rbbt-util 5.21.58 → 5.21.59

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 062604ecae4d86c8b4227e7e2456c976d85a3114
+  metadata.gz: 6af6b7d19c8318dff73f410c5e4094aeaa9466d7
+  data.tar.gz: cb78b1b85697ca27eb8716afe3b70513c4ffbe41
 SHA512:
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-  data.tar.gz: c6956c9de0dac01573c563822b8d17796414e2cc4935b87839a9cfa82dde09bd2cc4024156ce2ea65324e20e2213d038d74c088e19732f3cf0a037c2d487d84e
+  metadata.gz: 46bf19741a3c8d36219cd75fef3a103cad844dd89d4534ea8af5ec3c01fbc1d3632d07c55a1a397d5737550ad5d85961804af7ef3df19f1dee0e7ea777f4175b
+  data.tar.gz: 89ada9ba0db87dd8a2b10a2848e2d3f92c6bd2b0935177a1b50606604f7bee2a87667d6a02266842505965e79c4c3dac839a6b26bfd97eb9e1a6c21a0e02283d

data/lib/rbbt/tsv/manipulate.rb

@@ -379,11 +379,11 @@ module TSV
           end
         when :list, :flat
           through do |key, values|
-            new[key] = values if invert ^ (method.include? key or (method & values).any?)
+            new[key] = values if invert ^ (method.include? key or (method & values).length > 0)
           end
         else
           through do |key, values|
-            new[key] = values if invert ^ (method.include? key or (method & values.flatten).any?)
+            new[key] = values if invert ^ (method.include? key or (method & values.flatten).length > 0)
           end
         end
       end
@@ -517,7 +517,7 @@ module TSV
         with_unnamed do
           through :key, key do |key, values|
             values = [values] if type == :single
-            new[key] = self[key] if invert ^ (values.flatten.select{|v| v == method}.any?)
+            new[key] = self[key] if invert ^ (values.flatten.select{|v| v == method}.length > 0)
           end
         end
 
@@ -531,7 +531,7 @@ module TSV
         with_unnamed do
           through :key, key do |key, values|
             values = [values] if type == :single
-            new[key] = self[key] if invert ^ (values.flatten.select{|v| method.call(v)}.any?)
+            new[key] = self[key] if invert ^ (values.flatten.select{|v| method.call(v)}.length > 0)
           end
         end
       end

data/lib/rbbt/util/misc/math.rb

@@ -23,6 +23,13 @@ module Misc
     sum(list) / list.compact.length
   end
 
+  def self.median(array)
+    sorted = array.sort
+    len = sorted.length
+    (sorted[(len - 1) / 2] + sorted[len / 2]) / 2.0
+  end
+
+
   def self.sd(list)
     return nil if list.length < 3
     mean = mean(list)
@@ -79,12 +86,12 @@ module Misc
 
     label = "#{name1}: #{sizes[0]} (#{name2}: #{sizes[3]}, #{name3}: #{sizes[4]})"
     label << "|#{name2}: #{sizes[1]} (#{name1}: #{sizes[3]}, #{name3}: #{sizes[5]})"
-      label << "|#{name3}: #{sizes[2]} (#{name1}: #{sizes[4]}, #{name2}: #{sizes[5]})"
-      if total
-        label << "| INTERSECTION: #{sizes[6]} TOTAL: #{total}"
-      else
-        label << "| INTERSECTION: #{sizes[6]}"
-      end
+    label << "|#{name3}: #{sizes[2]} (#{name1}: #{sizes[4]}, #{name2}: #{sizes[5]})"
+    if total
+      label << "| INTERSECTION: #{sizes[6]} TOTAL: #{total}"
+    else
+      label << "| INTERSECTION: #{sizes[6]}"
+    end
 
     max = total || sizes.max
     sizes = sizes.collect{|v| (v.to_f/max * 100).to_i.to_f / 100}

data/lib/rbbt/workflow/accessor.rb

@@ -772,7 +772,7 @@ module Workflow
   def step_path(taskname, jobname, inputs, dependencies, extension = nil)
     #Proc.new{
       raise "Jobname makes an invalid path: #{ jobname }" if jobname =~ /\.\./
-      if inputs.any? or dependencies.any?
+      if inputs.length > 0 or dependencies.any?
         tagged_jobname = case TAG
                          when :hash
                            hash_str = Misc.obj2digest({:inputs => inputs, :dependencies => dependencies})

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.58
+  version: 5.21.59
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-11-30 00:00:00.000000000 Z
+date: 2016-12-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -491,83 +491,83 @@ signing_key:
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/rbbt/test_workflow.rb
+- test/test_helper.rb
 - test/rbbt/resource/test_path.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/util/test_concurrency.rb
 - test/rbbt/util/test_log.rb
+- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_semaphore.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_open.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_R.rb
 - test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
-- test/rbbt/util/misc/test_bgzf.rb
 - test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/misc/test_bgzf.rb
 - test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/misc/test_multipart_payload.rb
 - test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/R/test_model.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/test_association.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/test_resource.rb
 - test/rbbt/test_entity.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/test_tsv.rb
 - test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_doc.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_persist.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/tsv/test_field_index.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_task.rb
+- test/rbbt/test_association.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/parallel/test_through.rb
 - test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_matrix.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_parser.rb
-- test/rbbt/tsv/test_stream.rb
-- test/rbbt/tsv/test_util.rb
 - test/rbbt/tsv/test_excel.rb
 - test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_stream.rb
 - test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_matrix.rb
 - test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/parallel/test_through.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/test_field_index.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/tsv/test_parser.rb
+- test/rbbt/test_packed_index.rb
+- test/rbbt/test_persist.rb
 - test/rbbt/test_fix_width_table.rb
-- test/test_helper.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_lmdb.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/persist/test_tsv.rb
+- test/rbbt/test_tsv.rb