hanny 0.1.0 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: a911da20689134ebecdd01b88827a2d2cc65149b497103f32f528fa754590c15
+  metadata.gz: 2824f94d9113fc6605cf22f54a3cbabb594ade24cf27fee4c87bf44f173d8230
+  data.tar.gz: 7ae587eb0c54e706570463c45b067f664f18782689a3b9be2fae4cbb16f637bd
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+  data.tar.gz: 8ad6a5507f4efcd1afbdf9241931f9485780e9bf9e48d5048524944073a7d56e8ca693e710b5f8ea84b4f8aee595dc0339c61ab8409587d87169d9526e158dde

data/.coveralls.yml

@@ -1 +1 @@
-service_name: travis-ci
+service_name: github-ci

data/.github/workflows/build.yml

@@ -0,0 +1,21 @@
+name: build
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        ruby: [ '2.6', '2.7', '3.0' ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Ruby ${{ matrix.ruby }}
+        uses: actions/setup-ruby@v1
+        with:
+          ruby-version: ${{ matrix.ruby }}
+      - name: Build and test with Rake
+        run: |
+          gem install --no-document bundler
+          bundle install --jobs 4 --retry 3
+          bundle exec rake

data/.github/workflows/coverage.yml

@@ -0,0 +1,26 @@
+name: coverage
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  coverage:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Ruby 2.7
+        uses: actions/setup-ruby@v1
+        with:
+          ruby-version: '2.7'
+      - name: Build and test with Rake
+        run: |
+          gem install bundler
+          bundle install
+          bundle exec rake
+      - name: Coveralls GitHub Action
+        uses: coverallsapp/github-action@v1.1.2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}

data/.rubocop.yml

@@ -1,12 +1,16 @@
+require:
+  - rubocop-performance
+  - rubocop-rspec
+
 AllCops:
-  TargetRubyVersion: 2.1
+  TargetRubyVersion: 2.5
   DisplayCopNames: true
   DisplayStyleGuide: true
+  NewCops: enable
+  Exclude:
+    - 'hanny.gemspec'
 
-Documentation:
-  Enabled: false
-
-Metrics/LineLength:
+Layout/LineLength:
   Max: 140
   IgnoredPatterns: ['(\A|\s)#']
 
@@ -26,13 +30,13 @@ Metrics/BlockLength:
   Exclude:
     - 'spec/**/*'
 
-ParameterLists:
+Metrics/ParameterLists:
   Max: 10
 
 Security/MarshalLoad:
   Enabled: false
 
-Naming/UncommunicativeMethodParamName:
+Naming/MethodParameterName:
   Enabled: false
 
 Style/FormatStringToken:

data/CHANGELOG.md

@@ -0,0 +1,7 @@
+# 0.2.0
+- Add type declaration files.
+- Refactor some codes with type check.
+- Fix some configuration files.
+
+# 0.1.0
+- First release.

data/Gemfile

@@ -4,3 +4,11 @@ git_source(:github) { |repo_name| "https://github.com/#{repo_name}" }
 
 # Specify your gem's dependencies in hanny.gemspec
 gemspec
+
+gem 'bundler', '~> 2.0'
+gem 'rake', '~> 12.0'
+gem 'rspec', '~> 3.0'
+gem 'simplecov', '~> 0.19'
+gem 'simplecov-lcov', '~> 0.8'
+gem 'rbs', '~> 1.2'
+gem 'steep', '~> 0.44'

data/LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2017 yoshoku
+Copyright (c) 2017-2021 yoshoku
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

data/README.md

@@ -1,9 +1,10 @@
 # Hanny
 
-[![Build Status](https://travis-ci.org/yoshoku/Hanny.svg?branch=master)](https://travis-ci.org/yoshoku/Hanny)
-[![Coverage Status](https://coveralls.io/repos/github/yoshoku/Hanny/badge.svg?branch=master)](https://coveralls.io/github/yoshoku/Hanny?branch=master)
+[![Build Status](https://github.com/yoshoku/hanny/actions/workflows/build.yml/badge.svg)](https://github.com/yoshoku/hanny/actions/workflows/build.yml)
+[![Coverage Status](https://coveralls.io/repos/github/yoshoku/hanny/badge.svg?branch=main)](https://coveralls.io/github/yoshoku/hanny?branch=main)
 [![Gem Version](https://badge.fury.io/rb/hanny.svg)](https://badge.fury.io/rb/hanny)
-[![BSD 2-Clause License](https://img.shields.io/badge/License-BSD%202--Clause-orange.svg)](https://github.com/yoshoku/Hanny/blob/master/LICENSE.txt)
+[![BSD 2-Clause License](https://img.shields.io/badge/License-BSD%202--Clause-orange.svg)](https://github.com/yoshoku/Hanny/blob/main/LICENSE.txt)
+[![Documentation](https://img.shields.io/badge/api-reference-blue.svg)](https://yoshoku.github.io/hanny/doc/)
 
 Hanny is a Hash-based Approximate Nearest Neighbor (ANN) search library in Ruby.
 Hash-based ANN converts vector data into binary codes and builds a hash table by using the binary codes as hash keys.
@@ -27,6 +28,10 @@ Or install it yourself as:
 
     $ gem install hanny
 
+## Documentation
+
+- [Hanny API Documentation](https://yoshoku.github.io/hanny/doc/)
+
 ## Usage
 
 ```ruby
@@ -67,14 +72,14 @@ I confirmed the search speed of Hanny's LSH with [MNIST](https://www.csie.ntu.ed
 The experiment is carried out on MacBook Early 2016 (Core m3 1.1 GHz CPU and 8 GB memory).
 
 Code:
+
 ```ruby
 require 'benchmark'
-require 'svmkit'
+require 'rumale'
 require 'hanny'
 
 # Load MNIST data set.
-samples, labels = SVMKit::Dataset.load_libsvm_file('mnist')
-samples = Numo::DFloat.cast(samples)
+samples, labels = Rumale::Dataset.load_libsvm_file('mnist')
 queries = samples[0..5, true]
 targets = samples[6..-1, true]
 qlabels = labels[0..5]
@@ -111,6 +116,7 @@ end
 ```
 
 Result:
+
 ```bash
     user     system      total        real
 LSH
@@ -131,12 +137,6 @@ query label: 2, neighbors label: 2, 2, 2, 2, 2,
   6.350000   0.280000   6.630000 (  6.682365)
 ```
 
-## Development
-
-After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
-
-To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
-
 ## Contributing
 
 Bug reports and pull requests are welcome on GitHub at https://github.com/yoshoku/Hanny. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
@@ -147,4 +147,4 @@ The gem is available as open source under the terms of the [BSD 2-clause License
 
 ## Code of Conduct
 
-Everyone interacting in the Hanny project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/yoshoku/Hanny/blob/master/CODE_OF_CONDUCT.md).
+Everyone interacting in the Hanny project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/yoshoku/Hanny/blob/main/CODE_OF_CONDUCT.md).

data/Steepfile

@@ -0,0 +1,20 @@
+target :lib do
+  signature "sig"
+
+  check "lib"                       # Directory name
+#   check "Gemfile"                   # File name
+#   check "app/models/**/*.rb"        # Glob
+#   # ignore "lib/templates/*.rb"
+#
+#   # library "pathname", "set"       # Standard libraries
+  # library "numo-narray"           # Gems
+end
+
+# target :spec do
+#   signature "sig", "sig-private"
+#
+#   check "spec"
+#
+#   # library "pathname", "set"       # Standard libraries
+#   # library "rspec"
+# end

data/hanny.gemspec

@@ -27,12 +27,5 @@ MSG
   spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
   spec.require_paths = ['lib']
 
-  spec.required_ruby_version = '>= 2.1'
-
-  spec.add_runtime_dependency 'numo-narray', '>= 0.9.0'
-
-  spec.add_development_dependency 'bundler', '~> 1.16'
-  spec.add_development_dependency 'coveralls', '~> 0.8'
-  spec.add_development_dependency 'rake', '~> 10.0'
-  spec.add_development_dependency 'rspec', '~> 3.0'
+  spec.add_runtime_dependency 'numo-narray', '>= 0.9.1'
 end

data/lib/hanny/lsh_index.rb

@@ -65,13 +65,8 @@ module Hanny
     # @param random_seed [Integer/NilClass] The seed value using to initialize the random generator.
     def initialize(code_length: 256, random_seed: nil)
       @code_length = code_length
-      @n_samples = nil
-      @n_features = nil
-      @n_keys = nil
       @last_id = nil
       @weight_mat = nil
-      @hash_table = nil
-      @hash_codes = nil
       @random_seed = random_seed
       @random_seed ||= srand
       @rng = Random.new(@random_seed)
@@ -86,26 +81,27 @@ module Hanny
 
     # Build a search index.
     # @param x [Numo::DFloat] (shape: [n_samples, n_features]) The dataset for building search index.
-    # @return [SVC] The search index itself that has constructed the hash table.
+    # @return [LSHIndex] The search index itself that has constructed the hash table.
     def build_index(x)
       # Initialize some variables.
-      @n_samples, @n_features = x.shape
+      @n_samples = x.shape[0]
+      @n_features = x.shape[1]
       @hash_table = {}
-      @hash_codes = []
       @weight_mat = Utils.rand_normal([@n_features, @code_length], @rng)
       # Convert samples to binary codes.
       bin_x = hash_function(x)
       # Store samples to binary hash table.
+      codes = []
       @n_samples.times do |m|
         bin_code = bin_x[m, true]
         hash_key = symbolized_hash_key(bin_code)
         unless @hash_table.key?(hash_key)
-          @hash_codes.push(bin_code.to_a)
+          codes.push(bin_code.to_a)
           @hash_table[hash_key] = []
         end
         @hash_table[hash_key].push(m)
       end
-      @hash_codes = Numo::Bit.cast(@hash_codes)
+      @hash_codes = Numo::Bit.cast(codes)
       # Update some variables.
       @n_keys = @hash_codes.shape[0]
       @last_id = @n_samples
@@ -117,7 +113,7 @@ module Hanny
     # @return [Array<Integer>] The indices of appended data in search index
     def append_data(x)
       # Initialize some variables.
-      n_new_samples, = x.shape
+      n_new_samples = x.shape[0]
       bin_x = hash_function(x)
       added_data_ids = []
       # Store samples to binary hash table.
@@ -152,12 +148,14 @@ module Hanny
       removed_data_ids = []
       data_ids.each do |query_id|
         # Remove data id from hash table.
-        hash_key = @hash_table.keys.select { |k| @hash_table[k].include?(query_id) }.first
+        hash_key = @hash_table.keys.find { |k| @hash_table[k].include?(query_id) }
         next if hash_key.nil?
+
         @hash_table[hash_key].delete(query_id)
         removed_data_ids.push(query_id)
         # Remove the hash key if there is no data.
         next unless @hash_table[hash_key].empty?
+
         target_id = distances_to_hash_codes(decoded_hash_key(hash_key)).index(0)
         @hash_codes = @hash_codes.delete(target_id, 0)
       end
@@ -171,15 +169,17 @@ module Hanny
     # @return [Array<Integer>] The data indices of search result.
     def search_knn(q, n_neighbors: 10)
       # Initialize some variables.
-      n_queries, = q.shape
+      n_queries = q.shape[0]
       candidates = Array.new(n_queries) { [] }
       # Binarize queries.
       bin_q = hash_function(q)
       # Find k-nearest neighbors for each query.
       n_queries.times do |m|
-        sort_with_index(distances_to_hash_codes(bin_q[m, true])).each do |_, n|
+        sort_with_index(distances_to_hash_codes(bin_q[m, true])).each do |d, n|
           candidates[m] = candidates[m] | @hash_table[symbolized_hash_key(@hash_codes[n, true])]
-          break if candidates[m].size >= n_neighbors
+          # TODO: Investigate the cause of the steep Ruby::BreakTypeMismatch error.
+          # break if candidates[m].size >= n_neighbors
+          break [[d, n]] if candidates[m].size >= n_neighbors
         end
         candidates[m] = candidates[m].shift(n_neighbors)
       end
@@ -190,55 +190,25 @@ module Hanny
     # @param q [Numo::DFloat] (shape: [n_queries, n_features]) The data for search queries.
     # @param radius [Float] The hamming radius for search range.
     # @return [Array<Integer>] The data indices of search result.
-    def search_radius(q, radius: 1)
+    def search_radius(q, radius: 1.0)
       # Initialize some variables.
-      n_queries, = q.shape
+      n_queries = q.shape[0]
       candidates = Array.new(n_queries) { [] }
       # Binarize queries.
       bin_q = hash_function(q)
       # Find k-nearest neighbors for each query.
       n_queries.times do |m|
         sort_with_index(distances_to_hash_codes(bin_q[m, true])).each do |d, n|
-          break if d > radius
+          # TODO: Investigate the cause of the steep Ruby::BreakTypeMismatch error.
+          # break if d > radius
+          break [[d, n]] if d > radius
+
           candidates[m] = candidates[m] | @hash_table[symbolized_hash_key(@hash_codes[n, true])]
         end
       end
       candidates
     end
 
-    # Dump marshal data.
-    # @return [Hash] The marshal data for search index.
-    def marshal_dump
-      { code_length: @code_length,
-        n_samples: @n_samples,
-        n_features: @n_features,
-        n_keys: @n_keys,
-        last_id: @last_id,
-        weight_mat: @weight_mat,
-        bias_vec: @bias_vec,
-        hash_table: @hash_table,
-        hash_codes: @hash_codes,
-        random_seed: @random_seed,
-        rng: @rng }
-    end
-
-    # Load marshal data.
-    # @return [nil]
-    def marshal_load(obj)
-      @code_length = obj[:code_length]
-      @n_samples = obj[:n_samples]
-      @n_features = obj[:n_features]
-      @n_keys = obj[:n_keys]
-      @last_id = obj[:last_id]
-      @weight_mat = obj[:weight_mat]
-      @bias_vec = obj[:bias_vec]
-      @hash_table = obj[:hash_table]
-      @hash_codes = obj[:hash_codes]
-      @random_seed = obj[:random_seed]
-      @rng = obj[:rng]
-      nil
-    end
-
     private
 
     # Convert binary code to symbol as hash key.
@@ -266,7 +236,7 @@ module Hanny
     # @param hash_key [Symbol]
     # @return [Numo::Bit]
     def decoded_hash_key(hash_key)
-      bin_code = Zlib::Inflate.inflate(hash_key.to_s).split('').map(&:to_i)
+      bin_code = Zlib::Inflate.inflate(hash_key.to_s).chars.map(&:to_i)
       Numo::Bit[*bin_code]
     end
   end

data/lib/hanny/version.rb

@@ -2,6 +2,6 @@
 
 # Hanny is a hash-based approximate nearest neighbor search library.
 module Hanny
-  # @!visibility private
-  VERSION = '0.1.0'.freeze
+  # The version of Hanny you are using.
+  VERSION = '0.2.0'
 end

data/sig/hanny.rbs

@@ -0,0 +1,3 @@
+module Hanny
+  VERSION: String
+end

data/sig/hanny/lsh_index.rbs

@@ -0,0 +1,27 @@
+module Hanny
+  class LSHIndex
+    attr_reader code_length: Integer
+    attr_reader n_samples: Integer
+    attr_reader n_features: Integer
+    attr_reader n_keys: Integer
+    attr_reader hash_table: Hash[Symbol, Array[Integer]]
+    attr_reader hash_codes: Numo::Bit
+    attr_reader random_seed: untyped
+    attr_reader rng: Random
+
+    def initialize: (?code_length: Integer code_length, ?random_seed: Integer? random_seed) -> void
+    def hash_function: (Numo::DFloat x) -> Numo::Bit
+    def build_index: (Numo::DFloat x) -> LSHIndex
+    def append_data: (Numo::DFloat x) -> Array[Integer]
+    def remove_data: (Array[Integer] data_ids) -> Array[Integer]
+    def search_knn: (Numo::DFloat q, ?n_neighbors: Integer n_neighbors) -> Array[Array[Integer]]
+    def search_radius: (Numo::DFloat q, ?radius: Float radius) -> Array[Array[Integer]]
+
+    private
+
+    def symbolized_hash_key: (Numo::Bit bin_code) -> Symbol
+    def distances_to_hash_codes: (Numo::Bit bin_code) -> Array[Float]
+    def sort_with_index: (Array[Float] arr) -> Array[[Float, Integer]]
+    def decoded_hash_key: (Symbol hash_key) -> Numo::Bit
+  end
+end

data/sig/hanny/utils.rbs

@@ -0,0 +1,7 @@
+module Hanny
+  module Utils
+    def self.euclidean_distance: (Numo::DFloat x, ?Numo::DFloat? y) -> Numo::DFloat
+    def self.rand_uniform: (Array[Integer] shape, Random rng) -> Numo::DFloat
+    def self.rand_normal: (Array[Integer] shape, Random rng, ?Float mu, ?Float sigma) -> Numo::DFloat
+  end
+end

data/sig/patch.rbs

@@ -0,0 +1,30 @@
+module Numo
+  class NArray
+    def self.asarray: (untyped) -> untyped
+    def self.zeros: (*untyped) -> untyped
+    def concatenate: (*untyped arrays, ?axis: untyped) -> untyped
+    def delete: (untyped indice, ?untyped axis) -> untyped
+    def dot: (untyped b) -> untyped
+    def shape: () -> Array[Integer]
+  end
+
+  class DFloat < NArray
+    def self.[]: (*untyped) -> untyped
+    def -@: () -> untyped
+    def +: (untyped) -> untyped
+    def -: (untyped) -> untyped
+    def *: (untyped) -> untyped
+    def /: (untyped) -> untyped
+    def []: (*untyped) -> untyped
+    def []=: (*untyped) -> untyped
+  end
+
+  class Bit < NArray
+    def self.[]: (*untyped) -> untyped
+    def self.cast: (untyped) -> untyped
+    def []: (*untyped) -> untyped
+    def []=: (*untyped) -> untyped
+    def ^: (untyped) -> untyped
+    def to_a: () -> untyped
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: hanny
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors:
 - yoshoku
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2018-05-04 00:00:00.000000000 Z
+date: 2021-06-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: numo-narray
@@ -16,70 +16,14 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.9.0
+        version: 0.9.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.9.0
-- !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.16'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.16'
-- !ruby/object:Gem::Dependency
-  name: coveralls
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.8'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.8'
-- !ruby/object:Gem::Dependency
-  name: rake
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '10.0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '10.0'
-- !ruby/object:Gem::Dependency
-  name: rspec
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.0'
+        version: 0.9.1
 description: |
   Hanny is a Hash-based Approximate Nearest Neighbor (ANN) search library in Ruby.
   Hash-based ANN converts vector data into binary codes and builds a hash table by using the binary codes as hash keys.
@@ -93,22 +37,27 @@ extensions: []
 extra_rdoc_files: []
 files:
 - ".coveralls.yml"
+- ".github/workflows/build.yml"
+- ".github/workflows/coverage.yml"
 - ".gitignore"
 - ".rspec"
 - ".rubocop.yml"
-- ".travis.yml"
+- CHANGELOG.md
 - CODE_OF_CONDUCT.md
 - Gemfile
 - LICENSE.txt
 - README.md
 - Rakefile
-- bin/console
-- bin/setup
+- Steepfile
 - hanny.gemspec
 - lib/hanny.rb
 - lib/hanny/lsh_index.rb
 - lib/hanny/utils.rb
 - lib/hanny/version.rb
+- sig/hanny.rbs
+- sig/hanny/lsh_index.rbs
+- sig/hanny/utils.rbs
+- sig/patch.rbs
 homepage: https://github.com/yoshoku/hanny
 licenses:
 - BSD-2-Clause
@@ -121,15 +70,14 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '2.1'
+      version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.6
+rubygems_version: 3.1.6
 signing_key: 
 specification_version: 4
 summary: Hanny is a Hash-based Approximate Nearest Neighbor search library in Ruby.

data/.travis.yml

@@ -1,11 +0,0 @@
-sudo: false
-os: linux
-dist: trusty
-language: ruby
-rvm:
-  - 2.2
-  - 2.3
-  - 2.4
-  - 2.5
-before_install:
-  - gem install --no-document bundler -v '~> 1.16'

data/bin/console

@@ -1,14 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'bundler/setup'
-require 'hanny'
-
-# You can add fixtures and/or initialization code here to make experimenting
-# with your gem easier. You can also use a different console, if you like.
-
-# (If you use this, don't forget to add pry to your Gemfile!)
-# require "pry"
-# Pry.start
-
-require 'irb'
-IRB.start(__FILE__)

data/bin/setup

@@ -1,8 +0,0 @@
-#!/usr/bin/env bash
-set -euo pipefail
-IFS=$'\n\t'
-set -vx
-
-bundle install
-
-# Do any other automated setup that you need to do here