pycall 0.1.0.alpha → 0.1.0.alpha.20170224

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: 6d6ddea53f723b45bf9207c52746afaa083fba57
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+  metadata.gz: '08a91ee3157d872d18725d57ace058d991feb1855250307d9b9cd17feab5081a96ed03ab05941ecec073c22c3a63b2ed8c8c777c83735459e9e7b8e10e7220d7'
+  data.tar.gz: 2359c6d09f3bc687466e41c0e0de2287a89bd4b11587e3384d4a41dd0eb737cf75af387d149efbb8322baa69136d4483f3901728e6b2b36545a9dbc5e6fe8d35

data/.travis.yml

@@ -1,5 +1,19 @@
 sudo: false
 language: ruby
+
 rvm:
+  - 2.1.10
+  - 2.2.5
   - 2.3.1
-before_install: gem install bundler -v 1.13.2
+  - ruby-head
+
+addons:
+  apt:
+    packages:
+      - python3
+      - python3-dev
+      - python3-all
+
+before_install:
+  - gem update --system
+  - gem update bundler

data/Gemfile

@@ -2,3 +2,8 @@ source 'https://rubygems.org'
 
 # Specify your gem's dependencies in pycall.gemspec
 gemspec
+
+group :development do
+  gem 'guard-rspec', require: false
+  gem 'terminal-notifier-guard', require: false
+end

data/Guardfile

@@ -0,0 +1 @@
+./config/Guardfile

data/README.md

@@ -1,4 +1,6 @@
-# Pycall
+# PyCall
+
+[![Build Status](https://travis-ci.org/mrkn/pycall.svg?branch=master)](https://travis-ci.org/mrkn/pycall)
 
 Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/pycall`. To experiment with that code, run `bin/console` for an interactive prompt.
 
@@ -32,7 +34,7 @@ To install this gem onto your local machine, run `bundle exec rake install`. To
 
 ## Contributing
 
-Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/pycall.
+Bug reports and pull requests are welcome on GitHub at https://github.com/mrkn/pycall.
 
 
 ## License

data/bin/guard

@@ -0,0 +1,17 @@
+#!/usr/bin/env ruby
+# frozen_string_literal: true
+#
+# This file was generated by Bundler.
+#
+# The application 'guard' is installed as part of a gem, and
+# this file is here to facilitate running it.
+#
+
+require "pathname"
+ENV["BUNDLE_GEMFILE"] ||= File.expand_path("../../Gemfile",
+  Pathname.new(__FILE__).realpath)
+
+require "rubygems"
+require "bundler/setup"
+
+load Gem.bin_path("guard", "guard")

data/bin/rspec

@@ -0,0 +1,17 @@
+#!/usr/bin/env ruby
+# frozen_string_literal: true
+#
+# This file was generated by Bundler.
+#
+# The application 'rspec' is installed as part of a gem, and
+# this file is here to facilitate running it.
+#
+
+require "pathname"
+ENV["BUNDLE_GEMFILE"] ||= File.expand_path("../../Gemfile",
+  Pathname.new(__FILE__).realpath)
+
+require "rubygems"
+require "bundler/setup"
+
+load Gem.bin_path("rspec-core", "rspec")

data/config/Guardfile

@@ -0,0 +1,30 @@
+# More info at https://github.com/guard/guard#readme
+
+if RUBY_PLATFORM =~ /darwin/
+  notification :terminal_notifier, app_name: 'pycall.gem ::', activate: 'com.googlecode.iTerm2'
+end
+
+directories %w(config lib spec).select { |d|
+  Dir.exists?(d) ? d : UI.warning("Directory #{d} does not exist")
+}
+
+watch('config/Guardfile') do
+  UI.info "Exiting guard because config changed"
+  exit 0
+end
+
+guard :rspec, cmd: 'bin/rspec' do
+  require "guard/rspec/dsl"
+  dsl = Guard::RSpec::Dsl.new(self)
+
+  # RSpec files
+  rspec = dsl.rspec
+  watch(rspec.spec_helper) { rspec.spec_dir }
+  watch(rspec.spec_support) { rspec.spec_dir }
+  watch(rspec.spec_files)
+
+  # Ruby files
+  ruby = dsl.ruby
+  dsl.watch_spec_files_for(ruby.lib_files)
+  watch('lib/pycall/libpython.rb') { 'spec' }
+end

data/examples/classifier_comparison.rb

@@ -0,0 +1,130 @@
+require 'pycall/import'
+include PyCall::Import
+
+pyimport 'numpy', as: :np
+pyimport 'matplotlib.pyplot', as: :plt
+pyimport 'matplotlib.colors', as: :mplc
+pyfrom 'sklearn.cross_validation', import: :train_test_split
+pyfrom 'sklearn.preprocessing', import: :StandardScaler
+pyfrom 'sklearn.datasets', import: %i(make_moons make_circles make_classification)
+pyfrom 'sklearn.neighbors', import: :KNeighborsClassifier
+pyfrom 'sklearn.svm', import: :SVC
+pyfrom 'sklearn.tree', import: :DecisionTreeClassifier
+pyfrom 'sklearn.ensemble', import: %i(RandomForestClassifier AdaBoostClassifier)
+pyfrom 'sklearn.naive_bayes', import: :GaussianNB
+pyfrom 'sklearn.discriminant_analysis', import: %i(LinearDiscriminantAnalysis QuadraticDiscriminantAnalysis)
+
+h = 0.02  # step size in the mesh
+
+names = [
+  'Nearest Neighbors',
+  'Linear SVM',
+  'RBF SVM',
+  'Decision Tree',
+  'Random Forest',
+  'AdaBoost',
+  'Naive Bayes',
+  'Linear Discriminant Analysis',
+  'Quadratic Discriminant Analysis'
+]
+
+classifiers = [
+  KNeighborsClassifier.(3),
+  SVC.(kernel: 'linear', C: 0.025),
+  SVC.(gamma: 2, C: 1),
+  DecisionTreeClassifier.(max_depth: 5),
+  RandomForestClassifier.(max_depth: 5, n_estimators: 10, max_features: 1),
+  AdaBoostClassifier.(),
+  GaussianNB.(),
+  LinearDiscriminantAnalysis.(),
+  QuadraticDiscriminantAnalysis.()
+]
+
+x, y = make_classification.(
+  n_features: 2,
+  n_redundant: 0,
+  n_informative: 2,
+  random_state: 1,
+  n_clusters_per_class: 1
+)
+
+np.random.seed.(42)
+x += 2 * np.random.random_sample.(x.shape)
+linearly_separable = PyCall.tuple(x, y)
+
+datasets = [
+  make_moons.(noise: 0.3, random_state: 0),
+  make_circles.(noise: 0.2, factor: 0.5, random_state: 1),
+  linearly_separable
+]
+
+fig = plt.figure.(figsize: PyCall.tuple(27, 9))
+i = 1
+all = PyCall.slice(nil)
+datasets.each do |ds|
+  x, y = ds
+  x = StandardScaler.().fit_transform.(x)
+  x_train, x_test, y_train, y_test = train_test_split.(x, y, test_size: 0.4)
+
+  x_min, x_max = np.min.(x[all, 0]) - 0.5, np.max.(x[all, 0]) + 0.5
+  y_min, y_max = np.min.(x[all, 1]) - 0.5, np.max.(x[all, 1]) + 0.5
+
+  xx, yy = np.meshgrid.(
+    np.linspace.(x_min, x_max, ((x_max - x_min)/h).round),
+    np.linspace.(y_min, y_max, ((y_max - y_min)/h).round),
+  )
+  mesh_points = np.dstack.(PyCall.tuple(xx.ravel.(), yy.ravel.()))[0, all, all]
+
+  # just plot the dataset first
+  cm = plt.cm.RdBu
+  cm_bright = mplc.ListedColormap.(["#FF0000", "#0000FF"])
+  ax = plt.subplot.(datasets.length, classifiers.length + 1, i)
+  # plot the training points
+  ax.scatter.(x_train[all, 0], x_train[all, 1], c: y_train, cmap: cm_bright)
+  # and testing points
+  ax.scatter.(x_test[all, 0], x_test[all, 1], c: y_test, cmap: cm_bright, alpha: 0.6)
+
+  ax.set_xlim.(np.min.(xx), np.max.(xx))
+  ax.set_ylim.(np.min.(yy), np.max.(yy))
+  ax.set_xticks.(PyCall.tuple())
+  ax.set_yticks.(PyCall.tuple())
+  i += 1
+
+  # iterate over classifiers
+  names.zip(classifiers).each do |name, clf|
+    ax = plt.subplot.(datasets.length, classifiers.length + 1, i)
+    clf.fit.(x_train, y_train)
+    scor = clf.score.(x_test, y_test)
+
+    # Plot the decision boundary.  For that, we will assign a color to each
+    # point in the mesh [x_min, x_max]x[y_min, y_max]
+    begin
+      # not implemented for some
+      z = clf.decision_function.(mesh_points)
+    rescue
+      z = clf.predict_proba.(mesh_points)[all, 1]
+    end
+
+    # Put the result into a color plot
+    z = z.reshape.(xx.shape)
+    ax.contourf.(xx, yy, z, cmap: cm, alpha: 0.8)
+
+    # Plot also the training points
+    ax.scatter.(x_train[all, 0], x_train[all, 1], c: y_train, cmap: cm_bright)
+    # and testing points
+    ax.scatter.(x_test[all, 0], x_test[all, 1], c: y_test, cmap: cm_bright, alpha: 0.6)
+
+    ax.set_xlim.(np.min.(xx), np.max.(xx))
+    ax.set_ylim.(np.min.(yy), np.max.(yy))
+    ax.set_xticks.(PyCall.tuple())
+    ax.set_yticks.(PyCall.tuple())
+    ax.set_title.(name)
+
+    ax.text.(np.max.(xx) - 0.3, np.min.(yy) + 0.3, "%.2f" % scor, size: 15, horizontalalignment: 'right')
+
+    i += 1
+  end
+end
+
+fig.subplots_adjust.(left: 0.02, right: 0.98)
+plt.show.()

data/examples/hist.rb

@@ -0,0 +1,27 @@
+require 'pycall/import'
+include PyCall::Import
+
+pyimport 'numpy', as: 'np'
+pyimport 'matplotlib.mlab', as: 'mlab'
+pyimport 'matplotlib.pyplot', as: 'plt'
+
+np.random.seed.(0)
+
+mu = 100
+sigma = 15
+x = mu + sigma * np.random.randn.(437)
+
+num_bins = 50
+
+fig, ax = plt.subplots.()
+
+n, bins, patches = ax.hist.(x, num_bins, normed: 1)
+
+y = mlab.normpdf.(bins, mu, sigma)
+ax.plot.(bins, y, '--')
+ax.set_xlabel.('Smarts')
+ax.set_ylabel.('Probability density')
+ax.set_title.('Histogram of IQ: $\mu=100$, $\sigma=15$')
+
+fig.tight_layout.()
+plt.show.()

data/examples/plot_forest_importances_faces.rb

@@ -0,0 +1,41 @@
+require 'pycall/import'
+
+include PyCall::Import
+
+pyimport 'numpy', as: 'np'
+pyimport 'matplotlib.pyplot', as: 'plt'
+
+pyfrom 'sklearn.datasets', import: 'fetch_olivetti_faces'
+pyfrom 'sklearn.ensemble', import: 'ExtraTreesClassifier'
+
+# Number of cores to use to perform parallel fitting of the forest model
+n_jobs = 1
+
+# Load the faces datasets
+data = fetch_olivetti_faces.()
+x = data.images.reshape.(PyCall.tuple(PyCall.len(data.images), -1))
+y = data.target
+
+mask = y < 5  # Limit to 5 classes
+x = x[mask]
+y = y[mask]
+
+# Build a forest and compute the pixel importances
+puts "Fitting ExtraTreesClassifier on faces data with #{n_jobs} cores..."
+t0 = Time.now
+forest = ExtraTreesClassifier.(
+  n_estimators: 1_000,
+  max_features: 128,
+  n_jobs: n_jobs,
+  random_state: 0
+)
+
+forest = forest.fit.(x, y)
+puts "done in %0.3fs" % (Time.now - t0)
+importances = forest.feature_importances_
+importances = importances.reshape.(data.images[0].shape)
+
+# Plot pixel importances
+plt.matshow.(importances, cmap: plt.cm.hot)
+plt.title.("Pixel importances with forests of trees")
+plt.show.()

data/examples/sum_benchmarking.rb

@@ -0,0 +1,48 @@
+require 'pycall/import'
+include PyCall::Import
+
+require 'benchmark'
+pyimport :pandas, as: :pd
+pyimport :seaborn, as: :sns
+pyimport 'matplotlib.pyplot', as: :plt
+
+array = Array.new(100_000) { rand }
+
+trials = 100
+results = { method: [], runtime: [] }
+
+# Array#sum
+trials.times do
+  results[:method] << 'sum'
+  results[:runtime] << Benchmark.realtime { array.sum }
+end
+
+# Array#inject(:+)
+trials.times do
+  results[:method] << 'inject'
+  results[:runtime] << Benchmark.realtime { array.inject(:+) }
+end
+
+# while
+def while_sum(ary)
+  sum, i, n = 0, 0, ary.length
+  while i < n
+    sum += ary[i]
+    i += 1
+  end
+  sum
+end
+
+trials.times do
+  results[:method] << 'while'
+  results[:runtime] << Benchmark.realtime { while_sum(array) }
+end
+
+# visualization
+
+df = pd.DataFrame.(PyCall::Dict.new(results))
+sns.barplot.(x: 'method', y: 'runtime', data: df)
+plt.title.("Array summation benchmark (#{trials} trials)")
+plt.xlabel.('Summation method')
+plt.ylabel.('Average runtime [sec]')
+plt.show.()

data/lib/pycall.rb

@@ -1,5 +1,15 @@
 require "pycall/version"
-
-module Pycall
-  # Your code goes here...
-end
+require "pycall/libpython"
+require "pycall/pyobject"
+require "pycall/pyerror"
+require "pycall/eval"
+require "pycall/types"
+require "pycall/conversion"
+require "pycall/pyobject_wrapper"
+require "pycall/tuple"
+require "pycall/list"
+require "pycall/dict"
+require "pycall/set"
+require "pycall/slice"
+require "pycall/utils"
+require "pycall/init"

data/lib/pycall/conversion.rb

@@ -0,0 +1,120 @@
+module PyCall
+  module Conversions
+    def self.from_ruby(obj)
+      case obj
+      when PyObject
+        obj
+      when PyObjectWrapper
+        obj.__pyobj__
+      when TrueClass, FalseClass
+        LibPython.PyBool_FromLong(obj ? 1 : 0)
+      when Integer
+        LibPython.PyInt_FromSsize_t(obj)
+      when Float
+        LibPython.PyFloat_FromDouble(obj)
+      when String
+        case obj.encoding
+        when Encoding::US_ASCII, Encoding::BINARY
+          LibPython.PyString_FromStringAndSize(obj, obj.bytesize)
+        else
+          obj = obj.encode(Encoding::UTF_8)
+          LibPython.PyUnicode_DecodeUTF8(obj, obj.bytesize, nil)
+        end
+      when Symbol
+        from_ruby(obj.to_s)
+      when Array
+        PyCall::List.new(obj).__pyobj__
+      else
+        LibPython.Py_None
+      end
+    end
+
+    def self.convert_to_boolean(py_obj)
+      0 != LibPython.PyInt_AsSsize_t(py_obj)
+    end
+
+    def self.convert_to_integer(py_obj)
+      LibPython.PyInt_AsSsize_t(py_obj)
+    end
+
+    def self.convert_to_float(py_obj)
+      LibPython.PyFloat_AsDouble(py_obj)
+    end
+
+    def self.convert_to_complex(py_obj)
+      real = LibPython.PyComplex_RealAsDouble(py_obj)
+      imag = LibPython.PyComplex_ImagAsDouble(py_obj)
+      Complex(real, imag)
+    end
+
+    def self.convert_to_string(py_obj)
+      FFI::MemoryPointer.new(:string) do |str_ptr|
+        FFI::MemoryPointer.new(:int) do |len_ptr|
+          res = LibPython.PyString_AsStringAndSize(py_obj, str_ptr, len_ptr)
+          return nil if res == -1  # FIXME: error
+
+          len = len_ptr.get(:int, 0)
+          return str_ptr.get_pointer(0).read_string(len)
+        end
+      end
+    end
+
+    def self.convert_to_array(py_obj, force_list: true, array_class: Array)
+      case
+      when force_list || py_obj.kind_of?(LibPython.PyList_Type)
+        len = LibPython.PySequence_Size(py_obj)
+        array_class.new(len) do |i|
+          LibPython.PySequence_GetItem(py_obj, i).to_ruby
+        end
+      end
+    end
+
+    def self.convert_to_tuple(py_obj)
+      PyCall::Tuple.new(py_obj)
+    end
+  end
+
+  class PyObject
+    def to_ruby
+      return nil if self.null? || self.py_none?
+
+      case self
+      when LibPython.PyBool_Type
+        return Conversions.convert_to_boolean(self)
+
+      when LibPython.PyInt_Type
+        return Conversions.convert_to_integer(self)
+
+      when LibPython.PyLong_Type
+        # TODO: should make Bignum
+
+      when LibPython.PyFloat_Type
+        return Conversions.convert_to_float(self)
+
+      when LibPython.PyComplex_Type
+        return Conversions.convert_to_complex(self)
+
+      when LibPython.PyString_Type
+        return Conversions.convert_to_string(self)
+
+      when LibPython.PyUnicode_Type
+        py_str_ptr = LibPython.PyUnicode_AsUTF8String(self)
+        return Conversions.convert_to_string(py_str_ptr).force_encoding(Encoding::UTF_8)
+
+      when LibPython.PyList_Type
+        return Conversions.convert_to_array(self)
+
+      when LibPython.PyTuple_Type
+        return Conversions.convert_to_tuple(self)
+
+      when LibPython.PyDict_Type
+        return PyCall::Dict.new(self)
+
+      when LibPython.PySet_Type
+        return PyCall::Set.new(self)
+      end
+
+      self
+    end
+  end
+end