iroki 0.0.26 → 0.0.27
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- checksums.yaml +4 -4
- data/CHANGELOG.md +113 -0
- data/README.md +0 -110
- data/lib/iroki/core_ext/file/file.rb +0 -1
- data/lib/iroki/utils/utils.rb +0 -4
- data/lib/iroki/version.rb +1 -1
- metadata +3 -2
checksums.yaml
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SHA1:
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metadata.gz:
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metadata.gz: 3b2edb3ca335f17d6a626dfb3942e126406aee07
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data.tar.gz: 8ce0d9190c92bde7dd7df73002e2521fefd3fd90
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metadata.gz:
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metadata.gz: 1b88a8d47e9034dfc393020d54a011f986ea1cbb291479213ed779a8f1220cabc415c7c6c7cfcb2915e7b5e5e7306e9e33196d6f0cba0d6194c676c3ae1c4f07
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data.tar.gz: 32530d5109ff8868232d224e78d78a5ff88a8d549ebba7646772cc736eddbe15c84cf80808f17594e07863780371e3c8198198a056b0db7edf5b64a1d4aec6bf
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data/CHANGELOG.md
ADDED
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# Change Log #
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### 0.0.1 ###
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Migrate from [color_tree](https://github.com/mooreryan/color_tree) to
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Iroki.
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### 0.0.2 ###
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Add [iroki](https://github.com/mooreryan/iroki/blob/master/exe/iroki)
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executable, and use RubyGems for installation.
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### 0.0.3 ###
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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.
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### 0.0.4 ###
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Fix the `iroki_docker` install bug.
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### 0.0.5 ###
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Add `newick_to_phyloxml` script.
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### 0.0.6 ###
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Add branch length and bootstraps to `newick_to_phyloxml`.
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### 0.0.7 ###
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Add `reorder_nodes` script.
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### 0.0.8 ###
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- Add auto coloring with Kelly theme
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- Add ability to color branches and labels separately
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### 0.0.9 ###
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- Add single sample color gradients (one and two color)
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### 0.0.10 ###
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- Fix Jess's bug
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### 0.0.11 ###
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- Add two color, two group color gradients from biom files
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### 0.0.12 ###
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- Bug fixes
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### 0.0.13 ###
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- Handle bad command line input
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### 0.0.14 ###
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- Add more specs and various improvements
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### 0.0.15 ###
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- `.ruby-version` file was being weird when user didn't have the correct ruby
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### 0.0.16 ###
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- Allow unusual characters in label names ([GitHub issue](https://github.com/mooreryan/iroki/issues/2))
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- Fix no method `clean` bug ([GitHub issue](https://github.com/mooreryan/iroki/issues/3))
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### 0.0.17 ###
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- Color map can override color gradient from biom file
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### 0.0.18 ###
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- `Iroki::Main::main` returns `:success` (for `iroki.net`)
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### 0.0.19 ###
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- Remove assertion that color map cannot have entries that aren't in the newick file
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### 0.0.20 ###
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- Handle more examples of bad biom files and bad name maps
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### 0.0.21 ###
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- Fix empty branch tag bug (issue 6)
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### 0.0.22 ###
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- Strip whitespace from beginning and end of entries in color map and name map
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### 0.0.23 ###
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- `Iroki::Main::main` returns the nexus string (for `iroki.net`)
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### 0.0.24 ###
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- Add `Iroki::Main::iroki_job` runs Iroki w/o needing an output file (for `iroki.net`)
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### 0.0.25 ###
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- Bugfix
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### 0.0.26 ###
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- Basic validation of Newick files (issue 9)
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### 0.0.27 ###
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- Remove some debugging statements
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data/README.md
CHANGED
@@ -78,113 +78,3 @@ be a safe, welcoming space for collaboration, and contributors are
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expected to adhere to the
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[Contributor Covenant](http://contributor-covenant.org) code of
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conduct.
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## Version Info ##
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### 0.0.1 ###
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-
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Migrate from [color_tree](https://github.com/mooreryan/color_tree) to
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Iroki.
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-
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### 0.0.2 ###
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-
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Add [iroki](https://github.com/mooreryan/iroki/blob/master/exe/iroki)
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executable, and use RubyGems for installation.
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### 0.0.3 ###
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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.
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### 0.0.4 ###
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Fix the `iroki_docker` install bug.
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### 0.0.5 ###
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Add `newick_to_phyloxml` script.
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### 0.0.6 ###
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Add branch length and bootstraps to `newick_to_phyloxml`.
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### 0.0.7 ###
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Add `reorder_nodes` script.
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### 0.0.8 ###
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-
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- Add auto coloring with Kelly theme
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- Add ability to color branches and labels separately
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-
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### 0.0.9 ###
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-
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- Add single sample color gradients (one and two color)
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### 0.0.10 ###
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- Fix Jess's bug
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### 0.0.11 ###
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- Add two color, two group color gradients from biom files
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### 0.0.12 ###
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- Bug fixes
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### 0.0.13 ###
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- Handle bad command line input
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### 0.0.14 ###
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- Add more specs and various improvements
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### 0.0.15 ###
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- `.ruby-version` file was being weird when user didn't have the correct ruby
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### 0.0.16 ###
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-
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- Allow unusual characters in label names ([GitHub issue](https://github.com/mooreryan/iroki/issues/2))
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- Fix no method `clean` bug ([GitHub issue](https://github.com/mooreryan/iroki/issues/3))
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### 0.0.17 ###
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- Color map can override color gradient from biom file
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### 0.0.18 ###
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- `Iroki::Main::main` returns `:success` (for `iroki.net`)
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### 0.0.19 ###
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- Remove assertion that color map cannot have entries that aren't in the newick file
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### 0.0.20 ###
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- Handle more examples of bad biom files and bad name maps
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### 0.0.21 ###
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- Fix empty branch tag bug (issue 6)
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### 0.0.22 ###
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- Strip whitespace from beginning and end of entries in color map and name map
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### 0.0.23 ###
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- `Iroki::Main::main` returns the nexus string (for `iroki.net`)
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### 0.0.24 ###
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- Add `Iroki::Main::iroki_job` runs Iroki w/o needing an output file (for `iroki.net`)
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### 0.0.25 ###
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- Bugfix
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### 0.0.26 ###
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- Basic validation of Newick files (issue 9)
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data/lib/iroki/utils/utils.rb
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# clean the name no matter what
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if node.name
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# puts "before haha: #{node.name}"
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node.name = node.name #.clean_name
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# puts "after haha: #{node.name}"
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else
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node.name = nil
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end
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color = add_color_to_leaf_branch patterns, node, exact, iroki_to_name
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# add color to the name
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# p [:before, node.name]
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node.name = node.name + color[:branch] if color
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# p [:after, node.name]
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elsif !leaf?(tree, node)
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children = tree.children(node) # get the children
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children_colors = []
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data/lib/iroki/version.rb
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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.
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version: 0.0.27
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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: 2016-09-
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date: 2016-09-26 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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@@ -177,6 +177,7 @@ files:
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- ".gitignore"
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- ".rspec"
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- ".travis.yml"
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- CHANGELOG.md
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- CODE_OF_CONDUCT.md
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- COPYING
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- Dockerfile
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