umappp 0.1.2

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data/LICENSE.txt

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+BSD 2-Clause License
+
+Copyright (c) 2022, kojix2
+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.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

data/README.md

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+# Umappp - UMAP for Ruby
+
+[![test](https://github.com/kojix2/ruby-umappp/actions/workflows/ci.yml/badge.svg)](https://github.com/kojix2/ruby-umappp/actions/workflows/ci.yml)
+[![Gem Version](https://badge.fury.io/rb/umappp.svg)](https://badge.fury.io/rb/umappp)
+
+🗺️ [Umappp](https://github.com/LTLA/umappp) - Uniform Manifold Approximation and Projection - for Ruby
+
+![image](https://user-images.githubusercontent.com/5798442/155692246-fa8e0fb0-33c2-4265-a1bf-228d4f80ebdb.png)
+
+> Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction. 
+> ([original UMAP documentation](https://umap-learn.readthedocs.io/en/latest/index.html))
+
+* Ruby Umappp is a wrapper library for [C++ Umappp library](https://github.com/LTLA/umappp) created by Aaron Lun 
+* Compatible with [yaumap](https://github.com/LTLA/yaumap)
+* Support [Numo::NArray](https://github.com/ruby-numo/numo-narray)
+
+## Installation
+
+
+```
+gem install umappp
+```
+
+* [OpenMP](https://www.openmp.org) is required for multithreading.
+
+## Usage
+
+This Gem provides the module `Umappp` and its singular method `Umappp.run()`. The first argument of `Umappp.run()` is a two-dimensional Ruby array or a two-dimensional Numo array. [Numo](https://github.com/ruby-numo/numo-narray) is a library for performing N-dimensional array computing like NumPy. The argument is converted to `Numo::SFloat`. SFloat is a single precision floating point number type of Numo::NArray.
+
+```ruby
+Umappp.run(embedding) # embedding is two-dimensional Ruby array or Numo array
+
+# with parameters
+Umappp.run(pixels, num_threads: 8, a: 1.8956, b: 0.8006)
+```
+
+Available parameters and their default values
+
+| parameters           | default value                      |
+|----------------------|------------------------------------|
+| method               | :annoy (another option is :vptree) |
+| ndim                 | 2                                  |
+| tick                 | 0 (Not yet implemented)            |
+| local_connectivity   | 1.0                                |
+| bandwidth            | 1                                  |
+| mix_ratio            | 1                                  |
+| spread               | 1                                  |
+| min_dist             | 0.01                               |
+| a                    | 0                                  |
+| b                    | 0                                  |
+| repulsion_strength   | 1                                  |
+| num_epochs           | 500                                |
+| learning_rate        | 1                                  |
+| negative_sample_rate | 5                                  |
+| num_neighbors        | 15                                 |
+| seed                 | 1234567890                         |
+| batch                | false                              |
+| num_threads          | 1 (OpenMP required)                |
+
+## Development
+
+```
+git clone https://github.com/kojix2/ruby-umappp
+cd umap
+b ndle dle exec rake compile
+bundle exec rake test
+```
+
+### Ruby dependencies
+
+* [rice](https://github.com/jasonroelofs/rice) - Ruby Interface for C++ Extensions
+* [numo.hpp](https://github.com/ankane/numo.hpp) - C++ header for Numo and Rice
+
+### Umappp dependencies
+
+This Gem is a wrapper for [Umappp](https://github.com/LTLA/umappp). We store and distribute Umappp and other dependent C++ code in the Vendor directory. Umappp is compiled when the Gem is installed. Umappp's C++ modules have complex dependencies as shown in the figure below. It is not a good idea to manage them manually. Use `script/vendor.sh` to update them automatically. This actually runs cmake and moves the required directories to the vendor directory.
+
+
+```mermaid
+graph TD;
+    id1(eigen)-->CppIrlba;
+    aarand-->CppIrlba;
+    Annoy-->knncolle;
+    hnswlib-->knncolle;
+    CppKmeans-->knncolle;
+    aarand-->CppKmeans;
+    powerit-->CppKmeans;
+    aarand-->powerit;
+    knncolle-->umappp;
+    aarand-->umappp;
+    CppIrlba-->umappp;
+    style id1 fill:#f9f,stroke:#333
+```
+
+All modules except eigen are the work of Aaron Lun.
+
+## Contributing
+
+Welcome!
+
+    Do you need commit rights to my repository?
+    Do you want to get admin rights and take over the project?
+    If so, please feel free to contact us @kojix2.
+
+## License
+
+* As for the code I wrote, it is  BSD 2-Clause (or MIT).
+* The license of Umappp for C++ by Aaron Lun is BSD 2-Clause.
+* For other codes, please check on your own. (There are many dependencies)
+ 

data/ext/umappp/extconf.rb

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+# frozen_string_literal: true
+
+require "mkmf-rice"
+require "numo/narray"
+
+vendor = File.expand_path("../../vendor", __dir__)
+
+apple_clang = RbConfig::CONFIG["CC_VERSION_MESSAGE"] =~ /apple clang/i
+
+# check omp first
+if have_library("omp") || have_library("gomp")
+  $CXXFLAGS += " -Xclang" if apple_clang
+  $CXXFLAGS += " -fopenmp"
+end
+
+# numo-narray
+numo = File.join(Gem.loaded_specs["numo-narray"].require_path, "numo")
+abort "Numo header not found" unless find_header("numo/narray.h", numo)
+abort "Numo library not found" if Gem.win_platform? && !find_library("narray", nil, numo)
+find_header("numo.hpp", File.expand_path("../../include", __dir__))
+
+dir_config "umap", vendor, vendor
+dir_config "umappp", File.join(vendor, "umappp"), File.join(vendor, "umappp")
+
+create_makefile("umappp/umappp")