commons-math.git
3 months agoAdd GitHub workflows for build and coverage
aherbert [Tue, 7 Jun 2022 12:39:10 +0000 (13:39 +0100)] 
Add GitHub workflows for build and coverage

3 months agoEnable jacoco plugin using the commons parent profile
aherbert [Tue, 7 Jun 2022 12:38:45 +0000 (13:38 +0100)] 
Enable jacoco plugin using the commons parent profile

3 months agoCorrect javadoc tags to allow build on JDK 17
aherbert [Tue, 7 Jun 2022 11:58:37 +0000 (12:58 +0100)] 
Correct javadoc tags to allow build on JDK 17

Remove heading tags
Correctly close paragraph tags

5 months agoMATH-1644: Prevent computed probability from exceeding 1.
Gilles Sadowski [Sat, 9 Apr 2022 12:07:03 +0000 (14:07 +0200)] 
MATH-1644: Prevent computed probability from exceeding 1.

5 months agogit-wip-us => gitbox
Sebb [Tue, 5 Apr 2022 10:37:39 +0000 (11:37 +0100)] 
git-wip-us => gitbox

6 months agoHTML5 javadoc comments.
Gilles Sadowski [Thu, 3 Mar 2022 11:02:58 +0000 (12:02 +0100)] 
HTML5 javadoc comments.

As of Java 11, the "javadoc" command requires compliance.

7 months agoRedundant setting (POM).
Gilles Sadowski [Tue, 1 Feb 2022 00:10:12 +0000 (01:10 +0100)] 
Redundant setting (POM).

7 months agoUse specialized "pow" function.
Gilles Sadowski [Thu, 27 Jan 2022 14:09:34 +0000 (15:09 +0100)] 
Use specialized "pow" function.

7 months agoTrack changes.
Gilles Sadowski [Tue, 25 Jan 2022 00:30:07 +0000 (01:30 +0100)] 
Track changes.

7 months agoAdd "ElkanKMeansPlusPlusClusterer" to example application.
Gilles Sadowski [Tue, 25 Jan 2022 00:27:17 +0000 (01:27 +0100)] 
Add "ElkanKMeansPlusPlusClusterer" to example application.

7 months agoMATH-1371: Elkan's enhancement to "K-Means" algorithm.
Gilles Sadowski [Mon, 24 Jan 2022 18:05:14 +0000 (19:05 +0100)] 
MATH-1371: Elkan's enhancement to "K-Means" algorithm.

Original implementation is a old PR provided by Artem Barger.
Updated and changed to pass the code style checks.

I did not review how this algorithm departs from the other
implementations available in the same package, and whether
some other design could minimize duplicate codes (but it
would have been a pity to drop a potential performance
improvement).
A thorough examination should be considered, when tackling
the refactoring of the "clustering" package.

Closes #35.

7 months agoMATH-1580: "K-Means" clustering example.
Gilles Sadowski [Mon, 24 Jan 2022 17:14:59 +0000 (18:14 +0100)] 
MATH-1580: "K-Means" clustering example.

Adapted application moved to the "commons-math-examples" module.

* GUI dependencies have been removed.
* Any format supported by "Commons Imaging" can be used as input.
* Clustered image saved in PNG format.

7 months agoUnused "import".
Gilles Sadowski [Mon, 24 Jan 2022 17:12:52 +0000 (18:12 +0100)] 
Unused "import".

8 months agoMinor cosmetic change (POM).
Gilles Sadowski [Mon, 24 Jan 2022 05:37:38 +0000 (06:37 +0100)] 
Minor cosmetic change (POM).

8 months agoUpgrade dependency.
Gilles Sadowski [Mon, 24 Jan 2022 04:54:10 +0000 (05:54 +0100)] 
Upgrade dependency.

Commons Statistics 1.0-SNAPSHOT requires Commons Numbers 1.1-SNAPSHOT.

8 months agoMATH-1589: Remove spurious "throws" clause.
Gilles Sadowski [Mon, 24 Jan 2022 04:35:06 +0000 (05:35 +0100)] 
MATH-1589: Remove spurious "throws" clause.

8 months agoReplace deprecated calls.
Gilles Sadowski [Sun, 23 Jan 2022 02:56:07 +0000 (03:56 +0100)] 
Replace deprecated calls.

8 months agoUpgrade dependencies.
Gilles Sadowski [Sun, 23 Jan 2022 02:55:21 +0000 (03:55 +0100)] 
Upgrade dependencies.

8 months agoMATH-1640: Do not try to outguess the caller.
Gilles Sadowski [Sat, 22 Jan 2022 17:53:17 +0000 (18:53 +0100)] 
MATH-1640: Do not try to outguess the caller.

8 months agoAvoid array declarations written in C-style syntax and replace it with java.
Arturo Bernal [Tue, 18 Jan 2022 18:28:55 +0000 (19:28 +0100)] 
Avoid array declarations written in C-style syntax and replace it with java.

Closes #202.

8 months agoFix duplicate reference (POM).
Gilles Sadowski [Wed, 19 Jan 2022 04:21:00 +0000 (05:21 +0100)] 
Fix duplicate reference (POM).

8 months agoRelax tolerance (unit test).
Gilles Sadowski [Wed, 19 Jan 2022 04:19:47 +0000 (05:19 +0100)] 
Relax tolerance (unit test).

8 months agoMove "shade" plugin to a profile (POM).
Gilles Sadowski [Wed, 19 Jan 2022 03:54:26 +0000 (04:54 +0100)] 
Move "shade" plugin to a profile (POM).

Cf. https://markmail.org/message/xvsc75mt6fpz2k65

8 months agoRemove dependency fileset
Alex Herbert [Wed, 19 Jan 2022 00:12:21 +0000 (00:12 +0000)] 
Remove dependency fileset

8 months agoMerge branch 'master' of https://gitbox.apache.org/repos/asf/commons-math
Gilles Sadowski [Tue, 18 Jan 2022 19:01:21 +0000 (20:01 +0100)] 
Merge branch 'master' of https://gitbox.apache.org/repos/asf/commons-math

8 months agoDisable jacoco coverage check in core module
aherbert [Tue, 18 Jan 2022 18:21:29 +0000 (18:21 +0000)] 
Disable jacoco coverage check in core module

This should allow Travis to build.

8 months agoDo not perform site checkout by default
aherbert [Tue, 18 Jan 2022 17:55:15 +0000 (17:55 +0000)] 
Do not perform site checkout by default

8 months agoAdd a release profile
aherbert [Tue, 18 Jan 2022 17:35:17 +0000 (17:35 +0000)] 
Add a release profile

8 months agoRemove examples and correct artifact ids in dist-archive
aherbert [Tue, 18 Jan 2022 17:34:57 +0000 (17:34 +0000)] 
Remove examples and correct artifact ids in dist-archive

8 months agoReplace calls to deprecated classes and methods (unit tests).
Gilles Sadowski [Tue, 18 Jan 2022 03:37:54 +0000 (04:37 +0100)] 
Replace calls to deprecated classes and methods (unit tests).

8 months agoReplace "CMAESOptimizer.Sigma" with "Sigma".
Gilles Sadowski [Mon, 17 Jan 2022 01:37:20 +0000 (02:37 +0100)] 
Replace "CMAESOptimizer.Sigma" with "Sigma".

8 months agoRelax tolerance (unit tests).
Gilles Sadowski [Thu, 13 Jan 2022 14:51:32 +0000 (15:51 +0100)] 
Relax tolerance (unit tests).

8 months agoRemove spurious file.
Gilles Sadowski [Thu, 13 Jan 2022 14:50:22 +0000 (15:50 +0100)] 
Remove spurious file.

Thanks to Karl-Philipp Richter.

Closes #201.

8 months agoAllow successful build on Java 9+.
Gilles Sadowski [Tue, 11 Jan 2022 00:05:58 +0000 (01:05 +0100)] 
Allow successful build on Java 9+.

Currently "JdkMath" implements all "Math" methods only on Java 8 (or lower).

8 months agoTrack changes.
Gilles Sadowski [Sat, 8 Jan 2022 23:19:02 +0000 (00:19 +0100)] 
Track changes.

8 months agoRemove non-applicable terms from "LICENCE" and "NOTICE" files.
Gilles Sadowski [Sat, 8 Jan 2022 14:46:22 +0000 (15:46 +0100)] 
Remove non-applicable terms from "LICENCE" and "NOTICE" files.

The referred dependencies are not used in the "neuralnet" module.

8 months agoAdd accessors.
Gilles Sadowski [Sat, 8 Jan 2022 13:52:55 +0000 (14:52 +0100)] 
Add accessors.

Allow retrieval of the full state, e.g. for persistent storage (cf. MATH-1594).

8 months agoUpdate copyright notice (2022).
Gilles Sadowski [Thu, 6 Jan 2022 00:18:24 +0000 (01:18 +0100)] 
Update copyright notice (2022).

8 months agoRemove comparator.
Gilles Sadowski [Thu, 6 Jan 2022 00:04:31 +0000 (01:04 +0100)] 
Remove comparator.

Its usage is unnecessary within the library.

8 months agoUnused "import" statements.
Gilles Sadowski [Wed, 5 Jan 2022 23:26:11 +0000 (00:26 +0100)] 
Unused "import" statements.

8 months agoJavadoc.
Gilles Sadowski [Wed, 5 Jan 2022 23:16:40 +0000 (00:16 +0100)] 
Javadoc.

8 months agoMATH-1594: Remove "Serializable".
Gilles Sadowski [Thu, 30 Dec 2021 15:10:46 +0000 (16:10 +0100)] 
MATH-1594: Remove "Serializable".

8 months agoUnused "import" statements.
Gilles Sadowski [Sat, 1 Jan 2022 12:25:44 +0000 (13:25 +0100)] 
Unused "import" statements.

8 months agoMATH-1594: Remove "Serializable".
Gilles Sadowski [Fri, 31 Dec 2021 00:59:20 +0000 (01:59 +0100)] 
MATH-1594: Remove "Serializable".

8 months agoMATH-1594: Remove "Serializable".
Gilles Sadowski [Fri, 31 Dec 2021 00:44:22 +0000 (01:44 +0100)] 
MATH-1594: Remove "Serializable".

8 months agoMATH-1594: Remove "Serializable".
Gilles Sadowski [Thu, 30 Dec 2021 23:59:27 +0000 (00:59 +0100)] 
MATH-1594: Remove "Serializable".

8 months agoRemove spurious "throws" clause.
Gilles Sadowski [Thu, 30 Dec 2021 23:53:17 +0000 (00:53 +0100)] 
Remove spurious "throws" clause.

8 months agoMATH-1594: Remove "Serializable".
Gilles Sadowski [Thu, 30 Dec 2021 23:44:16 +0000 (00:44 +0100)] 
MATH-1594: Remove "Serializable".

8 months agoAdd unit tests.
Gilles Sadowski [Thu, 30 Dec 2021 23:34:07 +0000 (00:34 +0100)] 
Add unit tests.

8 months agoMATH-1594: Remove "Serializable".
Gilles Sadowski [Thu, 30 Dec 2021 23:31:49 +0000 (00:31 +0100)] 
MATH-1594: Remove "Serializable".

8 months agoMATH-1594: Remove "Serializable".
Gilles Sadowski [Thu, 30 Dec 2021 22:29:18 +0000 (23:29 +0100)] 
MATH-1594: Remove "Serializable".

8 months agoMATH-1594: Remove "Serializable".
Gilles Sadowski [Thu, 30 Dec 2021 17:12:41 +0000 (18:12 +0100)] 
MATH-1594: Remove "Serializable".

8 months agoMATH-1594: Remove "Serializable".
Gilles Sadowski [Thu, 30 Dec 2021 17:11:26 +0000 (18:11 +0100)] 
MATH-1594: Remove "Serializable".

8 months agoMATH-1594: Remove "Serializable".
Gilles Sadowski [Thu, 30 Dec 2021 16:27:48 +0000 (17:27 +0100)] 
MATH-1594: Remove "Serializable".

8 months agoObsolete package.
Gilles Sadowski [Thu, 30 Dec 2021 15:12:28 +0000 (16:12 +0100)] 
Obsolete package.

9 months agoTypo (userguide).
Gilles Sadowski [Sun, 12 Dec 2021 11:56:41 +0000 (12:56 +0100)] 
Typo (userguide).

9 months agoComment out test case that fails too often.
Gilles Sadowski [Wed, 1 Dec 2021 01:36:17 +0000 (02:36 +0100)] 
Comment out test case that fails too often.

9 months agoMATH-1635: Unit test demonstrating the reported issue.
Gilles Sadowski [Wed, 1 Dec 2021 01:27:51 +0000 (02:27 +0100)] 
MATH-1635: Unit test demonstrating the reported issue.

Test is set to "@Ignore" since the behaviour may be a known limitation.

9 months agoMATH-1636: Remove "isSupportedConnected" (as per STATISTICS-48).
Gilles Sadowski [Wed, 1 Dec 2021 01:06:16 +0000 (02:06 +0100)] 
MATH-1636: Remove "isSupportedConnected" (as per STATISTICS-48).

11 months agoJavadoc.
Gilles Sadowski [Sun, 17 Oct 2021 13:27:45 +0000 (15:27 +0200)] 
Javadoc.

11 months agoRemove methods that were calling the "Math" implementation.
Gilles Sadowski [Sun, 17 Oct 2021 00:03:42 +0000 (02:03 +0200)] 
Remove methods that were calling the "Math" implementation.

11 months agoClass "JdkMath" bridges user code and alternative implementations.
Gilles Sadowski [Sat, 16 Oct 2021 23:46:06 +0000 (01:46 +0200)] 
Class "JdkMath" bridges user code and alternative implementations.

It's a "drop-in" replacement for JDK's "Math" as of Java 8 (cf. MATH-1630).

"AccurateMath" contains pure Java, acccurate, implementations of "Math" functions.
But it is no longer required to implement all of them.

11 months agoAdd files in new maven module.
Gilles Sadowski [Sat, 16 Oct 2021 08:48:27 +0000 (10:48 +0200)] 
Add files in new maven module.

11 months agoRemove non-applicable rules (SpotBugs).
Gilles Sadowski [Sat, 16 Oct 2021 08:39:20 +0000 (10:39 +0200)] 
Remove non-applicable rules (SpotBugs).

11 months agoAdapt configuration to class being moved to another package.
Gilles Sadowski [Sat, 16 Oct 2021 08:33:39 +0000 (10:33 +0200)] 
Adapt configuration to class being moved to another package.

11 months agoTrack changes.
Gilles Sadowski [Sat, 16 Oct 2021 00:23:17 +0000 (02:23 +0200)] 
Track changes.

11 months agoMATH-1630: Runtime switch between JDK and CM implementations of the methods defined...
Gilles Sadowski [Thu, 14 Oct 2021 08:56:56 +0000 (10:56 +0200)] 
MATH-1630: Runtime switch between JDK and CM implementations of the methods defined in "java.lang.Math".

Default is to use the CM implementations in order to retain previous behaviour.
When using the JDK implementations, some unit tests fail (on Java 8).

Class "AccurateMath" was moved to "o.a.c.math4.core" package.
[Unit tests for that class were not moved because they depend on "legacy" classes.]

11 months agoMATH-1629: Throw "ArithmeticException" instead of "MathArithmeticException".
Gilles Sadowski [Tue, 28 Sep 2021 23:42:46 +0000 (01:42 +0200)] 
MATH-1629: Throw "ArithmeticException" instead of "MathArithmeticException".

11 months agoSpurious "throws" clauses.
Gilles Sadowski [Tue, 28 Sep 2021 23:00:15 +0000 (01:00 +0200)] 
Spurious "throws" clauses.

11 months agoJavadoc.
Gilles Sadowski [Tue, 28 Sep 2021 19:08:37 +0000 (21:08 +0200)] 
Javadoc.

11 months agoUse "valueOf".
Gilles Sadowski [Tue, 28 Sep 2021 09:56:02 +0000 (11:56 +0200)] 
Use "valueOf".

Call to constructor is deprecated in Java 11.

11 months agoUpdated tests to use factory constructors for Statistics distributions
aherbert [Wed, 13 Oct 2021 13:20:47 +0000 (14:20 +0100)] 
Updated tests to use factory constructors for Statistics distributions

11 months agoUpdated SpotBugs 3.1.8 to 4.3.0 to allow building on JDK 17.
aherbert [Wed, 13 Oct 2021 13:09:08 +0000 (14:09 +0100)] 
Updated SpotBugs 3.1.8 to 4.3.0 to allow building on JDK 17.

A generic exclusion has been added to allow the build to pass.

11 months agoUpdated to use factory constructors for Statistics distributions
aherbert [Wed, 13 Oct 2021 13:01:08 +0000 (14:01 +0100)] 
Updated to use factory constructors for Statistics distributions

11 months agoMATH-1462: Extend workaround for bins that contain up to 3 values.
Gilles Sadowski [Sun, 26 Sep 2021 23:02:54 +0000 (01:02 +0200)] 
MATH-1462: Extend workaround for bins that contain up to 3 values.

12 months agoMATH-1462: Reproduce the infinite quantile bug
Maciej Kwidzinski [Fri, 17 Sep 2021 11:58:19 +0000 (13:58 +0200)] 
MATH-1462: Reproduce the infinite quantile bug

12 months agoJavadoc.
Gilles Sadowski [Sat, 18 Sep 2021 01:05:51 +0000 (03:05 +0200)] 
Javadoc.

12 months agoUpgrade dependency.
Gilles Sadowski [Tue, 14 Sep 2021 11:34:44 +0000 (13:34 +0200)] 
Upgrade dependency.

12 months agoPMD.
Gilles Sadowski [Wed, 1 Sep 2021 11:36:40 +0000 (13:36 +0200)] 
PMD.

12 months agoRelax tolerance (unit tests).
Gilles Sadowski [Wed, 1 Sep 2021 11:34:56 +0000 (13:34 +0200)] 
Relax tolerance (unit tests).

12 months agoSpurious "throws" clauses.
Gilles Sadowski [Wed, 1 Sep 2021 09:25:20 +0000 (11:25 +0200)] 
Spurious "throws" clauses.

12 months agoReplace algorithm used in "best list" search.
Gilles Sadowski [Wed, 1 Sep 2021 01:43:05 +0000 (03:43 +0200)] 
Replace algorithm used in "best list" search.

Although efficient in terms of evaluations, "NelderMeadTransform" fails for
some higher-dimensional test functions.

12 months agoUpgrade dependency.
Gilles Sadowski [Sat, 28 Aug 2021 01:19:57 +0000 (03:19 +0200)] 
Upgrade dependency.

12 months agoUnused "import".
Gilles Sadowski [Fri, 27 Aug 2021 18:58:27 +0000 (20:58 +0200)] 
Unused "import".

12 months agoRemove obsolete helper class for unit testing.
Gilles Sadowski [Fri, 27 Aug 2021 17:16:03 +0000 (19:16 +0200)] 
Remove obsolete helper class for unit testing.

Retries are handled by the "surefire" plugin.

12 months agoRelax expectations (unit test).
Gilles Sadowski [Fri, 27 Aug 2021 17:15:17 +0000 (19:15 +0200)] 
Relax expectations (unit test).

12 months agoFix incorrect usage of "ROSENBROCK" test function (unit tests).
Gilles Sadowski [Fri, 27 Aug 2021 16:35:47 +0000 (18:35 +0200)] 
Fix incorrect usage of "ROSENBROCK" test function (unit tests).

12 months agoFavouring the "expanded" simplex over the "reflected" one.
Gilles Sadowski [Fri, 27 Aug 2021 15:24:51 +0000 (17:24 +0200)] 
Favouring the "expanded" simplex over the "reflected" one.

This modification decreases the number of function evaluations in several
test cases. Note however that the original description of the algorithm
uses the strict inequality...

12 months agoSimplex search in higher-dimensional cases (unit test).
Gilles Sadowski [Fri, 27 Aug 2021 03:37:49 +0000 (05:37 +0200)] 
Simplex search in higher-dimensional cases (unit test).

12 months agoAdd (back) "POwELL" standard test function for optimizers.
Gilles Sadowski [Thu, 26 Aug 2021 21:56:42 +0000 (23:56 +0200)] 
Add (back) "POwELL" standard test function for optimizers.

12 months agoUse default SA setup in "SimplexOptimizerTest" (unit test).
Gilles Sadowski [Thu, 26 Aug 2021 00:05:15 +0000 (02:05 +0200)] 
Use default SA setup in "SimplexOptimizerTest" (unit test).

A single additional search finds the optimum of the test functions.

12 months agoMATH-1622: Simulated annealing entails at least one additional search.
Gilles Sadowski [Wed, 25 Aug 2021 23:39:46 +0000 (01:39 +0200)] 
MATH-1622: Simulated annealing entails at least one additional search.

Also ensure that the "best list" contains at least two points.

13 months agoInput files for "SimplexOptimizerTest" (unit tests).
Gilles Sadowski [Tue, 24 Aug 2021 23:51:34 +0000 (01:51 +0200)] 
Input files for "SimplexOptimizerTest" (unit tests).

13 months agoMATH-1622: Simulated annealing variant of "NelderMeadTransform".
Gilles Sadowski [Tue, 24 Aug 2021 23:50:28 +0000 (01:50 +0200)] 
MATH-1622: Simulated annealing variant of "NelderMeadTransform".

13 months agoChange how simulated annealing affects the transformed simplex (cf. MATH-1622).
Gilles Sadowski [Tue, 24 Aug 2021 13:39:52 +0000 (15:39 +0200)] 
Change how simulated annealing affects the transformed simplex (cf. MATH-1622).

Compared with commit 97462b1a1b6f64ab10e06db331d5b6762d979aab, this commit is
more consistent with assumptions of the original (non-hybridized) algorithm.

13 months agoUseless local variable.
Gilles Sadowski [Tue, 24 Aug 2021 02:09:42 +0000 (04:09 +0200)] 
Useless local variable.

13 months agoInput files for "SimplexOptimizerTest" (unit tests).
Gilles Sadowski [Mon, 23 Aug 2021 23:28:43 +0000 (01:28 +0200)] 
Input files for "SimplexOptimizerTest" (unit tests).

13 months agoMATH-1622: Simulated annealing variant of "MultiDirectionalTransform".
Gilles Sadowski [Mon, 23 Aug 2021 23:18:16 +0000 (01:18 +0200)] 
MATH-1622: Simulated annealing variant of "MultiDirectionalTransform".

13 months agoUpdate exception fr locale to match changes to en locale
Alex Herbert [Mon, 23 Aug 2021 06:40:55 +0000 (07:40 +0100)] 
Update exception fr locale to match changes to en locale

13 months agoMATH-1627: Throw an exception when column or row sums are zero.
Alex Herbert [Sun, 22 Aug 2021 20:43:27 +0000 (21:43 +0100)] 
MATH-1627: Throw an exception when column or row sums are zero.