miga-base 1.3.21.3 → 1.3.21.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 94519dd1a0689d8a5c1b3c878394827a14ea1db4fa373078312c5db3fbf711b2
-  data.tar.gz: 59bd5e8151b87102544c44263422cf856405f53b2bbd224dc036beb0853d831a
+  metadata.gz: 9522358be2993d435fcece0ff3a1916919c955754bce64f02ebd32e50c1cdc11
+  data.tar.gz: c3277224287f994d56fb1f0e27b0adc8d5dc2010ac00f48f124ca60ba55beee9
 SHA512:
-  metadata.gz: 362f537d825f8cce8ef8413df35b5276abdccd189f6934b57e35f7c62017d552de6759e55dd1d55d0ef6d5f483a6412626c5e9092bf23122df32772ca48c181c
-  data.tar.gz: 2ab7d106c091d87da87631bfe2f73838f76c2a8355b28269dfa70656bc8ec39958d92b758fdc28c7fe02650a86e1e7d159d7286e4e113f155e16c4e8343bf31d
+  metadata.gz: 6cb5214b223052e199de0185960fe8371e2de08d82cdcc97dcd3e1089da28bf25e05438b3d33c4d2bb3d3ae9be4950144db9c0c79d48cbc2091292952cc88a26
+  data.tar.gz: 1be4517ab0285d5bdbaf01b7aaa3514f459e623489c4887712a403a217268beb46b57f778d6bcd010d32cfb9716da76736c568b015b5ffc31f5b345d63ffd570

data/lib/miga/cli/action/download/gtdb.rb

@@ -23,8 +23,9 @@ module MiGA::Cli::Action::Download::Gtdb
 
   def sanitize_cli
     cli.ensure_par(taxon: '-T')
-    unless cli[:taxon] =~ /^[a-z]__\S+$/
-      raise 'Taxon (-T) must be in GTDB format: s__Macondimonas_diazotrophica'
+    cli[:taxon].gsub!(' ', '%20')
+    unless cli[:taxon] =~ /^[a-z]__[\S ]+$/
+      raise 'Taxon (-T) must be in GTDB format: "s__Macondimonas diazotrophica"'
     end
     cli[:save_every] = 1 if cli[:dry]
   end

data/lib/miga/common/format.rb

@@ -51,7 +51,7 @@ module MiGA::Common::Format
           end
           next_seq = [">#{id.gsub(/[^A-Za-z0-9_\|\.]/, '_')}#{df}", '']
         else
-          next_seq[1] += ln.gsub(/[^A-Za-z\.\-]/, '')
+          next_seq[1] += ln.gsub(/[^A-Za-z]/, '')
         end
       end
       if next_seq[1].length >= min_len

data/lib/miga/daemon/base.rb

@@ -59,7 +59,7 @@ module MiGA::Daemon::Base
 
   ##
   # Returns the running option +opt+ in jobs for +what+. +what+ can be
-  # +:dataset+ or +:projects+
+  # +:dataset+ or +:project+
   def runopts_for(opt, what)
     runopts(:"#{opt}_#{what}") || runopts(opt)
   end

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 21, 3].freeze
+  VERSION = [1.3, 21, 5].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2024, 9, 28)
+  VERSION_DATE = Date.new(2025, 1, 16)
 
   ##
   # References of MiGA

data/test/format_test.rb

@@ -11,7 +11,7 @@ class FormatTest < Test::Unit::TestCase
 
   def test_clean_fasta
     c = ">MyFa|not-good\nACTG123ACTG-XXNN*\n>GoodOne + spaces!\n\nA C T G .\n"
-    cc = ">MyFa|not_good\nACTGACTG-XXNN\n>GoodOne + spaces!\nACTG.\n"
+    cc = ">MyFa|not_good\nACTGACTGXXNN\n>GoodOne + spaces!\nACTG\n"
     f = helper_write_file(c)
     assert_equal(c, File.read(f))
     MiGA::MiGA.clean_fasta_file(f)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.21.3
+  version: 1.3.21.5
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-09-28 00:00:00.000000000 Z
+date: 2025-01-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons