rbbt-dm 1.2.10 → 1.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 9d53609453e1c3bd589c95071569583bff5f11224a200850c0d9e85775e5a2ce
-  data.tar.gz: 501f436caff07c990c09adec4caa60d32fe577b35209a65e8f96418ab2acc422
+  metadata.gz: b6000c342688d159e651b0ad37f14890a859ea8a858f1e96a447ea4b059f9466
+  data.tar.gz: 7d7504d58ac03ef5c090cb9d3208e7998ce486a80712d0e88bf537b95c62753f
 SHA512:
-  metadata.gz: 4a53ccc8a5eac633e344beffd36073e1828d848d9743552f12e75a54cbda337050152b72fd95d7d97d4aeed50f811dcc8475c97bc292ba9bcdd57e9d32f0e91b
-  data.tar.gz: 30fef4ee2c023e141c0ef991ae35d1a0913d4444138fda778760b821ccc48d85d67dc44d4c251d7f84e3b1bbe6ecb6f3b64aee13fbdc443cb33bbed2b34a586a
+  metadata.gz: a9d76a1383e10a323d4c6f93f2224a68956d8d3a8738c34c7a52c96391a5f9c0b1ce5b849f0579f0c63551270e57190c23529d7e33ea8f9e991f42402a5ae072
+  data.tar.gz: c2d96d57dae1edb7afaeee0897898a36a439e1d00fa65742c0afeddfc933508d178f649f12c65599558817772507f4ad2172ce41e922fd90044419f7e0b67d60

data/lib/rbbt/vector/model/huggingface.rb

@@ -2,9 +2,22 @@ require 'rbbt/vector/model/torch'
 
 class HuggingfaceModel < TorchModel
 
+  attr_accessor :tokenizer
+  def init
+    @model, @tokenizer = self.instance_exec(&@init_model) if @model.nil?
+    [@model, @tokenizer]
+  end
+
+  def tokenizer
+    init
+    @tokenizer
+  end
+
   def initialize(task, checkpoint, dir = nil, model_options = {})
     super(dir, nil, model_options)
 
+    checkpoint = checkpoint.find if Path === checkpoint
+
     @model_options = Misc.add_defaults @model_options, :task => task, :checkpoint => checkpoint
 
     init_model do 

data/lib/rbbt/vector/model/torch/dataloader.rb

@@ -42,13 +42,12 @@ class TorchModel
   end
 
   def self.text_dataset(tsv_dataset_file, elements, labels = nil, class_labels = nil)
-    elements = elements.collect{|e| e.gsub("\n", ' ') }
+    elements = elements.compact.collect{|e| e.gsub("\n", ' ') }
     tsv = feature_tsv(elements, labels, class_labels)
+    tsv.fields[0] = "text"
     if labels.nil?
-      tsv.fields[0] = "text"
-      tsv.type = :single
+      tsv = tsv.to_single
     else
-      tsv.fields[0] = "text"
       tsv.type = :list
     end
     Open.write(tsv_dataset_file, tsv.to_s)

data/lib/rbbt/vector/model/torch.rb

@@ -2,7 +2,7 @@ require_relative 'python'
 
 class TorchModel < PythonModel
 
-  attr_accessor :model, :criterion, :optimizer, :training_args
+  attr_accessor :criterion, :optimizer, :training_args
 
   def initialize(...)
     TorchModel.init_python

data/lib/rbbt/vector/model.rb

@@ -482,8 +482,11 @@ cat(paste(label, sep="\\n", collapse="\\n"));
       @labels = orig_labels
     end unless folds == -1
 
-    self.reset_model if self.respond_to? :reset_model
-    self.train unless folds == 1
+    if folds != 1
+      self.reset_model if self.respond_to? :reset_model
+      self.train 
+    end
+
     res
   end
 end

data/share/R/MA.R

@@ -106,7 +106,8 @@ rbbt.dm.matrix.differential.limma <- function(data, main, contrast=NULL, log2=NU
        data <- DGEList(data)
        data <- calcNormFactors(data)
        data = cpm(data, log=TRUE, prior.count=3)
-       data <- data[-drop,]
+       if (length(drop) > 0)
+           data <- data[-drop,]
     }else{
        data[data == 0] = NA
        good.rows = apply(is.na(data),1,sum) != dim(data)[2]
@@ -181,7 +182,7 @@ rbbt.dm.matrix.differential <- function(file, main, contrast = NULL, type = 'lim
         contrast <- make.names(contrast);
     }
 
-    if (type == 'limma')
+    if (is.null(type) || type == 'limma')
         result = rbbt.dm.matrix.differential.limma(data, main, contrast, log2, two.channel, eBayes.trend)
     else
         result = rbbt.dm.matrix.differential.DESeq(data, main, contrast)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-dm
 version: !ruby/object:Gem::Version
-  version: 1.2.10
+  version: 1.3.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-12-20 00:00:00.000000000 Z
+date: 2024-05-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -174,7 +174,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.0.dev
+rubygems_version: 3.5.9
 signing_key: 
 specification_version: 4
 summary: Data-mining and statistics