LICENSE.txt should be exactly the same as https://github.com/numenta/nupic/blob/master/LICENSE.txt. Copyright header should be at the top of all source code files:

/* ---------------------------------------------------------------------
 * Numenta Platform for Intelligent Computing (NuPIC)
 * Copyright (C) 2014, Numenta, Inc.  Unless you have an agreement
 * with Numenta, Inc., for a separate license for this software code, the
 * following terms and conditions apply:
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License version 3 as
 * published by the Free Software Foundation.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 * See the GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses.
 *
 * http://numenta.org/licenses/
 * ---------------------------------------------------------------------
 */

These were mistakenly created without giving Chetan Surpur credit for authorship.

There are several methods for setup that are necessary to construct a SpatialPooler class.

This class and test should be created to follow the same idioms and structure as the Encoder.java and ScalarEncoder.java class. The CategoryEncoder, can be used as an example.

Add the implementation for the encode() method and its delegate encodeIntoArray()

This class and test should be created to follow the same idioms and structure as the Encoder.java and ScalarEncoder.java class. The CategoryEncoder, can be used as an example.

In the pom.xml we specify source & target Java versions of 1.7; likewise in build.gradle.

However, I see we aren't using 1.7 niceties such as 'diamonds', e.g.:
Map<Integer, String> map = new HashMap<>

Can I feel free to code against Java 7 or do we want to support Java 6 also? If the latter, I'll put in a ticket to update the pom.xml and build.gradle.

the de-"functionalization" of the encoder package requires redocumentation

The TemporalMemory class java doc needs to be filled in (doesn't exist). Needs documentation

I propose a few more step to finalize parameters:

1. Make constructor private. Only allow instantiation with Factory methods. This way we will never have erroneous Parameters with missing attributes. Right now we have just one Factory method: Parameters getDefaultParameters(). It return global defaults.
   But we can have different flavors of it, for example: Parameters getMonkeyBrainParameters()

2. I mark 27 parameters constructor(Parameters.java:365). as depriciated, we will have only default private constructor, see my comments

3. I marked method getMap(Parameters.java:433) as depriciated. We remove direct access to the map

4. I'll use following pattern for parameters in all plases

/All parameters set to default/
Parameters params = Parameters.getDefaultParameters();
/Now just change what you need/
params.setParameterByKey(Parameters.KEY.CELLS_PER_COLUMN, 20);
/Apply to what you need/
Parameters.apply(conn, params);

Any suggetions?

The Spatial Pooler setup methods need to have their tests written, and this would be a good time to complete those method tests

Need to establish a .travis.yml file that runs unit tests.

Finished major work on ScalarEncoder and parent class - a few smaller tests of peripheral methods remain

I perform code analisys for 9 files from my last commit here solovyevk@faa9928

Results below, errors related to not matching names in JavaDoc, there are many meaningfull warnings as you see:

Warning:(926, 11) Local variabls\development\htm.java\src\main\java\org\numenta\nupic\encoders\GeospatialCoordinateEncoder.java
Warning:Warning:line (25)[UNUSED_IMPORT] Unused import statement
Warning:Warning:line (26)[UNUSED_IMPORT] Unused import statement
Warning:Warning:line (64)Local variable 'radius' hides field in class 'GeospatialCoordinateEncoder'
Error:Error:line (94)Cannot resolve symbol 'lon'
Error:Error:line (95)Cannot resolve symbol 'lat'
Warning:Warning:line (117)Local variable 'radius' hides field in class 'GeospatialCoordinateEncoder'
Error:Error:line (123)Cannot resolve symbol 'EncoderBuilder'
Warning:Warning:line (168)'StringBuilder' can be replaced with 'String'
Warning:Warning:line (183)Casting 'this' to 'Builder' is redundant
Warning:Warning:line (193)Casting 'this' to 'Builder' is redundant
Z:\projects\development\htm.java\src\main\java\org\numenta\nupic\encoders\MultiEncoder.java
Warning:Warning:line (50)Field 'ncategories' is never used
Warning:Warning:line (52)Field 'categoryToIndex' is never used
Warning:Warning:line (52)Explicit type argument String can be replaced with <>
Warning:Warning:line (53)Field 'indexToCategory' is never used
Warning:Warning:line (53)Explicit type argument String can be replaced with <>
Warning:Warning:line (55)Field 'categoryList' is never used
Warning:Warning:line (75)Explicit type argument EncoderTuple, List can be replaced with <>
Warning:Warning:line (83)Local variable 'name' hides field in class 'MultiEncoder'
Warning:Warning:line (96)Local variable 'name' hides field in class 'MultiEncoder'
Warning:Warning:line (103)Manual array copy
Warning:Warning:line (110)Method 'encodeField(java.lang.String, java.lang.Object)' is never used
Warning:Warning:line (112)Local variable 'name' hides field in class 'MultiEncoder'
Warning:Warning:line (123)Method 'encodeEachField(java.lang.Object)' is never used
Warning:Warning:line (124)Explicit type argument int[] can be replaced with <>
Warning:Warning:line (127)Local variable 'name' hides field in class 'MultiEncoder'
Warning:Warning:line (150)Explicit type argument String can be replaced with <>
Error:Error:line (287)Cannot resolve symbol 'EncoderBuilder'
Z:\projects\development\htm.java\src\main\java\org\numenta\nupic\encoders\CategoryEncoder.java
Warning:Warning:line (80)Explicit type argument String can be replaced with <>
Warning:Warning:line (81)Explicit type argument String can be replaced with <>
Warning:Warning:line (182)Format string '"input: %s, val: %s, value: %d, output: %s"' does not match the type of its arguments
Warning:Warning:line (207)Explicit type argument MinMax can be replaced with <>
Warning:Warning:line (231)Explicit type argument String, RangeList can be replaced with <>
Warning:Warning:line (234)Redundant array creation for calling varargs method
Error:Error:line (261)Cannot resolve symbol 'returnType'
Warning:Warning:line (271)Local variable 'topDownMapping' hides field in class 'CategoryEncoder'
Warning:Warning:line (303)Local variable 'topDownMapping' hides field in class 'CategoryEncoder'
Warning:Warning:line (309)Method 'getCategoryList()' is never used
Error:Error:line (318)Cannot resolve symbol 'EncoderBuilder'
Error:Error:line (361)Cannot resolve symbol 'stuff'
Z:\projects\development\htm.java\src\main\java\org\numenta\nupic\encoders\CoordinateEncoder.java
Warning:Warning:line (92)Explicit type argument int[] can be replaced with <>
Warning:Warning:line (120)Explicit type argument Double, Integer can be replaced with <>
Warning:Warning:line (141)Missing '@OverRide' annotation on 'orderForCoordinate()'
Warning:Warning:line (218)'StringBuilder' can be replaced with 'String'
Z:\projects\development\htm.java\src\main\java\org\numenta\nupic\encoders\PassThroughEncoder.java
Warning:Warning:line (99)Variable 'r' initializer '0.0' is redundant
Warning:Warning:line (128)Missing '@OverRide' annotation on 'encodeIntoArray()'
Warning:Warning:line (130)Format string '"Different input (%i) and output (%i) sizes"' is malformed
Warning:Warning:line (132)Format string '"Input has %i bits but w was set to %i."' is malformed
Warning:Warning:line (141)Missing '@OverRide' annotation on 'decode()'
Warning:Warning:line (145)Result of 'String.format()' is ignored
Warning:Warning:line (147)Explicit type argument MinMax can be replaced with <>
Warning:Warning:line (150)Explicit type argument String, RangeList can be replaced with <>
Warning:Warning:line (154)Redundant array creation for calling varargs method
Error:Error:line (170)Cannot resolve symbol 'EncoderBuilder'
Z:\projects\development\htm.java\src\main\java\org\numenta\nupic\encoders\ScalarEncoder.java
Warning:Warning:line (174)Missing '@OverRide' annotation on 'isDelta()'
Warning:Warning:line (240)String values are compared using '==', not 'equals()'
Error:Error:line (247)Cannot resolve symbol 'c'
Error:Error:line (297)Cannot resolve symbol 'c'
Warning:Warning:line (341)Casting '((int)((input - getMinVal()) * getNInternal() / getRange()))' to 'int' is redundant
Warning:Warning:line (343)Casting '((int)(((input - getMinVal()) + getResolution()/2) / getResolution()))' to 'int' is redundant
Warning:Warning:line (346)Local variable 'minbin' is redundant
Error:Error:line (352)Cannot resolve symbol 'c'
Warning:Warning:line (366)Redundant array creation for calling varargs method
Warning:Warning:line (372)Missing '@OverRide' annotation on 'getWidth()'
Error:Error:line (408)Cannot resolve symbol 'getW()'
Error:Error:line (411)Cannot resolve symbol 'inputData'
Error:Error:line (412)Cannot resolve symbol 'getW()'
Warning:Warning:line (432)Local variable 'range' hides field in class 'ScalarEncoder'
Warning:Warning:line (458)Missing '@OverRide' annotation on 'decode()'
Warning:Warning:line (507)Missing '@OverRide' annotation on 'eval()'
Warning:Warning:line (511)Explicit type argument Tuple can be replaced with <>
Warning:Warning:line (532)Casting 'runs.get(l).get(0)' to 'Integer' is redundant
Warning:Warning:line (544)Variable 'left' initializer '0' is redundant
Warning:Warning:line (545)Variable 'right' initializer '0' is redundant
Warning:Warning:line (546)Explicit type argument MinMax can be replaced with <>
Warning:Warning:line (608)Explicit type argument String, RangeList can be replaced with <>
Warning:Warning:line (611)Redundant array creation for calling varargs method
Error:Error:line (641)Cannot resolve symbol 'c'
Warning:Warning:line (662)Local variable 'topDownMapping' hides field in class 'ScalarEncoder'
Warning:Warning:line (664)Explicit type argument int[] can be replaced with <>
Warning:Warning:line (667)Local variable 'topDownValues' hides field in class 'ScalarEncoder'
Warning:Warning:line (669)Local variable 'minVal' hides field in class 'ScalarEncoder'
Warning:Warning:line (670)Local variable 'maxVal' hides field in class 'ScalarEncoder'
Error:Error:line (705)Cannot resolve symbol 'returnType'
Warning:Warning:line (715)Local variable 'topDownMapping' hides field in class 'ScalarEncoder'
Warning:Warning:line (730)Local variable 'topDownMapping' hides field in class 'ScalarEncoder'
Warning:Warning:line (745)Redundant array creation for calling varargs method
Warning:Warning:line (756)Local variable 'topDownMapping' hides field in class 'ScalarEncoder'
Warning:Warning:line (771)Explicit type argument Tuple can be replaced with <>
Error:Error:line (795)Cannot resolve symbol 'EncoderBuilder'
Warning:Warning:line (834)[UnusedDeclaration] Parameter 'stuff' is never used
Z:\projects\development\htm.java\src\main\java\org\numenta\nupic\encoders\LogEncoder.java
Error:Error:line (226)Cannot resolve symbol 'getW()'
Error:Error:line (229)Cannot resolve symbol 'inputData'
Error:Error:line (230)Cannot resolve symbol 'getW()'
Warning:Warning:line (234)Missing '@OverRide' annotation on 'encodeIntoArray()'
Warning:Warning:line (239)'return' is unnecessary as the last statement in a 'void' method
Warning:Warning:line (254)Missing '@OverRide' annotation on 'decode()'
Warning:Warning:line (277)Casting 'outRanges.getRange(i)' to 'MinMax' is redundant
Warning:Warning:line (296)Explicit type argument String, RangeList can be replaced with <>
Warning:Warning:line (299)Explicit type argument String can be replaced with <>
Warning:Warning:line (334)Redundant array creation for calling varargs method
Warning:Warning:line (348)Redundant array creation for calling varargs method
Warning:Warning:line (355)Missing '@OverRide' annotation on 'closenessScores()'
Warning:Warning:line (377)Local variable 'err' is redundant
Error:Error:line (386)Cannot resolve symbol 'EncoderBuilder'
Warning:Warning:line (425)Method 'setStuff(int)' is never used
Warning:Warning:line (425)[UnusedDeclaration] Parameter 'stuff' is never used
Z:\projects\development\htm.java\src\main\java\org\numenta\nupic\encoders\Encoder.java
Error:Error:line (447)Cannot resolve symbol 'e'
Warning:Warning:line (453)Explicit type argument EncoderTuple, List can be replaced with <>
Warning:Warning:line (457)Variable 'childEncoders' initializer 'null' is redundant
Warning:Warning:line (459)Explicit type argument EncoderTuple can be replaced with <>
Warning:Warning:line (471)Explicit type argument EncoderTuple, List can be replaced with <>
Warning:Warning:line (499)Explicit type argument EncoderTuple, List can be replaced with <>
Warning:Warning:line (525)Method 'getFlattenedFieldTypeList(org.numenta.nupic.encoders.Encoder)' is never used
Warning:Warning:line (527)Explicit type argument Tuple, List can be replaced with <>
Warning:Warning:line (531)Variable 'fieldTypes' initializer 'null' is redundant
Warning:Warning:line (533)Explicit type argument FieldMetaType can be replaced with <>
Warning:Warning:line (563)Method 'getScalarNames()' is never used
Warning:Warning:line (572)Method 'setScalarNames(java.util.List<java.lang.String>)' is never used
Warning:Warning:line (586)Method 'isDelta()' is never used
Error:Error:line (620)Cannot resolve symbol 'encodeIntoArray(double, int[])'
Warning:Warning:line (642)Explicit type argument String can be replaced with <>
Warning:Warning:line (644)Local variable 'encoders' hides field in class 'Encoder'
Warning:Warning:line (647)Explicit type argument String can be replaced with <>
Warning:Warning:line (649)Local variable 'name' hides field in class 'Encoder'
Warning:Warning:line (678)Explicit type argument FieldMetaType can be replaced with <>
Warning:Warning:line (715)Local variable 'encoders' hides field in class 'Encoder'
Warning:Warning:line (715)Explicit type argument Encoder can be replaced with <>
Warning:Warning:line (751)Local variable 'encoders' hides field in class 'Encoder'
Warning:Warning:line (777)Method 'getEncodedValues(S)' is never used
Warning:Warning:line (778)Explicit type argument String can be replaced with <>
Warning:Warning:line (779)Local variable 'encoders' hides field in class 'Encoder'
Warning:Warning:line (801)Local variable 'encoders' hides field in class 'Encoder'
Warning:Warning:line (823)Local variable 'encoders' hides field in class 'Encoder'
Warning:Warning:line (844)Method 'scalarsToStr(java.util.List<?>, java.util.List<java.lang.String>)' is never used
Warning:Warning:line (852)Format string '", %s:%.2f"' does not match the type of its arguments
Warning:Warning:line (854)Format string '"%s:%.2f"' does not match the type of its arguments
Warning:Warning:line (884)Method 'encodedBitDescription(int, boolean)' is never used
Warning:Warning:line (886)Local variable 'description' hides field in class 'Encoder'
Warning:Warning:line (918)Method 'pprintHeader(java.lang.String)' is never used
Warning:Warning:line (921)Local variable 'description' hides field in class 'Encoder'
Warning:Warning:line (926)Local variable 'name' hides field in class 'Encoder'
Warning:Warning:line (947)Method 'pprint(int[], java.lang.String)' is never used
Warning:Warning:line (950)Local variable 'description' hides field in class 'Encoder'
Warning:Warning:line (1,030)Explicit type argument String, Tuple can be replaced with <>
Warning:Warning:line (1,031)Explicit type argument String can be replaced with <>
Warning:Warning:line (1,036)Local variable 'encoders' hides field in class 'Encoder'
Warning:Warning:line (1,040)Variable 'nextOffset' initializer '0' is redundant
Warning:Warning:line (1,112)Explicit type argument EncoderResult can be replaced with <>
Warning:Warning:line (1,115)Variable 'nextBucketOffset' initializer '-1' is redundant
Warning:Warning:line (1,116)Variable 'childEncoders' initializer 'null' is redundant
Warning:Warning:line (1,165)Explicit type argument EncoderResult can be replaced with <>
Warning:Warning:line (1,167)Local variable 'encoders' hides field in class 'Encoder'
Warning:Warning:line (1,194)Local variable 'encoders' hides field in class 'Encoder'
Warning:Warning:line (1,197)Variable 'closeness' initializer '-1' is redundant
Warning:Warning:line (1,204)Casting 'err' to 'double' is redundant
Warning:Warning:line (1,239)Casting 'matrix.getObject(i)' to 'int[]' is redundant
Error:Error:line (1,258)Cannot resolve symbol ''
Z:\projects\development\htm.java\src\main\java\org\numenta\nupic\encoders\SDRCategoryEncoder.java
Warning:Warning:line (379)Unchecked cast: 'java.util.Set<java.lang.String>' to 'java.util.Collection'
Warning:Warning:line (483)Method 'encoderSeed(int)' is never used

uhm yeah, that's what it needs. It also should have the corresponding CategoryEncoderTest

java.lang.OutOfMemoryError: Java heap space
at gnu.trove.list.array.TIntArrayList.(TIntArrayList.java:91)
at gnu.trove.list.array.TIntArrayList.(TIntArrayList.java:67)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)
at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:671)

The Encoder base class and ScalarEncoder were written to use the same "functional" pattern as the SpatialPooler and TemporalMemory. This pattern doesn't apply to the encoders and would be best implemented in the regular OO style. Requires re-writing all method signatures in classes and tests

We need a basic Encoder for experimentation that will be easy to work with. So I decided to do the SpatialEncoder. The RandomXXX and GEOXXX will follow. This will help me get familiar with encoders also and allow for the Encoder base class hierarchy development to be correct and checked.

Java Docs have not been generated since the beginning of development and need to be updated. Also, Matt should be consulted for Doxygen recommendations.

The repository wiki could be created to explain details of the code, architectural approach and roadmap for future development.

David,

I looked into SparseBinaryMatrix and it looks like it restricted to 2D(doesn't support more than 2 dimensions).
Please check https://github.com/solovyevk/htm.java/tree/test-sparse-matrix where I extend SparseBinaryMatrixTest to test backing and slicing for multiple dimensional matrix.
Failed to set value for 3D here org/numenta/nupic/util/SparseBinaryMatrix.java:144 because slice by first coordinate assumed to be a vector, not the case for 3D.
In some places looks like it is working with multiple dimensions, but loop here (org/numenta/nupic/util/SparseBinaryMatrix.java:64) not used, but last iteration result.
I'm going to modify it to support any number of dimensions. Let me know if you OK with it :)

This class and test should be created to follow the same idioms and structure as the Encoder.java and ScalarEncoder.java class. The CategoryEncoder, can be used as an example.

Should use only the Joda Date Library

This class and test should be created to follow the same idioms and structure as the Encoder.java and ScalarEncoder.java class. The CategoryEncoder, can be used as an example.

This class should extend the CoordinateEncoder which will also have to be created to act as a base class

To be completed in tandem with #19 due to concepts and structural formation spanning concepts in both modules.

Phase 1 is implementing the Encoder base class, and ScalarEncoder together with scalar encoder test(s).

Running the tests, I kept getting:

java.lang.OutOfMemoryError: Java heap space
    at gnu.trove.list.array.TIntArrayList.<init>(TIntArrayList.java:91)
    at gnu.trove.list.array.TIntArrayList.<init>(TIntArrayList.java:67)
    at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:668)
    at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:668)
    at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:668)
    at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:668)
    at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:668)
    at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:668)
    at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:668)
    at org.numenta.nupic.util.ArrayUtils.recurseAssembleCoordinates(ArrayUtils.java:668

testGetNeighborsND is the only test that fails.

I've tried:

export JAVA_OPTS=-Xms1024m -Xmx1024m
mvn test
gradle test

No luck. The recursion doesn't look right.

Maybe this has already been discussed, decided... but just in case.

We're using int[] arrays for storing zeros and ones, e.g. encoder output, and I presume the rest of the machinery work directly on these int[] arrays. I bring it up because each entry in the array is using 32 bits when it could use only 1. Now reading up a bit I can see how wasting the space might be useful to align better with bus width, but my guess is we would rather use a 64 bit wide value if that is our aim.

http://stackoverflow.com/questions/8804435/alternative-to-java-bitset-with-array-like-performance

https://github.com/lemire/RoaringBitmap

As part of the last of the basic CLA toolset, classifiers need to be ported.

Since you are using travis for your builds you don't actually need to supply a token - but if you did you should pass it via a mvn command line parameter -DrepoToken

Not a huge huge issue, as it would just let people submit "false" code coverage reports (in this case) - but I would still get your token changed/updated by coveralls.

A lot of classes have been added since the last time these notices were added. These should be added to the header of each class. As an example, please use one of the classes that already contains the copyright notice and copy it and paste it into all the new classes.

This class and test should be created to follow the same idioms and structure as the Encoder.java and ScalarEncoder.java class. The CategoryEncoder, can be used as an example.

Since this class is a "composite" of others, its understood to be ongoing, and other encoders should be added to it as they get developed.

This task is for a super enterprising individual who will stick with the effort and update as needed.

Now that there are 2 conceptual "modules" sharing the same core data model, the code could use a final scrubbing both functionally and conceptually to cement its readiness.

Travis CI and build support constructs need to allow JDK 1.8 build, using JDK 1.7 as a lower bound requirement. All support files and build configurations need to be adjusted to allow the build to take place on JDK 1.8 with JDK 1.7 code compliance minimum.

Encoder module will need corresponding additions to the Parameters object including expansion of initialization methods also for corresponding tests

This class and test should be created to follow the same idioms and structure as the Encoder.java and ScalarEncoder.java class. The CategoryEncoder, can be used as an example.

Next step to Java port is to add encoder functionality. This will be an ongoing issue until base encoder class and derivative classes (i.e. GEOSpatialEncoder) have be completed - and so will have an associated branch.

This class is a "catch-all" for all Encoder development work

The initialization of the classes in the encoder package should use the "builder" pattern to initialize. The ScalarEncoder and CategoryEncoder should be transformed and serve as an example for the initialization idiom

The "All Classes" list contains some duplicates, and this needs to be figured out.

Following this example: https://github.com/numenta/nupic/blob/master/tests/unit/py2/nupic/encoders/multi_test.py , lines 75-83.

Executing the following commands:

ScalarEncoder dow = ScalarEncoder.builder()
                .w(3)
                .resolution(1)
                .minVal(1)
                .maxVal(8)
                .periodic(true)
                .name("day of week")
                .forced(true)
                .build();
EncodeResult res = dow.topDownCompute(dow.encode(4.)).get(0);

should result in res.getValue() == 4.0; however, the actual result is

res = EncoderResult(value=4.5, scalar=4.5, encoding=[0, 0, 1, 1, 1, 0, 0]

The other example (involving myval=6) works as expected.

Maybe it's me, but it seems like when I create a ScalarEncoder with, say, minVal = 0.0 it looks like one of the following happens:
The encoder is put into incorrect state right from the start with resolution set to 0 by default and not changed due to a check in initEncoder. Is 0.0 prohibited or is it put there to check for default values?
0.0 seems like a valid value to me, it's that they can't be both 0.0 with maxVal that would make sense to me. This results in an endless loop when calling topDownCompute as it iterates with 0.0 increment - that is forever.

It looks as if the invariants are not properly preserved, if I did something wrong during construction a RuntimeException should have been thrown when invoking ScalarEncoder.build() method.

The following test results in OutOfMemoryError due to endless append operation to an primitive collection:

@Test
    public void endlessLoopInTopDownCompute() {
        ScalarEncoder encoder = ScalarEncoder.builder()
            .w( 5 )
            .n( 10 )
            .forced( true )
            .minVal( 0 )
            .maxVal( 100 )
            .build();
        encoder.topDownCompute( new int[] { 0, 0, 0, 0, 0, 0, 0, 0, 0, 1 } );
    }

Depends on #2.

Refine object model to complete form having a single location for Array manipulation utility methods (which emulate Numpy functionality), minimize object creation, and simplify containment and associative relationships

This class and test should be created to follow the same idioms and structure as the Encoder.java and ScalarEncoder.java class. The CategoryEncoder, can be used as an example.

The Javadoc html pages and wiki image resources should be hosted on an official Numenta server, and all links should be updated to point to the new resources

The KNNClassifier is required in order to have a full set of classifiers. In order to complete this, the swig wrapper class mapping of method implementations need to be identified. Namely these:

NearestNeighbor32: <-- I need to be able to view the implementation of these methods which I haven't been able to find in the NearestNeighbor.hpp file or any of their includes. I think that they are given aliases by swig generation or something? Anyway, if someone can point me to these I can begin work.

def rowDist(*args, **kwargs):
    """rowDist(self, row, xIn) -> Real"""
    return _math._NearestNeighbor32_rowDist(*args, **kwargs)

def vecLpDist(*args, **kwargs):
    """vecLpDist(self, p, xIn, take_root=True) -> PyObject"""
    return _math._NearestNeighbor32_vecLpDist(*args, **kwargs)

def LpNearest(*args, **kwargs):
    """LpNearest(self, p, row, k=1, take_root=True) -> PyObject"""
    return _math._NearestNeighbor32_LpNearest(*args, **kwargs)

def closestLp_w(*args, **kwargs):
    """closestLp_w(self, p, row) -> PyObject"""
    return _math._NearestNeighbor32_closestLp_w(*args, **kwargs)

def closestDot(*args, **kwargs):
    """closestDot(self, row) -> PyObject"""
    return _math._NearestNeighbor32_closestDot(*args, **kwargs)

def projLpNearest(*args, **kwargs):
    """projLpNearest(self, p, py_x, k=1, take_root=False) -> PyObject"""
    return _math._NearestNeighbor32_projLpNearest(*args, **kwargs)

def projRbf(*args, **kwargs):
    """projRbf(self, p, k, py_x) -> PyObject"""
    return _math._NearestNeighbor32_projRbf(*args, **kwargs)

I think what this class represents is a TemporalPooler, right?
https://github.com/numenta/htm.java/blob/master/src/main/java/org/numenta/nupic/research/TemporalMemory.java

If so, please consider renaming it to that, or TP...but temporal memory is used by the new "TM" code in nupic.research that maps a sequence to a SDR.

The javadoc shell script jdoc.sh should be used to automatically rebuild javadocs upon CI cycling. The jdoc.sh file should also have the functionality added to build a htmjava_docs.jar file. (Eventually, this stuff should be versioned with same versioning as the sister Python revision system to mark which "version" of the Python NuPIC distribution the code corresponds with.)

This should all be done automatically.

The example usage coding steps in the class java doc needs to be surrounded in <pre> </pre> tags so that the formatting is preserved.

This class and test should be created to follow the same idioms and structure as the Encoder.java and ScalarEncoder.java class. The CategoryEncoder, can be used as an example.

This class and test should be created to follow the same idioms and structure as the Encoder.java and ScalarEncoder.java class. The CategoryEncoder, can be used as an example.