tsne 0.1.1 → 0.2.0

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data/CHANGELOG.md

@@ -1,3 +1,10 @@
+## 0.2.0 (2023-05-11)
+
+- Added ARM shared libraries
+- Added support for OpenMP on Mac
+- Added support for boolean values to `verbose` option
+- Dropped support for Ruby < 3
+
 ## 0.1.1 (2020-02-11)
 
 - Fixed `Could not find Multicore t-SNE` error on some Linux platforms

data/LICENSE.txt

@@ -1,21 +1,21 @@
 BSD 3-Clause License
 
-Copyright (c) 2020, Andrew Kane
+Copyright (c) 2020-2023, Andrew Kane
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
 
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
 
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
 
-3. Neither the name of the copyright holder nor the names of its
-   contributors may be used to endorse or promote products derived from
-   this software without specific prior written permission.
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
 
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

data/README.md

@@ -1,13 +1,21 @@
-# t-SNE
+# t-SNE Ruby
 
-High performance t-SNE for Ruby, powered by [Multicore t-SNE](https://github.com/DmitryUlyanov/tsne)
+High performance t-SNE for Ruby, powered by [Multicore t-SNE](https://github.com/DmitryUlyanov/Multicore-TSNE)
+
+[![Build Status](https://github.com/ankane/tsne-ruby/workflows/build/badge.svg?branch=master)](https://github.com/ankane/tsne-ruby/actions)
 
 ## Installation
 
 Add this line to your application’s Gemfile:
 
 ```ruby
-gem 'tsne'
+gem "tsne"
+```
+
+On Mac, also install OpenMP:
+
+```sh
+brew install libomp
 ```
 
 ## Getting Started
@@ -15,7 +23,7 @@ gem 'tsne'
 Prep your data
 
 ```ruby
-x = Numo::DFloat.cast([[0, 0, 0], [0, 1, 1], [1, 0, 1], [1, 1, 1]])
+x = [[0, 0, 0], [0, 1, 1], [1, 0, 1], [1, 1, 1]]
 ```
 
 Run
@@ -31,6 +39,35 @@ Get Kullback-Leibler divergence
 tsne.kl_divergence
 ```
 
+## Full Example
+
+Install the [matplotlib](https://github.com/mrkn/matplotlib.rb) gem and download the [optdigits.tes](https://archive.ics.uci.edu/ml/machine-learning-databases/optdigits/optdigits.tes) from the [Optical Recognition of Handwritten Digits Data Set](https://archive.ics.uci.edu/ml/datasets/Optical+Recognition+of+Handwritten+Digits).
+
+```ruby
+require "csv"
+require "matplotlib/pyplot"
+require "tsne"
+
+data = []
+target = []
+CSV.foreach("optdigits.tes", converters: :numeric) do |row|
+  data << row[0...-1]
+  target << row[-1]
+end
+
+tsne = TSNE.new(n_jobs: 4)
+embeddings = tsne.fit_transform(data)
+
+vis_x = embeddings[true, 0]
+vis_y = embeddings[true, 1]
+
+plt = Matplotlib::Pyplot
+plt.scatter(vis_x.to_a, vis_y.to_a, c: target, cmap: plt.cm.get_cmap("jet", 10), marker: ".")
+plt.colorbar(ticks: 10.times.to_a)
+plt.clim(-0.5, 9.5)
+plt.show
+```
+
 ## Parameters
 
 ```ruby
@@ -49,24 +86,38 @@ TSNE.new(
 )
 ```
 
+## Data
+
+Data can be a Ruby array
+
+```ruby
+[[0, 0, 0], [0, 1, 1], [1, 0, 1], [1, 1, 1]]
+```
+
+Or a Numo array
+
+```ruby
+Numo::DFloat.new(4, 3).rand
+```
+
 ## History
 
-View the [changelog](https://github.com/ankane/tsne/blob/master/CHANGELOG.md)
+View the [changelog](https://github.com/ankane/tsne-ruby/blob/master/CHANGELOG.md)
 
 ## Contributing
 
 Everyone is encouraged to help improve this project. Here are a few ways you can help:
 
-- [Report bugs](https://github.com/ankane/tsne/issues)
-- Fix bugs and [submit pull requests](https://github.com/ankane/tsne/pulls)
+- [Report bugs](https://github.com/ankane/tsne-ruby/issues)
+- Fix bugs and [submit pull requests](https://github.com/ankane/tsne-ruby/pulls)
 - Write, clarify, or fix documentation
 - Suggest or add new features
 
 To get started with development:
 
 ```sh
-git clone https://github.com/ankane/tsne.git
-cd tsne
+git clone https://github.com/ankane/tsne-ruby.git
+cd tsne-ruby
 bundle install
 bundle exec rake vendor:all
 bundle exec rake test

data/lib/tsne/ffi.rb

@@ -7,7 +7,12 @@ module TSNE
       dlload Fiddle.dlopen(libs.shift)
     rescue Fiddle::DLError => e
       retry if libs.any?
-      raise e
+
+      if e.message =~ /Library not loaded: .+libomp/
+        raise LoadError, "OpenMP not found. Run `brew install libomp`"
+      else
+        raise e
+      end
     end
 
     typealias "bool", "char"

data/lib/tsne/model.rb

@@ -13,7 +13,15 @@ module TSNE
       @learning_rate = learning_rate
       @n_iter = n_iter
       @n_iter_early_exag = n_iter_early_exag
-      @verbose = verbose
+      @verbose =
+        case verbose
+        when true
+          1
+        when false
+          0
+        else
+          verbose
+        end
       @random_state = random_state
       @angle = angle
       @n_jobs = n_jobs

data/lib/tsne/version.rb

@@ -1,3 +1,3 @@
 module TSNE
-  VERSION = "0.1.1"
+  VERSION = "0.2.0"
 end

data/lib/tsne.rb

@@ -5,8 +5,8 @@ require "numo/narray"
 require "fiddle/import"
 
 # modules
-require "tsne/model"
-require "tsne/version"
+require_relative "tsne/model"
+require_relative "tsne/version"
 
 module TSNE
   class Error < StandardError; end
@@ -18,9 +18,17 @@ module TSNE
     if Gem.win_platform?
       "tsne_multicore.dll"
     elsif RbConfig::CONFIG["host_os"] =~ /darwin/i
-      "libtsne_multicore.dylib"
+      if RbConfig::CONFIG["host_cpu"] =~ /arm|aarch64/i
+        "libtsne_multicore.arm64.dylib"
+      else
+        "libtsne_multicore.dylib"
+      end
     else
-      "libtsne_multicore.so"
+      if RbConfig::CONFIG["host_cpu"] =~ /arm|aarch64/i
+        "libtsne_multicore.arm64.so"
+      else
+        "libtsne_multicore.so"
+      end
     end
   vendor_lib = File.expand_path("../vendor/#{lib_name}", __dir__)
   self.ffi_lib = [vendor_lib]

data/vendor/LICENSE-bhtsne.txt

@@ -0,0 +1,27 @@
+  Copyright (c) 2014, Laurens van der Maaten (Delft University of Technology)
+  All rights reserved.
+
+  Redistribution and use in source and binary forms, with or without
+  modification, are permitted provided that the following conditions are met:
+  1. Redistributions of source code must retain the above copyright
+     notice, this list of conditions and the following disclaimer.
+  2. Redistributions in binary form must reproduce the above copyright
+     notice, this list of conditions and the following disclaimer in the
+     documentation and/or other materials provided with the distribution.
+  3. All advertising materials mentioning features or use of this software
+     must display the following acknowledgement:
+     This product includes software developed by the Delft University of Technology.
+  4. Neither the name of the Delft University of Technology nor the names of
+     its contributors may be used to endorse or promote products derived from
+     this software without specific prior written permission.
+
+  THIS SOFTWARE IS PROVIDED BY LAURENS VAN DER MAATEN ''AS IS'' AND ANY EXPRESS
+  OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+  OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
+  EVENT SHALL LAURENS VAN DER MAATEN BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+  BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+  CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+  IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
+  OF SUCH DAMAGE.

data/vendor/{LICENSE.txt → LICENSE-multicore-tsne.txt}

@@ -1,7 +1,13 @@
+Created by Laurens van der Maaten.
+Copyright 2012, Delft University of Technology. All rights reserved.
+
+Multicore version by Dmitry Ulyanov, 2016. dmitry.ulyanov.msu@gmail.com
+
+--------------------------------------------------------------------------------
+
 BSD 3-Clause License
 
-Copyright (c) 2014, Laurens van der Maaten (Delft University of Technology)
-Copyright (c) 2016, Dmitry Ulyanov
+Copyright (c) [year], [fullname]
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: tsne
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.2.0
 platform: ruby
 authors:
 - Andrew Kane
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-02-12 00:00:00.000000000 Z
+date: 2023-05-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: numo-narray
@@ -24,50 +24,8 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-- !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: rake
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: minitest
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '5'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '5'
-description: 
-email: andrew@chartkick.com
+description:
+email: andrew@ankane.org
 executables: []
 extensions: []
 extra_rdoc_files: []
@@ -79,15 +37,18 @@ files:
 - lib/tsne/ffi.rb
 - lib/tsne/model.rb
 - lib/tsne/version.rb
-- vendor/LICENSE.txt
+- vendor/LICENSE-bhtsne.txt
+- vendor/LICENSE-multicore-tsne.txt
+- vendor/libtsne_multicore.arm64.dylib
+- vendor/libtsne_multicore.arm64.so
 - vendor/libtsne_multicore.dylib
 - vendor/libtsne_multicore.so
 - vendor/tsne_multicore.dll
-homepage: https://github.com/ankane/tsne
+homepage: https://github.com/ankane/tsne-ruby
 licenses:
-- MIT
+- BSD-3-Clause
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -95,15 +56,15 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '2.4'
+      version: '3'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.2
-signing_key: 
+rubygems_version: 3.4.10
+signing_key:
 specification_version: 4
 summary: High performance t-SNE for Ruby
 test_files: []