rubydown 0.1.0

checksums.yaml

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+---
+SHA256:
+  metadata.gz: 90da523f65d454d4aeb48b78fbfa2e2b35378c565a2823aae1a2e0dc07d1cf3d
+  data.tar.gz: 920bb095fd9c9855bd1dbb15c2a6a86d0d2e54e5d73b7d2d71644ec60709f5a2
+SHA512:
+  metadata.gz: 62cde3191b98f6dc8500a76722979bf022a88e83d156391f4362d33406bf80158f52da205e05ba4ec5b95efde689296766ae179a21e0a886b7dcc8784d698481
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data/.circleci/config.yml

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+# Ruby CircleCI 2.0 configuration file
+#
+# Check https://circleci.com/docs/2.0/language-ruby/ for more details
+#
+version: 2
+jobs:
+  build:
+    docker:
+       - image: ruby
+      
+    working_directory: ~/repo
+
+    steps:
+      - checkout
+
+      - run:
+          name: install rubydown
+          command: |
+            apt-get update
+            apt-get install -y gnuplot
+            gem build rubydown.gemspec
+            gem install rubydown-0.1.0.gem
+            gem install bio
+            
+      # run tests!
+      - run:
+          name: run tests
+          command: |
+            rubydown -i examples/bio.md -e templates/template.html.erb -o /tmp/bio.html
+            rubydown -i examples/table.md -e templates/template.html.erb -o /tmp/table.html
+            rubydown -i examples/graph.md -e templates/template.html.erb -o /tmp/graph.html
+            
+      # collect reports
+      - store_artifacts:
+          path: /tmp

data/.gitignore

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+vendor/
+pkg/
+.bundle/

data/Dockerfile

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+FROM ruby
+
+USER root
+
+RUN apt-get update && apt-get install -y emacs25-nox vim-nox mlocate locales-all tmux gnuplot && gem install numo-gnuplot\
+    git config --global alias.co checkout && \
+    git config --global alias.br branch && \
+    git config --global alias.ci commit && \
+    git config --global alias.st status

data/Gemfile

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+source "https://rubygems.org"
+
+git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
+
+# Specify your gem's dependencies in rubydown.gemspec
+gemspec
+
+gem "test-unit", "~> 3.2"

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    rubydown (0.1.0)
+      daru
+      kramdown
+      numo-gnuplot
+      numo-narray
+      pry
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    backports (3.11.4)
+    coderay (1.1.2)
+    daru (0.2.1)
+      backports
+      packable (~> 1.3.9)
+    kramdown (1.17.0)
+    method_source (0.9.2)
+    numo-gnuplot (0.2.4)
+    numo-narray (0.9.1.3)
+    packable (1.3.10)
+      backports
+    power_assert (1.1.3)
+    pry (0.12.2)
+      coderay (~> 1.1.0)
+      method_source (~> 0.9.0)
+    rake (10.5.0)
+    test-unit (3.2.9)
+      power_assert
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.17)
+  rake (~> 10.0)
+  rubydown!
+  test-unit
+
+BUNDLED WITH
+   1.17.3

data/LICENSE

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+MIT License
+
+Copyright (c) 2018 Yusuke Sangenya
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

data/README.md

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+# rubydown
+
+[![CircleCI](https://circleci.com/gh/sciruby-jp/rubydown/tree/master.svg?style=svg)](https://circleci.com/gh/sciruby-jp/rubydown/tree/master)
+[![Build status](https://ci.appveyor.com/api/projects/status/rroa24x9jgdwuka5?svg=true)](https://ci.appveyor.com/project/kozo2/rubydown)
+
+*rubydown* is pure-Ruby [R Markdown](https://rmarkdown.rstudio.com/) clone.
+It takes a markdown source file, executes the code chunks, captures the output, and stitches the output into the destination file.
+
+Python also has R Markdown like packages.
+If you have interest about making reproducible reports, please also refer to the following projects.
+
+https://github.com/jankatins/knitpy
+
+https://github.com/pystitch/stitch
+
+
+## Install
+
+```
+apt install gnuplot # When you use numo-gnuplot in your workflow markdown
+gem install specific_install
+gem specific_install https://github.com/sciruby-jp/rubydown
+```
+
+## Usage (example with [rumale](https://github.com/yoshoku/rumale) and [rdatasets](https://github.com/kojix2/rdatasets))
+
+```
+gem install rumale rdatasets
+git clone git://github.com/sciruby-jp/rubydown
+cd rubydown/examples
+rubydown -i rumale.md -o rumale.html
+```

data/Rakefile

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+require "bundler/gem_tasks"
+task :default => :spec

data/_config.yml

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+theme: jekyll-theme-cayman

data/appveyor.yml

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+# appveyor.yml
+install:
+  - set PATH=C:\Ruby25-x64\bin;%PATH%
+  - gem build rubydown.gemspec
+  - gem install rubydown-0.1.0.gem
+
+build: off
+
+before_test:
+  - ruby -v
+  - gem -v
+  - bundle -v
+  - rubydown --version
+  - gem install bio
+
+test_script:
+  - choco install gnuplot
+  - set PATH=C:\Program Files\gnuplot\bin;%PATH%
+  - gnuplot --version
+  - rubydown -i examples\bio.md -e templates\template.html.erb -o bio.html
+  - rubydown -i examples\graph.md -e templates\template.html.erb -o graph.html
+  - rubydown -i examples\table.md -e templates\template.html.erb -o table.html
+  
+artifacts:
+  - path: '*.html'

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "rubydown"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start(__FILE__)

data/bin/setup

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/docs/_config.yml

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+theme: jekyll-theme-cayman

data/docs/index.html

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+<div style="display: flex;">
+  <div>
+  
+  <b>Some Links:</b><br>
+  <a href="#">Link 1</a> |
+  <a href="#">Link 2</a> |
+  <iframe src="https://raw.githubusercontent.com/sciruby-jp/rubydown/master/examples/graph.html"></iframe>
+  <br><br>
+  
+  </div>
+  <div>
+    
+  <b>Some Links:</b><br>
+  <a href="#">Link 1</a> |
+  <a href="#">Link 2</a> |
+  <iframe src="https://raw.githubusercontent.com/sciruby-jp/rubydown/master/examples/graph.html"></iframe>
+  <br><br> 
+  
+  </div>  
+</div>

data/docs/sidebyside.md

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+

data/examples/bio.html

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+<!DOCTYPE html>
+<html>
+  <head>
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    <link href='https://cdnjs.cloudflare.com/ajax/libs/github-markdown-css/2.10.0/github-markdown.min.css' rel='stylesheet' type='text/css' />
+    <style>
+      article.markdown-body {
+        box-sizing: border-box;
+        min-width: 200px;
+        max-width: 980px;
+        margin: 0 auto;
+        padding: 45px;
+      }
+
+      span.line-numbers {
+        display: none;
+      }
+    </style>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js"></script>
+  </head>
+  <body>
+    <article class='markdown-body'>
+      <h1 id="bioruby-tutorial">BioRuby Tutorial</h1>
+
+<h2 id="trying-bioruby">Trying Bioruby</h2>
+
+<p>Now test the following:</p>
+
+<pre><code class="language-ruby">require 'bio'
+seq = Bio::Sequence::NA.new("atgcatgcaaaa")
+</code></pre>
+<p>  <pre><code>=&gt; atgcatgcaaaa
+</code></pre>
+</p>
+
+<pre><code class="language-ruby">seq.complement
+</code></pre>
+<p>  <pre><code>=&gt; ttttgcatgcat
+</code></pre>
+</p>
+
+<h2 id="working-with-nucleic--amino-acid-sequences-biosequence-class">Working with nucleic / amino acid sequences (Bio::Sequence class)</h2>
+
+<p>The <code>Bio::Sequence</code> class allows the usual sequence transformations and translations.</p>
+
+<p>In the example below the DNA sequence <code>atgcatgcaaaa</code> is converted into the complemental strand and spliced into a subsequence; next, the nucleic acid composition is calculated and the sequence is translated into the amino acid sequence, the molecular weight calculated, and so on. When translating into amino acid sequences, the frame can be specified and optionally the codon table selected (as defined in <a href="https://github.com/bioruby/bioruby/blob/master/lib/bio/data/codontable.rb">codontable.rb</a>).</p>
+
+<pre><code class="language-ruby">seq = Bio::Sequence::NA.new("atgcatgcaaaa")
+</code></pre>
+<p>  <pre><code>=&gt; atgcatgcaaaa
+</code></pre>
+</p>
+
+<pre><code class="language-ruby"># complemental sequence (Bio::Sequence::NA object)
+seq.complement
+</code></pre>
+<p>  <pre><code>=&gt; ttttgcatgcat
+</code></pre>
+</p>
+
+<pre><code class="language-ruby">seq.subseq(3,8) # gets subsequence of positions 3 to 8 (starting from 1)
+</code></pre>
+<p>  <pre><code>=&gt; gcatgc
+</code></pre>
+</p>
+
+<pre><code class="language-ruby">seq.gc_percent
+</code></pre>
+<p>  <pre><code>=&gt; 33
+</code></pre>
+</p>
+
+<pre><code class="language-ruby">seq.composition
+</code></pre>
+<p>  <pre><code>=&gt; {"a"=&gt;6, "t"=&gt;2, "g"=&gt;2, "c"=&gt;2}
+</code></pre>
+</p>
+
+<pre><code class="language-ruby">seq.translate
+</code></pre>
+<p>  <pre><code>=&gt; MHAK
+</code></pre>
+</p>
+
+<pre><code class="language-ruby">seq.translate(2)
+</code></pre>
+<p>  <pre><code>=&gt; CMQ
+</code></pre>
+</p>
+
+<pre><code class="language-ruby">seq.translate(1,11)
+</code></pre>
+<p>  <pre><code>=&gt; MHAK
+</code></pre>
+</p>
+
+<pre><code class="language-ruby">seq.translate.codes
+</code></pre>
+<p>  <pre><code>=&gt; ["Met", "His", "Ala", "Lys"]
+</code></pre>
+</p>
+
+<pre><code class="language-ruby">seq.translate.names
+</code></pre>
+<p>  <pre><code>=&gt; ["methionine", "histidine", "alanine", "lysine"]
+</code></pre>
+</p>
+
+<pre><code class="language-ruby">seq.translate.composition
+</code></pre>
+<p>  <pre><code>=&gt; {"M"=&gt;1, "H"=&gt;1, "A"=&gt;1, "K"=&gt;1}
+</code></pre>
+</p>
+
+<pre><code class="language-ruby">seq.translate.molecular_weight
+</code></pre>
+<p>  <pre><code>=&gt; 485.6050000000001
+</code></pre>
+</p>
+
+<pre><code class="language-ruby">seq.complement.translate
+</code></pre>
+<p>  <pre><code>=&gt; FCMH
+</code></pre>
+</p>
+
+    </article>
+  </body>
+</html>

data/examples/bio.md

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+# BioRuby Tutorial
+
+## Trying Bioruby
+
+Now test the following:
+
+~~~ruby
+require 'bio'
+seq = Bio::Sequence::NA.new("atgcatgcaaaa")
+~~~
+
+~~~ruby
+seq.complement
+~~~
+
+## Working with nucleic / amino acid sequences (Bio::Sequence class)
+
+The `Bio::Sequence` class allows the usual sequence transformations and translations.
+
+In the example below the DNA sequence `atgcatgcaaaa` is converted into the complemental strand and spliced into a subsequence; next, the nucleic acid composition is calculated and the sequence is translated into the amino acid sequence, the molecular weight calculated, and so on. When translating into amino acid sequences, the frame can be specified and optionally the codon table selected (as defined in [codontable.rb](https://github.com/bioruby/bioruby/blob/master/lib/bio/data/codontable.rb)).
+
+~~~ruby
+seq = Bio::Sequence::NA.new("atgcatgcaaaa")
+~~~
+
+~~~ruby
+# complemental sequence (Bio::Sequence::NA object)
+seq.complement
+~~~
+
+~~~ruby
+seq.subseq(3,8) # gets subsequence of positions 3 to 8 (starting from 1)
+~~~
+
+~~~ruby
+seq.gc_percent
+~~~
+
+~~~ruby
+seq.composition
+~~~
+
+~~~ruby
+seq.translate
+~~~
+
+~~~ruby
+seq.translate(2)
+~~~
+
+~~~ruby
+seq.translate(1,11)
+~~~
+
+~~~ruby
+seq.translate.codes
+~~~
+
+~~~ruby
+seq.translate.names
+~~~
+
+~~~ruby
+seq.translate.composition
+~~~
+
+~~~ruby
+seq.translate.molecular_weight
+~~~
+
+~~~ruby
+seq.complement.translate
+~~~