scipion-pyworkflow 3.10.2__py3-none-any.whl → 3.10.4__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 = '3.10.2'
+VERSION_3_0 = '3.10.4'
 
 # 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/executor.py

@@ -287,7 +287,7 @@ class ThreadStepExecutor(StepExecutor):
         # Some nodes/threads do not use gpus so may not be booked and not in the dictionary
         if gpus is not None:
             self.gpuDict.pop(node)
-            self.gpuDict[-node-1] = gpus
+            self.gpuDict[-node] = gpus
             logger.info("GPUs %s freed from step %s" % (gpus, node))
         else:
             logger.debug("step id %s not found in GPU slots" % node)
@@ -392,8 +392,6 @@ class QueueStepExecutor(ThreadStepExecutor):
         self.submitDict = submitDict
         # Command counter per thread
         self.threadCommands = {}
-        for threadId in range(nThreads):
-            self.threadCommands[threadId] = 0
 
         if nThreads > 1:
             self.runJobs = ThreadStepExecutor.runSteps
@@ -411,6 +409,15 @@ class QueueStepExecutor(ThreadStepExecutor):
 
         logger.debug("Updated gpus ids rebase starting from 0: %s per thread" %self.gpuDict)
 
+    def getThreadJobId(self, stepId):
+        """ Returns the job id extension assigned to each thread/step """
+        if not stepId in self.threadCommands:
+            self.threadCommands[stepId] = 0
+
+        self.threadCommands[stepId] += 1
+
+        return self.threadCommands[stepId]
+
     def runJob(self, log, programName, params, numberOfMpi=1, numberOfThreads=1, env=None, cwd=None, executable=None):
         threadId = threading.current_thread().thId
         submitDict = dict(self.hostConfig.getQueuesDefault())
@@ -418,8 +425,8 @@ class QueueStepExecutor(ThreadStepExecutor):
         submitDict['JOB_COMMAND'] = process.buildRunCommand(programName, params, numberOfMpi,
                                                             self.hostConfig, env,
                                                             gpuList=self.getGpuList())
-        self.threadCommands[threadId] += 1
-        subthreadId = '-%s-%s' % (threadId, self.threadCommands[threadId])
+        threadJobId = self.getThreadJobId(threadId)
+        subthreadId = '-%s-%s' % (threadId, threadJobId)
         submitDict['JOB_NAME'] = submitDict['JOB_NAME'] + subthreadId
         submitDict['JOB_SCRIPT'] = os.path.abspath(removeExt(submitDict['JOB_SCRIPT']) + subthreadId + ".job")
         submitDict['JOB_LOGS'] = os.path.join(getParentFolder(submitDict['JOB_SCRIPT']), submitDict['JOB_NAME'])

pyworkflow/protocol/protocol.py

@@ -362,17 +362,15 @@ class Protocol(Step):
     # prerequisites of steps, but is easier to keep it
     stepsExecutionMode = STEPS_SERIAL
 
-    @classmethod
-    def modeSerial(cls):
+    def modeSerial(self):
         """ Returns true if steps are run one after another"""
         # Maybe this property can be inferred from the
         # prerequisites of steps, but is easier to keep it
-        return cls.stepsExecutionMode == STEPS_SERIAL
+        return self.stepsExecutionMode == STEPS_SERIAL
 
-    @classmethod
-    def modeParallel(cls):
+    def modeParallel(self):
         """ Returns true if steps are run in parallel"""
-        return not cls.modeSerial()
+        return not self.modeSerial()
 
     def __init__(self, **kwargs):
         Step.__init__(self, **kwargs)
@@ -1934,7 +1932,9 @@ class Protocol(Step):
              'JOB_CORES': self.numberOfMpi.get() * self.numberOfThreads.get(),
              'JOB_HOURS': 72,
              'GPU_COUNT': len(self.getGpuList()),
-             'QUEUE_FOR_JOBS': 'N'
+             'QUEUE_FOR_JOBS': 'N',
+             'SCIPION_PROJECT': self.getProject().getShortName(),
+             'SCIPION_PROTOCOL': self.getRunName()
              }
         d.update(queueParams)
         return d

{scipion_pyworkflow-3.10.2.dist-info → scipion_pyworkflow-3.10.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scipion-pyworkflow
-Version: 3.10.2
+Version: 3.10.4
 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-3.10.2.dist-info → scipion_pyworkflow-3.10.4.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=GG3_xDU181oUFld0DkGbvKq5lN606DjaCLnOsuVMDDQ,7448
+pyworkflow/constants.py,sha256=EQ2RVEc4QdYO0vJVp-wW22WdBw5Yt1STFTlLJXgMBAQ,7448
 pyworkflow/exceptions.py,sha256=3VFxuNJHcIWxRnLPR0vYg0RFAQMmxPBJZLZSi87VI8E,507
 pyworkflow/object.py,sha256=yX3tBUuBssCI8aWGlTmyEKzFE59dJq_7NqllouVzMk0,55069
 pyworkflow/plugin.py,sha256=JJm5plPyOnPAR4To6I5rXVIBda-1Dg-53zicdnLSrac,28858
@@ -67,12 +67,12 @@ pyworkflow/project/scripts/stop.py,sha256=vCeCxkwPCoUkLbna5HCxKWJ1hrsI4U19Sg9JD4
 pyworkflow/protocol/__init__.py,sha256=bAdIpvUW4GAYdIuv92DZ44-OEkZ7lTtnp1S9T5cwtVs,1413
 pyworkflow/protocol/bibtex.py,sha256=mCUk1Hp5Vp_i2lozDM1BQNOw10e_RSu86oXvrR63sOA,2122
 pyworkflow/protocol/constants.py,sha256=DfuCs7eub-mLHJjEpHlIG9BW3fUpRwfTVwMYytNWv6U,3392
-pyworkflow/protocol/executor.py,sha256=x3v1q4NyF--iLMOMS2qsVpOEy-nge9IDuzWLllx5Tis,17769
+pyworkflow/protocol/executor.py,sha256=qWm5Baf8snMzS0DyvjeyPIBPqkYgfiRqDOUt_8kqTYg,17960
 pyworkflow/protocol/hosts.py,sha256=B9ENNclqYe75CPqAMOoPjwn-r3ST6HxTewXtsK_zWks,10453
 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=K-srKr4D220JLwYcDfAAlfBsAvrqf55gnyCZsSTt3uc,97442
+pyworkflow/protocol/protocol.py,sha256=AyeC_J_fA6Y_wgsJQNhbGO2g27zQZUwt9ezAoV8h9WM,97530
 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
@@ -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-3.10.2.dist-info/LICENSE.txt,sha256=ixuiBLtpoK3iv89l7ylKkg9rs2GzF9ukPH7ynZYzK5s,35148
-scipion_pyworkflow-3.10.2.dist-info/METADATA,sha256=-H5H84If9BMyHHX3bBRSZGwyJurbKwmlsUOHyi8U3_Y,4682
-scipion_pyworkflow-3.10.2.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-scipion_pyworkflow-3.10.2.dist-info/dependency_links.txt,sha256=D7r_CPRjYRtBb3q_OBocTdsaeXI5TwnYMu5ri0JFtzs,84
-scipion_pyworkflow-3.10.2.dist-info/entry_points.txt,sha256=oR-zwsOICjEPINm-FWVPp-RfnpXZanVal4_XG6BWkkQ,127
-scipion_pyworkflow-3.10.2.dist-info/top_level.txt,sha256=PzyJteyenJwLjAeSFP7oYrTN_U71GABQwET8oLZkh9k,27
-scipion_pyworkflow-3.10.2.dist-info/RECORD,,
+scipion_pyworkflow-3.10.4.dist-info/LICENSE.txt,sha256=ixuiBLtpoK3iv89l7ylKkg9rs2GzF9ukPH7ynZYzK5s,35148
+scipion_pyworkflow-3.10.4.dist-info/METADATA,sha256=e8izqpLT9VEfQO9i0SVwrQo_iDqr8mmX0Sy_2zU7rSc,4682
+scipion_pyworkflow-3.10.4.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
+scipion_pyworkflow-3.10.4.dist-info/dependency_links.txt,sha256=D7r_CPRjYRtBb3q_OBocTdsaeXI5TwnYMu5ri0JFtzs,84
+scipion_pyworkflow-3.10.4.dist-info/entry_points.txt,sha256=oR-zwsOICjEPINm-FWVPp-RfnpXZanVal4_XG6BWkkQ,127
+scipion_pyworkflow-3.10.4.dist-info/top_level.txt,sha256=PzyJteyenJwLjAeSFP7oYrTN_U71GABQwET8oLZkh9k,27
+scipion_pyworkflow-3.10.4.dist-info/RECORD,,

{scipion_pyworkflow-3.10.2.dist-info → scipion_pyworkflow-3.10.4.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.1.0)
+Generator: setuptools (75.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any