miga-base 0.3.8.0 → 0.3.8.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: c7f7bb9ba42ccdbed81ce05484031e17a43c6e688e89c5622327aadbee9d0f31
-  data.tar.gz: 3ca5e3189bb65b213fe43a948710d69ea304dac4c838c176838773fc87a88c5b
+  metadata.gz: bbf27a1aa7abe14e9b7fb0a32a3acaa82948f12034169dc1e065cbe05ec275f2
+  data.tar.gz: 854b0793698f158b73ba2aab35638610db3e7044acf91a760fcd6ab272b81172
 SHA512:
-  metadata.gz: 9fa0deb9770be85a71145fcedd3a8a590ad7a6584f274245ed47df7decde6ddcb8d48c635585773a7005ceca4b03d37e67620346faff3eea387803d113a726f8
-  data.tar.gz: 17eeaad6dc985ff89d813ece94d3e2837fac4a40223cde14063b3236ba5dbd7ff581c6e7df30a4919cb002dd6918a42ac820cf8a3045f99714486f05bbc252fe
+  metadata.gz: f90b4de8827dc552cd570072714de6e7383ca38e6baa1603a9d730d28a83a247f327bc598937a84cf5bc9bd3fab888b9a42d39dd501e311b18abe0d934daa8b0
+  data.tar.gz: 814bf34e30d1fde7e9f91403df099c61eecf6c0a7c4bf524e9cf70c0acd4c1b5052bc8168015c9883a35ed64f3ea813be033bc75ae0711094835597c3a9bafd7

data/actions/summary.rb

@@ -3,7 +3,7 @@
 # @package MiGA
 # @license Artistic-2.0
 
-o = {q:true, units:false, tabular:false}
+o = {q: true, units: false, tabular: false}
 opts = OptionParser.new do |opt|
   opt_banner(opt)
   opt_object(opt, o, [:project, :dataset_opt])
@@ -12,7 +12,7 @@ opts = OptionParser.new do |opt|
   opt.on("--tab",
     "Returns a tab-delimited table."){ |v| o[:tabular] = v }
   opt.on("--key STRING",
-    "Returns only the value of the requested key."){ |v| o[:key] = v }
+    "Returns only the value of the requested key."){ |v| o[:key_md] = v }
   opt.on("--with-units",
     "Includes units in each cell."){ |v| o[:units] = v }
   opt_common(opt, o)
@@ -42,8 +42,8 @@ stats = ds.map do |d|
   s = r.nil? ? {} : r[:stats]
   s.tap{ |i| i[:dataset] = d.name }
 end
-keys = o[:key].nil? ? stats.map(&:keys).flatten.uniq :
-      [:dataset, o[:key].downcase.miga_name.to_sym]
+keys = o[:key_md].nil? ? stats.map(&:keys).flatten.uniq :
+      [:dataset, o[:key_md].downcase.miga_name.to_sym]
 keys.delete :dataset
 keys.unshift :dataset
 

data/lib/miga/result/dates.rb

@@ -25,7 +25,7 @@ module MiGA::Result::Dates
   def running_time
     a = started_at or return nil
     b = done_at or return nil
-    (b - a).to_f * 24 * 60
+    (b - a).to_f / 60.0
   end
 
   private
@@ -34,6 +34,7 @@ module MiGA::Result::Dates
     # Internal function to detect start and end dates
     def date_at(event)
       date = self[event]
+      date ||= self[:started] if event == :start
       if date.nil?
         f = path event
         date = File.read(f) if File.size? f

data/lib/miga/version.rb

@@ -10,7 +10,7 @@ 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 = [0.3, 8, 0]
+  VERSION = [0.3, 8, 1]
   
   ##
   # Nickname for the current major.minor version.

data/utils/distance/commands.rb

@@ -80,9 +80,11 @@ module MiGA::DistanceRunner::Commands
     if o[:ani_p] == 'fastani'
       out = `fastANI -r "#{f1}" -q "#{f2}" \
             -o /dev/stdout 2>/dev/null`.chomp.split(/\s+/)
-      SQLite3::Database.new(db) do |conn|
-        conn.execute "insert into ani values(?, ?, ?, 0, ?, ?)",
-              [n1, n2, out[2], out[3], out[4]]
+      unless out.empty?
+        SQLite3::Database.new(db) do |conn|
+          conn.execute "insert into ani values(?, ?, ?, 0, ?, ?)",
+                [n1, n2, out[2], out[3], out[4]]
+        end
       end
       v = out[2]
     else

data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl

@@ -1 +1 @@
-utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.N50.pl
+../../Scripts/FastA.N50.pl

data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl

@@ -1 +1 @@
-utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.filterN.pl
+../../Scripts/FastA.filterN.pl

data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl

@@ -1 +1 @@
-utils/enveomics/Pipelines/assembly.pbs/../../Scripts/FastA.length.pl
+../../Scripts/FastA.length.pl

data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl

@@ -1 +1 @@
-utils/enveomics/Pipelines/blast.pbs/../../Scripts/FastA.split.pl
+../../Scripts/FastA.split.pl

data/utils/enveomics/Scripts/lib/enveomics.R

@@ -1 +1 @@
-utils/enveomics/Scripts/lib/../../enveomics.R
+../../enveomics.R

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.3.8.0
+  version: 0.3.8.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
@@ -496,8 +496,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.7
+rubygems_version: 3.0.2
 signing_key: 
 specification_version: 4
 summary: MiGA