes
Kakarot-SSJ4 Jul 12, 2019
5187fb2
pom
Kakarot-SSJ4 Jul 12, 2019
9170b66
recitfying
Kakarot-SSJ4 Jul 12, 2019
0129347
removed unnecessary changes
Kakarot-SSJ4 Jul 12, 2019
2940ec6
annotating
Kakarot-SSJ4 Jul 15, 2019
a87a7fe
made suggested changes
Kakarot-SSJ4 Jul 16, 2019
428f5fd
annotating FastMath.java
Kakarot-SSJ4 Jul 19, 2019
9ec2c44
OpenIntToDoubleHashMap.java
Kakarot-SSJ4 Jul 21, 2019
d9f54c8
OpenIntToFieldHashMap.java
Kakarot-SSJ4 Jul 22, 2019
1bf39c6
annotating
Kakarot-SSJ4 Jul 22, 2019
a57e7d0
fixing
Kakarot-SSJ4 Jul 22, 2019
6cee18b
fixing
Kakarot-SSJ4 Jul 22, 2019
dfe72f2
made suggested changes
Kakarot-SSJ4 Jul 23, 2019
a74ac32
made suggested changes
Kakarot-SSJ4 Jul 23, 2019
c608b71
made suggested changes
Kakarot-SSJ4 Jul 23, 2019
00e9867
made suggested changes
Kakarot-SSJ4 Jul 23, 2019
112248e
annotated FastMathCalc.java
Kakarot-SSJ4 Jul 23, 2019
f3cfb7e
checker version 2.9.0
Kakarot-SSJ4 Jul 24, 2019
855cf84
made suggested changes
Kakarot-SSJ4 Jul 25, 2019
e96b1a7
made suggested changes
Kakarot-SSJ4 Jul 25, 2019
ca5ae72
made suggested changes
Kakarot-SSJ4 Jul 25, 2019
abee324
Merge branch 'annotated-2' into annotated-3
Kakarot-SSJ4 Jul 25, 2019
5bbf6e7
made suggested changes
Kakarot-SSJ4 Jul 25, 2019
915e208
Merge branch 'annotated' into annotated-2
Kakarot-SSJ4 Jul 25, 2019
39f4314
Merge branch 'annotated-2' into annotated-3
Kakarot-SSJ4 Jul 25, 2019
dbb06b9
message
Kakarot-SSJ4 Jul 25, 2019
4e439f5
openjdk
Kakarot-SSJ4 Jul 31, 2019
53d47ef
IntRange
Kakarot-SSJ4 Aug 16, 2019
473c6de
@NonNegative
Kakarot-SSJ4 Aug 16, 2019
a59a8c5
error handled
Kakarot-SSJ4 Aug 16, 2019
07fe742
made suggested changes
Kakarot-SSJ4 Aug 16, 2019
566f7af
Merge pull request #3 from Kakarot-SSJ4/annotated-3
Kakarot-SSJ4 Aug 21, 2019
1102c66
Merge branch 'annotated' into annotated-2
Kakarot-SSJ4 Aug 21, 2019
a91c465
Merge pull request #1 from Kakarot-SSJ4/annotated-2
Kakarot-SSJ4 Aug 21, 2019
aed29ed
recctifying errors
Kakarot-SSJ4 Aug 21, 2019
dd1859e
resolved all the errors
Kakarot-SSJ4 Aug 21, 2019
623e052
skip test files
Kakarot-SSJ4 Aug 21, 2019
2cf074f
made suggested changes
Kakarot-SSJ4 Aug 29, 2019
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2 changes: 1 addition & 1 deletion .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ language: java
sudo: required

jdk:
- oraclejdk8
- openjdk8

env:
- MAVEN_OPTS="-Xmx6g -Xms2g"
Expand Down
187 changes: 144 additions & 43 deletions pom.xml
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Expand Up @@ -365,6 +365,19 @@
</contributors>

<dependencies>

<dependency>
<groupId>org.checkerframework</groupId>
<artifactId>checker-qual</artifactId>
<version>2.9.0</version>
</dependency>

<dependency>
<groupId>org.checkerframework</groupId>
<artifactId>jdk8</artifactId>
<version>2.9.0</version>
</dependency>

<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-statistics-distribution</artifactId>
Expand Down Expand Up @@ -460,6 +473,7 @@
</dependencies>

<properties>
<annotatedJdk>${org.checkerframework:jdk8:jar}</annotatedJdk>
<!-- Do not change: "math" is the name of the component even if the
name of the base package evolves with major release numbers
(see "commons.osgi.symbolicName", below). -->
Expand Down Expand Up @@ -515,50 +529,102 @@
</properties>

<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<plugins>
<plugin>
<!-- This plugin will set properties values using dependency information -->
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>properties</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.6.1</version>
<executions>
<execution>
<id>default-compile</id>
<phase>compile</phase>
<goals>
<goal>compile</goal>
</goals>
<configuration>
<!-- Fix for OpenJDK 8 now validating class-path attributes in Jar manifests. -->
<!-- See https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=912333#63 -->
<useSystemClassLoader>false</useSystemClassLoader>
<includes>
<include>**/*Test.java</include>
<include>**/*TestBinary.java</include>
<include>**/*TestPermutations.java</include>
</includes>
<excludes>
<exclude>**/*AbstractTest.java</exclude>
</excludes>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<descriptors>
<descriptor>src/assembly/src.xml</descriptor>
<descriptor>src/assembly/bin.xml</descriptor>
</descriptors>
<!-- There are a lot of long file names. Suppress the warnings. -->
<tarLongFileMode>gnu</tarLongFileMode>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>clirr-maven-plugin</artifactId>
<version>${math.clirr.version}</version>
<configuration>
<minSeverity>${minSeverity}</minSeverity>
<ignoredDifferencesFile>${basedir}/clirr-ignored.xml</ignoredDifferencesFile>
</configuration>
<executions>
<execution>
<goals>
</goals>
</execution>
</executions>
</plugin>
<source>1.8</source>
<target>1.8</target>
<compilerArguments>
<Xmaxerrs>10000</Xmaxerrs>
<Xmaxwarns>10000</Xmaxwarns>
</compilerArguments>
<annotationProcessorPaths>
<path>
<groupId>org.checkerframework</groupId>
<artifactId>checker</artifactId>
<version>2.9.0</version>
</path>
</annotationProcessorPaths>
<annotationProcessors>
<!-- Add all the checkers you want to enable here -->
<annotationProcessor>org.checkerframework.checker.index.IndexChecker</annotationProcessor>
</annotationProcessors>
<compilerArgs>
<!-- location of the annotated JDK, which comes from a Maven dependency -->
<arg>-Xbootclasspath/p:${annotatedJdk}</arg>
<arg>-AonlyDefs=^org\.apache\.commons\.math4\.util\.</arg>
<arg>-ArequirePrefixInWarningSuppressions</arg>
<arg>-AwarnUnneededSuppressions</arg>
</compilerArgs>
</configuration>
</execution>
</executions>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<!-- Fix for OpenJDK 8 now validating class-path attributes in Jar manifests. -->
<!-- See https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=912333#63 -->
<useSystemClassLoader>false</useSystemClassLoader>
<includes>
<include>**/*Test.java</include>
<include>**/*TestBinary.java</include>
<include>**/*TestPermutations.java</include>
</includes>
<excludes>
<exclude>**/*AbstractTest.java</exclude>
</excludes>
</configuration>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<descriptors>
<descriptor>src/assembly/src.xml</descriptor>
<descriptor>src/assembly/bin.xml</descriptor>
</descriptors>
<!-- There are a lot of long file names. Suppress the warnings. -->
<tarLongFileMode>gnu</tarLongFileMode>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>clirr-maven-plugin</artifactId>
<version>${math.clirr.version}</version>
<configuration>
<minSeverity>${minSeverity}</minSeverity>
<ignoredDifferencesFile>${basedir}/clirr-ignored.xml</ignoredDifferencesFile>
</configuration>
<executions>
<execution>
<goals>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-pmd-plugin</artifactId>
<version>${math.pmd.version}</version>
Expand Down Expand Up @@ -1048,5 +1114,40 @@
</plugins>
</build>
</profile>
<profile>
<id>mathjax-java8</id>
<activation><jdk>[1.8,)</jdk></activation>
<properties>
<!-- MathJax requires additional Javadoc qualifier for Java8+ -->
<allowscript.javadoc.qualifier>--allow-script-in-comments</allowscript.javadoc.qualifier>
</properties>
</profile>
<profile>
<id>checker</id>
<dependencies>
<dependency>
<groupId>org.checkerframework</groupId>
<artifactId>checker</artifactId>
<version>2.9.0</version>
<scope>provided</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.10</version>
<executions>
<execution>
<goals>
<goal>properties</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>
10 changes: 8 additions & 2 deletions src/main/java/org/apache/commons/math4/util/CentralPivotingStrategy.java
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Expand Up @@ -20,6 +20,11 @@

import org.apache.commons.math4.exception.MathIllegalArgumentException;

import org.checkerframework.checker.index.qual.IndexFor;
import org.checkerframework.checker.index.qual.LTEqLengthOf;
import org.checkerframework.checker.index.qual.Positive;
import org.checkerframework.checker.index.qual.LessThan;


/**
* A mid point strategy based on the average of begin and end indices.
Expand All @@ -38,10 +43,11 @@ public class CentralPivotingStrategy implements PivotingStrategyInterface, Seria
* @throws MathIllegalArgumentException when indices exceeds range
*/
@Override
public int pivotIndex(final double[] work, final int begin, final int end)
@SuppressWarnings("index:return.type.incompatible") // #1: begin + (end - begin)/2 = (begin + end)/2 where begin and end are @IndexFor("work"), hence, (begin + end)/2 is @IndexFor("work")
public @IndexFor("#1") int pivotIndex(final double[] work, final @LessThan("#3") @IndexFor("#1") int begin, final @Positive @LTEqLengthOf("#1") int end)
throws MathIllegalArgumentException {
MathArrays.verifyValues(work, begin, end-begin);
return begin + (end - begin)/2;
return begin + (end - begin)/2; // #1
}

}
20 changes: 14 additions & 6 deletions src/main/java/org/apache/commons/math4/util/CombinatoricsUtils.java
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Expand Up @@ -26,6 +26,9 @@
import org.apache.commons.numbers.combinatorics.Factorial;
import org.apache.commons.numbers.combinatorics.BinomialCoefficient;

import org.checkerframework.checker.index.qual.NonNegative;
import org.checkerframework.checker.index.qual.LessThan;

/**
* Combinatorial utilities.
*
Expand Down Expand Up @@ -57,7 +60,12 @@ private CombinatoricsUtils() {}
* k between 20 and n-2 (S(n,n-1) is handled specifically and does not overflow)
* @since 3.1
*/
public static long stirlingS2(final int n, final int k)
@SuppressWarnings("index:array.access.unsafe.high") /*
#1: i starts from 1, hence stirlingS2 has minimum 2 columns
#2: stirlingS2 has i + 1 columns, and j < i is checked
#3: k <= n as annotated and n < stirlingS2.length as annotated
*/
public static long stirlingS2(final @NonNegative int n, final @NonNegative @LessThan("#1 + 1") int k)
throws NotPositiveException, NumberIsTooLargeException, MathArithmeticException {
if (k < 0) {
throw new NotPositiveException(k);
Expand All @@ -78,12 +86,12 @@ public static long stirlingS2(final int n, final int k)
stirlingS2 = new long[maxIndex][];
stirlingS2[0] = new long[] { 1l };
for (int i = 1; i < stirlingS2.length; ++i) {
stirlingS2[i] = new long[i + 1];
stirlingS2[i][0] = 0;
stirlingS2[i][1] = 1;
stirlingS2[i] = new long[i + 1]; // #0.1
stirlingS2[i][0] = 0; // #1
stirlingS2[i][1] = 1; // #1
stirlingS2[i][i] = 1;
for (int j = 2; j < i; ++j) {
stirlingS2[i][j] = j * stirlingS2[i - 1][j] + stirlingS2[i - 1][j - 1];
stirlingS2[i][j] = j * stirlingS2[i - 1][j] + stirlingS2[i - 1][j - 1]; // #2
}
}

Expand All @@ -94,7 +102,7 @@ public static long stirlingS2(final int n, final int k)

if (n < stirlingS2.length) {
// the number is in the small cache
return stirlingS2[n][k];
return stirlingS2[n][k]; // #3
} else {
// use explicit formula to compute the number without caching it
if (k == 0) {
Expand Down
9 changes: 6 additions & 3 deletions src/main/java/org/apache/commons/math4/util/CompositeFormat.java
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Expand Up @@ -75,6 +75,7 @@ public static void parseAndIgnoreWhitespace(final String source,
* @param pos input/output parsing parameter.
* @return the first non-whitespace character.
*/
@SuppressWarnings("index:argument.type.incompatible") // #1: index < n (source.length) as checked by the condition of the loop and for the first time by the if statement
public static char parseNextCharacter(final String source,
final ParsePosition pos) {
int index = pos.getIndex();
Expand All @@ -84,7 +85,7 @@ public static char parseNextCharacter(final String source,
if (index < n) {
char c;
do {
c = source.charAt(index++);
c = source.charAt(index++); // #1
} while (Character.isWhitespace(c) && index < n);
pos.setIndex(index);

Expand All @@ -105,6 +106,7 @@ public static char parseNextCharacter(final String source,
* @param pos input/output parsing parameter.
* @return the special number.
*/
@SuppressWarnings("index:argument.type.incompatible") // #1: startIndex is @NonNegative, and as startIndex + n (@NonNegative) < source.length(), startIndex < source.length
private static Number parseNumber(final String source, final double value,
final ParsePosition pos) {
Number ret = null;
Expand All @@ -118,7 +120,7 @@ private static Number parseNumber(final String source, final double value,
final int startIndex = pos.getIndex();
final int endIndex = startIndex + n;
if (endIndex < source.length() &&
source.substring(startIndex, endIndex).compareTo(sb.toString()) == 0) {
source.substring(startIndex, endIndex).compareTo(sb.toString()) == 0) { // #1
ret = Double.valueOf(value);
pos.setIndex(endIndex);
}
Expand Down Expand Up @@ -166,6 +168,7 @@ public static Number parseNumber(final String source, final NumberFormat format,
* @param pos input/output parsing parameter.
* @return true if the expected string was there
*/
@SuppressWarnings("index:argument.type.incompatible") // pos.getIndex() is @NonNegative https://github.com/typetools/checker-framework/pull/2604
public static boolean parseFixedstring(final String source,
final String expected,
final ParsePosition pos) {
Expand All @@ -174,7 +177,7 @@ public static boolean parseFixedstring(final String source,
final int endIndex = startIndex + expected.length();
if ((startIndex >= source.length()) ||
(endIndex > source.length()) ||
(source.substring(startIndex, endIndex).compareTo(expected) != 0)) {
(source.substring(startIndex, endIndex).compareTo(expected) != 0)) { // #1
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I would expect this call to substring to not issue an error, because the expected type for both arguments is IndexOrHigh - which should both be established by the conditionals, as your suppress warning comment notes. Can you write a test case like this code and submit a bug? Thanks!

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The explanation @SuppressWarnings was wrong, it actually shows array.access.unsafe.low error as it cannot recognise pos.getIndex() as @NonNegative.
The PR with ParsePosition annotation is open, so I have provided a link in the comment.

// set index back to start, error index should be the start index
pos.setIndex(startIndex);
pos.setErrorIndex(startIndex);
Expand Down
4 changes: 3 additions & 1 deletion src/main/java/org/apache/commons/math4/util/DoubleArray.java
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Expand Up @@ -16,6 +16,8 @@
*/
package org.apache.commons.math4.util;

import org.checkerframework.checker.index.qual.NonNegative;


/**
* Provides a standard interface for double arrays. Allows different
Expand Down Expand Up @@ -57,7 +59,7 @@ public interface DoubleArray {
* @throws ArrayIndexOutOfBoundsException if <code>index</code> is less than
* zero.
*/
void setElement(int index, double value);
void setElement(@NonNegative int index, double value);

/**
* Adds an element to the end of this expandable array
Expand Down
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