iroki 0.0.26 → 0.0.27

checksums.yaml

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data/CHANGELOG.md

@@ -0,0 +1,113 @@
+# Change Log #
+
+### 0.0.1 ###
+
+Migrate from [color_tree](https://github.com/mooreryan/color_tree) to
+Iroki.
+
+### 0.0.2 ###
+
+Add [iroki](https://github.com/mooreryan/iroki/blob/master/exe/iroki)
+executable, and use RubyGems for installation.
+
+### 0.0.3 ###
+
+Add a [Dockerfile](https://github.com/mooreryan/iroki/blob/master/Dockerfile) and a [wrapper script](https://github.com/mooreryan/iroki/blob/master/exe/iroki_docker) for running Iroki with Docker.
+
+### 0.0.4 ###
+
+Fix the `iroki_docker` install bug.
+
+### 0.0.5 ###
+
+Add `newick_to_phyloxml` script.
+
+### 0.0.6 ###
+
+Add branch length and bootstraps to `newick_to_phyloxml`.
+
+### 0.0.7 ###
+
+Add `reorder_nodes` script.
+
+### 0.0.8 ###
+
+- Add auto coloring with Kelly theme
+- Add ability to color branches and labels separately
+
+### 0.0.9 ###
+
+- Add single sample color gradients (one and two color)
+
+### 0.0.10 ###
+
+- Fix Jess's bug
+
+### 0.0.11 ###
+
+- Add two color, two group color gradients from biom files
+
+### 0.0.12 ###
+
+- Bug fixes
+
+### 0.0.13 ###
+
+- Handle bad command line input
+
+### 0.0.14 ###
+
+- Add more specs and various improvements
+
+### 0.0.15 ###
+
+- `.ruby-version` file was being weird when user didn't have the correct ruby
+
+### 0.0.16 ###
+
+- Allow unusual characters in label names ([GitHub issue](https://github.com/mooreryan/iroki/issues/2))
+- Fix no method `clean` bug ([GitHub issue](https://github.com/mooreryan/iroki/issues/3))
+
+### 0.0.17 ###
+
+- Color map can override color gradient from biom file
+
+### 0.0.18 ###
+
+- `Iroki::Main::main` returns `:success` (for `iroki.net`)
+
+### 0.0.19 ###
+
+- Remove assertion that color map cannot have entries that aren't in the newick file
+
+### 0.0.20 ###
+
+- Handle more examples of bad biom files and bad name maps
+
+### 0.0.21 ###
+
+- Fix empty branch tag bug (issue 6)
+
+### 0.0.22 ###
+
+- Strip whitespace from beginning and end of entries in color map and name map
+
+### 0.0.23 ###
+
+- `Iroki::Main::main` returns the nexus string (for `iroki.net`)
+
+### 0.0.24 ###
+
+- Add `Iroki::Main::iroki_job` runs Iroki w/o needing an output file (for `iroki.net`)
+
+### 0.0.25 ###
+
+- Bugfix
+
+### 0.0.26 ###
+
+- Basic validation of Newick files (issue 9)
+
+### 0.0.27 ###
+
+- Remove some debugging statements

data/README.md

@@ -78,113 +78,3 @@ be a safe, welcoming space for collaboration, and contributors are
 expected to adhere to the
 [Contributor Covenant](http://contributor-covenant.org) code of
 conduct.
-
-## Version Info ##
-
-### 0.0.1 ###
-
-Migrate from [color_tree](https://github.com/mooreryan/color_tree) to
-Iroki.
-
-### 0.0.2 ###
-
-Add [iroki](https://github.com/mooreryan/iroki/blob/master/exe/iroki)
-executable, and use RubyGems for installation.
-
-### 0.0.3 ###
-
-Add a [Dockerfile](https://github.com/mooreryan/iroki/blob/master/Dockerfile) and a [wrapper script](https://github.com/mooreryan/iroki/blob/master/exe/iroki_docker) for running Iroki with Docker.
-
-### 0.0.4 ###
-
-Fix the `iroki_docker` install bug.
-
-### 0.0.5 ###
-
-Add `newick_to_phyloxml` script.
-
-### 0.0.6 ###
-
-Add branch length and bootstraps to `newick_to_phyloxml`.
-
-### 0.0.7 ###
-
-Add `reorder_nodes` script.
-
-### 0.0.8 ###
-
-- Add auto coloring with Kelly theme
-- Add ability to color branches and labels separately
-
-### 0.0.9 ###
-
-- Add single sample color gradients (one and two color)
-
-### 0.0.10 ###
-
-- Fix Jess's bug
-
-### 0.0.11 ###
-
-- Add two color, two group color gradients from biom files
-
-### 0.0.12 ###
-
-- Bug fixes
-
-### 0.0.13 ###
-
-- Handle bad command line input
-
-### 0.0.14 ###
-
-- Add more specs and various improvements
-
-### 0.0.15 ###
-
-- `.ruby-version` file was being weird when user didn't have the correct ruby
-
-### 0.0.16 ###
-
-- Allow unusual characters in label names ([GitHub issue](https://github.com/mooreryan/iroki/issues/2))
-- Fix no method `clean` bug ([GitHub issue](https://github.com/mooreryan/iroki/issues/3))
-
-### 0.0.17 ###
-
-- Color map can override color gradient from biom file
-
-### 0.0.18 ###
-
-- `Iroki::Main::main` returns `:success` (for `iroki.net`)
-
-### 0.0.19 ###
-
-- Remove assertion that color map cannot have entries that aren't in the newick file
-
-### 0.0.20 ###
-
-- Handle more examples of bad biom files and bad name maps
-
-### 0.0.21 ###
-
-- Fix empty branch tag bug (issue 6)
-
-### 0.0.22 ###
-
-- Strip whitespace from beginning and end of entries in color map and name map
-
-### 0.0.23 ###
-
-- `Iroki::Main::main` returns the nexus string (for `iroki.net`)
-
-### 0.0.24 ###
-
-- Add `Iroki::Main::iroki_job` runs Iroki w/o needing an output file (for `iroki.net`)
-
-### 0.0.25 ###
-
-- Bugfix
-
-### 0.0.26 ###
-
-- Basic validation of Newick files (issue 9)

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

@@ -45,7 +45,6 @@ module Iroki
         first_char = str[0]
         last_char = str[-1]
 
-        p [:ryan, first_char, last_char]
         first_char == "(" && last_char == ";"
       end
 

data/lib/iroki/utils/utils.rb

@@ -69,9 +69,7 @@ module Iroki
 
       # clean the name no matter what
       if node.name
-        # puts "before haha: #{node.name}"
         node.name = node.name #.clean_name
-        # puts "after  haha: #{node.name}"
       else
         node.name = nil
       end
@@ -89,9 +87,7 @@ module Iroki
         color = add_color_to_leaf_branch patterns, node, exact, iroki_to_name
 
         # add color to the name
-        # p [:before, node.name]
         node.name = node.name + color[:branch] if color
-        # p [:after, node.name]
       elsif !leaf?(tree, node)
         children = tree.children(node) # get the children
         children_colors = []

data/lib/iroki/version.rb

@@ -18,7 +18,7 @@
 
 # Library metadata
 module Iroki
-  VERSION = "0.0.26"
+  VERSION = "0.0.27"
   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: 0.0.26
+  version: 0.0.27
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-09-23 00:00:00.000000000 Z
+date: 2016-09-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -177,6 +177,7 @@ files:
 - ".gitignore"
 - ".rspec"
 - ".travis.yml"
+- CHANGELOG.md
 - CODE_OF_CONDUCT.md
 - COPYING
 - Dockerfile