optimus-ep 0.6.91 → 0.8.0

data/spec/transformers/timing_extractor_spec.rb

@@ -1,17 +1,17 @@
 # Part of the Optimus package for managing E-Prime data
 # 
-# Copyright (C) 2008 Board of Regents of the University of Wisconsin System
+# Copyright (C) 2008-09 Board of Regents of the University of Wisconsin System
 # 
 # Written by Nathan Vack <njvack@wisc.edu>, at the Waisman Laborotory for Brain
 # Imaging and Behavior, University of Wisconsin - Madison
 
 require File.join(File.dirname(__FILE__),'../spec_helper')
-require File.join(File.dirname(__FILE__), '../../lib/eprime')
+require File.join(File.dirname(__FILE__), '../../lib/optimus')
 require 'transformers/timing_extractor'
-include EprimeTestHelper
-include Eprime::Transformers
+include OptimusTestHelper
+include Optimus::Transformers
 
-describe Eprime::Transformers::TimingExtractor do
+describe Optimus::Transformers::TimingExtractor do
   before :each do
     @data = mock_edata
     @tx = TimingExtractor.new(@data)
@@ -42,7 +42,7 @@ describe Eprime::Transformers::TimingExtractor do
   end
   
   it "should extract from computed columns" do
-    @tx.computed_column 'foo', 'a'
+    @tx.computed_column 'foo', "'a'"
     @tx.columns.should include('foo')
     @tx.extract_stimulus('foo', 'foo', 'foo')
     @tx.extracted_data.size.should == @data.size
@@ -63,8 +63,8 @@ describe Eprime::Transformers::TimingExtractor do
     before :each do
       @data = mock_edata
       @tx = TimingExtractor.new(@data)
-      @tx.computed_column('stim_name','stim')
-      @tx.computed_column('fix_name', 'fixation')
+      @tx.computed_column('stim_name',"'stim'")
+      @tx.computed_column('fix_name', "'fixation'")
       @tx.computed_column('stim_offset', '{stim_time} + 500 - {run_start}')
       @tx.computed_column('fix_offset', '{fix_time}+130-{run_start}')
       @tx.extract_stimulus('stim_name', 'stim_time', 'stim_time')

data/spec/writers/stimtimes_writer_spec.rb

@@ -1,16 +1,16 @@
 # Part of the Optimus package for managing E-Prime data
 # 
-# Copyright (C) 2008 Board of Regents of the University of Wisconsin System
+# Copyright (C) 2008-09 Board of Regents of the University of Wisconsin System
 # 
 # Written by Nathan Vack <njvack@wisc.edu>, at the Waisman Laborotory for Brain
 # Imaging and Behavior, University of Wisconsin - Madison
 
 
 require File.join(File.dirname(__FILE__),'../spec_helper')
-require File.join(File.dirname(__FILE__), '../../lib/eprime')
+require File.join(File.dirname(__FILE__), '../../lib/optimus')
 require File.join(File.dirname(__FILE__), '../../lib/writers/stimtimes_writer')
 
-describe Eprime::StimtimesWriter do
+describe Optimus::StimtimesWriter do
   # I don't actually know how to spec this out. I'm a bit worried.
   
 end

metadata

@@ -1,78 +1,110 @@
 --- !ruby/object:Gem::Specification 
 name: optimus-ep
 version: !ruby/object:Gem::Version 
-  version: 0.6.91
+  hash: 63
+  prerelease: false
+  segments: 
+  - 0
+  - 8
+  - 0
+  version: 0.8.0
 platform: ruby
 authors: 
-- Nathan Vack
+- Nate Vack
 autorequire: 
 bindir: bin
 cert_chain: []
 
-date: 2009-03-10 00:00:00 -05:00
+date: 2010-11-01 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: rparsec
-  type: :runtime
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        hash: 15
+        segments: 
+        - 1
+        - 0
         version: "1.0"
-    version: 
+  type: :runtime
+  version_requirements: *id001
 - !ruby/object:Gem::Dependency 
-  name: hoe
-  type: :development
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
+  name: rspec
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 1.8.2
-    version: 
-description: A collection of utilities for working with Eprime data files
-email: 
-- njvack@freshforever.net
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id002
+description: Utilities to process behavioral data generated by E-Prime
+email: njvack@wisc.edu
 executables: 
 - eprime2tabfile
 - extract_timings
 extensions: []
 
 extra_rdoc_files: 
-- GPL.txt
-- History.txt
-- License.txt
-- Manifest.txt
-- README.txt
-- spec/samples/bad_excel_tsv.txt
-- spec/samples/corrupt_log_file.txt
-- spec/samples/eprime_tsv.txt
-- spec/samples/excel_tsv.txt
-- spec/samples/optimus_log.txt
-- spec/samples/short_columns.txt
-- spec/samples/sorted_columns.txt
-- spec/samples/std_columns.txt
-- spec/samples/unknown_type.txt
+- CHANGELOG
+- LICENSE
+- README
+- bin/eprime2tabfile
+- bin/extract_timings
+- lib/eprimetab_parser.rb
+- lib/excel_parser.rb
+- lib/expression_parser/evaluators.rb
+- lib/expression_parser/expressions.rb
+- lib/log_file_parser.rb
+- lib/optimus.rb
+- lib/optimus_data.rb
+- lib/optimus_reader.rb
+- lib/parsed_calculator.rb
+- lib/raw_tab_parser.rb
+- lib/runners/generic_runner.rb
+- lib/runners/yaml_template/option_parser.rb
+- lib/runners/yaml_template/runner.rb
+- lib/tabfile_parser.rb
+- lib/tabfile_writer.rb
+- lib/transformers/basic_transformer.rb
+- lib/transformers/column_calculator.rb
+- lib/transformers/multipasser.rb
+- lib/transformers/row_filter.rb
+- lib/transformers/timing_extractor.rb
+- lib/version.rb
+- lib/writers/stimtimes_writer.rb
 files: 
+- CHANGELOG
 - GPL.txt
-- History.txt
-- License.txt
-- Manifest.txt
-- README.txt
+- LICENSE
+- Manifest
+- README
 - Rakefile
+- autotest/discover.rb
 - bin/eprime2tabfile
 - bin/extract_timings
-- lib/calculator.rb
-- lib/eprime.rb
-- lib/eprime_data.rb
-- lib/eprime_reader.rb
 - lib/eprimetab_parser.rb
 - lib/excel_parser.rb
+- lib/expression_parser/evaluators.rb
+- lib/expression_parser/expressions.rb
 - lib/log_file_parser.rb
+- lib/optimus.rb
+- lib/optimus_data.rb
+- lib/optimus_reader.rb
+- lib/parsed_calculator.rb
 - lib/raw_tab_parser.rb
 - lib/runners/generic_runner.rb
+- lib/runners/yaml_template/option_parser.rb
+- lib/runners/yaml_template/runner.rb
 - lib/tabfile_parser.rb
 - lib/tabfile_writer.rb
 - lib/transformers/basic_transformer.rb
@@ -82,18 +114,25 @@ files:
 - lib/transformers/timing_extractor.rb
 - lib/version.rb
 - lib/writers/stimtimes_writer.rb
-- spec/calculator_spec.rb
-- spec/eprime_data_spec.rb
-- spec/eprime_reader_spec.rb
 - spec/eprimetab_parser_spec.rb
 - spec/excel_parser_spec.rb
+- spec/expression_parser/evaluators_spec.rb
+- spec/expression_parser/expressions_spec.rb
 - spec/log_file_parser_spec.rb
+- spec/optimus_data_spec.rb
+- spec/optimus_reader_spec.rb
+- spec/parsed_calculator_spec.rb
+- spec/raw_tab_parser_spec.rb
 - spec/runners/generic_runner_spec.rb
+- spec/runners/yaml_template/option_parser_spec.rb
+- spec/runners/yaml_template/runner_spec.rb
 - spec/samples/bad_excel_tsv.txt
 - spec/samples/corrupt_log_file.txt
 - spec/samples/eprime_tsv.txt
 - spec/samples/excel_tsv.txt
 - spec/samples/optimus_log.txt
+- spec/samples/optimus_log_utf16le.txt
+- spec/samples/raw_tsv.txt
 - spec/samples/short_columns.txt
 - spec/samples/sorted_columns.txt
 - spec/samples/std_columns.txt
@@ -108,32 +147,46 @@ files:
 - spec/transformers/row_filter_spec.rb
 - spec/transformers/timing_extractor_spec.rb
 - spec/writers/stimtimes_writer_spec.rb
+- optimus-ep.gemspec
 has_rdoc: true
-homepage: http://code.google.com/p/optimus-ep
-post_install_message: ""
+homepage: http://github.com/njvack/optimus-ep
+licenses: []
+
+post_install_message: 
 rdoc_options: 
+- --line-numbers
+- --inline-source
+- --title
+- Optimus-ep
 - --main
-- README.txt
+- README
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
       version: "0"
-  version: 
 required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      version: "0"
-  version: 
+      hash: 11
+      segments: 
+      - 1
+      - 2
+      version: "1.2"
 requirements: []
 
 rubyforge_project: optimus-ep
-rubygems_version: 1.3.1
+rubygems_version: 1.3.7
 signing_key: 
-specification_version: 2
-summary: A collection of utilities for working with Eprime data files
+specification_version: 3
+summary: Utilities to process behavioral data generated by E-Prime
 test_files: []
 

data/History.txt

@@ -1,45 +0,0 @@
-== 0.6.9.1 3/10/2008
-* Bug fix:
-  * Fix for parsing eprime log files in which leaf frames don't occur at the
-    highest log level
-
-== 0.6.9 2/25/2008
-* New features:
-  * Supports parsing raw tab-delmimted files
-  * Allows Procs as starting values for ComputedColumns
-* Bug fixes:
-  * No longer jumbles the order of Eprime log files
-
-== 0.6.5 9/2/2008
-* New features:
-  * Speed! Speed! Speed! Should be something like 10x faster.
-  * Procs are now allowed in ComputedColumns -- so if you want to do really
-    arbitrary things in your column computation, have at it.
-
-== 0.6.0 7/14/2008
-* New features:
-  * Added extract_timings, a script to pull stimulus timing data from eprime
-    files.
-  * Added a GenericRunner -- a class that greatly eases end-to-end
-    transformation of eprime data. See extract_timings for an example of
-    its use.
-
-== 0.5.5 7/09/2008
-* New features:
-  * Supports making multiple passes through data, to allow extracting multiple
-    stimuli that occur on the same row
-  * Created a general-purpose stimulus extractor to pull data out in the
-    format:
-    stimulus \t onset__time \t offset__time
-* Architectural changes:
-  * Created a BasicTransformer that performs all of the basic operations to
-    datasets: column calculation, row filtering, and multipass
-  * Moved ColumnCalculator, RowFilter, and Multipasser into a Transformers
-    module
-  * Support release via hoe / rubygems
-
-== 0.5.0 6/26/2008
-
-* First public gem release
-  * Supports converting general Eprime files into tab-delimited files
-  * Supports converting Eprime files into AFNI stim_times files

data/lib/calculator.rb

@@ -1,51 +0,0 @@
-# Part of the Optimus package for managing E-Prime data
-# 
-# Copyright (C) 2008 Board of Regents of the University of Wisconsin System
-# 
-# Written by Nathan Vack <njvack@wisc.edu>, at the Waisman Laborotory for Brain
-# Imaging and Behavior, University of Wisconsin - Madison
-#
-# Calculator code adapted from rparsec infix calculator demo
-# at http://docs.codehaus.org/display/JPARSEC/Ruby+Parsec
-# rparsec (C) Ben Yu
-
-require 'rubygems'
-require 'rparsec'
-include RParsec
-
-module Eprime
-  class Calculator
-    include Parsers
-    include Functors
-    
-    Mod = lambda { |x, y| x.to_i % y.to_i }
-    Eql = lambda { |x, y| x.to_s == y.to_s }
-    
-    def initialize
-      ops = OperatorTable.new.
-        infixl(char('+') >> Plus, 20).
-        infixl(char('-') >> Minus, 20).
-        infixl(char('*') >> Mul, 40).
-        infixl(char('/') >> Div, 40).
-        infixl(char('%') >> Mod, 40).
-        prefix(char('-') >> Neg, 60)
-      expr = nil
-      float_parser = number.map(&To_f)
-      string_parser = regexp(/[_a-z]\S*/i)
-      grouping_parser = char('(') >>(lazy{expr})<< char(')')
-      term = alt(float_parser, grouping_parser, string_parser)
-      delim = whitespace.many_
-      expr = delim >> Expressions.build(term, ops, delim)
-      @parser = expr << eof
-    end
-    
-    def compute(expression)
-      ans = @parser.parse(expression)
-      return ans if ans.is_a?(String)
-      if (ans - ans.to_i) == 0
-        ans = ans.to_i
-      end
-      return ans.to_s
-    end
-  end
-end

data/lib/eprime.rb

@@ -1,24 +0,0 @@
-# Part of the Optimus package for managing E-Prime data
-# 
-# Copyright (C) 2008 Board of Regents of the University of Wisconsin System
-# 
-# Written by Nathan Vack <njvack@wisc.edu>, at the Waisman Laborotory for Brain
-# Imaging and Behavior, University of Wisconsin - Madison
-
-# Add our lib to the search path
-$: << File.expand_path(File.join(File.dirname(__FILE__), "..", "lib"))
-
-require 'eprime_data'
-require 'version'
-require 'tabfile_writer'
-require 'eprime_reader'
-
-module Eprime
-
-  # Raised whenever an input file's type can't be detemined by Eprime::Reader
-  class UnknownTypeError < Exception; end
-  
-  # Raised whenever an input file seems to be damaged
-  class DamagedFileError < Exception; end
-  
-end

data/spec/calculator_spec.rb

@@ -1,70 +0,0 @@
-# Part of the Optimus package for managing E-Prime data
-# 
-# Copyright (C) 2008 Board of Regents of the University of Wisconsin System
-# 
-# Written by Nathan Vack <njvack@wisc.edu>, at the Waisman Laborotory for Brain
-# Imaging and Behavior, University of Wisconsin - Madison
-
-require File.join(File.dirname(__FILE__),'spec_helper')
-require File.join(File.dirname(__FILE__), '../lib/eprime')
-require 'calculator'
-
-include EprimeTestHelper
-
-describe Eprime::Calculator do
-  before :all do
-    @calc = Eprime::Calculator.new
-  end
-  
-  it "should compute constants" do
-    @calc.compute(es(:const)).should == ev(:const)
-  end
-  
-  it "should allow strings" do
-    @calc.compute(es(:str_const)).should == ev(:str_const)
-  end
-  
-  it "should allow string concatentation" do
-    @calc.compute(es(:str_cat)).should == ev(:str_cat)
-  end
-
-  it "should not allow concatenating numbers with strings" do
-    lambda {
-      @calc.compute("1 + a")
-    }.should raise_error
-  end
-  
-  it "should add" do
-    @calc.compute(es(:add)).should == ev(:add)
-  end
-  
-  it "should multiply" do
-    @calc.compute(es(:mul)).should == ev(:mul)
-  end
-  
-  it "should handle negation" do
-    @calc.compute(es(:add_neg)).should == ev(:add_neg)
-  end
-  
-  it "should handle grouping" do
-    @calc.compute(es(:add_mul_group)).should == ev(:add_mul_group)
-  end
-  
-  it "should handle fdiv" do
-    @calc.compute(es(:fdiv)).should == ev(:fdiv)
-  end
-  
-  it "should handle fmul" do
-    @calc.compute(es(:fmul)).should == ev(:fmul)
-  end
-  
-  it "should handle mod" do
-    @calc.compute(es(:mod)).should == ev(:mod)
-  end
-  
-  it "should fail with infix garbage" do
-    lambda {
-      @calc.compute("1 broken 2")
-    }.should raise_error(RParsec::ParserException)
-  end
-end