miga-base 1.3.6.1 → 1.3.7.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 7dced09173180bd58d8ba0feef1a90ecf00d3fc55154ebae4c34d861b0e1e566
+  metadata.gz: b5e0216cf49c600ae5776ea4e45bfcc2441ffed928908b20bbfc32541b08351a
+  data.tar.gz: a826116aa5208524e029bd2c6324a89d1805653dd20659a9738e627439192ad1
 SHA512:
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+  metadata.gz: 8da516f7f72b162e643202d1e84e57646f36afe895f7e57695bb281a937e6a80ee8cdbd333fe83e24f2708d2306e10d9d216adc86c510e07bf2dcdf3a02372d6
+  data.tar.gz: 3cbc31c7152861e678858420e213c35f4283c668586d0770a1d933e6d788589f006de645b9de292bbc991511c72a375bc97881981aa40c412271063b9434c83b

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

@@ -172,11 +172,10 @@ class MiGA::Cli::Action::Db < MiGA::Cli::Action
   end
 
   def version_requested(db)
-    if cli[:version] == :latest
-      cli[:version] = db[:latest].to_sym
-    end
+    cli[:version] = db[:latest].to_sym if cli[:version] == :latest
     ver = db[:versions][cli[:version]]
     raise 'Cannot find database version' if ver.nil?
+    ver[:version] = cli[:version]
 
     cli.puts "# Database size: #{version_size(ver)}"
     ver
@@ -252,12 +251,13 @@ class MiGA::Cli::Action::Db < MiGA::Cli::Action
 
   def register_database(manif, db, ver)
     cli.say "Registering database locally"
-    reg = local_manifest.merge(last_update: Time.now.to_s)
+    reg = (local_manifest || {}).merge(last_update: Time.now.to_s)
     reg[:databases] ||= {}
     reg[:databases][cli[:database]] ||= {}
     reg[:databases][cli[:database]][:manif_last_update] = manif[:last_update]
     reg[:databases][cli[:database]][:manif_host] = manif[:host]
     reg[:databases][cli[:database]].merge! db
+    reg[:databases][cli[:database]].delete(:versions)
     reg[:databases][cli[:database]][:local_version] = ver
     MiGA::Json.generate(reg, local_manifest_file)
   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, 6, 1].freeze
+  VERSION = [1.3, 7, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2023, 5, 1)
+  VERSION_DATE = Date.new(2023, 6, 4)
 
   ##
   # References of MiGA

data/utils/distance/commands.rb

@@ -224,7 +224,10 @@ module MiGA::DistanceRunner::Commands
         else
           out[6] = out[6].to_f
         end
-        aai_data[out[1]] = [out[6], 0, 0, 0]
+
+        # AAI-hat can result in 0.0 values (e.g., "<30%") when low-quality
+        # genome comparisons produce unrealistically small estimates. 
+        aai_data[out[1]] = [out[6], 0, 0, 0] unless out[6].zero?
       end
     end
     $stderr.puts "Results: #{haai_data.size} | Inferences: #{aai_data.size}"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.6.1
+  version: 1.3.7.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-05-01 00:00:00.000000000 Z
+date: 2023-06-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons