miga-base 0.7.5.0 → 0.7.6.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 6361b203b4612214936255e8b285959cbf556e7e64f88119a058e167774264f9
-  data.tar.gz: 1a3d8df11d57a363a49eecc88011a5337ddb40573cf8727942eea24e5071ecf5
+  metadata.gz: 2b881cdffbe06953931fafa52599b97d7e8b66d17fb37ca3d16d774df4162f23
+  data.tar.gz: 57253881d9af0a362102853d8bd8e876ad8da50f496eff72a77cac0a20fad46a
 SHA512:
-  metadata.gz: 53786e1830ed8b3c56bffbf1fc581745185084e96b68631323b01fd9994c2b59cdeac582c2f4cef8d0ed622136a2c2cf4f68e06cc3a9e7dbf580d10d1aedc9e5
-  data.tar.gz: 26322daf6a52906466c4f28cc93ef455bac22e98e115fc6f6b3ad685998d58854454c8044126491e5a886910ce5ddceece2713e94acafaf86459442970617f4f
+  metadata.gz: 39a1a13da018cee4512620b014c140f3a661ee0fe658fd8d1d5d727884116d872bc45b77e23a50045e133c8d901acf51edb5a27ec1706d2c9f0ffb5e96969535
+  data.tar.gz: d34f900c757d290d143846bd77c4d6dc331b7cbfdadea7170c6ca9421dc8b112991c2e664658d11b2e36d312bb0d8e588321e29c97642d968defc580deaa00c9

data/lib/miga/cli/action/init.rb

@@ -66,8 +66,10 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
   end
 
   def run_r_cmd(cli, paths, cmd)
-    run_cmd(cli,
-            "echo #{cmd.shellescape} | #{paths['R'].shellescape} --vanilla -q 2>&1")
+    run_cmd(
+      cli,
+      "echo #{cmd.shellescape} | #{paths['R'].shellescape} --vanilla -q 2>&1"
+    )
   end
 
   def test_r_package(cli, paths, pkg)
@@ -81,16 +83,21 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
   end
 
   def test_ruby_gem(cli, paths, pkg)
-    run_cmd(cli,
-            "#{paths['ruby'].shellescape} -r #{pkg.shellescape} -e '' 2>/dev/null")
+    run_cmd(
+      cli,
+      "#{paths['ruby'].shellescape} -r #{pkg.shellescape} -e '' 2>/dev/null"
+    )
     $?.success?
   end
 
   def install_ruby_gem(cli, paths, pkg)
     gem_cmd = "Gem::GemRunner.new.run %w(install --user #{pkg})"
-    run_cmd(cli, "#{paths['ruby'].shellescape} \
+    run_cmd(
+      cli,
+      "#{paths['ruby'].shellescape} \
         -r rubygems -r rubygems/gem_runner \
-        -e #{gem_cmd.shellescape} 2>&1")
+        -e #{gem_cmd.shellescape} 2>&1"
+    )
   end
 
   def list_requirements
@@ -99,7 +106,7 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
       'no', %w(yes no)
     ) == 'yes'
       cli.puts ''
-      req_path = File.expand_path('utils/requirements.txt', MiGA.root_path)
+      req_path = File.join(MiGA.root_path, 'utils', 'requirements.txt')
       File.open(req_path, 'r') do |fh|
         fh.each_line { |ln| cli.puts ln }
       end
@@ -205,18 +212,18 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
   def check_additional_files(paths)
     if cli[:mytaxa]
       cli.puts 'Looking for MyTaxa databases:'
-      mt = File.dirname paths["MyTaxa"]
+      mt = File.dirname paths['MyTaxa']
       cli.print 'Looking for scores... '
       unless Dir.exist?(File.expand_path('db', mt))
-        cli.puts "no.\nExecute 'python2 #{mt}/utils/download_db.py'."
+        cli.puts "no\nExecute 'python2 #{mt}/utils/download_db.py'"
         exit(1)
       end
-      cli.puts 'yes.'
+      cli.puts 'yes'
       cli.print 'Looking for diamond db... '
       unless File.exist?(File.expand_path('AllGenomes.faa.dmnd', mt))
-        cli.puts "no.\nDownload " \
+        cli.puts "no\nDownload " \
           "'http://enve-omics.ce.gatech.edu/data/public_mytaxa/" \
-          "AllGenomes.faa.dmnd' into #{mt}."
+          "AllGenomes.faa.dmnd' into #{mt}"
         exit(1)
       end
       cli.puts ''
@@ -228,7 +235,7 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
     %w(ape cluster vegan).each do |pkg|
       cli.print "Testing #{pkg}... "
       if test_r_package(cli, paths, pkg)
-        cli.puts 'yes.'
+        cli.puts 'yes'
       else
         cli.puts 'no, installing'
         cli.print '' + install_r_package(cli, paths, pkg)
@@ -245,7 +252,7 @@ class MiGA::Cli::Action::Init < MiGA::Cli::Action
     %w(sqlite3 daemons json).each do |pkg|
       cli.print "Testing #{pkg}... "
       if test_ruby_gem(cli, paths, pkg)
-        cli.puts 'yes.'
+        cli.puts 'yes'
       else
         cli.puts 'no, installing'
         # This hackey mess is meant to ensure the test and installation are done

data/lib/miga/version.rb

@@ -8,7 +8,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.7, 5, 0]
+  VERSION = [0.7, 6, 0]
 
   ##
   # Nickname for the current major.minor version.
@@ -16,7 +16,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 5, 13)
+  VERSION_DATE = Date.new(2020, 5, 19)
 
   ##
   # Reference of MiGA.

data/test/remote_dataset_test.rb

@@ -31,13 +31,15 @@ class RemoteDatasetTest < Test::Unit::TestCase
       assert_equal(MiGA::Taxonomy, tx.class, msg)
       assert_equal('Lentivirus', tx[:g], msg)
       assert_equal(
-        'ns:ncbi o:Ortervirales f:Retroviridae ' \
-          'g:Lentivirus s:Human_immunodeficiency_virus_2',
+        'ns:ncbi k:Pararnavirae p:Artverviricota c:Revtraviricetes ' \
+          'o:Ortervirales f:Retroviridae g:Lentivirus ' \
+          's:Human_immunodeficiency_virus_2',
         tx.to_s, msg
       )
       assert_equal(
-        'ns:ncbi d: k: p: c: o:Ortervirales f:Retroviridae ' \
-          'g:Lentivirus s:Human_immunodeficiency_virus_2 ssp: str: ds:',
+        'ns:ncbi d: k:Pararnavirae p:Artverviricota c:Revtraviricetes ' \
+          'o:Ortervirales f:Retroviridae g:Lentivirus ' \
+          's:Human_immunodeficiency_virus_2 ssp: str: ds:',
         tx.to_s(true), msg
       )
       assert_equal('ncbi', tx.namespace, msg)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.5.0
+  version: 0.7.6.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-05-13 00:00:00.000000000 Z
+date: 2020-05-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -44,14 +44,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: '1.3'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: '1.3'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement