iroki 0.0.32 → 0.0.33

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Files changed (11) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +7 -3
  3. data/assets/images/iroki_logo3.png +0 -0
  4. data/assets/kelly_info/kelly.graffle +0 -0
  5. data/assets/kelly_info/kelly.pdf +0 -0
  6. data/assets/kelly_info/kelly.png +0 -0
  7. data/assets/kelly_info/kelly_color_key.html +31 -0
  8. data/lib/iroki/color/palette/palette.rb +21 -0
  9. data/lib/iroki/main/main.rb +7 -3
  10. data/lib/iroki/version.rb +1 -1
  11. metadata +7 -2
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+ data.tar.gz: 1270cc9ede4186ba4c191085ab776a6e5cc7a9f97cd3710c91db92ef39584ba436f0a6c4d8b0e01e2aaabd3f193a84e935c29b93d21b178a82d173afc588c174
data/README.md CHANGED
@@ -1,4 +1,4 @@
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- [![Iroki](https://github.com/mooreryan/iroki/blob/master/assets/images/iroki_logo2.png)](https://github.com/mooreryan/iroki/blob/master/assets/images/iroki_logo2.png)
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+ [![Iroki](https://github.com/mooreryan/iroki/blob/master/assets/images/iroki_logo3.png)](https://github.com/mooreryan/iroki/blob/master/assets/images/iroki_logo3.png)
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  # Iroki #
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@@ -13,10 +13,10 @@ customization program.
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  ## Citation ##
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- Iroki is research software. If you use Iroki, please cite the Iroki preprint:
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+ Iroki is research software. If you use Iroki, please cite the Iroki [preprint](http://biorxiv.org/content/early/2017/04/25/106138.1):
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  ```
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- Moore RM, Harrison AO, McAllister SM, Marine R, Chan C, Wommack KE. 2017. Iroki: automatic customization for phylogenetic trees. doi: https://doi.org/10.1101/106138
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+ Moore RM, Harrison AO, McAllister SM , Marine RL, Chan CS, and Wommack KE. 2017. Iroki: automatic customization for phylogenetic trees. bioRxiv doi:10.1101/106138
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  ```
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  ## Documentation ##
@@ -25,6 +25,10 @@ For in depth docs and examples, please see the [Iroki wiki](https://github.com/m
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  ## Installation ##
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+ ### Using the web app
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+
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+ Iroki has a web app ([iroki.net](http://www.iroki.net/)). The [code](https://github.com/mooreryan/iroki_web) for that is also on GitHub.
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+
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  ### Running with Docker ###
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  See the [wiki](https://github.com/mooreryan/iroki/wiki).
data/assets/images/iroki_logo3.png ADDED
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data/assets/kelly_info/kelly.graffle ADDED
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data/assets/kelly_info/kelly.pdf ADDED
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data/assets/kelly_info/kelly.png ADDED
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data/assets/kelly_info/kelly_color_key.html ADDED
@@ -0,0 +1,31 @@
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+ <!DOCTYPE html>
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+ <html>
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+
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+ <head>
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+ <title>Jess's Key</title>
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+ </head>
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+
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+ <body>
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+
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+ <p><span style="background-color: #875692; font-size: 200%;">1: Purple (#875692)</span></p>
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+ <p><span style="background-color: #F38400; font-size: 200%;">2: Orange (#F38400)</span></p>
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+ <p><span style="background-color: #A1CAF1; font-size: 200%;">3: Light Blue (#A1CAF1)</span></p>
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+ <p><span style="background-color: #BE0032; font-size: 200%;">4: Red (#BE0032)</span></p>
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+ <p><span style="background-color: #C2B280; font-size: 200%;">5: Buff (#C2B280)</span></p>
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+ <p><span style="background-color: #848482; font-size: 200%;">6: Grey (#848482)</span></p>
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+ <p><span style="background-color: #008856; font-size: 200%;">7: Green (#008856)</span></p>
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+ <p><span style="background-color: #E68FAC; font-size: 200%;">8: Purplish pink (#E68FAC)</span></p>
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+ <p><span style="background-color: #0067A5; font-size: 200%;">9: Blue (#0067A5)</span></p>
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+ <p><span style="background-color: #F99379; font-size: 200%;">10: Yellowish pink (#F99379)</span></p>
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+ <p><span style="background-color: #604E97; font-size: 200%;">11: Violet (#604E97)</span></p>
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+ <p><span style="background-color: #F6A600; font-size: 200%;">12: Orange yellow (#F6A600)</span></p>
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+ <p><span style="background-color: #B3446C; font-size: 200%;">13: Purplish red (#B3446C)</span></p>
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+ <p><span style="background-color: #882D17; font-size: 200%;">14: Reddish brown (#882D17)</span></p>
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+ <p><span style="background-color: #8DB600; font-size: 200%;">15: Yellow green (#8DB600)</span></p>
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+ <p><span style="background-color: #654522; font-size: 200%;">16: Yellowish brown (#654522)</span></p>
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+ <p><span style="background-color: #E25822; font-size: 200%;">17: Reddish orange (#E25822)</span></p>
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+ <p><span style="background-color: #2B3D26; font-size: 200%;">18: Olive green (#2B3D26)</span></p>
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+ <p><span style="background-color: #F3C300; font-size: 200%;">19: Yellow (#F3C300)</span></p>
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+ </body>
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+
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+ </html>
data/lib/iroki/color/palette/palette.rb CHANGED
@@ -34,6 +34,27 @@ module Iroki
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  "18" => { name: "olive_green", hex: "#2B3D26" },
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  "19" => { name: "yellow", hex: "#F3C300" },
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  }
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+
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+ KELLY_TEXT = " 1: Purple (#875692)
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+ 2: Orange (#F38400)
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+ 3: Light Blue (#A1CAF1)
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+ 4: Red (#BE0032)
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+ 5: Buff (#C2B280)
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+ 6: Grey (#848482)
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+ 7: Green (#008856)
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+ 8: Purplish pink (#E68FAC)
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+ 9: Blue (#0067A5)
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+ 10: Yellowish pink (#F99379)
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+ 11: Violet (#604E97)
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+ 12: Orange yellow (#F6A600)
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+ 13: Purplish red (#B3446C)
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+ 14: Reddish brown (#882D17)
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+ 15: Yellow green (#8DB600)
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+ 16: Yellowish brown (#654522)
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+ 17: Reddish orange (#E25822)
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+ 18: Olive green (#2B3D26)
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+ 19: Yellow (#F3C300)"
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+
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  end
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  end
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  end
data/lib/iroki/main/main.rb CHANGED
@@ -147,7 +147,9 @@ module Iroki
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  name_map_f: nil,
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  auto_color: nil,
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  display_auto_color_options: nil,
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- newick_f: nil)
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+ newick_f: nil,
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+ min_lumin: 35,
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+ max_lumin: 70)
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  begin
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  out_f = Tempfile.new "foo"
@@ -163,7 +165,9 @@ module Iroki
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  auto_color: auto_color,
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  display_auto_color_options: display_auto_color_options,
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  newick_f: newick_f,
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- out_f: out_f)
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+ out_f: out_f,
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+ min_lumin: min_lumin,
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+ max_lumin: max_lumin)
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  ensure
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  if out_f
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  out_f.close
@@ -193,7 +197,7 @@ module Iroki
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  if display_auto_color_options
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  STDERR.puts "\n Choices for --auto-color ..."
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- STDERR.print " - kelly: up to 19 high contrast colors (purple, orange, light blue, red, ...)\n\n"
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+ STDERR.print " - kelly: up to 19 high contrast colors\n\n#{Iroki::Color::Palette::KELLY_TEXT}\n\n"
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  exit
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  end
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data/lib/iroki/version.rb CHANGED
@@ -18,7 +18,7 @@
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  # Library metadata
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  module Iroki
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- VERSION = "0.0.32"
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+ VERSION = "0.0.33"
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  COPYRIGHT = "2015 - 2017 Ryan Moore"
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  CONTACT = "moorer@udel.edu"
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  WEBSITE = "https://github.com/mooreryan/iroki"
metadata CHANGED
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  --- !ruby/object:Gem::Specification
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  name: iroki
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  version: !ruby/object:Gem::Version
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- version: 0.0.32
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+ version: 0.0.33
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  platform: ruby
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  authors:
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  - Ryan Moore
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  autorequire:
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  bindir: exe
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  cert_chain: []
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- date: 2017-04-23 00:00:00.000000000 Z
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+ date: 2017-04-28 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bundler
@@ -188,6 +188,7 @@ files:
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  - assets/images/iroki_logo2.idraw
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  - assets/images/iroki_logo2.png
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  - assets/images/iroki_logo2.svg
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+ - assets/images/iroki_logo3.png
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  - assets/images/iroki_text.graffle
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  - assets/images/iroki_text.idraw
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  - assets/images/iroki_text.pdf
@@ -195,6 +196,10 @@ files:
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  - assets/images/iroki_text.svg
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  - assets/images/iroki_text_omni.pdf
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  - assets/images/iroki_text_omni.svg
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+ - assets/kelly_info/kelly.graffle
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+ - assets/kelly_info/kelly.pdf
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+ - assets/kelly_info/kelly.png
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+ - assets/kelly_info/kelly_color_key.html
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  - bin/console
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  - bin/iroki_docker
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  - bin/setup