rbbt-util 5.26.84 → 5.26.85

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: a7a03e9e9cec9f84ea91902fe393037932b4bc155abc38ef4145573dea832171
-  data.tar.gz: dc7030fb86e929d468bd8481eea26a8fd55e679c99cc8709507b9cff3a1044b8
+  metadata.gz: b150d8b85d7565e2ec820343f002c8bfc80e46302d5a35d83b10f132d2ebfc94
+  data.tar.gz: 66359a6ec5533d41ab1bb2344bf6795844e0f4ca46332523647ba13319a7d6e8
 SHA512:
-  metadata.gz: c67e91543978c2b151b1bfc77083de1decd53e2912da81beaac2925190db85531255fcca48056f6c7a2b02ee91a03017b74390531ae44bec6777bfea1b23c100
-  data.tar.gz: 285ba9a06af9cec0377b828a24949250ee5cc62825a0ad59fd207fdd7f44acc1e3469a495773e2818198eb414dc8090283117021276b5b2525c7f5e3f2e6d783
+  metadata.gz: 1cf80ad89a6007b291518458b7eb995b2a589ce34230a8fea9b03e83cf196df787f7c46376dfb80d0c8a4d3fdbb83cc906a8a1240ac26bbee25c8bebc67c606c
+  data.tar.gz: 6a9fc1eee7bf113ccefa6aef14d704406fbe68a07a24f0c603102e2cfe3e9863ec4b88a01a3029885b2e98754ad85c215956e2a267b71d894659c041da62ae43

data/lib/rbbt/resource/path.rb

@@ -402,6 +402,11 @@ module Path
     self.annotate(new_path)
   end
 
+  def remove_extension(new_extension = nil)
+    self.sub(/\.[^\.\/]{1,5}$/,'')
+  end
+
+
   def self.get_extension(path)
     path.match(/\.([^\.\/]{1,5})$/)[1]
   end

data/lib/rbbt/util/R/plot.rb

@@ -138,6 +138,7 @@ module R
       options[:R_open] ||= "colClasses=c('character'," + field_classes * ", " + ')'
 
       data.R <<-EOF, :plot, options
+rbbt.require('ggplot2')
 plot = { #{script} }
 
 ggsave('#{filename}', plot, width = #{R.ruby2R width}, height = #{R.ruby2R height})

data/lib/rbbt/util/cmd.rb

@@ -20,7 +20,7 @@ module CMD
         if test
           CMD.cmd(test)
         else
-          CMD.cmd("#{cmd} --help")
+          CMD.cmd("#{tool} --help")
         end
       rescue
         if claim

data/lib/rbbt/util/config.rb

@@ -24,7 +24,7 @@ module Rbbt::Config
   end
 
   def self.load_config
-    Rbbt.etc.config.find_all.each do |file|
+    Rbbt.etc.config.find_all.reverse.each do |file|
       self.load_file(file)
     end
   end
@@ -110,7 +110,7 @@ module Rbbt::Config
       end
     end
 
-    value = priorities.empty? ? default : priorities.collect{|p| p }.sort_by{|p,v| p}.first.last.first
+    value = priorities.empty? ? default : priorities.collect{|p| p }.sort_by{|p,v| p}.first.last.last
     value = false if value == 'false'
 
     Log.debug "Value #{value.inspect} for config key '#{ key }': #{tokens * ", "}"

data/lib/rbbt/util/open.rb

@@ -338,6 +338,7 @@ module Open
     source = source.find if Path === source
     target = target.find if Path === target
 
+    target = File.join(target, File.basename(source)) if File.directory? target
     FileUtils.mkdir_p File.dirname(target) unless File.exists?(File.dirname(target))
     FileUtils.rm target if File.exists?(target)
     FileUtils.ln_s source, target

data/lib/rbbt/util/python.rb

@@ -4,19 +4,27 @@ require 'pycall/import'
 
 module RbbtPython
   extend PyCall::Import
-  def self.run(mod = nil, &block)
+  def self.run(mod = nil, imports = nil, &block)
     begin
-      pyimport mod unless mod.nil?
-      case block.arity
-      when 0
-        yield 
-      when 1
-        yield self.send(mod)
-      else
-        raise "Unknown arity on block of code #{block.arity}"
+      if mod
+        if imports
+          pyfrom mod, :import => imports
+        else
+          pyimport mod 
+        end
       end
+
+      module_eval(&block)
+
     rescue
       Log.exception $!
     end
   end
+
+  def self.add_path(path)
+    self.run 'sys' do
+      sys.path.append path
+    end
+  end
+
 end

data/share/Rlib/util.R

@@ -485,6 +485,7 @@ rbbt.model.inpute <- function(data, formula, ...){
 }
 
 rbbt.tsv.melt <- function(tsv, variable = NULL, value = NULL, key.field = NULL){
+    rbbt.require('reshape2')
     if (is.null(key.field)){ key.field = attributes(data)$key.field;}
     if (is.null(key.field)){ key.field = "ID" }
 

data/share/install/software/lib/install_helpers

@@ -404,7 +404,7 @@ setup(){
     else
         local old_pwd="`expand_path $(pwd)`"
 
-        for exe in ` find "$pkg_dir/" "$pkg_dir/source/" "$pkg_dir/src/" -maxdepth 1 -type f -executable`; do
+        for exe in ` find "$pkg_dir/" "$pkg_dir/build"  "$pkg_dir/source/" "$pkg_dir/src/" -maxdepth 1 -type f -executable`; do
             orig=$exe
             exe=$(basename $exe)
             echo "EXE $exe"

data/share/rbbt_commands/migrate

@@ -55,7 +55,7 @@ puts path.glob_all.collect{|p| File.directory?(p) ? p + "/" : p } * "\n"
           [path, paths.collect{|p| [options[:source], p] * ":"}]
         else
           if File.exists?(path)
-            path = resource.identify(path) 
+            path = resource.identify(path)
           else
             path = Path.setup(path)
           end

data/share/rbbt_commands/system/purge

@@ -2,7 +2,6 @@
 
 options = SOPT.get("-a--app*")
 
-
 CMD.cmd("rbbt workflow monitor --quick -c -a -d #{Rbbt.var.jobs.find}").read
 CMD.cmd("rm -f  #{ Rbbt.tmp.tsv_open_locks.find.glob("*").collect{|f| "'#{f}'" } * " " }").read
 CMD.cmd("find #{Rbbt.share.find_all.collect{|f| "'#{f}'" } * " " } -name '*.lock' -delete").read 

data/test/rbbt/util/test_python.rb

@@ -0,0 +1,44 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/util/python'
+
+class TestPython < Test::Unit::TestCase
+  def test_python
+    TmpFile.with_file do |tmpdir|
+      code =<<-EOF
+def python_test(a, b):
+	c = a + b
+	return c
+      EOF
+      Open.write(File.join(tmpdir, 'file1.py'), code)
+      Open.write(File.join(tmpdir, 'file2.py'), code)
+      Open.write(File.join(tmpdir, 'file3.py'), code)
+      Open.write(File.join(tmpdir, 'file4.py'), code)
+      RbbtPython.add_path tmpdir
+
+      res = nil
+
+      RbbtPython.run 'file2', :python_test do 
+        res = python_test(1, 3)
+      end
+      assert_equal 4, res
+
+      RbbtPython.run do
+        pyfrom :file3, :import => :python_test
+        res = python_test(1, 4)
+      end
+      assert_equal 5, res
+
+      RbbtPython.run do
+        pyimport :file4
+        res = file4.python_test(1, 4)
+      end
+      assert_equal 5, res
+
+      RbbtPython.run 'file1' do 
+        res = file1.python_test(1, 2)
+      end
+      assert_equal 3, res
+    end
+  end
+end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.84
+  version: 5.26.85
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-10-25 00:00:00.000000000 Z
+date: 2019-11-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -502,6 +502,7 @@ files:
 - test/rbbt/util/test_log.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_open.rb
+- test/rbbt/util/test_python.rb
 - test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_simpleDSL.rb
 - test/rbbt/util/test_simpleopt.rb
@@ -530,7 +531,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubygems_version: 3.0.6
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
@@ -565,6 +566,7 @@ test_files:
 - test/rbbt/util/simpleopt/test_parse.rb
 - test/rbbt/util/simpleopt/test_setup.rb
 - test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/test_python.rb
 - test/rbbt/util/test_filecache.rb
 - test/rbbt/util/concurrency/test_processes.rb
 - test/rbbt/util/concurrency/test_threads.rb