iroki 0.0.27 → 0.0.28

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 3b2edb3ca335f17d6a626dfb3942e126406aee07
-  data.tar.gz: 8ce0d9190c92bde7dd7df73002e2521fefd3fd90
+  metadata.gz: 7fb0a7ac745f83ec8341cbfbac699f9ac3c5f54b
+  data.tar.gz: decf8043b7d513ce31aef186155133d63758ddcb
 SHA512:
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-  data.tar.gz: 32530d5109ff8868232d224e78d78a5ff88a8d549ebba7646772cc736eddbe15c84cf80808f17594e07863780371e3c8198198a056b0db7edf5b64a1d4aec6bf
+  metadata.gz: 0e823649d07424f55164ed15ecf1af65d2a72f2b7aeb1e6e57003cef2ee009b2b5c6d0b6a3a68c64cf32805499b3f99093a5a60b4842b41f9b3ed3583fa77fa7
+  data.tar.gz: 33f53a9b7853311080a57af7815ff5572d4f00fd2e19099b3a9bb615d14b641adbaad35b22a32fffa9fe44aebce9710e86a904b325a2044700af4d3bbcdd286e

data/.gitignore

@@ -18,3 +18,4 @@ spec/test_files/nexus_files/output.nex
 .idea
 .DS_Store
 spec/.DS_Store
+TODO.md

data/CHANGELOG.md

@@ -111,3 +111,8 @@ Add `reorder_nodes` script.
 ### 0.0.27 ###
 
 - Remove some debugging statements
+
+### 0.0.28 ###
+
+- Update `Dockerfile`
+- Let user choose default color (issue 15)

data/bin/iroki_docker

@@ -5,17 +5,35 @@ use File::Spec;
 my @args = ();
 
 foreach my $arg (@ARGV) {
-    if ($arg =~ /^-/) {
+    if ($arg =~ /^-/) { # arg is a flag
         push @args, $arg;
-    } else {
+
+        # check if next arg should expand (these are file inputs)
+        if ($arg eq "-c" || $arg eq "--color-map" ||
+            $arg eq "-i" || $arg eq "--biom" ||
+            $arg eq "-f" || $arg eq "--infile" ||
+            $arg eq "-o" || $arg eq "--outfile" ||
+            $arg eq "-n" || $arg eq "--name-map") {
+
+            $expand = 1;
+        } else {
+            $expand = 0;
+        }
+    } elsif ($expand) { # an arg that is a path, expand it
         my $path = File::Spec->rel2abs($arg);
+
         push @args, $path;
+    } else { # an arg that is not a path and not a flag
+        push @args, $arg;
     }
 }
 
 my $img = "mooreryan/iroki";
-my $cmd = "docker run -v \"\$HOME:\$HOME\" $img @args";
+my $pull = "docker pull $img";
+my $run = "docker run -v \"\$HOME:\$HOME\" $img @args";
 
-print "\nRUNNING COMMAND: $cmd\n";
+print "\n\n\nRUNNING COMMAND: $pull\n\n\n";
+system("$pull");
 
-exec("$cmd");
+print "\n\n\nRUNNING COMMAND: $run\n\n\n";
+exec("$run");

data/exe/iroki

@@ -30,6 +30,8 @@ opts = Trollop.options do
 
   Iroki command line program.
 
+  See https://github.com/mooreryan/iroki/wiki for the Iroki manual.
+
   Options:
   EOS
 
@@ -78,6 +80,11 @@ opts = Trollop.options do
   opt(:outfile,
       "Name of outfile",
       type: :string)
+
+  opt(:default_color,
+      "Default color",
+      type: :string,
+      default: "black")
 end
 
 Iroki::Main.main(
@@ -92,5 +99,6 @@ Iroki::Main.main(
   auto_color:                 opts[:auto_color],
   display_auto_color_options: opts[:display_auto_color_options],
   newick_f:                   opts[:infile],
-  out_f:                      opts[:outfile]
+  out_f:                      opts[:outfile],
+  default_color:              opts[:default_color]
 )

data/lib/iroki/color/color.rb

@@ -731,5 +731,13 @@ module Iroki
       hex = colors[col]
       %Q{[&!color="#{hex.upcase}"]}
     end
+
+    def self.default_color_tag= tag_hash
+      @@default_color = tag_hash
+    end
+
+    def self.default_color_tag
+      @@default_color ||= nil
+    end
   end
 end

data/lib/iroki/main/main.rb

@@ -183,7 +183,8 @@ module Iroki
                   auto_color: nil,
                   display_auto_color_options: nil,
                   newick_f: nil,
-                  out_f: nil)
+                  out_f: nil,
+                  default_color: "black")
 
       args = method(__method__).parameters.map { |arg| arg[1] }
       AbortIf::logger.info "Args " + args.map { |arg| "#{arg} = #{eval(arg.to_s).inspect}" }.join(', ')
@@ -345,6 +346,18 @@ module Iroki
         patterns = nil
       end
 
+      # set default color if needed
+      if default_color && default_color != "black"
+
+        abort_if !default_color.hex? && !Iroki::Color::COLORS[default_color],
+                 "--default-color must be a hex code (don't forget the '#' or a valid color. Got '#{default_color}'."
+
+        Iroki::Color::default_color_tag = { label: Iroki::Color.get_tag(default_color),
+                                            branch: Iroki::Color.get_tag(default_color), }
+      end
+
+
+
       ####################
       # get color patterns
       #################################################################

data/lib/iroki/utils/utils.rb

@@ -32,6 +32,10 @@ module Iroki
         if patterns.has_key? node_s
           color = patterns[node_s]
 
+          return color
+        elsif Iroki::Color::default_color_tag
+          color = Iroki::Color::default_color_tag
+
           return color
         else
           return nil

data/lib/iroki/version.rb

@@ -18,7 +18,7 @@
 
 # Library metadata
 module Iroki
-  VERSION = "0.0.27"
+  VERSION = "0.0.28"
   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: 0.0.27
+  version: 0.0.28
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-09-26 00:00:00.000000000 Z
+date: 2016-10-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler