cmd_stan_rb 0.3.0 → 0.4.0

data/examples/linear_regression.ipynb

@@ -9,22 +9,46 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/robin/.rvm/gems/ruby-2.6.5/gems/cmd_stan_rb-0.3.0/lib/cmd_stan_rb/version.rb:2: warning: already initialized constant CmdStanRb::VERSION\n",
-      "/Users/robin/private_projects/cmd_stan_rb/lib/cmd_stan_rb/version.rb:2: warning: previous definition of VERSION was here\n"
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/cmd_stan_rb-0.3.1/lib/cmd_stan_rb/version.rb:2: warning: already initialized constant CmdStanRb::VERSION\n",
+      "/Users/robin.neumann/private_projects/cmd_stan_rb/lib/cmd_stan_rb/version.rb:2: warning: previous definition of VERSION was here\n"
      ]
     },
     {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "☑️"
+     "ename": "LoadError",
+     "evalue": "cannot load such file -- rubystats",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[31mLoadError\u001b[0m: cannot load such file -- rubystats",
+      "/Users/robin.neumann/.rvm/rubies/ruby-2.6.5/lib/ruby/site_ruby/2.6.0/rubygems/core_ext/kernel_require.rb:54:in `require'",
+      "/Users/robin.neumann/.rvm/rubies/ruby-2.6.5/lib/ruby/site_ruby/2.6.0/rubygems/core_ext/kernel_require.rb:54:in `require'",
+      "(pry):3:in `<main>'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/pry-0.13.1/lib/pry/pry_instance.rb:290:in `eval'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/pry-0.13.1/lib/pry/pry_instance.rb:290:in `evaluate_ruby'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/pry-0.13.1/lib/pry/pry_instance.rb:659:in `handle_line'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/pry-0.13.1/lib/pry/pry_instance.rb:261:in `block (2 levels) in eval'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/pry-0.13.1/lib/pry/pry_instance.rb:260:in `catch'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/pry-0.13.1/lib/pry/pry_instance.rb:260:in `block in eval'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/pry-0.13.1/lib/pry/pry_instance.rb:259:in `catch'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/pry-0.13.1/lib/pry/pry_instance.rb:259:in `eval'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/iruby-0.4.0/lib/iruby/backend.rb:66:in `eval'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/iruby-0.4.0/lib/iruby/backend.rb:12:in `eval'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/iruby-0.4.0/lib/iruby/kernel.rb:90:in `execute_request'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/iruby-0.4.0/lib/iruby/kernel.rb:49:in `dispatch'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/iruby-0.4.0/lib/iruby/kernel.rb:38:in `run'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/iruby-0.4.0/lib/iruby/command.rb:110:in `run_kernel'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/iruby-0.4.0/lib/iruby/command.rb:40:in `run'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/gems/iruby-0.4.0/bin/iruby:5:in `<top (required)>'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/bin/iruby:23:in `load'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/bin/iruby:23:in `<main>'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/bin/ruby_executable_hooks:24:in `eval'",
+      "/Users/robin.neumann/.rvm/gems/ruby-2.6.5/bin/ruby_executable_hooks:24:in `<main>'"
      ]
     }
    ],

data/lib/cmd_stan_rb/version.rb

@@ -1,3 +1,3 @@
 module CmdStanRb
-  VERSION = "0.3.0"
+  VERSION = "0.4.0"
 end

data/lib/stan/examples.rb

@@ -18,6 +18,19 @@
           }
         }
       end
+
+      # Convenience method to cross check on bundle console if all pieces
+      # are glued together correctly. Should get supported by far more test
+      # cases, but until I managed this this is a good assistence 😅
+      def run_bernoulli_integration_test
+        model = Stan::Model.new("test_#{rand(1000000)}") do
+          Stan::Examples.bernoulli
+        end
+        model.compile
+        model.data = {"N"=>4, "y"=>[1,1,0,0]}
+        result = model.fit(warm_up: 5, samples: 10)
+        result.theta
+      end
     end
   end
 end

data/lib/stan/model.rb

@@ -1,9 +1,11 @@
 module Stan
   class Model
     class NoDataGivenError < StandardError ;; end
+    class InvalidNameError < StandardError ;; end
 
-    attr_accessor :compiled_model_path, :name, :data
-    attr_reader :model_string, :model_file
+    attr_accessor :data
+    attr_reader :compiled_model_path, :model_string, :model_file,
+                :name, :last_compiled_at
 
     class << self
       def load(name)
@@ -12,18 +14,11 @@
     end
 
     def initialize(name, &block)
+      raise InvalidNameError.new("Please ensure that the model name does not start with a number!") if (name.to_s =~ /^\d/)
       @name = name
-
-      # I'd like to invent a convenient DSL that
-      # is similar to writing "direct" Stan code,
-      # but to do so I need to get a better understanding
-      # of Stan as a language/DSL itself. Until that
-      # I "approximate" my goal by using a block for initialization,
-      # where the block always needs to return the Stan model
-      # as a string. You can load it from a file or write in directly!
       @model_string = block.call if block_given?
 
-      `mkdir -p #{model_directory}` unless Dir.exists?(model_directory)
+      FileUtils.mkdir_p(model_directory) unless Dir.exists?(model_directory)
 
       if File.exists?(filename)
         load_model_file
@@ -37,15 +32,38 @@
     #
 
     def compile
-      system(commands[:compile])
-      {state: :ok, target: target, working_directory: working_directory}
+      if system(commands[:compile].to_s)
+        @last_compiled_at = Time.now
+        true
+      else
+        false
+      end
     end
 
-    def fit
+    def fit(warmup: 1000, samples: 1000, save_warmup: false, thin: 1)
       raise NoDataGivenError.new("Please specify your model's data before running simulations!") if data.nil?
-      `chmod +x #{CmdStanRb.configuration.model_dir}/#{name}/#{name}`
-      `#{commands[:fit]}`
-      {state: :ok, data: data}
+
+      additional_arguments =
+       [
+         "num_samples=#{samples.to_i}",
+         "num_warmup=#{warmup.to_i}",
+         "save_warmup=#{!!save_warmup ? 1 : 0}",
+         "thin=#{thin}",
+       ].join(" ")
+
+      FileUtils.chmod(0755, "#{CmdStanRb.configuration.model_dir}/#{name}/#{name}")
+
+      commands[:fit] = [
+        commands[:model_binary],
+        "sample",
+        additional_arguments,
+        "data",
+        "file=#{data_file.path}"
+      ].join(" ")
+
+      `#{commands[:fit].to_s}`
+
+      Stan::FitResult.new(output_csv)
     end
 
     def show
@@ -53,16 +71,15 @@
     end
 
     def destroy
-      path = "#{CmdStanRb.configuration.model_dir}/#{name}"
-      `rm -rvf #{path}`
-      {state: :ok, destroyed_path: path}
+      FileUtils.rm_rf(model_directory)
     end
 
     def commands
-      {
-        compile: "make -C #{CmdStanRb.configuration.cmdstan_dir} #{target}",
-        fit: "#{CmdStanRb.configuration.model_dir}/#{name}/#{name} sample data file=#{data_file.path}"
-      }
+      @commands ||=
+        {
+          compile: "make -C #{CmdStanRb.configuration.cmdstan_dir} #{target}",
+          model_binary: "#{CmdStanRb.configuration.model_dir}/#{name}/#{name}"
+        }
     end
 
     private
@@ -102,5 +119,11 @@
       "#{CmdStanRb.configuration.model_dir}/#{name}/#{name}.stan"
     end
 
+    def output_csv
+      File.read("output.csv")
+    rescue
+      ""
+    end
+
   end
 end

metadata

@@ -1,16 +1,16 @@
 --- !ruby/object:Gem::Specification
 name: cmd_stan_rb
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.4.0
 platform: ruby
 authors:
 - 'Robin Neumann
 
   '
-autorequire: 
+autorequire:
 bindir: exe
 cert_chain: []
-date: 2020-05-29 00:00:00.000000000 Z
+date: 2020-08-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
@@ -52,6 +52,7 @@ files:
 - demo.ipynb
 - examples/exponential.ipynb
 - examples/linear_regression.ipynb
+- examples/scumazon_sales_data.csv
 - lib/cmd_stan_rb.rb
 - lib/cmd_stan_rb/configuration.rb
 - lib/cmd_stan_rb/version.rb
@@ -66,7 +67,7 @@ metadata:
   homepage_uri: https://github.com/neumanrq/cmd_stan_rb
   source_code_uri: https://github.com/neumanrq/cmd_stan_rb
   changelog_uri: https://github.com/neumanrq/cmd_stan_rb
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -81,8 +82,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
-signing_key: 
+rubygems_version: 3.0.8
+signing_key:
 specification_version: 4
 summary: Ruby interface to CmdStan, the command line interface to Stan, a high performance
   statistical computing platform