scipion-pyworkflow 3.9.1__tar.gz → 3.10.0__tar.gz

{scipion_pyworkflow-3.9.1 → scipion_pyworkflow-3.10.0}/CHANGES.txt

@@ -1,3 +1,8 @@
+V3.10.0
+developers:
+  -  stepsExecutionMode = STEPS_SERIAL at class level. Should a class attribute for future versions. Now both approaches are valid.
+
+V3.9.2 - hotfix: rescue commented methods: Protocol._insertRunJobStep and Protocol._insertCopyFileStep
 V3.9.1 - hotfix: loading related objects (CTF - Mics in particle extraction)
 V3.9.0
   - Project can have a comment (tooltip over the project name and click will edit it). Will be populated with templates description.

{scipion_pyworkflow-3.9.1/scipion_pyworkflow.egg-info → scipion_pyworkflow-3.10.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scipion-pyworkflow
-Version: 3.9.1
+Version: 3.10.0
 Summary: Simple workflow platform used in scientific applications, initially developed within the Scipion framework for image processing in Electron Microscopy.
 Home-page: https://github.com/scipion-em/scipion-pyworkflow
 Author: J.M. De la Rosa Trevin, Roberto Marabini, Grigory Sharov, Josue Gomez Blanco, Pablo Conesa, Yunior Fonseca Reyna

{scipion_pyworkflow-3.9.1 → scipion_pyworkflow-3.10.0}/pyworkflow/constants.py

@@ -43,7 +43,7 @@ VERSION_1 = '1.0.0'
 VERSION_1_1 = '1.1.0'
 VERSION_1_2 = '1.2.0'
 VERSION_2_0 = '2.0.0'
-VERSION_3_0 = '3.9.1'
+VERSION_3_0 = '3.10.0'
 
 # For a new release, define a new constant and assign it to LAST_VERSION
 # The existing one has to be added to OLD_VERSIONS list.

{scipion_pyworkflow-3.9.1 → scipion_pyworkflow-3.10.0}/pyworkflow/protocol/protocol.py

@@ -358,6 +358,10 @@ class Protocol(Step):
     _package = None
     _plugin = None
 
+    # Maybe this property can be inferred from the
+    # prerequisites of steps, but is easier to keep it
+    stepsExecutionMode = STEPS_SERIAL
+
     def __init__(self, **kwargs):
         Step.__init__(self, **kwargs)
         self._size = None
@@ -410,9 +414,6 @@ class Protocol(Step):
         if not hasattr(self, 'hostFullName'):
             self.hostFullName = String()
 
-        # Maybe this property can be inferred from the
-        # prerequisites of steps, but is easier to keep it
-        self.stepsExecutionMode = STEPS_SERIAL
 
         # Run mode
         self.runMode = Integer(kwargs.get('runMode', MODE_RESUME))
@@ -1139,20 +1140,17 @@ class Protocol(Step):
 
         return self.__insertStep(step,prerequisites)
 
-    # def _insertRunJobStep(self, progName, progArguments, resultFiles=[],
-    #                       **kwargs):
-    #     """ Insert an Step that will simple call runJob function
-    #     **args: see __insertStep
-    #     """
-    #     return self._insertFunctionStep('runJob', progName, progArguments,
-    #                                     **kwargs)
-    #
-    # def _insertCopyFileStep(self, sourceFile, targetFile, **kwargs):
-    #     """ Shortcut function to insert a step for copying a file to a destiny. """
-    #     step = FunctionStep(pwutils.copyFile, 'copyFile', sourceFile,
-    #                         targetFile,
-    #                         **kwargs)
-    #     return self.__insertStep(step, **kwargs)
+    def _insertRunJobStep(self, progName, progArguments, resultFiles=[],
+                          **kwargs):
+        """ Insert a Step that will simply call runJob function
+        **args: see __insertStep
+        """
+        return self._insertFunctionStep('runJob', progName, progArguments, **kwargs)
+
+    def _insertCopyFileStep(self, sourceFile, targetFile, **kwargs):
+        """ Shortcut function to insert a step for copying a file to a destiny. """
+        step = FunctionStep(pwutils.copyFile, 'copyFile', sourceFile, targetFile, **kwargs)
+        return self.__insertStep(step, **kwargs)
 
     def _enterDir(self, path):
         """ Enter into a new directory path and store the current path.
@@ -2454,6 +2452,7 @@ def runProtocolMain(projectPath, protDbPath, protId):
         executor = StepExecutor(hostConfig,
                                 gpuList=protocol.getGpuList())
 
+    logger.info("Running protocol using the %s executor." % executor)
     protocol.setStepsExecutor(executor)
     # Finally run the protocol
     protocol.run()

{scipion_pyworkflow-3.9.1 → scipion_pyworkflow-3.10.0}/pyworkflow/utils/path.py

@@ -292,10 +292,11 @@ def createAbsLink(source, dest):
     """ Creates a link to a given file path"""
     if os.path.islink(dest):
         os.remove(dest)
-        
+
     if os.path.exists(dest):
         raise Exception('Destination %s os.path.exists and is not a link' % dest)
-
+    
+    source = os.path.abspath(source)
     os.symlink(source, dest)
 
 

{scipion_pyworkflow-3.9.1 → scipion_pyworkflow-3.10.0}/pyworkflow/utils/utils.py

@@ -498,7 +498,9 @@ class LazyDict(object):
 def parseBibTex(bibtexStr):
     """ Parse a bibtex file and return a dictionary. """
 
-    return bibtexparser.loads(bibtexStr).entries_dict
+    return bibtexparser.loads(bibtexStr,
+                              parser=bibtexparser.bparser.BibTexParser(common_strings=True)
+                              ).entries_dict
 
 
 

{scipion_pyworkflow-3.9.1 → scipion_pyworkflow-3.10.0/scipion_pyworkflow.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scipion-pyworkflow
-Version: 3.9.1
+Version: 3.10.0
 Summary: Simple workflow platform used in scientific applications, initially developed within the Scipion framework for image processing in Electron Microscopy.
 Home-page: https://github.com/scipion-em/scipion-pyworkflow
 Author: J.M. De la Rosa Trevin, Roberto Marabini, Grigory Sharov, Josue Gomez Blanco, Pablo Conesa, Yunior Fonseca Reyna