bel 0.3.0.beta6 → 0.3.0

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data/INSTALL.md

@@ -1,7 +1,7 @@
 Install
 =======
 
-This library requires [Ruby](https://www.ruby-lang.org) (**>= 1.9.2**).  See [how to install ruby](https://github.com/OpenBEL/bel.rb/blob/master/INSTALL_RUBY.md).
+This library requires [Ruby](https://www.ruby-lang.org) (**>= 2.0.0**).  See [how to install ruby](https://github.com/OpenBEL/bel.rb/blob/master/INSTALL_RUBY.md).
 
 Install from [RubyGems.org](http://rubygems.org/gems/bel)
 

data/INSTALL_RUBY.md

@@ -4,7 +4,7 @@
 ## Install Ruby (Windows)
 
 1. Download [RubyInstaller](http://rubyinstaller.org/downloads).
-   * Versions 1.9.3 and 2.x.x are supported.
+   * Versions 2.x.x are supported.
 2. Install RubyInstaller version.
    * Enable the _Add Ruby executables to your PATH_ option presented during installation.
 3. Open a command prompt (Windows Key + R then type `cmd`).

data/README.md

@@ -13,7 +13,7 @@ Dependencies
 
 - Required
 
-    - Ruby 1.9.2 or greater ([how to install ruby](INSTALL_RUBY.md))
+    - Ruby 2.0.0 or greater ([how to install ruby](INSTALL_RUBY.md))
 
 - Optional
 
@@ -35,62 +35,115 @@ branches
 executable commands
 -------------------
 
-**bel_upgrade**: Upgrade namespaces in BEL content to another version (i.e. *1.0* to *20131211*)
+**bel**: A single executable command with subcommands.
 
 ```bash
 
-    # using BEL file and change log JSON file
-    bel_upgrade --bel small_corpus.bel --changelog change_log.json
-
-    # using BEL file and change log from a URL
-    bel_upgrade --bel small_corpus.bel --changelog http://resource.belframework.org/belframework/20131211/change_log.json
-
-    # using BEL from STDIN and change log from a URL
-    cat small_corpus.bel | bel_upgrade --changelog http://resource.belframework.org/belframework/20131211/change_log.json
+    NAME
+        bel - Command line utilities for BEL.
+
+    SYNOPSIS
+        bel [global options] command [command options] [arguments...]
+
+    VERSION
+        0.3.0
+
+    GLOBAL OPTIONS
+        --help         - Show this message
+        --[no-]verbose - Enables verbose output.
+        --version      - Display the program version
+
+    COMMANDS
+        bel2rdf.rb   - Converts BEL to RDF.
+        compare   - Compares knowledge in two BEL script.
+        help      - Shows a list of commands or help for one command
+        parse     - Shows parse of BEL script.
+        rdfschema - Outputs the RDFS (e.g. RDF Schema) for BEL.
+        summarize - Show summary statistics. for knowledge in provided BEL script.
+        translate - Translates BEL evidence between file formats.
+        upgrade   - Upgrades BEL knowledge and annotation.
 ```
 
-**bel_rdfschema**: Dumps the RDF Schema triples for BEL.
-
-```bash
-
-    # dumps schema in ntriples format (default)
-    bel_rdfschema
-
-    # dumps schema in turtle format
-    # note: requires the 'rdf-turtle' gem
-    bel_rdfschema --format turtle
-```
 
-**bel2rdf**: Converts BEL to RDF.
+**bel2rdf.rb**: Converts BEL to RDF.
 
 ```bash
 
     # dumps RDF to standard out in ntriples format (default)
     #   (from file)
-    bel2rdf --bel small_corpus.bel
+    bel2rdf.rb --bel small_corpus.bel
 
     #   (from standard in)
-    cat small_corpus.bel | bel2rdf
+    cat small_corpus.bel | bel2rdf.rb
 
     # dumps RDF to standard out in turtle format
     #   (from file)
-    bel2rdf --bel small_corpus.bel --format turtle
+    bel2rdf.rb --bel small_corpus.bel --format turtle
 
     #   (from standard in)
-    cat small_corpus.bel | bel2rdf --format turtle
+    cat small_corpus.bel | bel2rdf.rb --format turtle
+```
+
+
+**bel_compare.rb**: Compares knowledge in two BEL script files.
+
+```bash
+
+    bel_compare.rb small_corpus.bel large_corpus.bel
 ```
 
-**bel_parse**: Show parsed objects from BEL content for debugging purposes
+
+**bel_parse.rb**: Show parsed objects from BEL content for debugging purposes
 
 ```bash
 
     # ...from file
-    bel_parse --bel small_corpus.bel
+    bel_parse.rb --bel small_corpus.bel
 
     # ...from standard in
-    cat small_corpus.bel | bel_parse
+    cat small_corpus.bel | bel_parse.rb
+```
+
+
+**bel_rdfschema.rb**: Dumps the RDF Schema triples for BEL.
+
+```bash
+
+    # dumps schema in ntriples format (default)
+    bel_rdfschema.rb
+
+    # dumps schema in turtle format
+    # note: requires the 'rdf-turtle' gem
+    bel_rdfschema.rb --format turtle
+```
+
+
+**bel_summarize.rb**: Show summary statistics for knowledge in BEL script.
+
+```bash
+    # using BEL file
+    bel_summarize.rb --bel small_corpus.bel
+
+    # using BEL from STDIN
+    cat small_corpus.bel | bel_summarize.rb
 ```
 
+
+**bel_upgrade.rb**: Upgrade namespaces in BEL content to another version (i.e. *1.0* to *20131211*)
+
+```bash
+
+    # using BEL file and change log JSON file
+    bel_upgrade.rb --bel small_corpus.bel --changelog change_log.json
+
+    # using BEL file and change log from a URL
+    bel_upgrade.rb --bel small_corpus.bel --changelog http://resource.belframework.org/belframework/20131211/change_log.json
+
+    # using BEL from STDIN and change log from a URL
+    cat small_corpus.bel | bel_upgrade.rb --changelog http://resource.belframework.org/belframework/20131211/change_log.json
+```
+
+
 api examples
 ------------
 

data/bel.gemspec

@@ -1,4 +1,4 @@
-require_relative 'lib/bel/version'
+require './lib/bel/version'
 
 Gem::Specification.new do |spec|
   spec.name                     = 'bel'

data/bin/bel_summarize.rb

@@ -58,6 +58,7 @@ CSV do |csv_out|
       fx = fx.respond_to?(:long_form) ?
              fx.long_form.to_s :
              fx.to_s
+      fx = FUNCTIONS[fx.to_sym][:long_form]
       report["fx_#{fx}"] += 1
     end
     if obj.is_a? BEL::Model::Statement

data/lib/bel/libbel.rb

@@ -11,8 +11,6 @@ module LibBEL
     def extension_path(ruby_version = RUBY_VERSION)
       version =
         case ruby_version
-        when /^1\.9/
-          '1.9'
         when /^2\.0/
           '2.0'
         when /^2\.1/

data/lib/bel/version.rb

@@ -1,3 +1,3 @@
 module BEL
-  VERSION = '0.3.0.beta6'
+  VERSION = '0.3.0'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bel
 version: !ruby/object:Gem::Version
-  version: 0.3.0.beta6
+  version: 0.3.0
 platform: ruby
 authors:
 - Anthony Bargnesi
@@ -287,9 +287,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: 2.0.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">"
+  - - ">="
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
 rubyforge_project: 
 rubygems_version: 2.4.5