Browse Source

Rewrite website from staticmatic to middleman

remotes/origin/middleman
Adam Stankiewicz 6 years ago
parent
commit
102ecb84b0
100 changed files with 324 additions and 531 deletions
  1. +3
    -6
      .gitignore
  2. +14
    -10
      Gemfile
  3. +90
    -18
      Gemfile.lock
  4. +5
    -10
      INSTALL.md
  5. +1
    -1
      README.rdoc
  6. +13
    -14
      Rakefile
  7. +90
    -83
      bin/fetch-geminfo.rb
  8. +0
    -0
      bin/fetch-src.rb
  9. +2
    -2
      bin/rss.rb
  10. +38
    -0
      config.rb
  11. +0
    -10
      create_biolinux_tab.sh
  12. +0
    -39
      create_website.sh
  13. +0
    -23
      doc/generate.md
  14. +0
    -267
      index.html
  15. +3
    -5
      lib/helpers/biolinux_helpers.rb
  16. +4
    -6
      lib/helpers/content_helpers.rb
  17. +0
    -3
      show_website.sh
  18. +29
    -0
      source/_footer.haml
  19. +11
    -11
      source/_header.haml
  20. +0
    -0
      source/_news.haml
  21. +6
    -6
      source/biolinux.haml
  22. +0
    -2
      source/bioruby.haml
  23. +0
    -0
      source/doc/README_rdoc.html
  24. +0
    -0
      source/doc/Tutorial_rdoc.html
  25. +0
    -0
      source/doc/rdoc.css
  26. +9
    -9
      source/howto.haml
  27. +0
    -0
      source/images/anvil.png
  28. BIN
      source/images/background.png
  29. +0
    -0
      source/images/biolinux.png
  30. +0
    -0
      source/images/bioruby-bg.gif
  31. +0
    -0
      source/images/bioruby-console.png
  32. +0
    -0
      source/images/bioruby-gem.png
  33. +0
    -0
      source/images/bioruby-icon-dev.png
  34. +0
    -0
      source/images/bioruby-icon-doc.png
  35. +0
    -0
      source/images/bioruby-icon-download.png
  36. +0
    -0
      source/images/bioruby-icon-ipa.png
  37. +0
    -0
      source/images/bioruby-icon-keynote.png
  38. +0
    -0
      source/images/bioruby-icon-link.png
  39. +0
    -0
      source/images/bioruby-icon-mail.png
  40. +0
    -0
      source/images/bioruby-icon-shell.png
  41. +0
    -0
      source/images/bioruby-link.gif
  42. +0
    -0
      source/images/book-large-1.jpg
  43. +0
    -0
      source/images/book_open.png
  44. +0
    -0
      source/images/books_64.png
  45. +0
    -0
      source/images/commit.png
  46. +0
    -0
      source/images/down1.png
  47. +0
    -0
      source/images/git-logo.png
  48. +0
    -0
      source/images/hp_fav_star.png
  49. BIN
      source/images/middleman.png
  50. +0
    -0
      source/images/pickaxe.png
  51. +0
    -0
      source/images/reference.png
  52. +0
    -0
      source/images/reference2.png
  53. +0
    -0
      source/images/rss-small.png
  54. +0
    -0
      source/images/science_64.png
  55. +0
    -0
      source/images/up1.png
  56. +6
    -6
      source/index.haml
  57. +0
    -0
      source/javascripts/OpenLayer/OpenLayers.js
  58. +0
    -0
      source/javascripts/OpenLayer/img/blank.gif
  59. +0
    -0
      source/javascripts/OpenLayer/img/cloud-popup-relative.png
  60. +0
    -0
      source/javascripts/OpenLayer/img/drag-rectangle-off.png
  61. +0
    -0
      source/javascripts/OpenLayer/img/drag-rectangle-on.png
  62. +0
    -0
      source/javascripts/OpenLayer/img/east-mini.png
  63. +0
    -0
      source/javascripts/OpenLayer/img/layer-switcher-maximize.png
  64. +0
    -0
      source/javascripts/OpenLayer/img/layer-switcher-minimize.png
  65. +0
    -0
      source/javascripts/OpenLayer/img/marker-blue.png
  66. +0
    -0
      source/javascripts/OpenLayer/img/marker-gold.png
  67. +0
    -0
      source/javascripts/OpenLayer/img/marker-green.png
  68. +0
    -0
      source/javascripts/OpenLayer/img/marker.png
  69. +0
    -0
      source/javascripts/OpenLayer/img/measuring-stick-off.png
  70. +0
    -0
      source/javascripts/OpenLayer/img/measuring-stick-on.png
  71. +0
    -0
      source/javascripts/OpenLayer/img/north-mini.png
  72. +0
    -0
      source/javascripts/OpenLayer/img/panning-hand-off.png
  73. +0
    -0
      source/javascripts/OpenLayer/img/panning-hand-on.png
  74. +0
    -0
      source/javascripts/OpenLayer/img/slider.png
  75. +0
    -0
      source/javascripts/OpenLayer/img/south-mini.png
  76. +0
    -0
      source/javascripts/OpenLayer/img/west-mini.png
  77. +0
    -0
      source/javascripts/OpenLayer/img/zoom-minus-mini.png
  78. +0
    -0
      source/javascripts/OpenLayer/img/zoom-plus-mini.png
  79. +0
    -0
      source/javascripts/OpenLayer/img/zoom-world-mini.png
  80. +0
    -0
      source/javascripts/OpenLayer/img/zoombar.png
  81. +0
    -0
      source/javascripts/OpenLayer/textfile.txt
  82. +0
    -0
      source/javascripts/OpenLayer/theme/default/framedCloud.css
  83. +0
    -0
      source/javascripts/OpenLayer/theme/default/google.css
  84. +0
    -0
      source/javascripts/OpenLayer/theme/default/google.tidy.css
  85. +0
    -0
      source/javascripts/OpenLayer/theme/default/ie6-style.css
  86. +0
    -0
      source/javascripts/OpenLayer/theme/default/ie6-style.tidy.css
  87. +0
    -0
      source/javascripts/OpenLayer/theme/default/img/add_point_off.png
  88. +0
    -0
      source/javascripts/OpenLayer/theme/default/img/add_point_on.png
  89. +0
    -0
      source/javascripts/OpenLayer/theme/default/img/blank.gif
  90. +0
    -0
      source/javascripts/OpenLayer/theme/default/img/close.gif
  91. +0
    -0
      source/javascripts/OpenLayer/theme/default/img/drag-rectangle-off.png
  92. +0
    -0
      source/javascripts/OpenLayer/theme/default/img/drag-rectangle-on.png
  93. +0
    -0
      source/javascripts/OpenLayer/theme/default/img/draw_line_off.png
  94. +0
    -0
      source/javascripts/OpenLayer/theme/default/img/draw_line_on.png
  95. +0
    -0
      source/javascripts/OpenLayer/theme/default/img/draw_point_off.png
  96. +0
    -0
      source/javascripts/OpenLayer/theme/default/img/draw_point_on.png
  97. +0
    -0
      source/javascripts/OpenLayer/theme/default/img/draw_polygon_off.png
  98. +0
    -0
      source/javascripts/OpenLayer/theme/default/img/draw_polygon_on.png
  99. +0
    -0
      source/javascripts/OpenLayer/theme/default/img/editing_tool_bar.png
  100. +0
    -0
      source/javascripts/OpenLayer/theme/default/img/move_feature_off.png

+ 3
- 6
.gitignore View File

@@ -1,11 +1,8 @@
website/site/images/
pkg/
contrib/
var/
website/site/*.html
website/site/*.xml
website/site/stylesheets/
bio-projects.yaml
*.swp
*#
*~
source/rss.xml
build/
data/

+ 14
- 10
Gemfile View File

@@ -1,17 +1,21 @@
source "http://rubygems.org"
# Add dependencies required to use your gem here.
# Example:
gem "staticmatic", ">= 0"
gem "haml"

gem "middleman", "~>3.2.0"

# Live-reloading plugin
gem "middleman-livereload", "~> 3.1.0"

# For faster file watcher updates on Windows:
gem "wdm", "~> 0.1.0", :platforms => [:mswin, :mingw]

# Add dependencies to develop your gem here.
# Include everything needed to run rake, tests, features, etc.
group :development do
gem "rake"
gem "yard", "~> 0.7.4"
gem "rspec", "~> 2.5.0"
gem "bundler", "~> 1.3.5"
gem "nokogiri", "~> 1.5.2"
gem "cucumber", "~> 1.2.0"
gem "compass", "~> 0.11.7"
gem "yard", "~> 0.7"
gem "rspec", "~> 2.5"
gem "bundler", "~> 1.3"
gem "nokogiri", "~> 1.5"
gem "cucumber", "~> 1.2"
gem "thread", "~> 0.1.3"
end

+ 90
- 18
Gemfile.lock View File

@@ -1,9 +1,16 @@
GEM
remote: http://rubygems.org/
specs:
activesupport (3.2.16)
i18n (~> 0.6, >= 0.6.4)
multi_json (~> 1.0)
builder (3.2.0)
chunky_png (1.2.8)
compass (0.11.7)
chunky_png (1.2.9)
coffee-script (2.2.0)
coffee-script-source
execjs
coffee-script-source (1.6.3)
compass (0.12.2)
chunky_png (~> 1.2)
fssm (>= 0.2.7)
sass (~> 3.1)
@@ -13,15 +20,68 @@ GEM
gherkin (~> 2.11.7)
multi_json (~> 1.3)
diff-lcs (1.1.3)
em-websocket (0.5.0)
eventmachine (>= 0.12.9)
http_parser.rb (~> 0.5.3)
eventmachine (1.0.3)
execjs (1.4.0)
multi_json (~> 1.0)
ffi (1.9.3)
fssm (0.2.10)
gherkin (2.11.8)
multi_json (~> 1.3)
haml (4.0.2)
haml (4.0.4)
tilt
hike (1.2.3)
http_parser.rb (0.5.3)
i18n (0.6.9)
kramdown (1.2.0)
listen (1.3.1)
rb-fsevent (>= 0.9.3)
rb-inotify (>= 0.9)
rb-kqueue (>= 0.2)
middleman (3.2.0)
coffee-script (~> 2.2.0)
compass (>= 0.12.2)
execjs (~> 1.4.0)
haml (>= 3.1.6)
kramdown (~> 1.2)
middleman-core (= 3.2.0)
middleman-sprockets (>= 3.1.2)
sass (>= 3.1.20)
uglifier (~> 2.1.0)
middleman-core (3.2.0)
activesupport (~> 3.2.6)
bundler (~> 1.1)
i18n (~> 0.6.1)
listen (~> 1.1)
rack (>= 1.4.5)
rack-test (~> 0.6.1)
thor (>= 0.15.2, < 2.0)
tilt (~> 1.3.6)
middleman-livereload (3.1.0)
em-websocket (>= 0.2.0)
middleman-core (>= 3.0.2)
multi_json (~> 1.0)
rack-livereload
middleman-sprockets (3.2.0)
middleman-core (~> 3.2)
sprockets (~> 2.1)
sprockets-helpers (~> 1.0.0)
sprockets-sass (~> 1.0.0)
multi_json (1.7.2)
nokogiri (1.5.9)
rack (1.5.2)
rack-livereload (0.3.15)
rack
rack-test (0.6.2)
rack (>= 1.0)
rake (10.0.4)
rb-fsevent (0.9.3)
rb-inotify (0.9.2)
ffi (>= 0.5.0)
rb-kqueue (0.2.0)
ffi (>= 0.5.0)
rspec (2.5.0)
rspec-core (~> 2.5.0)
rspec-expectations (~> 2.5.0)
@@ -30,24 +90,36 @@ GEM
rspec-expectations (2.5.0)
diff-lcs (~> 1.1.2)
rspec-mocks (2.5.0)
sass (3.2.8)
staticmatic (0.11.1)
compass (>= 0.10.0)
haml (>= 2.0.0)
rack (>= 1.0)
tilt (1.4.0)
yard (0.7.5)
sass (3.2.12)
sprockets (2.10.1)
hike (~> 1.2)
multi_json (~> 1.0)
rack (~> 1.0)
tilt (~> 1.1, != 1.3.0)
sprockets-helpers (1.0.1)
sprockets (~> 2.0)
sprockets-sass (1.0.2)
sprockets (~> 2.0)
tilt (~> 1.1)
thor (0.18.1)
thread (0.1.3)
tilt (1.3.7)
uglifier (2.1.2)
execjs (>= 0.3.0)
multi_json (~> 1.0, >= 1.0.2)
yard (0.8.7.3)

PLATFORMS
ruby

DEPENDENCIES
bundler (~> 1.3.5)
compass (~> 0.11.7)
cucumber (~> 1.2.0)
haml
nokogiri (~> 1.5.2)
bundler (~> 1.3)
cucumber (~> 1.2)
middleman (~> 3.2.0)
middleman-livereload (~> 3.1.0)
nokogiri (~> 1.5)
rake
rspec (~> 2.5.0)
staticmatic
yard (~> 0.7.4)
rspec (~> 2.5)
thread (~> 0.1.3)
wdm (~> 0.1.0)
yard (~> 0.7)

+ 5
- 10
INSTALL.md View File

@@ -1,7 +1,7 @@
# INSTALL

Biogem.info is a staticmatic generated website, which can be viewed with
staticmatic. It comes with a number of scripts and rake tasks which generate
Biogem.info is a middleman generated website.
It comes with a number of scripts and rake tasks which generate
the information displayed on the site in YAML format (usually to STDOUT).

## Installation
@@ -17,8 +17,7 @@ Install Ruby with openssl support
rvm remove 1.9.2
rvm install 1.9.2 -C --with-openssl-dir=$HOME/.rvm/usr,--with-iconv-dir=$HOME/.rvm/usr

Checkout the source code and run bundler. See also the create_website.sh and
show_website.sh scripts, to see the latest commands.
Checkout the source code and run bundler. See also the create_data.sh.

bundle update

@@ -28,15 +27,11 @@ To run the cucumber tests

To run a 'quick' test run

./create_website.sh --test
bundle exec rake -- --test

which will generate the site with just a few biogems. Next run

bundle exec staticmatic preview website/

The rakefile has some useful tasks, which can be viewed with

rake -T
bundle exec middleman server

## Trouble shooting



+ 1
- 1
README.rdoc View File

@@ -60,7 +60,7 @@ issues and stargazers for each gem.

To get around this, go to the applications tab on your GitHub
settings page and generate a new "Personal API access token". Then
copy that token (but not into the repository!), and before running the ./create_website.sh script,
copy that token (but not into the repository!), and before running the ./create_data.sh script,
set the GITHUB_API_TOKEN environment variable like this:

export GITHUB_API_TOKEN="copy-here-the-token-string-from-github"


+ 13
- 14
Rakefile View File

@@ -1,19 +1,18 @@
$:.unshift File.join(File.dirname(__FILE__),'lib')

BIOGEMS = './var/bio-projects.yaml'
RUBYGEMS = './var/ruby-projects.yaml'
BIOGEMS = './data/biogems.yaml'
RUBYGEMS = './data/rubygems.yaml'
GENERATE_DATA_FILES = [
BIOGEMS,
RUBYGEMS,
'./var/news.yaml'
'./data/news.yaml'
]

file RUBYGEMS do |t|
require 'biogems/fetch'
File.open(t.name,'w'){|f| f.print fetch('--rubygems') }
end
file BIOGEMS => [ :biogems ]

file RUBYGEMS => [ :biogems ]

file "./website/site/rss.xml" => ["./var/bio-projects.yaml", "./etc/blogs.yaml"] do |t|
file "./source/rss.xml" => ["./data/biogems.yaml", "./etc/blogs.yaml"] do |t|
require 'biogems/rss'
projects, blogs = t.prerequisite_tasks.map(&:name)
File.open(t.name,'w') do |f|
@@ -21,7 +20,7 @@ file "./website/site/rss.xml" => ["./var/bio-projects.yaml", "./etc/blogs.yaml"]
end
end

file "./var/news.yaml" =>"./website/site/rss.xml" do |t|
file "./data/news.yaml" =>"./source/rss.xml" do |t|
require 'yaml'
require 'rss'

@@ -38,15 +37,15 @@ file "./var/news.yaml" =>"./website/site/rss.xml" do |t|
File.open(t.name,'w'){|f| YAML.dump(site_news,f) }
end

task :rss => [ "./website/site/rss.xml" ]
task :rss => [ "./source/rss.xml" ]

desc "Fetch gem info and write YAML to stdout (optionally use -- --test)"
task :biogems => [ BIOGEMS ] do |t|
load 'bin/fetch-geminfo.rb'
desc "Fetch gem info and write to data directory (optionally use -- --test)"
task :biogems do |t|
%x{./bin/create_data.sh #{ARGV.join(' ')} 1>&2}
end

task :default => [ :biogems ] do
`staticmatic build website/`
`bundle exec middleman build`
end



+ 90
- 83
bin/fetch-geminfo.rb View File

@@ -1,4 +1,4 @@
#! /usr/bin/env ruby
#!/usr/bin/env ruby
#
# This script fetches information of bioruby gems, first querying the gem
# tool, followed by visiting rubygems.org and github.com.
@@ -10,6 +10,7 @@ require 'yaml'
require 'net/http'
require 'uri'
require 'biogems'
require 'thread/pool'

include BioGemInfo
include BioGemInfo::GitHub
@@ -38,7 +39,6 @@ $stderr.print "Querying gem list\n" if $is_debug
list = []
if is_biogems
# We re-read the last information from the resident YAML file.
# projects = YAML::load('var/bio-projects.yaml')
if is_testing
list = ['bio-logger', 'bio-table']
else
@@ -154,95 +154,102 @@ end

list_in_random_order = list.uniq.sort_by { rand }

pool = Thread.pool(15)

list_in_random_order.each do | name |
$stderr.print name,"\n" if $is_debug
info = Hash.new
# Fetch the gem YAML definition of the project
fetch = `bundle exec gem specification -r #{name.strip}`
if fetch != ''
spec = YAML::load(fetch)
# print fetch
# p spec
# When you get undefined method `authors' for #<Syck::Object:0x000000028cf3f0> (NoMethodError) make sure you try with 'bundle exec' instead!
info[:authors] = spec.authors
info[:summary] = spec.summary
info[:version] = spec.version.to_s
info[:release_date] = spec.date
info[:homepage] = spec.homepage
info[:licenses] = spec.licenses.join(' ')
info[:description] = spec.description
else
info[:version] = 'pre'
info[:status] = 'pre'
end
# Query rubygems.org directly
uri = URI.parse("http://rubygems.org/api/v1/gems/#{name}.yaml")
http = Net::HTTP.new(uri.host, uri.port)
request = Net::HTTP::Get.new(uri.request_uri)
response = http.request(request)
if response.code.to_i==200
# print response.body
biogems = YAML::load(response.body)
info[:downloads] = biogems["downloads"]
info[:version_downloads] = biogems["version_downloads"]
info[:gem_uri] = biogems["gem_uri"]
info[:homepage_uri] = check_url(biogems["homepage_uri"])
info[:project_uri] = check_url(biogems["project_uri"])
info[:source_code_uri] = biogems["sourcecode_uri"]
info[:docs_uri] = check_url(biogems["documentation_uri"])
info[:dependencies] = biogems["dependencies"]
# query for recent downloads
else
raise Exception.new("Response code for #{name} is "+response.code)
end
info[:docs_uri] = "http://rubydoc.info/gems/#{name}/#{info[:version]}/frames" if not info[:docs_uri]
versions = get_versions(name)
info[:downloads90] = get_downloads90(name, versions)
# if a gem is less than one month old, mark it as new
if versions.size <= 5
is_new = true
versions.each do | ver |
date = ver['built_at']
date.to_s =~ /^(\d\d\d\d)\-(\d\d)\-(\d\d)/
t = Time.new($1.to_i,$2.to_i,$3.to_i)
if Time.now - t > IS_NEW_IN_DAYS*24*3600
is_new = false
break
pool.process do
$stderr.print name,"\n" if $is_debug
info = Hash.new
# Fetch the gem YAML definition of the project
fetch = `bundle exec gem specification -r #{name.strip}`
if fetch != ''
spec = YAML::load(fetch)
# print fetch
# p spec
# When you get undefined method `authors' for #<Syck::Object:0x000000028cf3f0> (NoMethodError) make sure you try with 'bundle exec' instead!
info[:authors] = spec.authors
info[:summary] = spec.summary
info[:version] = spec.version.to_s
info[:release_date] = spec.date
info[:homepage] = spec.homepage
info[:licenses] = spec.licenses.join(' ')
info[:description] = spec.description
else
info[:version] = 'pre'
info[:status] = 'pre'
end
# Query rubygems.org directly
uri = URI.parse("http://rubygems.org/api/v1/gems/#{name}.yaml")
http = Net::HTTP.new(uri.host, uri.port)
request = Net::HTTP::Get.new(uri.request_uri)
response = http.request(request)
if response.code.to_i==200
# print response.body
biogems = YAML::load(response.body)
info[:downloads] = biogems["downloads"]
info[:version_downloads] = biogems["version_downloads"]
info[:gem_uri] = biogems["gem_uri"]
info[:homepage_uri] = check_url(biogems["homepage_uri"])
info[:project_uri] = check_url(biogems["project_uri"])
info[:source_code_uri] = biogems["sourcecode_uri"]
info[:docs_uri] = check_url(biogems["documentation_uri"])
info[:dependencies] = biogems["dependencies"]
# query for recent downloads
else
raise Exception.new("Response code for #{name} is "+response.code)
end
info[:docs_uri] = "http://rubydoc.info/gems/#{name}/#{info[:version]}/frames" if not info[:docs_uri]
versions = get_versions(name)
info[:downloads90] = get_downloads90(name, versions)
# if a gem is less than one month old, mark it as new
if versions.size <= 5
is_new = true
versions.each do | ver |
date = ver['built_at']
date.to_s =~ /^(\d\d\d\d)\-(\d\d)\-(\d\d)/
t = Time.new($1.to_i,$2.to_i,$3.to_i)
if Time.now - t > IS_NEW_IN_DAYS*24*3600
is_new = false
break
end
end
info[:status] = 'new' if is_new
end
info[:status] = 'new' if is_new
end
# Now parse etc/biogems/name.yaml
fn = "./etc/biogems/#{name}.yaml" if is_biogems
fn = "./etc/rubygems/#{name}.yaml" if is_rubygems
if File.exist?(fn)
added = YAML::load(File.new(fn).read)
added = {} if not added
info = info.merge(added)
end
# Replace http with https
for uri in [:source_code_uri, :homepage, :homepage_uri, :project_uri] do
if info[uri] =~ /^http:\/\/github/
info[uri] = info[uri].sub(/^http:\/\/github\.com/,"https://github.com")
# Now parse etc/biogems/name.yaml
fn = "./etc/biogems/#{name}.yaml" if is_biogems
fn = "./etc/rubygems/#{name}.yaml" if is_rubygems
if File.exist?(fn)
added = YAML::load(File.new(fn).read)
added = {} if not added
info = info.merge(added)
end
# Replace http with https
for uri in [:source_code_uri, :homepage, :homepage_uri, :project_uri] do
if info[uri] =~ /^http:\/\/github/
info[uri] = info[uri].sub(/^http:\/\/github\.com/,"https://github.com")
end
end
end

# Check github stuff
# print info
for uri in [:source_code_uri, :homepage, :homepage_uri, :project_uri] do
if info[uri] =~ /^https:\/\/github\.com/
info[:num_issues] = get_github_issues(info[uri]).size
info[:num_stargazers] = get_github_stargazers(info[uri]).size
user,project = get_github_user_project(info[uri])
info[:github_user] = user
info[:github_project] = project
info[:commit_stats] = get_github_commit_stats(info[uri])
break
# Check github stuff
# print info
for uri in [:source_code_uri, :homepage, :homepage_uri, :project_uri] do
if info[uri] =~ /^https:\/\/github\.com/
info[:num_issues] = get_github_issues(info[uri]).size
info[:num_stargazers] = get_github_stargazers(info[uri]).size
user,project = get_github_user_project(info[uri])
info[:github_user] = user
info[:github_project] = project
info[:commit_stats] = get_github_commit_stats(info[uri])
break
end
end
end

projects[name] = info
projects[name] = info
end
end

pool.shutdown

# Read the status of bio-core, bio-core-ext and bio-biolinux
# packages
update_status(projects) if is_biogems


+ 0
- 0
bin/fetch-src.rb View File


+ 2
- 2
bin/rss.rb View File

@@ -8,7 +8,7 @@ require_relative '../lib/biogems/rss.rb'
is_testing = ARGV.index('--test')

# First fetch all information
feed = generate_biogems_rss_feed "./var/bio-projects.yaml", "./etc/blogs.yaml", 50, is_testing
feed = generate_biogems_rss_feed "./data/biogems.yaml", "./etc/blogs.yaml", 50, is_testing

site_news = []
feed.items.each do | item |
@@ -21,7 +21,7 @@ end
# print site_news

# write a YAML file for the site
File.open('./var/news.yaml','w') do | f |
File.open('./data/news.yaml','w') do | f |
YAML.dump(site_news,f)
end



+ 38
- 0
config.rb View File

@@ -0,0 +1,38 @@
require 'lib/helpers/content_helpers'
require 'lib/helpers/biolinux_helpers'

helpers ContentHelpers
helpers BiolinuxHelpers

page "/usersmap.html", :layout => "usersmap_layout"
page "/bioruby.html", :layout => "bioruby_layout"
page "/news.html", :layout => "news_layout"

# Automatic image dimensions on image_tag helper
# activate :automatic_image_sizes

# Reload the browser automatically whenever files change
activate :livereload

set :css_dir, 'stylesheets'

set :js_dir, 'javascripts'

set :images_dir, 'images'

configure :build do
# For example, change the Compass output style for deployment
# activate :minify_css

# Minify Javascript on build
# activate :minify_javascript

# Enable cache buster
# activate :asset_hash

# Use relative URLs
# activate :relative_assets

# Or use a different image path
# set :http_prefix, "/Content/images/"
end

+ 0
- 10
create_biolinux_tab.sh View File

@@ -1,10 +0,0 @@
#! /bin/sh
#
# Create the website (partial)

# Download stats
./bin/create-biolinux-db.rb $* > ./var/biolinux-packages.yaml

# Generate site into website/site/
staticmatic build website/


+ 0
- 39
create_website.sh View File

@@ -1,39 +0,0 @@
#! /bin/bash
#
# Create the website


# Helper functions

## GitHub stats
function print_github_limits {
RATE_LIMIT_URL="https://api.github.com/rate_limit"

if [ -z "$GITHUB_API_TOKEN" ]; then
curl $RATE_LIMIT_URL
else
curl -H "Authorization: token $GITHUB_API_TOKEN" $RATE_LIMIT_URL
fi
}


# Work starts here

echo Github token=$GITHUB_API_TOKEN
print_github_limits

# curl http://github.com/api/v2/json/issues/list/pjotrp/bioruby-affy/open
bundle exec ./bin/fetch-geminfo.rb $* > ./var/bio-projects.yaml1
sed -e 's/!!null//g' < ./var/bio-projects.yaml1 > ./var/bio-projects.yaml
bundle exec ./bin/fetch-geminfo.rb --rubygems > ./var/ruby-projects.yaml1
sed -e 's/!!null//g' < ./var/ruby-projects.yaml1 > ./var/ruby-projects.yaml
# bundle exec ./bin/fetch-geminfo.rb > ./var/bio-projects.yaml

# Create RSS feed for others to use
bundle exec ./bin/rss.rb > website/site/rss.xml

# Generate site into website/site/
staticmatic build website/

print_github_limits


+ 0
- 23
doc/generate.md View File

@@ -1,23 +0,0 @@
= Biogems.info =

Biogems.info is a generated site (using staticmatic).

== News feeds ==

News is gathered from multiple RSS feeds. You can add a blog by
editing ./etc/blogs.yaml. When running

rake rss

or alternatively

./bin/rss.rb

both an XML RSS file and a YAML file gets generated. The information gets
collected into ./website/site/rss.xml - this is the file that is available as a
general news feed from http://biogems.info/rss.xml, which includes project
updates. Also a file ./var/news.yaml gets written - this is the file that is
used by staticmatic to generate the news feed on the website.




+ 0
- 267
index.html View File

@@ -1,267 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>BioRuby</title>
<link href="bioruby.css" media="screen" rel="Stylesheet" type="text/css" />
</head>

<body>

<div id="content">

<div id="side">
<div class="title">News</div>
<ul>
<li>2011/08/26 <p><a href="http://bioruby.org/archive/bioruby-1.4.2.tar.gz">BioRuby 1.4.2</a> released (<a href="https://github.com/bioruby/bioruby/blob/1.4.2/ChangeLog">ChangeLog</a>)</p></li>
<li>2010/12/24 <p>BioRuby <a href="http://bioruby.open-bio.org/wiki/Plugins">plugin system</a> is released</li>
<li>2010/10/22 <p><a href="http://bioruby.org/archive/bioruby-1.4.1.tar.gz">BioRuby 1.4.1</a> released (<a href="http://github.com/bioruby/bioruby/blob/1.4.1/ChangeLog">ChangeLog</a>)</p></li>
<li>2010/08/25 <p><a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq475">BioRuby paper</a> is published</li>
<li>2009/12/29 <p><a href="http://bioruby.org/archive/bioruby-1.4.0.tar.gz">BioRuby 1.4.0</a> released (<a href="http://github.com/bioruby/bioruby/blob/1.4.0/ChangeLog">ChangeLog</a>)</p></li>
<li>2009/09/03 <p><a href="http://bioruby.org/archive/bioruby-1.3.1.tar.gz">BioRuby 1.3.1</a> released (<a href="http://github.com/bioruby/bioruby/blob/1.3.1/ChangeLog">ChangeLog</a>)</p></li>
<li>2009/03/15-21 <p><a href="http://hackathon2.dbcls.jp/">BioHackathon 2009</a></p></li>
<li>2009/02/24 <p><a href="http://bioruby.org/archive/bioruby-1.3.0.tar.gz">BioRuby 1.3.0</a> released (<a href="http://github.com/bioruby/bioruby/blob/1.3.0/ChangeLog">ChangeLog</a>)</p></li>
<li>2008/09/01 <p><a href="http://lists.open-bio.org/pipermail/bioruby/2008-September/000700.html">BioRuby has officially moved from CVS to git</a></p></li>
<li>2008/02/18 <p>New site hosted at <a href="http://open-bio.org/">(O|B|F)</a></p></li>
<li>2008/02/11-15 <p><a href="http://hackathon.dbcls.jp/">BioHackathon 2008</a></p></li>
<li>2007/12/30 <p><a href="http://bioruby.org/archive/bioruby-1.2.1.tar.gz">BioRuby 1.2.1</a> released (<a href="http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioruby/ChangeLog?rev=1.79&cvsroot=bioruby&content-type=text/vnd.viewcvs-markup">ChangeLog</a>)</p></li>
<li>2007/12/15 <p><a href="http://bioruby.org/archive/bioruby-1.2.0.tar.gz">BioRuby 1.2.0</a> released (<a href="http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioruby/ChangeLog?rev=1.71&cvsroot=bioruby&content-type=text/vnd.viewcvs-markup">ChangeLog</a>)</p></li>
<li>2007/07/19-20 <p><a href="http://www.open-bio.org/wiki/BOSC_2007">BOSC 2007</a> (<a href="http://bioruby.org/archive/doc/BR070719-bosc.pdf">PDF</a>)</p></li>
<li><a href="http://bioruby.open-bio.org/wiki/History">... more ...</a></li>
</ul>

<div class="title">Links</div>
<ul>
<li><a href="http://www.ruby-lang.org/">Ruby</a><br />
+ <a href="http://raa.ruby-lang.org/list.rhtml?name=BioRuby">Ruby Application Archive</a><br />
+ <a href="http://rubyforge.org/projects/bioruby/">RubyForge</a></li>
<li><a href="http://open-bio.jp/">O|B|J</a><br />
+ <a href="http://www.chemruby.org/">ChemRuby</a></li>
<li><a href="http://open-bio.org/">O|B|F</a><br />
+ <a href="http://www.bioperl.org/">BioPerl</a><br />
+ <a href="http://www.biopython.org/">BioPython</a><br />
+ <a href="http://www.biojava.org/">BioJava</a></li>
<li>Misc<br />
+ <a href="http://www.biolisp.org/">BioLisp</a><br />
+ <a href="http://www.biodas.org/">BioDAS</a><br />
+ <a href="http://www.biomoby.org/">BioMOBY</a><br />
+ <a href="http://bioinformatics.org/">Bioinformatics.org</a></li>
</ul>

<br />
<a href="http://bioruby.org/"><img src="images/bioruby-link.gif" alt="bioruby.org" border="0" /></a>
</div><!-- side -->

<div id="title">
<p class="titletop">BioRuby</p>
<p class="titlesub">Open source bioinformatics library for Ruby</p>
</div><!-- title -->

<div id="main">

<div id="main_top">
<div class="section_title">Announcements</div>
<ul>
<li><a href="http://gems.bioruby.org/">Biogem</a> is community developed plugins for the BioRuby. See the <a href="http://biogems.info/">complete list</a>, <a href="http://bioruby.open-bio.org/wiki/Plugins">generic information</a>, <a href="http://www.biogems.info/doc/README_rdoc.html">README</a>, <a href="http://www.biogems.info/howto.html">HOWTO</a> and <a href="http://www.biogems.info/doc/Tutorial_rdoc.html">Tutorial</a>.</li>
<li>We will discontinue our bug tracking system on <a href="http://rubyforge.org/projects/bioruby/">RubyForge</a>. Instead, please use <a href="https://redmine.open-bio.org/projects/bioruby">Redmine system provided at O|B|F</a> for bug reports.</li>
<li>We had the first BioRuby world wide IRC conference on Dec 19th 2010 and agreed to continue weekly IRC meeting on every Thursday (<a href="http://bioruby.open-bio.org/wiki/BioRuby_IRC_conference">details</a>). The log is available <a href="http://irc.bioruby.org/">here</a>.</li>
</ul>

<div class="section_title">Project overview</div>
<p>BioRuby project provides an integrated environment in bioinformatics for the <a href="http://www.ruby-lang.org/">Ruby</a> language. This project is supported by <a href="http://www.hgc.jp/">University of Tokyo</a> (Human Genome Center), <a href="http://www.bic.kyoto-u.ac.jp/">Kyoto University</a> (Bioinformatics Center) and the <a href="http://open-bio.org/">Open Bio Foundation</a>.</p>
<div class="section_title">Reference</div>
<p>
BioRuby: Bioinformatics software for the Ruby programming language<br/>
Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama<br/>
<i>Bioinformatics</i> (2010) 26(20): 2617-2619. <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq475">doi: 10.1093/bioinformatics/btq475</a>
</p>
</div>

<div id="main_left">

<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-doc.png" alt="documentation" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">Documentation</div>
<ul>
<li><a href="http://bioruby.open-bio.org/wiki/">Wiki page</a><br />
+ <a href="http://bioruby.open-bio.org/wiki/Tutorial">Tutorial</a><br />
+ <a href="http://bioruby.open-bio.org/wiki/SampleCodes">Sample codes</a><br /></li>
<li><a href="http://dev.bioruby.org/ja/">Japanese Wiki page</a></li>
<li><a href="http://bioruby.org/rdoc/">API documentation</a></li>
</ul>
</div>
</td>
</tr>
</table>
</div>

<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-keynote.png" alt="presentations" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">Presentations</div>
<ul>
<li><a href="http://bioruby.org/archive/doc/">English slides</a></li>
<li><a href="http://bioruby.org/archive/doc/Japanese">Japanese slides</a></li>
<li><a href="http://bioruby.org/archive/doc/Japanese/BR070326-ws-k.mov">Video cast</a></li>
</ul>
</div>
</td>
</tr>
</table>
</div>

<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-dev.png" alt="development" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">Development</div>
<ul>
<li><a href="http://github.com/bioruby/bioruby">GitHub</a></li>
<li><a href="https://redmine.open-bio.org/projects/bioruby">Bug report</a></li>
<!--
<li><a href="http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=bioruby">BioRuby CVS repository</a> hosted by <a href="http://www.open-bio.org/wiki/SourceCode">(O|B|F)</a> is now deprecated.</li>
-->
</ul>
</div>
</td>
</tr>
</table>
</div>

<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-shell.png" alt="bioruby shell" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">BioRuby shell</div>
<p>BioRuby comes with an <a href="http://bioruby.open-bio.org/wiki/BioRubyOnRails">interactive shell</a> also capable as a plugin for the <a href="http://rubyonrails.org/">Ruby on Rails</a></p>
</div>
</td>
</tr>
</table>
</div>

</div><!-- main_left -->

<div id="main_right">

<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-download.png" alt="download" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">Download</div>
<ul>
<li><a href="http://rubyforge.org/projects/bioruby/">RubyGems package</a></li>
<li><a href="http://bioruby.org/archive/">Source code archive</a></li>
<li><a href="http://gems.bioruby.org/">Plugins</a> (<a href="http://bioruby.open-bio.org/wiki/Plugins">usage</a>)</li>
<li><a href="http://bioruby.org/contrib/">Contributed codes</a></li>
</ul>
</div>
</td>
</tr>
</table>
</div>

<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-mail.png" alt="mailing list" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">Mailng lists</div>
<ul>
<li><a href="http://lists.open-bio.org/mailman/listinfo/bioruby">English list</a></li>
<li><a href="http://lists.open-bio.org/mailman/listinfo/bioruby-ja">Japanese list</a></li>
<!-- <li><a href="http://lists.open-bio.org/mailman/listinfo/bioruby-cvs">CVS commit log</a></li> -->
</ul>
</div>
</td>
</tr>
</table>
</div>

<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-link.png" alt="community" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">Community</div>
<ul>
<li><a href="http://bioruby.open-bio.org/wiki/Contributors">Contributors</li>
<li><a href="http://bioruby.open-bio.org/wiki/Links#Blogs">Blogs</a></li>
</ul>
</div>
</td>
</tr>
</table>
</div>

<div class="section">
<table>
<tr>
<td>
<div class="section_image">
<img src="images/bioruby-icon-ipa.png" alt="IPA" />
</div>
</td>
<td>
<div class="section_text">
<div class="section_title">IPA</div>
<p>Our project was supported by Information-technology Promotion Agency (<a href="http://www.ipa.go.jp/">IPA</a>) as an <a href="http://www.ipa.go.jp/jinzai/esp/">Exploratory Software Project</a> in 2005</p>
</div>
</td>
</tr>
</table>
</div>

</div><!-- main_right -->

</div><!-- main -->

</div><!-- content -->

</body>

</html>

website/src/helpers/biolinux_helper.rb → lib/helpers/biolinux_helpers.rb View File

@@ -1,9 +1,8 @@
require 'ostruct'

module BiolinuxHelper
module BiolinuxHelpers
def news_items
news = YAML::load(File.new("./var/news.yaml").read)
news.each do | item |
data.news.each do | item |
item[:date].to_s =~ /(\d+-\d+-\d+)/
item[:short_date] = $1
yield item
@@ -11,8 +10,7 @@ module BiolinuxHelper
end

def biolinux_by_popularity(type = nil)
projects_fn = "./var/biolinux-packages.yaml"
packages = YAML::load(File.new(projects_fn).read)
packages = data.biolinux
packages = {} if not packages
# packages.each do |name,pkg|
# $stderr.print name,"\n"

website/src/helpers/content_helper.rb → lib/helpers/content_helpers.rb View File

@@ -3,10 +3,9 @@ require 'yaml'
MAX_WORDS = 7
NUM_AUTHORS = 3

module ContentHelper
module ContentHelpers
def news_items
news = YAML::load(File.new("./var/news.yaml").read)
news.each do | item |
data.news.each do | item |
item[:date].to_s =~ /(\d+-\d+-\d+)/
item[:short_date] = $1
yield item
@@ -14,9 +13,8 @@ module ContentHelper
end

def by_popularity(type = nil)
projects_fn = "./var/bio-projects.yaml"
projects_fn = "./var/ruby-projects.yaml" if type == :rubygems
spec = YAML::load(File.new(projects_fn).read)
spec = (type == :rubygems ? data.rubygems : data.biogems)

spec = {} if not spec
sorted = spec.sort { |a, b| b[1][:downloads] <=> a[1][:downloads] }
# rank trend

+ 0
- 3
show_website.sh View File

@@ -1,3 +0,0 @@
#! /bin/sh

bundle exec staticmatic preview website/

+ 29
- 0
source/_footer.haml View File

@@ -0,0 +1,29 @@
- if false
#footer
%hr
#links
%table
%tr
%td
= link_to "biogems.info", "https://github.com/bioruby/biogems.info"
website by
= link_to "Pjotr Prins", "http://thebird.nl/"
using
= link_to "middleman", "http://middlemanapp.com/"
,
= link_to "haml", "http://haml-lang.com/"
and
= link_to "sass", "http://sass-lang.com/"
%td
= link_to "Biogem README", "/doc/README_rdoc.html"
|
= link_to "Create a Biogem!", "/howto.html"
|
= link_to "BioRuby.org", "http://bioruby.org/"
project website and mailing list
|
= link_to "People", "/usersmap.html"
|
%a{:href => "/rss.xml"}
%img#git{:src => "/images/rss-small.png", :height => 10, :alt => "RSS"}


website/src/partials/header.haml → source/_header.haml View File

@@ -3,7 +3,7 @@
%img#logo{:src => "./images/bioruby-gem.png", :alt => "biogems.info"}
%div
.maintitle
= link "Biogems.info", "/"
= link_to "Biogems.info", "/"
%div{ :style => "background-color: #" + "%06x" % (rand * 0xffffff) }
&nbsp;
%div
@@ -13,27 +13,27 @@
|
- if current_page == '/index.html'
%span{ :style => "background-color: #550009" }
= link "&nbsp;Biogems&nbsp;", "/"
= link_to "&nbsp;Biogems&nbsp;", "/"
- else
= link "Biogems", "/"
= link_to "Biogems", "/"
|
- if current_page == '/rubygems.html'
%span{ :style => "background-color: #550009" }
= link "&nbsp;Rubygems&nbsp;", "/rubygems.html"
= link_to "&nbsp;Rubygems&nbsp;", "/rubygems.html"
- else
= link "Rubygems", "/rubygems.html"
= link_to "Rubygems", "/rubygems.html"
|
- if current_page == '/biolinux.html'
%span{ :style => "background-color: #550009" }
= link "&nbsp;BioLinux&nbsp;", "/biolinux.html"
= link_to "&nbsp;BioLinux&nbsp;", "/biolinux.html"
- else
= link "BioLinux", "/biolinux.html"
= link_to "BioLinux", "/biolinux.html"
|
- if current_page == '/usersmap.html'
%span{ :style => "background-color: #550009" }
= link "&nbsp;People&nbsp;", "/usersmap.html"
= link_to "&nbsp;People&nbsp;", "/usersmap.html"
- else
= link "People", "/usersmap.html"
= link_to "People", "/usersmap.html"
|
.rightheader
%span{ :align => "right", :style => "float: right" }
@@ -41,9 +41,9 @@
%i
%small
The future is bright for Ruby in bioinformatics!&nbsp;&nbsp;&nbsp;
= link "Create a Biogem!", "/howto.html"
= link_to "Create a Biogem!", "/howto.html"
|
= link "BioRuby", "http://bioruby.org/"
= link_to "BioRuby", "http://bioruby.org/"
|
%a{:href => "/rss.xml"}
%img#git{:src => "/images/rss-small.png", :height => 16 , :alt => "RSS"}

website/src/partials/news.haml → source/_news.haml View File


website/src/pages/biolinux.haml → source/biolinux.haml View File

@@ -55,14 +55,14 @@
%img#uparrow{:src => "./images/bioruby-gem.png", :width=>"20", :title => "new biogem!", :alt => "!"}
%td{ :class => "#{rowclass}" }
.name
= link pkg.name.gsub(/[_-]/,' '), pkg.url
= link_to pkg.name.gsub(/[_-]/,' '), pkg.url
%td{ :class => "#{rowclass}" }
.origin
= pkg.origin
%td{ :class => "#{rowclass}" }
.descr
= pkg.descr
= link " (...)", pkg.home
= link_to " (...)", pkg.home
%td.authors{ :class => "#{rowclass}" }
= pkg.author
%td{ :class => "#{rowclass}" }
@@ -75,14 +75,14 @@
// (moved to descr)
%td{ :align => "right", :class => "#{rowclass}" }
.version
= link pkg.version, pkg.version_url if pkg.version_url
= link_to pkg.version, pkg.version_url if pkg.version_url
= pkg.version if not pkg.version_url
// %td{ :align => "right", :class => "#{rowclass}" }
// .released
// = pkg.released
// %td{ :class => "#{rowclass}" }
// .issues
// = link pkg.num_issues.to_s, pkg.issues
// = link_to pkg.num_issues.to_s, pkg.issues
// %td{ :align => "center", :class => "#{rowclass}" }
// .commit
// - if pkg.src =~ /git/
@@ -92,12 +92,12 @@
// .citest
%td{ :align => "right", :class => "#{rowclass}" }
.dl
= link pkg.downloads.to_s, "http://popcon.debian.org/by_vote" if pkg.downloads>0
= link_to pkg.downloads.to_s, "http://popcon.debian.org/by_vote" if pkg.downloads>0
// %td{ :align => "right", :class => "#{rowclass}" }
// .dl
.footnote
<b>*)</b> package updates (total &amp; last 90 days) from
= link "Debian popularity index", "http://popcon.debian.org/by_vote"
= link_to "Debian popularity index", "http://popcon.debian.org/by_vote"
as of
= Time.now.to_s.split[0]
// %br

website/src/pages/bioruby.haml → source/bioruby.haml View File

@@ -1,5 +1,3 @@
- @layout = "bioruby"

#content
#side
.title News

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website/site/doc/rdoc.css → source/doc/rdoc.css View File


website/src/pages/howto.haml → source/howto.haml View File

@@ -13,7 +13,7 @@
%p
Biogem aims to encourage open source software development, and provide
tools to support
= link "bazaar", "http://en.wikipedia.org/wiki/The_Cathedral_and_the_Bazaar"
= link_to "bazaar", "http://en.wikipedia.org/wiki/The_Cathedral_and_the_Bazaar"
programming. In our interpretation:
%ul
%li Every good work of software starts by scratching a developer's personal itch
@@ -35,24 +35,24 @@
%p
%ul
%li
= link "Biogem README", "/doc/README_rdoc.html"
= link_to "Biogem README", "/doc/README_rdoc.html"
%li
= link "Create a Biogem!", "/doc/Tutorial_rdoc.html"
= link_to "Create a Biogem!", "/doc/Tutorial_rdoc.html"
%li
= link "Hacking the Biogem tool (DRY)!", "https://github.com/pjotrp/bioruby-gem/blob/master/doc/biogem-hacking.md"
= link_to "Hacking the Biogem tool (DRY)!", "https://github.com/pjotrp/bioruby-gem/blob/master/doc/biogem-hacking.md"
%li
= link "Source code for Biogem", "https://github.com/helios/bioruby-gem"
= link_to "Source code for Biogem", "https://github.com/helios/bioruby-gem"
%li
= link "Source code for the biogems.info website", "https://github.com/pjotrp/biogems.info"
= link_to "Source code for the biogems.info website", "https://github.com/pjotrp/biogems.info"

%p
Other important links
%ul
%li
= link "BioRuby", "http://bioruby.org/"
= link_to "BioRuby", "http://bioruby.org/"
%li
= link "The Ruby programming language", "http://www.ruby-lang.org/en/"
= link_to "The Ruby programming language", "http://www.ruby-lang.org/en/"
%li
= link "RVM - for running multiple Ruby versions", "https://rvm.beginrescueend.com/"
= link_to "RVM - for running multiple Ruby versions", "https://rvm.beginrescueend.com/"


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website/site/images/biolinux.png → source/images/biolinux.png View File


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website/site/images/bioruby-gem.png → source/images/bioruby-gem.png View File


website/site/images/bioruby-icon-dev.png → source/images/bioruby-icon-dev.png View File


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website/site/images/pickaxe.png → source/images/pickaxe.png View File


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website/src/pages/index.haml → source/index.haml View File

@@ -61,12 +61,12 @@
%img#uparrow{:src => "./images/bioruby-gem.png", :width=>"20", :title => "new biogem!", :alt => "!"}
%td{ :class => "#{rowclass}" }
.name
= link name.gsub(/[_-]/,' '), "http://rubygems.org/gems/#{name}"
= link_to name.gsub(/[_-]/,' '), "http://rubygems.org/gems/#{name}"
%td{ :class => "#{rowclass}" }
.descr
= descr
- if docs and docs != ''
= link " (...)", docs
= link_to " (...)", docs
- if name == 'bio' or name == 'bio-core' or name == 'bio-core-ext' or name == 'bio-biolinux' or status == 'core' or status == 'bio'
%img#uparrow{:src => "./images/bioruby-gem.png", :width=>"15", :title => "BioRuby core gem!", :alt => "!", :align => "right" }
- elsif status == 'bio-core'
@@ -91,14 +91,14 @@
// (moved to descr)
%td{ :align => "right", :class => "#{rowclass}" }
.version
= link version, "http://rubygems.org/gems/#{name}"
= link_to version, "http://rubygems.org/gems/#{name}"
%td{ :align => "right", :class => "#{rowclass}" }
.released
= released
%td{ :class => "#{rowclass}" }
.stargazers
- if num_stargazers > 0
= link num_stargazers.to_s, stargazers
= link_to num_stargazers.to_s, stargazers
%td{ :class => "#{rowclass}" }
.stargazers
- if num_stargazers > 0
@@ -106,7 +106,7 @@
%img#git{:src => "/images/hp_fav_star.png", :width => "25", :alt => "star"}
%td{ :class => "#{rowclass}" }
.issues
= link num_issues.to_s, issues
= link_to num_issues.to_s, issues
%td{ :align => "center", :class => "#{rowclass}" }
.commit
- if src =~ /git/
@@ -142,7 +142,7 @@
= c90.to_s
.footnote
<b>*)</b> gem downloads (total &amp; last 90 days) from
= link "rubygems.org", "http://rubygems.org"
= link_to "rubygems.org", "http://rubygems.org"
as of
= Time.now.to_s.split[0]
%br

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