rbbt-util 5.33.21 → 5.34.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 563841b942e1b0cf4a97bed6900bd51c96df63ec993d3a5280faadbf7b8eb753
-  data.tar.gz: c2cd78f5dfe5061f97021fd2121dd415d7b6c36c1fef2fc9f496c2cc985e4c4d
+  metadata.gz: cebda38db6f69e3dafffde7a38d5b35c87ead40eee194d4f69563577673a19e8
+  data.tar.gz: 565788a963e37d0850fe14fe9877d644e05d1131d2c56fa27a78fac5e9081efe
 SHA512:
-  metadata.gz: 6382e73cdb35ff7ab7dcd3de894a192353c39edef06ddaeb030ec376089b638acb0f62f468153433dfb0e3b0242a44146bfaeb1770ef35ee7175200caeea5e12
-  data.tar.gz: '08b8ce8d556f25269c671b6307972669927b468975c77d188b572e2285627968989a2db68de7fa2983908cb7d4cf3a236f0908a78d3917ea46ad84f82c60f536'
+  metadata.gz: 63dc077571b4c7931ca6a29e880294462c0b1928fce06ae280702f343ba5b51bb383234524e8eb766963a516dd8a5ae8afe83433ac9f56e9e83f20b892cad971
+  data.tar.gz: a956cfeccbb20ced8cbee407159378e8b02490cced6fd56f83b3d62a7bbce9c3f27d0331ed4776fa3c7bf3e945c40e444c4fc409a3965ce2fcaef9c2ff7400d6

data/lib/rbbt/hpc/orchestrate.rb

@@ -31,6 +31,7 @@ module HPC
       options.delete "detach"
       options.delete "jobname"
       options.delete "load_inputs"
+      options.delete "provenance"
 
       Log.high "Prepare for exec"
       prepare_for_execution(job)

data/lib/rbbt/util/misc/inspect.rb

@@ -56,7 +56,8 @@ module Misc
       ":" << obj.to_s
     when String
       if obj.length > 100
-        "'" << obj.slice(0,30) << "<...#{obj.length}...>" << obj.slice(-10,30)<< "'"
+        digest = Misc.digest(obj)
+        "'" << obj.slice(0,30) << "<...#{obj.length} - #{digest[0..4]}...>" << obj.slice(-10,30)<< "'"
       else 
         "'" << obj << "'"
       end

data/lib/rbbt/util/open.rb

@@ -678,7 +678,7 @@ module Open
       if Open.exists? notification_file
         key = Open.read(notification_file).strip
         key = nil if key.empty?
-        if key.include?("@")
+        if key && key.include?("@")
           to = from = key
           subject = "Wrote " << file
           message = "Content attached"

data/lib/rbbt/workflow.rb

@@ -542,8 +542,17 @@ module Workflow
     step_path = step_path.call if Proc === step_path
     persist = input_values.nil? ? false : true
     persist = false
+
+    if ! (Path === step_path ? step_path.find : File.exists?(step_path)) && step_path.split("/").length == 3 && File.exists?(new_path = Rbbt.var.jobs[step_path].find)
+      step_path = new_path
+    end
+    
     key = Path === step_path ? step_path.find : step_path
 
+    if ! File.exists?(step_path) && step_path.split("/").length == 3 && File.exists?(new_path = Rbbt.var.jobs[step_path].find)
+      step_path = new_path
+    end
+
     step = Step.new step_path, task, input_values, dependencies
 
     set_step_dependencies(step) unless dependencies
@@ -703,7 +712,15 @@ module Workflow
 
   def self.load_step(path)
     path = Path.setup(path.dup) unless Path === path
-    path = path.find
+
+    if ! (Path === path ? path.exists? : File.exists?(path)) && path.split("/").length == 3 
+      new_path = Rbbt.var.jobs[path]
+      if new_path.exists? || new_path.set_extension('info').exists?
+        path = new_path
+      end
+    end
+
+    path = path.find if Path === path
 
     begin
       _load_step(path)

data/share/Rlib/svg.R

@@ -20,9 +20,11 @@ rbbt.SVG.extract <- function(plot, size=NULL, prefix=NULL, ...){
         resolution = 72 * (size/7)
 
         if (length(plot$theme) == 0) plot <- plot + theme_light();
+
         if (length(plot$theme$text) == 0) plot <- plot + theme(text = element_text(size=base.size));
 
-        plot$theme$text$size = base.size
+        if (is.null(plot$theme$text$size))
+          plot$theme$text$size = base.size
 
         print(plot, type='cairo')
         mysvg <- grid.export(res=resolution, prefix=prefix, ...)

data/share/rbbt_commands/workflow/prov

@@ -36,7 +36,7 @@ file = ARGV.shift
 
 $seen = []
 def get_step(file)
-  file = File.expand_path(file)
+  file = File.expand_path(file) if File.exists?(file)
   file = file.sub(/\.(info|files)$/,'')
   $seen << file
   Workflow.load_step file

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.33.21
+  version: 5.34.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-06-03 00:00:00.000000000 Z
+date: 2022-06-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake