scipion-pyworkflow 3.9.1__py3-none-any.whl → 3.10.0__py3-none-any.whl

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.

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()

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)
 
 

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.dist-info → scipion_pyworkflow-3.10.0.dist-info}/METADATA

@@ -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.dist-info → scipion_pyworkflow-3.10.0.dist-info}/RECORD

@@ -1,6 +1,6 @@
 pyworkflow/__init__.py,sha256=Wr-MVKMQJy_Cy-rpPPB0-pyv8-8tx7GPPaLSNBrV1AI,1246
 pyworkflow/config.py,sha256=_sq6YCRfcfE4WUNXLShgbICbBeTSLpD2KmPVapR1Wos,22306
-pyworkflow/constants.py,sha256=nBscFi3ZRqUZA6daTMWVM2_xbStXn98BNC659zN_UNM,7447
+pyworkflow/constants.py,sha256=R9MnxV0n3oPb4pwacP6L80gj6inmkuP7yMS572s6OHQ,7448
 pyworkflow/exceptions.py,sha256=3VFxuNJHcIWxRnLPR0vYg0RFAQMmxPBJZLZSi87VI8E,507
 pyworkflow/object.py,sha256=yX3tBUuBssCI8aWGlTmyEKzFE59dJq_7NqllouVzMk0,55069
 pyworkflow/plugin.py,sha256=JJm5plPyOnPAR4To6I5rXVIBda-1Dg-53zicdnLSrac,28858
@@ -72,7 +72,7 @@ pyworkflow/protocol/hosts.py,sha256=B9ENNclqYe75CPqAMOoPjwn-r3ST6HxTewXtsK_zWks,
 pyworkflow/protocol/launch.py,sha256=7WKAiHma2tSuhqK4xVnxD_SnVt7Y5qyDFdQwTo8BLF0,11267
 pyworkflow/protocol/package.py,sha256=L6x3HHKtbrhDQRJHD07SG3DQKNMGaRQ0ROoLEY3SuRQ,1444
 pyworkflow/protocol/params.py,sha256=gP6QImgULvzCr-f0iseArIp1bjXm1JuUr9padmuMs7M,25901
-pyworkflow/protocol/protocol.py,sha256=Uwa5AT26wlIogPHLgmvqOTcs3tdV-CB88duE1GJKzvc,97219
+pyworkflow/protocol/protocol.py,sha256=pwgaQzcnuJOkpBDJ8k7ZEc0DJ6m_BrZz627HvWZoW2E,97145
 pyworkflow/resources/Imagej.png,sha256=nU2nWI1wxZB_xlOKsZzdUjj-qiCTjO6GwEKYgZ5Risg,14480
 pyworkflow/resources/chimera.png,sha256=AKCuwMqmZo0Cg2sddMUjBWUhmAq-nPsAVCBpVrYNeiQ,815
 pyworkflow/resources/fa-exclamation-triangle_alert.png,sha256=31_XvRu0CkJ2dvHSpcBAR43378lIJTWwiag_A7SuUQc,585
@@ -102,13 +102,13 @@ pyworkflow/utils/dataset.py,sha256=141u2xb-FTe8nF6OVJBJtTNHWz7eDWd24veBWX7eoTI,1
 pyworkflow/utils/echo.py,sha256=ZXJRrmxUaTT4Xxf7_pQwg7Th341iFafTs66VEKNOZmE,3442
 pyworkflow/utils/graph.py,sha256=z3Hcj0I38du97DQEqNT5gk--SCDTRPlKotaCszoZfX8,4981
 pyworkflow/utils/log.py,sha256=8SIg1jwOKMQzGgDqutB7ZD42ZzLHslxULPvK-f1sDD0,10693
-pyworkflow/utils/path.py,sha256=k689N4OpN8stfZf1KSyF8U2JjELloxymwrsgyu9y2eI,16770
+pyworkflow/utils/path.py,sha256=hDisc13HhfB6CxpBcI1JBd5er_S6yVTKw1MFSw1AR3U,16803
 pyworkflow/utils/process.py,sha256=m6gZ_9vHTJyzXOCGGIIwFCbXXoH7XC-Okn5SJzs1P1U,4717
 pyworkflow/utils/profiler.py,sha256=BC0KkAgfYqf-CV40zLcRxo5Td79f5jw1gzvaDH8iqt8,2218
 pyworkflow/utils/progressbar.py,sha256=VntEF_FTdQHjMKawfR1R4IoNgYNTEMmnLUIDvUXurxk,5903
 pyworkflow/utils/properties.py,sha256=D1LHkVn0cbxCHhedJE4XAw5ZwOufb_4z48IeJ0L0fWc,23960
 pyworkflow/utils/reflection.py,sha256=48cvIDO73JinBsFn3XMiVR56AcivfdJoiMXGM7ZwUDY,4429
-pyworkflow/utils/utils.py,sha256=t5QVNEI2-RJ1B457mozwJj3c_nwwoT_n4cYT23zoNy8,26205
+pyworkflow/utils/utils.py,sha256=1Sm7UXBhZVL1ZvWHG_QCg32M66OE7OInGJZmPqX60mU,26329
 pyworkflow/utils/which.py,sha256=KuyKYE4GnkwMpBJoKgOMnx-hNZjHf6OTyqxEsdHIftI,8627
 pyworkflow/webservices/__init__.py,sha256=CfkvvoFQp2t2Tt5p7uOF_tpkZVWPHOl9TLlAtBlKPJ8,294
 pyworkflow/webservices/config.py,sha256=CuJeul6ToLvWPHIp3hmxFe0v0pbLGYa3owUdBhIDDsg,577
@@ -131,10 +131,10 @@ pyworkflowtests/tests/test_protocol_export.py,sha256=z18nKPkOnrYLMU8KqcnVsF6-ylQ
 pyworkflowtests/tests/test_protocol_output.py,sha256=8gnIFMRNmwPnIBRCG29WHJB6mqK4FLGn1jiXHtTD6pY,5980
 pyworkflowtests/tests/test_streaming.py,sha256=vOH-bKCM-fVUSsejqNnCX5TPXhdUayk9ZtJHsNVcfCY,1615
 pyworkflowtests/tests/test_utils.py,sha256=_pTYGCuXC7YNMdCBzUYNfSBCR3etrHsxHfIhsQi4VPc,7465
-scipion_pyworkflow-3.9.1.dist-info/LICENSE.txt,sha256=ixuiBLtpoK3iv89l7ylKkg9rs2GzF9ukPH7ynZYzK5s,35148
-scipion_pyworkflow-3.9.1.dist-info/METADATA,sha256=bZIJBBArE8J_ILTTWYZrB76dEJqP0bjut66guo2JT0s,4681
-scipion_pyworkflow-3.9.1.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-scipion_pyworkflow-3.9.1.dist-info/dependency_links.txt,sha256=D7r_CPRjYRtBb3q_OBocTdsaeXI5TwnYMu5ri0JFtzs,84
-scipion_pyworkflow-3.9.1.dist-info/entry_points.txt,sha256=oR-zwsOICjEPINm-FWVPp-RfnpXZanVal4_XG6BWkkQ,127
-scipion_pyworkflow-3.9.1.dist-info/top_level.txt,sha256=PzyJteyenJwLjAeSFP7oYrTN_U71GABQwET8oLZkh9k,27
-scipion_pyworkflow-3.9.1.dist-info/RECORD,,
+scipion_pyworkflow-3.10.0.dist-info/LICENSE.txt,sha256=ixuiBLtpoK3iv89l7ylKkg9rs2GzF9ukPH7ynZYzK5s,35148
+scipion_pyworkflow-3.10.0.dist-info/METADATA,sha256=VMXHL5VKBHV-p3EyaKLc1yk_E7tUVSUkH2bQSBnLX7w,4682
+scipion_pyworkflow-3.10.0.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+scipion_pyworkflow-3.10.0.dist-info/dependency_links.txt,sha256=D7r_CPRjYRtBb3q_OBocTdsaeXI5TwnYMu5ri0JFtzs,84
+scipion_pyworkflow-3.10.0.dist-info/entry_points.txt,sha256=oR-zwsOICjEPINm-FWVPp-RfnpXZanVal4_XG6BWkkQ,127
+scipion_pyworkflow-3.10.0.dist-info/top_level.txt,sha256=PzyJteyenJwLjAeSFP7oYrTN_U71GABQwET8oLZkh9k,27
+scipion_pyworkflow-3.10.0.dist-info/RECORD,,