rbbt-util 5.35.1 → 5.35.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 1b7f34c9cb59d5936762531df4e004728071a90f4fcf3a4dce009e58071d7ffa
+  metadata.gz: 7fc87aa89e132735c535df80f34cfd0f31fb44475d55d08fb194ee50e045f884
+  data.tar.gz: e1c380d68af04bd683a3a06e675b6e8744497869d95ac96620e7864f05e8aeb7
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+  metadata.gz: dd65fb3be5c880288fa1718d6a2327d1e799f7c9b415785cdcb5f1cd9d18d02664347e6dc16dde2a78d727ab86ab292d272fc2a608ea7a9a1eb7c0e88f213131
+  data.tar.gz: 603ca603814e8405dcc88ed0a499ddb92658d2831887d8c8110ba60737a83317ee7d68e00a3b51a48734a6bb90f2539d654169b07a8609a60fe02351d8426394

data/lib/rbbt/util/python/util.rb

@@ -31,4 +31,23 @@ module RbbtPython
     tsv
   end
 
+  def self.list2ruby(list)
+    return list unless PyCall::List === list 
+    list.collect do |e|
+      list2ruby(e)
+    end
+  end
+
+  def self.numpy2ruby(numpy)
+    list2ruby(numpy.tolist)
+  end
+
+  def self.obj2hash(obj)
+    hash = {}
+    RbbtPython.iterate obj.keys do |k|
+      hash[k] = obj[k]
+    end
+    hash
+  end
+
 end

data/lib/rbbt/util/python.rb

@@ -5,6 +5,16 @@ require 'rbbt/util/python/util'
 module RbbtPython
   extend PyCall::Import
 
+  class RbbtPythonException < StandardError; end
+
+  class Binding
+    include PyCall::Import
+
+    def run(*args, &block)
+      instance_exec(*args, &block)
+    end
+  end
+
   def self.script(text, options = {})
     Log.debug "Running python script:\n#{text.dup}"
     text = StringIO.new text unless IO === text
@@ -12,8 +22,13 @@ module RbbtPython
   end
 
   def self.add_path(path)
-    self.run 'sys' do
-      sys.path.append path
+    begin
+      self.run 'sys' do
+        sys.path.append path
+      end
+    rescue
+      raise RbbtPythonException, 
+        "Could not add path #{Misc.fingerprint path} to python sys: " + $!.message
     end
   end
 
@@ -26,19 +41,64 @@ module RbbtPython
   end
 
   def self.init_rbbt
-    if ! defined?(@@__init_rbbt) || ! @@__init_rbbt 
+    if ! defined?(@@__init_rbbt_python) || ! @@__init_rbbt_python
       Log.debug "Loading python 'rbbt' module into pycall RbbtPython module"
       RbbtPython.add_paths(Rbbt.python.find_all)
       RbbtPython.pyimport("rbbt")
-      @@__init_rbbt = true
+      @@__init_rbbt_python = true
     end
   end
 
+  def self.import_method(module_name, method_name, as = nil)
+    RbbtPython.pyfrom module_name, import: method_name
+    RbbtPython.method(method_name)
+  end
+
   def self.exec(script)
     PyCall.exec(script)
   end
 
-  def self.iterate(iterator, options = {})
+  def self.iterate_index(elem, options = {})
+    iii :interate_index
+    bar = options[:bar]
+
+    len = PyCall.len(elem)
+    case bar
+    when TrueClass
+      bar = Log::ProgressBar.new nil, :desc => "RbbtPython iterate"
+    when String
+      bar = Log::ProgressBar.new nil, :desc => bar
+    end
+
+    len.times do |i|
+      begin
+        yield elem[i]
+        bar.tick if bar
+      rescue PyCall::PyError
+        if $!.type.to_s == "<class 'StopIteration'>"
+          break
+        else
+          raise $!
+        end
+      rescue
+        bar.error if bar
+        raise $!
+      end
+    end
+
+    Log::ProgressBar.remove_bar bar if bar
+    nil
+  end
+
+  def self.iterate(iterator, options = {}, &block)
+    if ! iterator.respond_to?(:__next__)
+      if iterator.respond_to?(:__iter__)
+        iterator = iterator.__iter__
+      else
+        return iterate_index(iterator, options, &block)
+      end
+    end
+
     bar = options[:bar]
 
     case bar
@@ -50,7 +110,8 @@ module RbbtPython
 
     while true
       begin
-        yield iterator.__next__
+        elem = iterator.__next__
+        yield elem
         bar.tick if bar
       rescue PyCall::PyError
         if $!.type.to_s == "<class 'StopIteration'>"
@@ -79,12 +140,12 @@ module RbbtPython
 
   def self.run(mod = nil, imports = nil, &block)
     if mod
-      if Array === imports
-        pyfrom mod, :import => imports
-      elsif Hash === imports
+      if Hash === imports
         pyimport mod, **imports
-      else
+      elsif imports.nil?
         pyimport mod 
+      else
+        pyfrom mod, :import => imports
       end
     end
 
@@ -124,4 +185,13 @@ module RbbtPython
       module_eval(&block)
     end
   end
+
+  def self.new_binding
+    Binding.new
+  end
+
+  def self.binding_run(binding = nil, *args, &block)
+    binding = new_binding
+    binding.instance_exec *args, &block
+  end
 end

data/test/rbbt/util/python/test_util.rb

@@ -13,5 +13,13 @@ class TestPythonUtil < Test::Unit::TestCase
     assert_equal tsv, new_tsv
   end
 
+  def test_numpy
+    ra = RbbtPython.run :numpy, :as => :np do
+      na = np.array([[[1,2,3], [4,5,6]]])
+      RbbtPython.numpy2ruby na
+    end
+    assert_equal 6, ra[0][1][2]
+  end
+
 end
 

data/test/rbbt/util/test_python.rb

@@ -81,5 +81,55 @@ def python_print():
     end
     assert defined
   end
+
+  def test_iterate
+    a2, b2 = nil, nil
+    RbbtPython.run :numpy, as: :np do 
+      a = np.array([1,2])
+      a2 = RbbtPython.collect a do |e|
+        e * 2
+      end
+      b = PyCall.tuple([1,2])
+      b2 = RbbtPython.collect b do |e|
+        e * 2
+      end
+    end
+    assert_equal [2,4], a2
+    assert_equal [2,4], b2
+  end
+
+  def test_lambda
+    l = PyCall.eval "lambda e: e + 2"
+    assert_equal 5, l.(3)
+  end
+
+  def test_binding
+    raised = false
+    RbbtPython.binding_run do
+      pyimport :torch
+      pyfrom :torch, import: ["nn"]
+      begin
+        torch
+      rescue
+        raised = true
+      end
+    end
+    assert ! raised
+
+    raised = false
+    RbbtPython.binding_run do
+      begin
+        torch
+      rescue
+        raised = true
+      end
+    end
+    assert raised
+  end
+
+  def test_import_method
+    random = RbbtPython.import_method :torch, :rand, :random
+    assert random.call(1).numpy.to_f > 0
+  end
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.35.1
+  version: 5.35.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-01-23 00:00:00.000000000 Z
+date: 2023-02-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -613,113 +613,113 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.4
+rubygems_version: 3.1.2
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
+- test/test_helper.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_association.rb
+- test/rbbt/hpc/test_orchestrate.rb
+- test/rbbt/hpc/test_slurm.rb
+- test/rbbt/hpc/orchestrate/test_batches.rb
+- test/rbbt/hpc/orchestrate/test_rules.rb
+- test/rbbt/hpc/orchestrate/test_chains.rb
+- test/rbbt/hpc/test_batch.rb
+- test/rbbt/persist/test_tsv.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_lmdb.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
+- test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/test_packed_index.rb
 - test/rbbt/test_entity.rb
+- test/rbbt/test_fix_width_table.rb
 - test/rbbt/workflow/test_remote_workflow.rb
+- test/rbbt/workflow/test_doc.rb
+- test/rbbt/workflow/step/test_save_load_inputs.rb
+- test/rbbt/workflow/step/test_dependencies.rb
+- test/rbbt/workflow/test_schedule.rb
 - test/rbbt/workflow/util/test_archive.rb
 - test/rbbt/workflow/util/test_orchestrator.rb
 - test/rbbt/workflow/util/test_data.rb
-- test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/test_schedule.rb
-- test/rbbt/workflow/test_step.rb
-- test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/step/test_save_load_inputs.rb
 - test/rbbt/workflow/test_task.rb
-- test/rbbt/resource/test_path.rb
-- test/rbbt/util/test_colorize.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/test_tsv.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/util/test_migrate.rb
+- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/test_misc.rb
+- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_procpath.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_plot.rb
+- test/rbbt/util/test_open.rb
+- test/rbbt/util/test_tmpfile.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_concurrency.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_config.rb
 - test/rbbt/util/python/test_util.rb
-- test/rbbt/util/misc/test_development.rb
+- test/rbbt/util/test_log.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/test_python.rb
+- test/rbbt/util/test_chain_methods.rb
 - test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/misc/test_pipes.rb
-- test/rbbt/util/misc/test_serialize.rb
-- test/rbbt/util/misc/test_format.rb
-- test/rbbt/util/misc/test_communication.rb
 - test/rbbt/util/misc/test_lock.rb
 - test/rbbt/util/misc/test_multipart_payload.rb
 - test/rbbt/util/misc/test_bgzf.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/R/test_plot.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/util/R/test_model.rb
-- test/rbbt/util/test_config.rb
-- test/rbbt/util/test_log.rb
-- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/util/misc/test_development.rb
+- test/rbbt/util/misc/test_serialize.rb
+- test/rbbt/util/misc/test_format.rb
+- test/rbbt/util/misc/test_communication.rb
+- test/rbbt/util/misc/test_pipes.rb
 - test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_R.rb
-- test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/test_python.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/test_semaphore.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_migrate.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_attach.rb
-- test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_marshal.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/resource/test_path.rb
+- test/rbbt/test_hpc.rb
+- test/rbbt/test_persist.rb
 - test/rbbt/tsv/test_parser.rb
 - test/rbbt/tsv/test_csv.rb
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_manipulate.rb
 - test/rbbt/tsv/test_field_index.rb
 - test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_stream.rb
 - test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_marshal.rb
+- test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_excel.rb
-- test/rbbt/tsv/parallel/test_through.rb
+- test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_index.rb
 - test/rbbt/tsv/parallel/test_traverse.rb
-- test/rbbt/tsv/test_stream.rb
-- test/rbbt/test_association.rb
-- test/rbbt/hpc/test_batch.rb
-- test/rbbt/hpc/orchestrate/test_chains.rb
-- test/rbbt/hpc/orchestrate/test_rules.rb
-- test/rbbt/hpc/orchestrate/test_batches.rb
-- test/rbbt/hpc/test_slurm.rb
-- test/rbbt/hpc/test_orchestrate.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/test_tsv.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/test_fix_width_table.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/test_hpc.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_persist.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/test_helper.rb
+- test/rbbt/tsv/parallel/test_through.rb