scout-essentials 1.6.1 → 1.6.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 2fe20bd6954a0372235430a8baa5990efbd23d00b5ebd37048dbeb253ebdb78d
-  data.tar.gz: 41ba7642cc7c683d482e1173c27d0f23a632c3651856d8adaf9d150b81904e2e
+  metadata.gz: 8ff597b1b0d5a5a8582e92677aa951559d3ddf2f56cec76bbbfd5f0c90ea180e
+  data.tar.gz: 298441b06d0c2d048732fa7fb525a51c4ff93a31e39b1882211048f06978c1b9
 SHA512:
-  metadata.gz: 1badc3ef7083453c39ff6778c1a1f516865ea3e59d7c01c7f0e1047bda5e9835d7ee490db35de6ac684b85d63bdac3369a442e669a32cc14b3242f6f1ee1092d
-  data.tar.gz: 671d77a07f9d9b847bc6397e365b9f944a85261818edd70aaf9a6cc5c75beef3d4e255b52081bc01b3762bb68df5632a5e10cf0041bb4472e360c8eea774d6c6
+  metadata.gz: 91c63f92b747ea2c39b291430b8a63a7db63bf28465eb66b5d7cceda88f07ceaefef1c7718a589bd5f8f040ff082f9a90232edfa16d4c28a5ba75877ac5a34b9
+  data.tar.gz: 10d3e562974232b7fe87954a6970cc9008799e341d2bb01e454406d3ceec5386bb27542dcc8b6622a27fd5382d29320561766b1abfd0467eee939d7c82af0a84

data/.vimproject

@@ -50,6 +50,7 @@ scout-essentials=/$PWD filter="*.rb *.txt *.md *.conf *.yaml" {
     find.rb
     tmpfile.rb
     util.rb
+    digest.rb
    }
    concurrent_stream.rb
    cmd.rb
@@ -59,6 +60,7 @@ scout-essentials=/$PWD filter="*.rb *.txt *.md *.conf *.yaml" {
     remote.rb
     stream.rb
     util.rb
+    bgzf.rb
    }
    resource.rb
    resource=resource{

data/VERSION

@@ -1 +1 @@
-1.6.1
+1.6.3

data/lib/scout/annotation/array.rb

@@ -9,6 +9,7 @@ module AnnotatedArray
   end
 
   def annotate_item(obj, position = nil)
+    return obj if obj.nil?
     obj = obj.dup if obj.frozen?
     obj.extend AnnotatedArray if Array === obj
     obj.extend AnnotatedArrayItem
@@ -37,6 +38,15 @@ module AnnotatedArray
     end
   end
 
+  def select(&block)
+    selected = []
+    each do |item|
+      selected << item if block.call(item)
+    end
+
+    self.annotate(selected)
+  end
+
   def each(&block)
     i = 0
     super do |item|

data/lib/scout/cmd.rb

@@ -41,7 +41,10 @@ module CMD
         if claim
           claim.produce
         else
-          block.call
+          res = block.call
+          if Hash === res
+            Resource.install res, tool.to_s
+          end
         end
       end
       version_txt = ""

data/lib/scout/concurrent_stream.rb

@@ -51,7 +51,7 @@ module ConcurrentStream
       end
     end
 
-    stream.filename = filename.nil? ? stream.inspect.split(":").last[0..-2] : filename
+    stream.filename = filename if filename
 
     stream.lock = lock unless lock.nil?
 
@@ -60,6 +60,10 @@ module ConcurrentStream
     stream
   end
 
+  def filename 
+    @filename || self.inspect.split(":").last[0..-2]
+  end
+
   def annotate(stream)
     ConcurrentStream.setup(stream, :threads => threads, :pids => pids, :callback => callback, :abort_callback => abort_callback, :filename => filename, :autojoin => autojoin, :lock => lock)
     stream

data/lib/scout/log.rb

@@ -146,7 +146,7 @@ module Log
       else
         begin
           STDERR.write str
-        rescue
+        rescue IOError
         end
       end
     end

data/lib/scout/misc/digest.rb

@@ -1,19 +1,11 @@
 module Misc
   MAX_ARRAY_DIGEST_LENGTH = 100_000
+
   def self.digest_str(obj)
     if obj.respond_to?(:digest_str)
       obj.digest_str
     else
       case obj
-      when Path
-        case
-        when File.directory?(obj)
-          "Directory MD5: #{digest_str(Dir.glob(File.join(obj, "*")))}"
-        when obj.located? && File.exist?(obj)
-          "File MD5: #{Misc.digest_file(obj)}"
-        else
-          '\'' << obj << '\''
-        end
       when String
         if Path.is_filename?(obj) && Open.exists?(obj)
           if File.directory?(obj)

data/lib/scout/misc/format.rb

@@ -36,9 +36,7 @@ module Misc
     end
   end
 
-
-  
-  MAX_TTY_LINE_WIDTH = 100
+  MAX_TTY_LINE_WIDTH = 160
   def self.format_paragraph(text, size = nil, indent = nil, offset = nil)
     size ||= Log.tty_size || MAX_TTY_LINE_WIDTH
     size = MAX_TTY_LINE_WIDTH if size > MAX_TTY_LINE_WIDTH

data/lib/scout/misc/helper.rb

@@ -28,14 +28,23 @@ module Misc
     counts
   end
 
-  def self.chunk(array, num)
+  # Divides the array into chunks of size +size+ by taking
+  # consecutive elements. If a block is given it runs it
+  # instead of returning the chunks
+  def self.chunk(array, size)
     total = array.length
     current = 0
+    res = [] unless block_given?
     while current < total
-      last = current + num - 1
-      yield array[current..last]
+      last = current + size - 1
+      if block_given?
+        yield array[current..last]
+      else
+        res << array[current..last]
+      end
       current = last + 1
     end
+    block_given? ? nil : res
   end
 
   # Divides the array into +num+ chunks of the same size by placing one

data/lib/scout/misc/monitor.rb

@@ -1,5 +1,6 @@
 module Misc
   def self.pid_alive?(pid)
+    return true if Process.pid == pid
     !! Process.kill(0, pid) rescue false
   end
 

data/lib/scout/named_array.rb

@@ -100,8 +100,8 @@ module NamedArray
 
   def to_hash
     hash = {}
-    self.fields.zip(self) do |field,value|
-      hash[field] = value
+    self.fields.each do |field|
+      hash[field] = self[field]
     end
     IndiferentHash.setup hash
   end

data/lib/scout/open/stream.rb

@@ -440,7 +440,7 @@ module Open
   #  StringIO.new stream.read.split("\n").sort.uniq * "\n"
   #end
 
-  def self.collapse_stream(s, line: nil, sep: "\t", header: nil, &block)
+  def self.collapse_stream(s, line: nil, sep: "\t", header: nil, compact: false, &block)
     sep ||= "\t"
     Open.open_pipe do |sin|
 
@@ -458,8 +458,13 @@ module Open
           current_key = key
         when current_key == key
           parts.each_with_index do |part,i|
-            if current_parts[i].nil?
-              current_parts[i] = "|" << part
+            next if compact and part.nil? || part.empty?
+            if current_parts[i].nil? || current_parts[i].empty?
+              if compact
+                current_parts[i] = part.dup
+              else
+                current_parts[i] = "|" << part
+              end
             else
               current_parts[i] = current_parts[i] << "|" << part
             end

data/lib/scout/open/util.rb

@@ -11,7 +11,7 @@ module Open
                end
              end
 
-  def self.grep(stream, grep, invert = false, fixed = nil)
+  def self.grep(stream, grep, invert = false, fixed = nil, options = {})
     case 
     when Array === grep
       TmpFile.with_file(grep * "\n", false) do |f|
@@ -236,11 +236,17 @@ module Open
     begin
       Open.ln(source, target, options)
     rescue
+      Log.debug "Could not make regular link, trying symbolic: #{Misc.fingerprint(source)} -> #{Misc.fingerprint(target)}"
       Open.ln_s(source, target, options)
     end
     nil
   end
 
+  def self.link_dir(source, target)
+    Log.debug "Copy with hard-links #{Log.fingerprint source}->#{Log.fingerprint target}"
+    FileUtils.cp_lr(source, target)
+  end
+
   def self.list(file)
     file = file.produce_and_find if Path === file
     Open.read(file).split("\n")

data/lib/scout/open.rb

@@ -31,13 +31,13 @@ module Open
     File.open(file, mode)
   end
 
-  def self.file_open(file, grep = false, mode = 'r', invert_grep = false, options = {})
+  def self.file_open(file, grep = false, mode = 'r', invert_grep = false, fixed_grep = true, options = {})
     Open.mkdir File.dirname(file) if mode.include? 'w'
 
     stream = get_stream(file, mode, options)
 
     if grep
-      grep(stream, grep, invert_grep)
+      grep(stream, grep, invert_grep, fixed_grep)
     else
       stream
     end
@@ -72,7 +72,7 @@ module Open
 
     options[:noz] = true if mode.include? "w"
 
-    io = file_open(file, options[:grep], mode, options[:invert_grep], options)
+    io = file_open(file, options[:grep], mode, options[:invert_grep], options[:fixed_grep], options)
 
     io = unzip(io)   if ((String === file and zip?(file))   and not options[:noz]) or options[:zip]
     io = gunzip(io)  if ((String === file and gzip?(file))  and not options[:noz]) or options[:gzip]

data/lib/scout/path/digest.rb

@@ -0,0 +1,13 @@
+require_relative '../misc/digest'
+module Path
+  def digest_str
+    case
+    when File.directory?(self)
+      "Directory MD5: #{Misc.digest_str(Dir.glob(File.join(self, "*")))}"
+    when self.located? && File.exist?(self)
+      "File MD5: #{Misc.digest_file(self)}"
+    else
+      '\'' << self << '\''
+    end
+  end
+end

data/lib/scout/path.rb

@@ -2,6 +2,7 @@ require_relative 'annotation'
 require_relative 'path/find'
 require_relative 'path/util'
 require_relative 'path/tmpfile'
+require_relative 'path/digest'
 
 module Path
   extend Annotation

data/lib/scout/persist/serialize.rb

@@ -145,6 +145,8 @@ module Persist
       Open.marshal(file)
     when :stream
       Open.open(file)
+    when :path
+      Path === file ? file : Path.setup(file)
     when :file
       value = Open.read(file)
       value.sub!(/^\./, File.dirname(file)) if value.start_with?("./")

data/scout-essentials.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: scout-essentials 1.6.1 ruby lib
+# stub: scout-essentials 1.6.3 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "scout-essentials".freeze
-  s.version = "1.6.1".freeze
+  s.version = "1.6.3".freeze
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Miguel Vazquez".freeze]
-  s.date = "2024-06-17"
+  s.date = "2024-10-04"
   s.description = "Things a scout can use anywhere".freeze
   s.email = "mikisvaz@gmail.com".freeze
   s.extra_rdoc_files = [
@@ -63,6 +63,7 @@ Gem::Specification.new do |s|
     "lib/scout/open/stream.rb",
     "lib/scout/open/util.rb",
     "lib/scout/path.rb",
+    "lib/scout/path/digest.rb",
     "lib/scout/path/find.rb",
     "lib/scout/path/tmpfile.rb",
     "lib/scout/path/util.rb",
@@ -106,6 +107,7 @@ Gem::Specification.new do |s|
     "test/scout/open/test_remote.rb",
     "test/scout/open/test_stream.rb",
     "test/scout/open/test_util.rb",
+    "test/scout/path/test_digest.rb",
     "test/scout/path/test_find.rb",
     "test/scout/path/test_util.rb",
     "test/scout/persist/test_open.rb",

data/test/scout/misc/test_helper.rb

@@ -6,6 +6,11 @@ class TestMiscHelper < Test::Unit::TestCase
     assert_equal 2, Misc.divide(%w(1 2 3 4 5 6 7 8 9),2).length
   end
 
+  def test_chunk
+    assert_equal %w(1 2), Misc.chunk(%w(1 2 3 4 5 6 7 8 9),2)[0]
+  end
+
+
   def test_ordered_divide
     assert_equal 5, Misc.ordered_divide(%w(1 2 3 4 5 6 7 8 9),2).length
   end

data/test/scout/open/test_stream.rb

@@ -393,6 +393,34 @@ row2 aa bb cc
     s = StringIO.new text
     assert Open.collapse_stream(s, sep: " ").read =~  /\|cc$/
   end
+
+  def test_collapse_stream_compact
+    text=<<-EOF
+row1	A	B	C
+row1	a	b	c
+row2		BB	CC
+row2	aa	bb	cc
+row2	aaa		ccc
+    EOF
+
+    s = StringIO.new text
+    stream = Open.collapse_stream(s, sep: "\t", compact: false)
+    txt = stream.read
+    assert_include txt, "A|a"
+    assert_include txt, "B|b"
+    assert_include txt, "C|c"
+    assert_include txt, "|aa"
+
+    s = StringIO.new text
+    stream = Open.collapse_stream(s, sep: "\t", compact: true)
+    txt = stream.read
+    assert_include txt, "A|a"
+    assert_include txt, "B|b"
+    assert_include txt, "C|c"
+    assert_not_include txt, "|aa\t"
+    assert_not_include txt, "bb|"
+  end
+
   #
   #
   #  def test_paste_stream

data/test/scout/open/test_util.rb

@@ -63,10 +63,25 @@ class TestOpenUtil < Test::Unit::TestCase
       file1 = directory.subdir1.file
       file2 = directory.subdir2.file
       Open.write(file1, "TEST")
-      Open.ln_s file1, file2
+      Open.ln_h file1, file2
+      assert_equal "TEST", Open.read(file2)
+      Open.write(file1, "TEST2")
+      assert_equal "TEST2", Open.read(file2)
+      assert_equal File.stat(file1).ino, File.stat(file2).ino
+    end
+  end
+
+  def test_ln_recursive
+    TmpFile.with_file do |directory|
+      Path.setup(directory)
+      file1 = directory.subdir1.file
+      file2 = directory.subdir2.file
+      Open.write(file1, "TEST")
+      Open.link_dir directory.subdir1, directory.subdir2
       assert_equal "TEST", Open.read(file2)
       Open.write(file1, "TEST2")
       assert_equal "TEST2", Open.read(file2)
+      assert_equal File.stat(file1).ino, File.stat(file2).ino
     end
   end
 end

data/test/scout/path/test_digest.rb

@@ -0,0 +1,20 @@
+require File.expand_path(__FILE__).sub(%r(/test/.*), '/test/test_helper.rb')
+require File.expand_path(__FILE__).sub(%r(.*/test/), '').sub(/test_(.*)\.rb/,'\1')
+
+class TestClass < Test::Unit::TestCase
+  def test_digest_path
+    TmpFile.with_path("TEXT") do |file|
+      assert_include file.digest_str, "File MD5"
+    end
+
+    TmpFile.with_path do |dir|
+      Open.write(dir.test, "TEXT")
+      assert_include dir.digest_str, "Directory"
+    end
+
+    TmpFile.with_path do |file|
+      assert_include "'#{file}'", file.digest_str
+    end
+  end
+end
+

data/test/scout/test_named_array.rb

@@ -39,5 +39,10 @@ ValueB (Entity type)
     assert_equal 1, a.a
     assert_equal 2, a.b
   end
-end
 
+  def test_to_hash
+    a = NamedArray.setup([1,2], [:a, :b])
+    assert_equal 1, a.to_hash[:a]
+    assert_equal 2, a.to_hash[:b]
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: scout-essentials
 version: !ruby/object:Gem::Version
-  version: 1.6.1
+  version: 1.6.3
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-06-17 00:00:00.000000000 Z
+date: 2024-10-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
@@ -160,6 +160,7 @@ files:
 - lib/scout/open/stream.rb
 - lib/scout/open/util.rb
 - lib/scout/path.rb
+- lib/scout/path/digest.rb
 - lib/scout/path/find.rb
 - lib/scout/path/tmpfile.rb
 - lib/scout/path/util.rb
@@ -203,6 +204,7 @@ files:
 - test/scout/open/test_remote.rb
 - test/scout/open/test_stream.rb
 - test/scout/open/test_util.rb
+- test/scout/path/test_digest.rb
 - test/scout/path/test_find.rb
 - test/scout/path/test_util.rb
 - test/scout/persist/test_open.rb