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Merge dev commits to master for the 1.0 release (#145)
* 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]
@@ -33,6 +33,8 @@ Ounce your pull request is integrated, some cleanups are required:
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- remove your branch from your fork
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- close the issue (tips: you can automatically close the issue n, by inserting the sentence: **close #n** when you merge your pull request).
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You will need from time to time to sync your fork with the original repo. You can do it on the command line with: https://help.github.com/articles/syncing-a-fork/ or in the browser like : https://github.com/KirstieJane/STEMMRoleModels/wiki/Syncing-your-fork-to-the-original-repository-via-the-browser You can also kill and redo a fork very easily.
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# Release management
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This project use semantic versionning to define the releases, meaning that each stable release of the project will be assigned a version number of the form `vX.Y.Z`.
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# Branch management
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This project uses gitflow management.
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This project uses trunk-based development: https://trunkbaseddevelopment.com/
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This project contains two main branches:
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-**master** : This branch is a stable branch. Each version on this branch should be a stable release of PolyMath, and ideally each commit modifying the source code of the project should be tagged with a version number.
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-**development** : This branch contains the current development of this project.
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-**release** : This branch contains the releases of this project.
[](http://www.repostatus.org/#active)
You can load the code in a fresh Pharo 6.1 image with:
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<imgwidth="1675"alt="Screenshot 2019-04-24 at 11 12 57"src="https://user-images.githubusercontent.com/327334/56652094-66eb7780-6682-11e9-9753-101be18df67c.png">
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You can load the code in a fresh Pharo 7.0 image with:
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```Smalltalk
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Metacello new
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load
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```
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We have **767** green tests !
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PolyMath is a Smalltalk project, similar to existing scientific libraries like NumPy, SciPy for Python or SciRuby for Ruby. PolyMath already provide the following basic functionalities:
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We have **806** green tests ! At the moment, all the development happens in the development branch.
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PolyMath is a Pharo project, similar to existing scientific libraries like NumPy, SciPy for Python or SciRuby for Ruby. PolyMath already provide the following basic functionalities:
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- complex and quaternions extensions,
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- random number generators,
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- fuzzy algorithms,
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- KDE-trees,
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-Didier Besset's numerical methods,
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-Numerical methods,
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- Ordinary Differential Equation (ODE) solvers.
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[](https://twitter.com/SergeStinckwich/status/457039376111788032)
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A book about PolyMath called "Numerical Methods" is available online: https://github.com/SquareBracketAssociates/NumericalMethods/releases/tag/snapshot-2016-01-17
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A book about PolyMath called "PolyMath book" is available online: https://github.com/SquareBracketAssociates/PolyMath-book
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Some documentation (to be cleaned and reorganized) about PolyMath is available on the Wiki here:
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https://github.com/PolyMathOrg/PolyMath/wiki
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## Install PolyMath
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To install PolyMath on your Pharo image you can just execute the following script:
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To install PolyMath in your Pharo image you can just execute the following script:
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```Smalltalk
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Metacello new
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