iroki 0.0.13 → 0.0.14

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: d8a7ec7990c34342fb7505e0aaeae2167f7e67ce
+  metadata.gz: 95a7ef76c36216350d0b539cd3e4b259e725e588
+  data.tar.gz: 9701c392d7bbba6e02bccafe2d12461567a8c5dd
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+  data.tar.gz: d3aed5abfb0cd2b89c06e0e963e47414c7ff082b46d55c467ab5746c85c317b9ff08d97cf682b6e0c75817a72e0f857662ebc7fcbeb660612ac6dce82446578a

data/.ruby-version

@@ -1 +1 @@
-ruby-2.2.4
+ruby-2.3.1

data/.travis.yml

@@ -1,4 +1,4 @@
 language: ruby
 rvm:
-  - 2.2.4
+  - 2.3.1
 before_install: gem install bundler -v 1.11.2

data/README.md

@@ -131,3 +131,7 @@ Add `reorder_nodes` script.
 ### 0.0.13 ###
 
 - Handle bad command line input
+
+### 0.0.14 ###
+
+- Add more specs and various improvements

data/iroki.gemspec

@@ -19,7 +19,7 @@ Gem::Specification.new do |spec|
   spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
   spec.require_paths = ["lib"]
 
-  spec.required_ruby_version = ">= 2.2.4"
+  spec.required_ruby_version = ">= 2.3.1"
 
   spec.add_development_dependency "bundler", "~> 1.11"
   spec.add_development_dependency "rake", "~> 10.0"

data/lib/iroki/biom.rb

@@ -23,11 +23,22 @@ module Iroki
     def parse
       samples = []
       counts  = []
+      lineno = -1
+      first_line_count = -1
 
-      self.each_line do |line|
+      self.each_line.with_index do |line, idx|
         unless line.start_with? "#"
+          lineno += 1
           sample, *the_counts = line.chomp.split "\t"
 
+          if lineno.zero?
+            first_line_count = the_counts.count
+          else
+            abort_unless first_line_count == the_counts.count,
+                         "The biom file has rows with different " +
+                         "numbers of columns"
+          end
+
           samples << sample
 
           if the_counts.length == 1

data/lib/iroki/color/color.rb

@@ -698,7 +698,7 @@ module Iroki
     WHITE = HSL.from_fraction WHITE_HUE, FULLY_SATURATED, PURE_LIGHT
 
     DARK_GREEN = RGB.by_hex(COLORS["darkgreen"])
-    GRAY =       RGB.by_hex(COLORS["gray"])
+    GRAY       = RGB.by_hex(COLORS["gray"])
 
     def self.get_tag str, palette=nil
       if str.hex?
@@ -725,13 +725,10 @@ module Iroki
         colors = COLORS
       end
 
-      if colors.has_key? col
-        hex = colors[col]
-      else
-        # if passed color other than one defined, return black
-        hex = colors["black"]
-      end
+      abort_unless colors.has_key?(col),
+                   "Color '#{col}' is not defined."
 
+      hex = colors[col]
       %Q{[&!color="#{hex.upcase}"]}
     end
   end

data/lib/iroki/color/single_group_gradient.rb

@@ -22,6 +22,10 @@ module Iroki
       attr_accessor :counts, :rel_abunds
 
       def initialize samples, counts, single_color=false
+        abort_unless samples.count == counts.count,
+                     "Samples (#{samples.count}) and counts " +
+                     "#{counts.count} are different size."
+
         @single_color = single_color
         @samples = samples
         @counts = counts

data/lib/iroki/core_ext/file/file.rb

@@ -55,7 +55,7 @@ module Iroki
 
 
         patterns = {}
-        Object::File.open(fname).each_line do |line|
+        Object::File.open(fname, "rt").each_line do |line|
           unless line.start_with? "#"
             label_tag = ""
             branch_tag = ""
@@ -131,7 +131,7 @@ module Iroki
         check_file fname, :name_map
 
         name_map = {}
-        Object::File.open(fname).each_line do |line|
+        Object::File.open(fname, "rt").each_line do |line|
           unless line.start_with? "#"
             oldname, newname = line.chomp.split "\t"
 

data/lib/iroki/main/main.rb

@@ -98,7 +98,7 @@ module Iroki
                                    exact_matching: exact,
                                    auto_color: auto_color_hash
       else
-        samples, counts, is_single_group = Biom.open(biom_f).parse
+        samples, counts, is_single_group = Biom.open(biom_f, "rt").parse
 
         if is_single_group
           patterns = SingleGroupGradient.new(samples, counts, single_color).patterns

data/lib/iroki/version.rb

@@ -18,7 +18,7 @@
 
 # Library metadata
 module Iroki
-  VERSION = "0.0.13"
+  VERSION = "0.0.14"
   COPYRIGHT = "2015 - 2016 Ryan Moore"
   CONTACT   = "moorer@udel.edu"
   WEBSITE   = "https://github.com/mooreryan/iroki"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: iroki
 version: !ruby/object:Gem::Version
-  version: 0.0.13
+  version: 0.0.14
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-08-03 00:00:00.000000000 Z
+date: 2016-08-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -222,7 +222,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 2.2.4
+      version: 2.3.1
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
@@ -230,7 +230,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.8
+rubygems_version: 2.5.1
 signing_key: 
 specification_version: 4
 summary: Command line app and library code for Iroki, a phylogenetic tree customization