[Issue 62] - Rename packages that have DHB in their names (Part 1) - #102
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* Added convenience methods with tests #atAllPut: (Matrix instance protocol) #atColumn:put:repeat: #initializeRows:columns: #rows:columns: (Matrix class protocol) #rows:columns:element: (Matrix class protocol) * Clean class PMFloatingPointMachine and sync with the book * Cleaning * Code cleaning during book sync session * Typos * Sync with book chap 6 * Cleaning code * Clean PCA code * Cleaning * Add a class similar to StandardScaler in Scikit-learn * Add scale for PMStandardizationScaler * Use PMMatrix for PMDataTransformer classes * Add a transform test * Close #77. Implement class PMStandardizationScaler for doing standardization cleaning on matrices + abstract class PMDataTransformer. 5 unit tests include. * Add a fit: and transform: methods to PCA but apparently there is a bug. Results different from what you obtain from Python ... * Clean PMSingularValueDecomposition * Some optimisation for PMStandardizationScaler>>transform: * Refactor PMPrincipalComponentAnalyser in order to have 2 implementation classes (Jacobi transformation of the covariance matrix and SVD) and one abstract classes for all PCA. Still 2 unit tests not green. * Cleanup setUp in PMSingularValueDecompositionTest * Clean and sync with book * Add flattenOnColumns and flattenOnRows + tests Close #79 * Add argMaxOnColumns + argMaxOnRows for PMMatrix and argMax on vector. Close #80 * Following discussion #79 and #80, I rename the flatten methods and add more tests for argmax. * Remove unecessary code in cos, cosh, log, sin, sinh, sqrt, tan and tanh on a matrix * Add a sign op on PMMAtrix + one test * Remove PMPrincipalComponentAnalysisServer and tests because we change completely the API and old version got some problems with encapsulation ... * Commit tests for PCA. * Add one example with PCA with SVD on IRIS dataset * Update CONTRIBUTING.md - changed 8 space indentation to 4 spaces * Update CONTRIBUTING.md * Moved the tests to a more sensible package * Moved the tests to a more sensible package. * Moved the tests to a more sensible package. * Moved the tests to a more sensible package. * Corrected the test - of course PMMatrix does not have the assert message as part of its interface. * Add .project metadata * Rename Quaternion as PMQuaternion * QuantileTest => PMQuantileTest * Working on #16 * Add PM prefix for Math-Tests-Random classes #16 * Add PM prefix for Math-Tests-KolmogorovSmirnov classes #16 * Fix #16 for Math-Tests-KDTree * #16 for Math-Tests-FastFourierTransform * Continue to work on #16 * More on #16 * [issue-85] Moved the TestCase classes to more sensible packages. * [issue-88] Corrected the type. * [issue-81] Added a test for the eigevalues of a 2 x 2 identity matrix as a starting point. * [issue-81] Added another missing test to confirm that the eigenvectors of I are the unit basis vectors. * [issue-81] Simplified the test a bit. * [issue-81] Extracted Scikit Learn's algorithm to its own class to allow a little more isolated testing. * [issue-81] Refactor - improved the name of the method. * [issue-81] Added a method to demonstrate how the argMax message works for vectors over the field of real numbers. * [issue-81] The signs computed by the computeSignsFromU message match Sci-Kit Learn. * [issue-81] To make it easier to understand the algebra, return the signs as a vector object. * [issue-81] Extracted a helper method and added a test, where the example is taken from scikit-learn. * [issue-81] Simplified initialisation of the algorithm, removed obselete method. * [issue-81] Inlined a local variable. * [issue-81] Developed a method that computes the sign matrix for the U matrix. * [issue-81] Removed an unused variable. * [issue-81] Spelling error. * [issue-81] Removed an obselete comment. * [issue-81] Store the flipped matrices in better named state variables. * [issue-81] Removed unused accessor methods. * [issue-81] Corrected the comment. * [issue-81] Added a test for uFlipped. * [issue-81] Fixed the comment, again. * [issue-81] Added a test for vFlipped, corrected an existing test. * [issue-81] Removed unused state variables. * [issue-81] Removed the unused method. * [issue-81] Extracted duplicate arrange code to an intent-revealing set up helper. * [issue-81] Use the helper as it generates the same set up. * [issue-81] Use the signMatrixForU message to be consistent with vFlipped. * [issue-81] Moved the duplicated comments to a more sensible place. * [issue-81] We now have a working SVD flip algorithm. * [issue-81] Improved the name of the instanciation method. * Update .smalltalk.ston * Reverse * [issue-81] The sign flipping is now working in that the test for the SVD-based PCA implementation is now failing rather than erroring. * [issue-81] Name of the class now conforms to the PolyMath codestyle. * Support for principalDiagonal function #91 (#92) * Update .travis.yml * Update PMMatrixTest.class.st * missing PM before a class name ... * [Issue 81] - 2 PCA implementations that give same results but different from Python scikit-learn implementation (#96) * [issue-81] Categorised the methods, removed duplication to the set up method. * [issue-81] Added additional tests from the example in the Sandia sign ambiguity paper. * [issue-81] Added tests to confirm that we would get the same flipped U and V. * [issue-81] Renamed the set up method to follow convention. * [issue-81] Mobbing with colleagues we decided that it sufficed, because of sign ambiguity, to compare the moduli of the matrices. * [issue-81] Removed the computation of argMax to an certain level of precision. After discussion with colleagues it was deemed inadvisable. * [issue-81] Extracted expected outputs to a local variable with a good name. * [Issue 81] 2 PCA implementations that give same results but different from Python scikit-learn implementation (#97) * [issue-81] Added an acceptance test with the mean-centred data from the Lindsay Smith PCA Tutorial paper. * [issue-81] Improved the name of the test method. * [issue-81] Added an acceptance for the Jacobi-based transform: message. * [Issue 81] Refactoring/Clean Up (#98) * [issue-81] Improved the name of the variables. * [issue-81] Improved the name of the categories. * [issue-81] Removed obselete comments. * [issue-81] Emphasised the polymorphism of the two implementations of PCA in their respective tests. * [issue-81] Removed duplicate code to set up messages. * [issue-81] Removed unused instance variables. * [issue-81] Use an existing message that has the same method. * [issue-81] Moved the duplicate acceptance tests to a more sensible place. * Add missing tests in BaselineOf * Add more missing tests package * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * [Issue 62] - Rename packages that have DHB in their names (Part 1) (#102) * [issue-62] Removed an empty test case. * [issue-62] Moved the tests to a more appropriate package. * [issue-62] Moved the test class to a more appropriate package. * [issue-62] Removed DHB from the package names. (#103) * Remove all DHB in baseline * Missing packages in the baseline * Missing Math-Tests-Core package * Remove all DHB (even in comments) * Remove copyright comments * Rename tests to use CamelCase * Update README.md * Rename initialize to setUp in some tests * - Remove print1On: print2On: methods and use properly printOn: - Rename PMKolmogorovSmirnov to PMKolmogorovSmirnovSample * Working on #62 rename TSNE => PMSTE * - Remove Manifest classes - work on #62 to rename classes with PM prefix * Close #62 * Close #62 * Close #62 * fix typo. * Don't test if a package has been loaded or not, this is manage by Baseline. * Clean comments * Still comments fixes * Clean some tests * More tests cleaning * Remove dependancy between PM-RandomDistributionBased and PM-Polynomials * Ongoing work on #105. Remove Math-RandomDistributionBased package and merge classes with Math-Random. * Update .travis.yml * Update .travis.yml * Update appveyor.yml * Remove all Transcript show from tests. * Update .smalltalk.ston * Update README.md * Update appveyor.yml * Update .smalltalk.ston * [issue-104] Set the seed to zero for more certainty. (#107) * [Issue 104] Some tests methods fail randomly (#111) * [issue-104] Removed obselete code. * [issue-104] Corrected the method category, improved the formatting of the code in the test method. * [issue-104] Removed unnecessary code. * [issue-104] Improved code formatting. * [issue-104] Extracted the computation to an intention-revealing variable. * [issue-104] Improved code formatting, used data from a series from slides from QMUL * [issue-104] Separated the assert from the arrange. * [issue-104] Improved code formatting. * [issue-104] Removed obselete method. * [issue-104] We need to call the super class method according to the Pharo style guide. * [issue-104] Corrected the category of the method. * [issue-104] Removed obselete code - here I removed them and re-ran the tests. They remained green. * [issue-104] Corrected formatting. * [issue-104] Improved formatting, used data from the Oxford University Statistics Dept lecture notes. * [issue-104] Corrected the link to the data source * Removed == operator from PMVector (#108) The == operator should not be overridden. Removed that block entirely due to no it having no real application. * Issue 29 - PMVector/PMMatrix >> #dot: does not compute a dot product. (#119) * [issue-29] Marked PMMatrix's dot message as deprecated and introduced the hadamard product in its place. Replaced calls to dot in places where we can be confident nothing breaks. * [issue-29] Introduce the new and better-named elementwiseTimes message. * [issue-29] Marked the PMVector dot message as deprecated. * [issue-29] Added a separate test for the Hadamard product and reverted the element-wise multiply test to its original state. * [issue-29] Improved the name of the method. * Removed PMVector sum for speedup (#126) * Implementing the t-SNE algorithm (#117) * Added "Hbeta" function for PMTSNE with test It is named as `entropyOf: andPRow: withBeta:`. Added a test for the method ensuring: - Original pVector reference is maintained - entropy is calculated correctly - pVector is calculated correctly * Added `reduceXToInputDims:` method for PMTSNE - Added corresponding test for new method. - Renamed `ndims` to `outputDims` - Renamed `initialdims` to `initialDims` - Added accessor `x` * Added method to get pairwise affinities in PMTSNE - The new function is called `computePairwiseAffinities` (as in original paper) - The old one is renamed to `computeLowDimentionalAffinities` - Removed x2p function (translated it's code to `computePairwiseAffinities`) - Also added tests * Added progress bar(Job) for PMTSNE Moved contents of the `start` method to `initializeJob`. * Added gradient descent in PMTSNE - Also added various accessors and instance vars - Classified existing methods - Added a test for `computePValues` * [Issue 29] PMVector/PMMatrix >> #dot: does not compute a dot product. (#127) * [issue-29] Removed test for a deprecated message. * [issue-29] Replaced a call to a deprecated message, corrected a style violation. * [issue-29] Removed deprecated messages. * Update README.md * Added test cases for subtraction between scalars and vectors and suggested quickfix (#121) * Added Basic Scalar subtraction test * added test for subtract PMVector from a Number * QuickFix of the scalar subtraction with PMVector Issue * Fixed ZeroDivideError in PMStandardizationScaler (#128) This happened when one of the input features was constant. - Set scale to 1 for the feature which is constant - Added two tests for this case * Remove old Math-RandomDistributionBased package from repo * Refactored PMTSNE to include steps (#131) New methods `step` and `postStep` have been added. `postStep` will contain all viz and debug methods. A new `stateVariables` contains required variables for the steps. * [Issue 105] Math-Random Package Is Messy - Improve Naming, Refactor Tests (#132) * [issue-105] Removed an obselete test. * [issue-105] Improved the name of the class. The class comment says it is a generator. * [issue-105] Improved the name of the class. * [issue-105] Extracted duplicate code to an intention-revealing method. * [issue-105] Extracted duplicate code to a helper method. * [issue-105] Inlined the method as it's only used in one place. * [issue-105] Improved the name of the method. * [issue-105] Corrected code style. * [issue-105] Improved the name of the method. * [issue-105] Removed obselete code. * [issue-105] Corrected the category. * [issue-105] Improved the names of the methods. * [issue-105] Improved the names of the method. * [issue-105] Removed obselete test. * [issue-105] Brought back a test deleted accidentally. * [issue-105] Made similar code even more similar. * [issue-105] Moved the code to a better place, an intention-revealing method. * [issue-105] Made the code consistent with that of the other tests. This reads a little better now. * [issue-105] Made similar code look the same, improved the name of a test method by using domain language. * Added vizualization examples for PMTSNE (#133) - Renamed variable `computeErrorEvery` to `updateErrorEvery` - Added `updateError` variable which calculates error only when true - Added grid vizualization example - Added linked-rings vizualization and generator * Ability to convert vectors to matrices and vice versa (#129) * Added Basic Scalar subtraction test * added test for subtract PMVector from a Number * QuickFix of the scalar subtraction with PMVector Issue * Added methods for intuitive conversion between vectors and matrices * Tests for matrix <-> vector interconversions * Fixed implementation of reshape * [Issue 105] Refactor Math-Random Tests Package (#134) * [issue-105] Removed unnecessary dot. * [issue-105] The code is doing the same thing differently, so I have made it look exactly the same in order that we can extract the duplication elsewhere later. * [issue-105] Extracted code to an intention-revealing method. * [issue-105] Improved the name of the test method and extracted generation of a sample to an intention revealing variable. * [issue-105] Extracted the generation of a sample to an intention-revealing method. * [issue-105] In the case of the Poisson generator I understand that lambda is the mean/expected value (cf. wikipedia). * [issue-105] Introduced the expectedValue message for consistency, in view of removing the mean message completely. * [issue-105] Corrected the message name to conform to the Pharo style. * [issue-105] Extracted duplicate code to a test helper class. * [issue-105] Removed obselete comment. * [issue-105] Made the assertion the same as used in the exponential generator test in hopes of moving it to a super class. * [issue-105] Corrected and improved the name of the class and the method therein. * [issue-105] Improved code formatting, replaced implicitly duplicate code with the random sample generator class. * [issue-105] Improved the names of the temporary variables. * [issue-105] Improved the name of the assertion. * [issue-105] Removed an obselete comment. * [issue-105] Improved the name of the assertion. * [issue-105] Made the name of the test clearer. * [issue-105] Inlined the temp variable as it does not enhance understandability. * [#122] Fix PMVector comparison operators (#123) - Also added relevant tests for the operators * [Issue 105] Math-Random package is messy (#135) * [issue-105] Moved the incrementing to the bottom so we can extract the tempering to a method in the next refactor. * [issue-105] Extracted the tempering section to an intention-revealing method. * [issue-105] Corrected the categorisation to match the super class's. * [issue-105] Corrected the categorisation to match the super class's. * [issue-105] Corrected the initialisation. * [Issue 106] Support For coveralls.io (#137) * [issue-106] Fake it til we make it - just test the random package for now. * [issue-106] Corrected structure. * [issue-106] Added another package to track. * [issue-106] Added another two packages. * [issue-106] Added the benchmark packages. * [issue-106] Added the Chromosome, Clustering, Complex and Core packages. * [issue-106] Added the Distribution packages. * [issue-106] Added the FFT and FunctionFit packages. * [issue-106] The FFT and FunctionFit packages seem broken so we replace it with the K-packages. * [issue-106] Added the Math-Matrix (and any Math-M*) package. * [issue-106] Added all Math-N* packages. * [issue-106] Added the Math-O* packages. * [issue-106] The Math-ODE packages seems to cause the CI job to run out of memory, so let's proceed to the Math-P* packages. * [issue-106] Added the Math-Q* packages. * [issue-106] Added the coverage status to the README. * [issue-106] Replaced hard-coded package name with something that keeps overage open to additional R-packages. * [issue-106] Added the TNSE package. * [issue-106] Support For coveralls.io (#138) * [issue-106] The link to the badge should point to the development branch. * [issue-106] We can at least cover the FunctionFit package. * [Issue 106] Refactor Math-Accuracy (#139) * [issue-106] Improved message names. * [issue-106] The happy path should not be the guard clause; normally the subclass should respond to the message. * [issue-106] Improved the name of the block variable. * [issue-106] Moved related code closer together. initRest goes on to populate parameters, arguments and results. * [issue-106] The asString message send is redundant. * [issue-106] Improved the name of the temp variable. * [issue-106] Improved the names of the block variables. * [issue-106] The asString is redundant as the tests remain green. * [issue-106] Extracted code to an intention-revealing method. * [issue-106] Simplified the calculation of the occurence of a key. * [issue-106] Inlined the temporary variable as it is now redundant. * [issue-106] Extracted an code to an intention-revealing local temp and improved ormatting. * [issue-106] Inlined the variable as it over wrote the earlier assignment. * [issue-106] The initialize call looks like a special case, so transformed it into a guard clause. * [issue-106] Improved code formatting. * [issue-106] The check is redundant now because we have got passed the guard clause. * [issue-106] The nil check is unnecessary now given the ifNone: call. The call to join: is for efficiency (O(n) vs O(n^2) for concatenation). This was recommended by Pharo. * [issue-106] Reverted the change as we are only concatenating two strings which is not super inefficient. * [issue-106] Removed obselete code. * [Issue 106] Get Math-ODE Covered By Coveralls.io (#140) * [issue-106] Cover all packages starting with Math-O. * [issue-106] Back to hard-coding the package name (Travis ran out of memory). * Use double dispatch for PMDualNumber (#142) * Clean tests of AutomaticDifferenciation * Use double dispatch for + * Double dispatch for * in DualNumber * Use double dispatch for *,+ and /. Now all tests are green again * Add a test about derivatives * PMDualNumber is now a subclass of Number and not Magnitude. * Add conjugated and real method (to support dual numbers with complex numbers). Add support in PMComplex classes also. Add green tests. * Use absSquared instead of abs2 * Remove constant comments * Fix formatting * Reformat correctly PMHyperDualNumber * [skip ci] * [skip CI] * Update README.md * [skip CI] * [skip CI] * [skip CI] * [skip CI] * [skip CI] * Update README.md * [skip CI]
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This is the first part of renaming the packages with DHB in their names. Initially, I started by doing a bit of necessary clean up.
After each refactor I ran all the tests using Pharo 7.0's test runner and all tests are green.