umappp 0.1.4 → 0.1.6

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data/README.md

@@ -16,7 +16,6 @@
 
 ## Installation
 
-
 ```
 gem install umappp
 ```
@@ -28,10 +27,12 @@ gem install umappp
 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
+# The embedding is two-dimensional Ruby array or Numo array
+# Returns Numo::SFloat
+r = Umappp.run(embedding)
 
-# with parameters
-Umappp.run(pixels, num_threads: 8, a: 1.8956, b: 0.8006)
+# Run with parameters
+r = Umappp.run(pixels, num_threads: 8, a: 1.8956, b: 0.8006)
 ```
 
 Available parameters and their default values

data/ext/umappp/umappp.cpp

@@ -1,7 +1,6 @@
 // Uniform Manifold Approximation and Projection for Ruby
 // https://github.com/kojix2/ruby-umappp
 
-
 #include <rice/rice.hpp>
 #include <rice/stl.hpp>
 #include "numo.hpp"
@@ -52,7 +51,7 @@ Object umappp_run(
 {
   // Parameters are taken from a Ruby Hash object.
   // If there is key, set the value.
-  
+
   auto umap_ptr = new Umap;
 
   double local_connectivity = Umap::Defaults::local_connectivity;
@@ -159,7 +158,7 @@ Object umappp_run(
     num_threads = params.get<int>(Symbol("num_threads"));
     umap_ptr->set_num_threads(num_threads);
   }
-  
+
   // initialize_from_matrix
 
   const float *y = data.read_ptr();
@@ -181,12 +180,16 @@ Object umappp_run(
   std::vector<Float> embedding(ndim * nobs);
 
   auto status = umap_ptr->initialize(knncolle_ptr.get(), ndim, embedding.data());
-
+  if (nobs < 0 || ndim < 0)
+  {
+    throw std::runtime_error("nobs or ndim is negative");
+  }
   if (tick == 0)
   {
     status.run(ndim, embedding.data(), 0);
 
-    auto na = numo::SFloat({(uint)nobs, (uint)ndim});
+    // it is safe to cast to unsigned int
+    auto na = numo::SFloat({(unsigned int)nobs, (unsigned int)ndim});
     std::copy(embedding.begin(), embedding.end(), na.write_ptr());
 
     return na;
@@ -201,7 +204,8 @@ Object umappp_run(
 
       status.run(ndim, embedding.data(), epoch_limit);
 
-      auto na = numo::SFloat({(uint)nobs, (uint)ndim});
+      //it is safe to cast to unsigned int
+      auto na = numo::SFloat({(unsigned int)nobs, (unsigned int)ndim});
       std::copy(embedding.begin(), embedding.end(), na.write_ptr());
 
       rb_ary_push(ret, na.value());

data/lib/umappp/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Umappp
-  VERSION = "0.1.4"
+  VERSION = "0.1.6"
 end

data/lib/umappp.rb

@@ -37,6 +37,7 @@ module Umappp
   # @param seed [Integer]
   # @param batch [Boolean]
   # @param num_threads [Integer]
+  # @return [Numo::SFloat] the final embedding
 
   def self.run(embedding, method: :annoy, ndim: 2, tick: 0, **params)
     unless (u = (params.keys - default_parameters.keys)).empty?

data/vendor/umappp/NeighborList.hpp

@@ -1,6 +1,9 @@
 #ifndef UMAPPP_NEIGHBOR_LIST_HPP
 #define UMAPPP_NEIGHBOR_LIST_HPP
 
+#include <utility>
+#include <vector>
+
 /**
  * @file NeighborList.hpp
  *

data/vendor/umappp/Umap.hpp

@@ -38,7 +38,7 @@ enum InitMethod { SPECTRAL, SPECTRAL_ONLY, RANDOM, NONE };
 /**
  * @cond
  */
-int choose_num_epochs(int num_epochs, size_t size) {
+inline int choose_num_epochs(int num_epochs, size_t size) {
     if (num_epochs < 0) {
         // Choosing the number of epochs. We use a simple formula to decrease
         // the number of epochs with increasing size, with the aim being that

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: umappp
 version: !ruby/object:Gem::Version
-  version: 0.1.4
+  version: 0.1.6
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-10-12 00:00:00.000000000 Z
+date: 2022-11-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: numo-narray