mathjax-yard 0.1.0 → 1.0.1

data/lib/mathjax-yard.rb

@@ -1,11 +1,11 @@
 require "mathjax-yard/version"
+require "mathjax-yard/script"
 require 'optparse'
 require 'yaml'
 require 'fileutils'
-
+require 'systemu'
 
 module MathJaxYard
-    # Your code goes here...
   class Command
     def self.run(argv=[])
       new(argv).execute
@@ -19,7 +19,6 @@ module MathJaxYard
     end
 
     def execute
-      # @argv << '--help' if @argv.size==0
       command_parser = OptionParser.new do |opt|
         opt.on('-v', '--version','show program Version.') { |v|
           opt.version = Yardmath::VERSION
@@ -37,6 +36,10 @@ module MathJaxYard
           revert(directory)
           exit
         }
+        opt.on('-i', '--init','initiation for mathjax extension on yard layout.') {
+          init_yard()
+          exit
+        }
       end
       command_parser.banner = "Usage: yardmath [options] [DIRECTORY]"
       command_parser.parse!(@argv)
@@ -45,23 +48,44 @@ module MathJaxYard
       exit
     end
 
+    def init_yard()
+      target_dir=get_yard_layout_dir()
+      FileUtils.cd(target_dir){
+        tmp_dir='mathjax' # 'math2'
+        FileUtils.cp_r('default',tmp_dir)
+        modify_layout("#{tmp_dir}/layout/html/layout.erb")
+        modify_layout("#{tmp_dir}/onefile/html/layout.erb")
+      }
+    end
+
+    def get_yard_layout_dir()
+      status, stdout, stderr  = systemu('gem env | grep INSTALLATION ')
+      p inst_dir= stdout.split("\n")[0].split(': ')[1]
+      status, stdout, stderr  = systemu('yard -v')
+      p yard_num= stdout.split(' ')[0]+'-'+stdout.split(' ')[1]
+      p target_dir = File.join(inst_dir,'gems',yard_num,"templates")
+      return target_dir
+    end
+
+    def modify_layout(file_name)
+      p file_name
+      src=Ffile.read(file_name)
+      src.gsub!(ORIGINAL,MATH_SCRIPT+ORIGINAL)
+      File.write(file_name,src)
+    end
+
     def post_operation
-      file = File.open("./mathjax.yml",'r')
-      src = file.read
+      src = File.read("./mathjax.yml")
       p data = YAML.load(src)
       data.each_pair{|file, tags|
         File.basename(file).scan(/(.+)\.md/)
         p basename = $1
         target = "./doc/file.#{basename}.html"
-        file = File.open(target,'r')
-        src = file.read
-        file.close
+        src = File.read(target)
         tags.each_pair{|tag,eq|
           src.gsub!(tag,eq)
         }
-        file = File.open(target,'w')
-        file.print(src)
-        file.close
+        File.write(target,src)
       }
     end
 
@@ -85,33 +109,15 @@ module MathJaxYard
           @eq_data.delete(file) 
         else
           write_output_on_target(file,output)
-#          write_output_on_backup(file,output,'.mjx')
         end
       }
-      save_yaml(@eq_data,"mathjax.yml")
-    end
-
-    def write_output_on_backup(file,output,extention='.mjx')
-      file.scan(/(.+)\.md/)
-      p basename = $1
-      b_file = File.open(basename+extention+'.md','w')
-      b_file.print output
-      b_file.close
+      File.write("mathjax.yml",YAML.dump(@eq_data))
     end
 
     def write_output_on_target(file,output)
       b_file = file+'.back'
       FileUtils.mv(file,b_file)
-      t_file = File.open(file,'w')
-      t_file.print output
-      t_file.close
-    end
-
-    def save_yaml(data,file)
-      print yaml_data=YAML.dump(data)
-      math_file = File.open(file,'w')
-      math_file.print(yaml_data)
-      math_file.close
+      File.write(file,output)
     end
 
     def mk_tags(lines,file_name)
@@ -121,18 +127,22 @@ module MathJaxYard
         if @in_eq_block #inside in eq block
           if line =~/^\$\$/ #closing
             stored_eq << "$"
-            output << store_eq_data(stored_eq,file_name)
+            output << store_eq_data("$#{stored_eq}$",file_name)
             stored_eq=""
             @in_eq_block = !@in_eq_block
           else #normal op. in eq block
             p stored_eq << line
           end
         else #outside eq block
-          if line =~ /\$(.+)\$/ #normal op. in line eq.
-            p converted =check_multiple_match($1,file_name)
-            output <<  $`+converted+$'
-          elsif line =~/^\$\$/ # opening in eq block
-            p line
+          case line
+          when /\\\$(.*?)\\\$/
+            output << line # tryed to change $$ but failed.
+          when /\$(.+?)\$/
+            line.gsub!(/\$(.+?)\$/){|equation|
+              store_eq_data(equation,file_name)
+            }
+            output << line
+          when /^\$\$/ # opening in eq block
             @in_eq_block = !@in_eq_block
             stored_eq << "$"
           else  #normal op (no eq)
@@ -146,32 +156,9 @@ module MathJaxYard
     def store_eq_data(equation,file_name)
       @eq_number+=1
       tag="$MATHJAX#{@eq_number}$"
-      @eq_data[file_name][tag] = "$#{equation}$"
+      @eq_data[file_name][tag] = equation
       return tag
     end
-
-    def check_multiple_match(line,file)
-      if !line.include?('$') or
-          (line=~/^\$(.+)\$$/) then
-        return store_eq_data(line,file)
-      end
-      inline_eq = true
-      equation,text="",""
-      line.each_char{|char|
-        if char == '$'
-          if inline_eq then
-            text << store_eq_data(equation,file)
-            equation = ""
-          else
-          end
-          inline_eq = !inline_eq
-        else
-          inline_eq ? equation << char : text << char
-        end
-      }
-      text << store_eq_data(equation,file)
-      return text
-    end
   end
 end
 

data/lib/mathjax-yard/script.rb

@@ -0,0 +1,20 @@
+MATH_SCRIPT= <<EOS
+    <script type="text/x-mathjax-config">
+      MathJax.Hub.Config({
+                           tex2jax:{
+      inlineMath: [ ['$','$'], ["\\(","\\)"] ],
+      displayMath: [ ['$$','$$'], ["\\[","\\]"] ]
+                           }
+                         });
+    </script>
+    <script type="text/javascript"
+            src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AM\
+S_HTML">
+    </script>
+    <meta http-equiv="X-UA-Compatible" CONTENT="IE=EmulateIE7" />
+EOS
+
+ORIGINAL = <<EOS
+    <%= erb(:headers) %>
+  </head>
+EOS

data/lib/mathjax-yard/version.rb

@@ -1,3 +1,3 @@
 module MathJaxYard
-    VERSION = "0.1.0"
+    VERSION = "1.0.1"
 end

data/mathjax-yard.gemspec

@@ -11,7 +11,7 @@ Gem::Specification.new do |spec|
 
   spec.summary       = %q{mathjax-yard provides mathjax extention to yard.}
   spec.description   = %q{mathjax-yard provides mathjax extention to yard.}
-  spec.homepage      = "http://nishitani0.kwansei.ac.jp/Open/mathjax-yad"
+  spec.homepage      = "https://github.com/daddygongon/mathjax-yard"
   spec.license       = "MIT"
 
   # Prevent pushing this gem to RubyGems.org by setting 'allowed_push_host', or
@@ -27,8 +27,10 @@ Gem::Specification.new do |spec|
   spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
   spec.require_paths = ["lib"]
 
+  spec.required_ruby_version = ">= 2.0.0"
   spec.add_development_dependency "bundler", "~> 1.11"
   spec.add_development_dependency "rake", "~> 10.0"
   spec.add_development_dependency "rspec", "~> 3.0"
   spec.add_development_dependency "yard", "~> 0.8"  
+  spec.add_runtime_dependency "systemu"
 end

data/mathjax.yml

@@ -1,5 +1,5 @@
 ---
-lib/../docs/atom.md:
+lib/../mathjax-yard.wiki/atom.md:
   "$MATHJAX1$": "$i$"
   "$MATHJAX2$": |-
     $$E_i = \sum_j\phi \left( r_j \right) + f(\rho)
@@ -20,8 +20,8 @@ lib/../docs/atom.md:
     $$E_v = -\frac{E_c}{2} \frac{2-poq}{1-poq}
     $$
   "$MATHJAX14$": "$q$"
-lib/../docs/potential2.md:
-  "$MATHJAX15$": "$$ F(s)=\\int_{0}^{\\infty}f(t)e^{-st}dt $$"
+lib/../mathjax-yard.wiki/potential2.md:
+  "$MATHJAX15$": "$$ F(s)=\\int_{0}^{\\infty}f(t)e^{-st}dt $"
   "$MATHJAX16$": |-
     $$
     r_1=r/r_0

data/mathjax.yml.bk

@@ -0,0 +1,28 @@
+---
+lib/../mathjax-yard.wiki/atom.md:
+  "$MATHJAX1$": "$i$"
+  "$MATHJAX2$": |-
+    $$E_i = \sum_j\phi \left( r_j \right) + f(\rho)
+    $$
+  "$MATHJAX3$": "$r_j$"
+  "$MATHJAX4$": "$j$"
+  "$MATHJAX5$": "$E_i$"
+  "$MATHJAX6$": "$i$"
+  "$MATHJAX7$": |-
+    $$f(\rho) =\sqrt{\rho}=\sqrt{\sum_j h^2 \left( r_j \right) }
+    $$
+  "$MATHJAX8$": "$\\rho$"
+  "$MATHJAX9$": "$NPT$"
+  "$MATHJAX10$": "$E-V$"
+  "$MATHJAX11$": "$T=0.1$"
+  "$MATHJAX12$": "$E_v$"
+  "$MATHJAX13$": |-
+    $$E_v = -\frac{E_c}{2} \frac{2-poq}{1-poq}
+    $$
+  "$MATHJAX14$": "$q$"
+lib/../mathjax-yard.wiki/potential2.md:
+  "$MATHJAX15$": "$$ F(s)=\\int_{0}^{\\infty}f(t)e^{-st}dt $"
+  "$MATHJAX16$": |-
+    $$r_1=r/r_0 \\
+    \frac{ d_0 \left( r_1^{-n}m-  r_1^{-m} n \right) }{ -n + m }
+    $$

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: mathjax-yard
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 1.0.1
 platform: ruby
 authors:
 - Shigeto R. Nishitani
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-06-21 00:00:00.000000000 Z
+date: 2016-06-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -66,6 +66,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
+- !ruby/object:Gem::Dependency
+  name: systemu
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 description: mathjax-yard provides mathjax extention to yard.
 email:
 - shigeto_nishitani@me.com
@@ -85,15 +99,34 @@ files:
 - Rakefile
 - bin/console
 - bin/setup
-- docs/README_ja.md
-- docs/atom.md
-- docs/potential2.md
+- doc/MathJaxYard.html
+- doc/MathJaxYard/Command.html
+- doc/_index.html
+- doc/class_list.html
+- doc/css/common.css
+- doc/css/full_list.css
+- doc/css/style.css
+- doc/file.Home.html
+- doc/file.README.html
+- doc/file.README_ja.html
+- doc/file.atom.html
+- doc/file.potential2.html
+- doc/file_list.html
+- doc/frames.html
+- doc/index.html
+- doc/js/app.js
+- doc/js/full_list.js
+- doc/js/jquery.js
+- doc/method_list.html
+- doc/top-level-namespace.html
 - exe/mathjax-yard
 - lib/mathjax-yard.rb
+- lib/mathjax-yard/script.rb
 - lib/mathjax-yard/version.rb
 - mathjax-yard.gemspec
 - mathjax.yml
-homepage: http://nishitani0.kwansei.ac.jp/Open/mathjax-yad
+- mathjax.yml.bk
+homepage: https://github.com/daddygongon/mathjax-yard
 licenses:
 - MIT
 metadata: {}
@@ -105,7 +138,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 2.0.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="

data/docs/README_ja.md

@@ -1,77 +0,0 @@
-# MathJaxYard
-
-mathjax-yardはyardによるmarkdown変換においてmathjaxを使えるようにする拡張機能です．
-
-## Installation
-
-Add this line to your application's Gemfile:
-
-```ruby
-gem 'mathjax-yard'
-```
-
-And then execute:
-
-    $ bundle
-
-Or install it yourself as:
-
-    $ gem install mathjax-yard
-
-## Usage
-
-mathjax-yardはcommand line toolとしての使用を意図して作られています．例えば，Rakefileでの使用例は次の通りです．
-
-```
-desc "make documents by yard"
-task :yard do
-  system('mathjax-yard')
-  YARD::Rake::YardocTask.new
-end
-
-desc "make documents with yardmath"
-task :mathjax do
-  system('mathjax-yard --post')
-end
-```
-
-yardのデフォルトでの動作をなぞって，動作するように作られています．
-* mathjax-yardは./*/*.mdを探索し，それらの中に'$...$'あるいは'$$...$$'があると$MATHJAX**$というタグに付け替え，
-* *.md.backとしたファイルに元ファイルのバックアップを取り，*.mdにタグ付け替えした内容を保存します．
-*また，同時に，  'mathjax.yml'にそれらのhash関係をyaml形式で保存します．
-* 通常のrake yardで変換したのち，
-* 'mathjax-yard --post'によって，'doc/file.*.html'に残されたtagを元に戻します．
-* また同時に，backファイルを元に戻します．
-
-yardのoptionは，.yardoptsに
-
-```
--t mathjax -p templates
--
-spec/*.md
-```
-
-としています．また，htmlのhead部分にmathjaxのscriptを埋め込んだlayoutを用意しています．
-
-```csh
-bob% bundle exec exe/mathjax-yard --help
-Usage: yardmath [options] [DIRECTORY]
-    -v, --version                    show program Version.
-    -r, --revert                     revert mjx file to orig file.
-    -p, --post                       post operation.
-```
-
-## Development
-
-After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment. Run `bundle exec mathjax-yard` to use the gem in this directory, ignoring other installed copies of this gem.
-
-To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
-
-## Contributing
-
-Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/mathjax-yard. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
-
-
-## License
-
-The gem is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).

data/docs/atom.md

@@ -1,121 +0,0 @@
-# 概要
-# EAM
-EAM(Embedded atom method)は1980年代以降に，盛んに使われるようになった経験的原子間ポテンシャルである．
-
-## エネルギー表記
-EAMは原子$i$のエネルギーを
-
-$$
-E_i = \sum_j\phi \left( r_j \right) + f(\rho)
-$$
-
-と表記する．右辺第1項は単なる2体間の相互作用を表わす．
-右辺第2項が多体項と呼ばれるEAMに特徴的な項である．
-この工夫によって原子空孔を初め多くの金属物性を
-うまく表現することが可能となった．詳しくは西谷・赤本参照．
-
-さて，$r_j$はこの場合原子$j$との距離を意味しており，$E_i$は原子$i$の周りの原子との和によって求まる．多体項は，一般的に
-
-$$
-f(\rho) =\sqrt{\rho}=\sqrt{\sum_j h^2 \left( r_j \right) }
-$$
-
-によって求められる．$\rho$は強結合(tight binding)理論の2次モーメント近似と捉えると，電子密度を表わすとされている．
-
-## 具体例
-### for phi(r0)=-3.39, Ev=0.8, p=3.0 at r0=2.8577
-```maple
-
-A0,B0,P,POQ,Q:=69.1378255, 12.47431958,
-2.148157653, 2.893854749, 0.7423170267;
-
--3.39*32;
-                            -108.48
-```
-```
-n:=12;
-ene:=r->n*A0*exp(-P*r);
-h:=r->B0*exp(-Q*r);
-rho:=r->12*h(r)^2;
-plot(ene(r)-sqrt(rho(r)),r=2..4);
-```
-![](eam_ev_plot.gif)
-```
-r0:=fsolve(diff(ene(r)-sqrt(rho(r)),r),r=3);
-                          2.857701344
-evalf(subs(r=r0,ene(r)-sqrt(rho(r))));
-                          -3.390000002
-```
-```math
-E_i = \sum _ j\phi \left( r_{{j}} \right) + \h \left( r_{{j}} \right)
-```
-
-# LJ
-LJ(Lennard-Jones)はもっとも簡単な2体のポテンシャル．
-
-## エネルギー表記
-
-## 具体例
-```maple
-A0:=1.587401051*0.7071067812/2.857701314;
-E0:=-1*4.0/12.0;
-
-A:=18.19007708;
-B:=89.22765864;
-phi:=r-> 12*(-A*(1/r**3)+B*(1/r**5));
-r0:=fsolve(diff(phi(r),r),r=3);
-                          2.859281101
-phi(r0);
-                          -3.735125644
-```
-
-![](lj_ev_plot.gif)
-
-# EAM fitting
-
-EAM potentialの種々の構築手法を詳解する．
-## background
-MCにおいて$NPT$一定の計算がうまくいっていない．
-- 覚埜式の$E-V$プロットをすると小体積でのエネルギの上がりが低い．
-- $T=0.1$[eV]で融けているよう
-なので，もう少し精密にEAMポテンシャルを構築してみる．
-
-## poq fixed
-
-EAM potentialにおいて単原子空孔の生成エネルギ$E_v$は
-
-$$
-E_v = -\frac{E_c}{2} \frac{2-poq}{1-poq}
-$$
-
-の関係がある．したがって，
-```maple
-Ev:=0.8;                         
-Ec:=3.39;                    
-eq1:=Ev=Ec/2*(2-poq)/(1-poq);
-solve(eq1,poq);              
-                          2.893854749
-```
-
-さらにこの値を使ってポテンシャルのパラメータを求めるのは以下の通り．ここで，$q$を設定している．
-
-```
-phi:=r->12.0*A*exp(-p*r)-sqrt(12.0*(B*exp(-q*r))^2);
-poq:=2.893854749;
-q:=3.00*0.2474390089;
-a0:=8.0828/2;     
-r0:=evalf(a0*sqrt(2)/2.0); #2.857701345
-eq1:=phi(r0)=-3.39;
-s2:=solve(eq1,A);
-p:=poq*q; #2.148157653
-eq2:=subs(r=r0,diff(phi(r),r));
-#plot(subs(A=s2,eq2),B=0..20);
-b0:=fsolve(subs(A=s2,eq2),B=10);
-a0:=subs(B=b0,s2);
-phi0:=unapply(subs({A=a0,B=b0},phi(r)),r);
-plot(phi0(r),r=2..5);
-phi0(r0);
-a0,b0,p,poq,q;
-#69.1378255, 12.47431958, 2.148157653, 2.893854749, 0.7423170267
-```
-![](eam_ev.png)