scipion-pyworkflow 3.10.6__py3-none-any.whl → 3.11.1__py3-none-any.whl

pyworkflow/utils/log.py

@@ -82,9 +82,9 @@ class LoggingConfigurator:
     customLoggingActive = False  # Holds if a custom logging configuration has taken place.
 
     @classmethod
-    def setupLogging(cls, logFile=None, console=True):
+    def setupLogging(cls, logFile=None, console=True, consoleLevel='ERROR'):
         if not cls.loadCustomLoggingConfig():
-            cls.setupDefaultLogging(logFile=logFile, console=console)
+            cls.setupDefaultLogging(logFile=logFile, console=console, consoleLevel=consoleLevel)
 
     @classmethod
     def loadCustomLoggingConfig(cls):
@@ -104,13 +104,13 @@ class LoggingConfigurator:
         return False
 
     @staticmethod
-    def setupDefaultLogging(logFile=None, console=True):
+    def setupDefaultLogging(logFile=None, console=True, consoleLevel="ERROR"):
         """ Configures logging in a default way that is to file (rotating) and console
 
         :param logFile: Optional, path to the log file. Defaults to SCIPION_LOG variable value. If folder
-            does not exists it will be created.
+            does not exist it will be created.
         :param console: Optional, defaults to True, so log messages are sent to the terminal as well
-
+        :param consoleLevel: Optional, defaults to ERROR. Only error messages are sent to the console.
         """
         from pyworkflow import Config
 
@@ -147,7 +147,7 @@ class LoggingConfigurator:
 
         if console:
             config["handlers"][CONSOLE_HANDLER] = {
-                        'level': 'ERROR', #Config.SCIPION_LOG_LEVEL,
+                        'level': consoleLevel,
                         'class': 'logging.StreamHandler',
                         'formatter': 'standard',
                         }
@@ -282,3 +282,12 @@ def getExtraLogInfo(measurement, status, project_name=None, prot_id=None, prot_n
 
     except Exception as e:
         print("getExtraLogInfo failed: %s.Params were: dbFilename %s" % (e, dbfilename))
+
+
+def changeLogLevel(newLoglevel):
+    """ Changes "on-the-fly" the log level iterating through the handlders"""
+
+    logger = logging.getLogger()
+    logger.setLevel(newLoglevel)
+    for handler in logger.handlers:
+        handler.setLevel(newLoglevel)

pyworkflow/utils/properties.py

@@ -121,11 +121,8 @@ class Message:
     LABEL_RUNNAME = 'Run name'
     LABEL_EXECUTION = 'Run mode'
     LABEL_RUNMODE = 'Mode'
-    LABEL_PARALLEL = 'Parallel'
+    LABEL_PARALLEL = 'Program compute'
     LABEL_HOST = 'Host'
-    LABEL_THREADS = 'Threads'
-    LABEL_SCIPION_THREADS = 'Scipion threads'
-    LABEL_MPI = 'MPI'
     LABEL_QUEUE = 'Use a queue engine?'
 
     LABEL_WAIT_FOR = 'Wait for'
@@ -144,17 +141,6 @@ will clean the whole run directory and start from scratch.
     """
 
     HELP_PARALLEL_HEADER = 'Define the number of processors to be used in the execution.\nCheck %s for more detailed info.\n\n' % DOCSITEURLS.THREADS_MPIS_AND_GPUS
-    HELP_PARALLEL_MPI = ("*MPI*:\nThis is a number of independent processes"
-                         " that communicate through message passing "
-                         "over the network (or the same computer).\n")
-    HELP_PARALLEL_THREADS = ("*Threads*:\nThis refers to different execution threads in the same process that "
-                             "can share memory. They run in the same computer. This value is an argument"
-                             " passed to the program integrated")
-
-    HELP_SCIPION_THREADS = ("*Scipion threads*:\n threads created by Scipion to run the steps."
-                            " 1 thread is always used by the master/main process. Then extra threads will allow"
-                            " this protocol to run several steps at the same time, taking always into account "
-                            "restrictions to previous steps and 'theoretical GPU availability'")
 
     HELP_USEQUEUE = """
     Click Yes if you want to send this execution to a queue engine like Slurm, Torque, ...
@@ -478,54 +464,54 @@ class Sprite:
 # To get font awesome icons into png use: http://fa2png.io/
 class Icon:
     # Protocols status
-    PROT_DISABLED = SpriteImage(16,32,'prot_disabled.png',bottom=32,right=64)
-    BETA = SpriteImage(0,0,'beta.png',bottom=16,right=32)
-    NEW = SpriteImage(32,0,'new.png',bottom=48,right=32)
-    PRODUCTION = SpriteImage(32,32,'production.png',bottom=48,right=64)
-    UPDATED = SpriteImage(16,0,'updated.png',bottom=32,right=32)
-
-    GROUP = SpriteImage(80, 224,'class_obj.png')
-    FAVORITE = SpriteImage(80,256,'bookmark.png')
-    DEBUG = SpriteImage(64,288,'debug.png')
-    DOWNLOAD = SpriteImage(48,272,'fa-download.png')
-    FIND = SpriteImage(80,272,'binoculares.png')
-    SELECT_ALL = SpriteImage(0,32,'workflow.png')
+    PROT_DISABLED = SpriteImage(16,32, 'prot_disabled.png', bottom=32, right=64)
+    BETA = SpriteImage(0, 0, 'beta.png', bottom=16, right=32)
+    NEW = SpriteImage(32, 0, 'new.png', bottom=48, right=32)
+    PRODUCTION = SpriteImage(32, 32, 'production.png', bottom=48, right=64)
+    UPDATED = SpriteImage(16, 0, 'updated.png', bottom=32, right=32)
+
+    GROUP = SpriteImage(80, 224, 'class_obj.png')
+    FAVORITE = SpriteImage(80, 256, 'bookmark.png')
+    DEBUG = SpriteImage(64, 288, 'debug.png')
+    DOWNLOAD = SpriteImage(48, 272, 'fa-download.png')
+    FIND = SpriteImage(80, 272, 'binoculares.png')
+    SELECT_ALL = SpriteImage(0, 32, 'workflow.png')
 
     # Project window icons
-    RUNS_TREE = SpriteImage(16,272,'fa-sitemap.png')
-    ACTION_NEW = SpriteImage(80,304,'fa-plus-circle.png')
-    ACTION_EDIT = SpriteImage(32,272,'fa-pencil.png')
-    ACTION_SELECT_FROM = SpriteImage(64,272,'fa-arrow-down.png')
-    ACTION_SELECT_TO = SpriteImage(64,256,'fa-arrow-up.png')
-    ACTION_COPY = SpriteImage(80,208,'clipboard-regular.png')
-    ACTION_PASTE = SpriteImage(0,64,'paste-solid.png')
-    ACTION_DUPLICATE = SpriteImage(48,208,'fa-files-o.png')
-    ACTION_DELETE = SpriteImage(16,176,'fa-trash-o.png')
-    ACTION_REFRESH = SpriteImage(32,144, 'fa-refresh.png')
-    ACTION_RENAME = SpriteImage(0,48,'rename.png')
-    ACTION_BROWSE = SpriteImage(32,304,'fa-folder-open.png')
-    ACTION_DB = SpriteImage(48,288,'fa-database.png')
-    ACTION_STOP = SpriteImage(16,256,'fa-stop.png')
-    ACTION_CONTINUE = SpriteImage(32,256,'fa-play-circle-o.png')
-    ACTION_STOP_WORKFLOW = SpriteImage(16,240,'fa-stop-workflow.png')
-    ACTION_RESULTS = SpriteImage(48,240,'fa-eye.png')
-    ACTION_SAVE = SpriteImage(32,112, 'fa-save.png')
+    RUNS_TREE = SpriteImage(16, 272, 'fa-sitemap.png')
+    ACTION_NEW = SpriteImage(80, 304, 'fa-plus-circle.png')
+    ACTION_EDIT = SpriteImage(32, 272, 'fa-pencil.png')
+    ACTION_SELECT_FROM = SpriteImage(64, 272, 'fa-arrow-down.png')
+    ACTION_SELECT_TO = SpriteImage(64, 256, 'fa-arrow-up.png')
+    ACTION_COPY = SpriteImage(80, 208, 'clipboard-regular.png')
+    ACTION_PASTE = SpriteImage(0, 64, 'paste-solid.png')
+    ACTION_DUPLICATE = SpriteImage(48, 208, 'fa-files-o.png')
+    ACTION_DELETE = SpriteImage(16, 176, 'fa-trash-o.png')
+    ACTION_REFRESH = SpriteImage(32, 144, 'fa-refresh.png')
+    ACTION_RENAME = SpriteImage(0, 48, 'rename.png')
+    ACTION_BROWSE = SpriteImage(32, 304, 'fa-folder-open.png')
+    ACTION_DB = SpriteImage(48, 288, 'fa-database.png')
+    ACTION_STOP = SpriteImage(16, 256, 'fa-stop.png')
+    ACTION_CONTINUE = SpriteImage(32, 256, 'fa-play-circle-o.png')
+    ACTION_STOP_WORKFLOW = SpriteImage(16, 240, 'fa-stop-workflow.png')
+    ACTION_RESULTS = SpriteImage(48, 240, 'fa-eye.png')
+    ACTION_SAVE = SpriteImage(32, 112, 'fa-save.png')
     ACTION_VISUALIZE = ACTION_RESULTS
-    ACTION_WIZ = SpriteImage(32,288,'fa-magic.png')
-    ACTION_HELP = SpriteImage(32,160,'fa-question-circle.png')
-    ACTION_REFERENCES = SpriteImage(48,256,'link')
+    ACTION_WIZ = SpriteImage(32, 288, 'fa-magic.png')
+    ACTION_HELP = SpriteImage(32, 160, 'fa-question-circle.png')
+    ACTION_REFERENCES = SpriteImage(48, 256, 'link')
     ACTION_EXPORT = ACTION_REFERENCES
-    ACTION_EXPORT_UPLOAD = SpriteImage(16,96, 'fa-upload.png')
-    ACTION_SEARCH = SpriteImage(32,96, 'fa-search.png')
-    SETTINGS = SpriteImage(48,304,'fa-cogs.png')
+    ACTION_EXPORT_UPLOAD = SpriteImage(16, 96, 'fa-upload.png')
+    ACTION_SEARCH = SpriteImage(32, 96, 'fa-search.png')
+    SETTINGS = SpriteImage(48, 304, 'fa-cogs.png')
     ACTION_EXECUTE = SETTINGS
-    ACTION_IN = SpriteImage(16,304,'fa-sign-in.png')
-    ACTION_OUT = SpriteImage(16,288,'fa-sign-out.png')
-    ACTION_FIND_NEXT = SpriteImage(32,208,'fa-next.png')
-    ACTION_FIND_PREVIOUS = SpriteImage(32,192,'fa-previous.png')
-    ACTION_COLLAPSE = SpriteImage(32,240,'fa-minus-square.png')
-    ACTION_EXPAND = SpriteImage(32,224,'fa-plus-square.png')
-    ACTION_CIRCLE = SpriteImage(48,192,'circle.png')
+    ACTION_IN = SpriteImage(16, 304, 'fa-sign-in.png')
+    ACTION_OUT = SpriteImage(16, 288, 'fa-sign-out.png')
+    ACTION_FIND_NEXT = SpriteImage(32, 208, 'fa-next.png')
+    ACTION_FIND_PREVIOUS = SpriteImage(32, 192, 'fa-previous.png')
+    ACTION_COLLAPSE = SpriteImage(32, 240, 'fa-minus-square.png')
+    ACTION_EXPAND = SpriteImage(32, 224, 'fa-plus-square.png')
+    ACTION_CIRCLE = SpriteImage(48, 192, 'circle.png')
     ACTION_PICKING = SpriteImage(64, 192, 'picking.png')
     ACTION_STATS = SpriteImage(80, 192, 'stats.png')
     ACTION_ZOOM = SpriteImage(64, 176, 'zoom.png')
@@ -536,38 +522,38 @@ class Icon:
 
 
     # Host template
-    BUTTON_SELECT = SpriteImage(64,224,'fa-check.png')
-    BUTTON_CANCEL = SpriteImage(64,240,'fa-ban.png')
+    BUTTON_SELECT = SpriteImage(64, 224, 'fa-check.png')
+    BUTTON_CANCEL = SpriteImage(64, 240, 'fa-ban.png')
     ACTION_CLOSE = BUTTON_CANCEL
     BUTTON_CLOSE = ACTION_CLOSE
     BUTTON_SAVE = ACTION_SAVE
 
     ARROW_UP = ACTION_SELECT_TO
-    TAGS = SpriteImage(16,224,'fa-tags.png')
-    HOME = SpriteImage(0,304,'fa-home.png')
-    LIGHTBULB = SpriteImage(32,80,'fa-lightbulb-o.png')
-    ROCKET = SpriteImage(32,128, 'fa-rocket.png')
+    TAGS = SpriteImage(16, 224, 'fa-tags.png')
+    HOME = SpriteImage(0, 304, 'fa-home.png')
+    LIGHTBULB = SpriteImage(32, 80, 'fa-lightbulb-o.png')
+    ROCKET = SpriteImage(32, 128, 'fa-rocket.png')
 
     # File browser icons
     FOLDER_OPEN = ACTION_BROWSE
-    DB = SpriteImage(0,144,'file_sqlite.png')
-    TXT_FILE = SpriteImage(0,96,'file_text.png')
-    FILE_VOL = SpriteImage(0,80,'file_vol.png')
-    FILE_STACK = SpriteImage(0,112,'file_stack.png')
-    FILE_STACK_LINK = SpriteImage(0,128, 'file_stack_link.png')
-    PYTHON_FILE = SpriteImage(0,160,'file_python.png')
-    FILE_METADATA = SpriteImage(0,176,'file_md.png')
-    FILE_METADATA_LINK = SpriteImage(0,192, 'file_md_link.png')
-    FILE_IMAGE = SpriteImage(0,208, 'file_image.png')
-    FILE_IMAGE_LINK = SpriteImage(0,224, 'file_image_link.png')
-    FILE = SpriteImage(0,240, 'file_generic.png')
-    FILE_LINK = SpriteImage(0,256, 'file_generic_link.png')
-    FOLDER = SpriteImage(0,272, 'file_folder.png')
-    FOLDER_LINK = SpriteImage(0,288, 'file_folder_link.png')
-
-    BROOM = SpriteImage(80,240,'broom-solid.png')
-    BACKWARD = SpriteImage(80,288,'backward-solid.png')
-    CODE_BRANCH = SpriteImage(64,304,'code-branch-solid.png')
+    DB = SpriteImage(0, 144, 'file_sqlite.png')
+    TXT_FILE = SpriteImage(0, 96, 'file_text.png')
+    FILE_VOL = SpriteImage(0, 80, 'file_vol.png')
+    FILE_STACK = SpriteImage(0, 112, 'file_stack.png')
+    FILE_STACK_LINK = SpriteImage(0, 128, 'file_stack_link.png')
+    PYTHON_FILE = SpriteImage(0, 160, 'file_python.png')
+    FILE_METADATA = SpriteImage(0, 176, 'file_md.png')
+    FILE_METADATA_LINK = SpriteImage(0, 192, 'file_md_link.png')
+    FILE_IMAGE = SpriteImage(0, 208, 'file_image.png')
+    FILE_IMAGE_LINK = SpriteImage(0, 224, 'file_image_link.png')
+    FILE = SpriteImage(0, 240, 'file_generic.png')
+    FILE_LINK = SpriteImage(0, 256, 'file_generic_link.png')
+    FOLDER = SpriteImage(0, 272, 'file_folder.png')
+    FOLDER_LINK = SpriteImage(0, 288, 'file_folder_link.png')
+
+    BROOM = SpriteImage(80, 240, 'broom-solid.png')
+    BACKWARD = SpriteImage(80, 288, 'backward-solid.png')
+    CODE_BRANCH = SpriteImage(64, 304, 'code-branch-solid.png')
 
     # Dialog icons
     ERROR = 'fa-times-circle_alert.png'
@@ -585,20 +571,20 @@ class Icon:
     CHIMERA = 'chimera.png'
 
     # PLUGIN MANAGER ICONS
-    CHECKED = SpriteImage(64,208,'fa-checked.png')
-    UNCHECKED = SpriteImage(16,160,'fa-unchecked.png')
-    INSTALL = SpriteImage(32,64,'fa-install.png')
+    CHECKED = SpriteImage(64, 208, 'fa-checked.png')
+    UNCHECKED = SpriteImage(16, 160, 'fa-unchecked.png')
+    INSTALL = SpriteImage(32, 64, 'fa-install.png')
     UNINSTALL = ACTION_CLOSE
-    TO_INSTALL = SpriteImage(32,256,'fa-to_install.png')
-    INSTALLED = SpriteImage(16, 64,'fa-installed.png')
-    PROCESSING = SpriteImage(32, 176, 'fa-processing.png',48,192)
-    FAILURE = SpriteImage(48,224,'fa-failure.png')
+    TO_INSTALL = SpriteImage(32, 256, 'fa-to_install.png')
+    INSTALLED = SpriteImage(16, 64, 'fa-installed.png')
+    PROCESSING = SpriteImage(32, 176, 'fa-processing.png', 48, 192)
+    FAILURE = SpriteImage(48, 224, 'fa-failure.png')
     DELETE_OPERATION = ACTION_DELETE
-    TO_UPDATE = SpriteImage(32,144,'fa-update.png')
+    TO_UPDATE = SpriteImage(32, 144, 'fa-update.png')
     WAITING = 'wait.gif'
-    ACTION_UNDO = SpriteImage(16,144,'fa-undo.png')
+    ACTION_UNDO = SpriteImage(16, 144, 'fa-undo.png')
 
-    PLUGIN_AUTHORS = SpriteImage(16,80,'users.png')
+    PLUGIN_AUTHORS = SpriteImage(16, 80, 'users.png')
     PLUGIN_DESCRIPTION = FILE_STACK
     PLUGIN_RELEASE_DATE = ACTION_EXPORT_UPLOAD
     PLUGIN_VERSION = FILE_VOL

pyworkflow/utils/utils.py

@@ -22,6 +22,7 @@
 # *
 # **************************************************************************
 import logging
+
 logger = logging.getLogger(__name__)
 
 import contextlib
@@ -36,7 +37,7 @@ import sysconfig
 import bibtexparser
 import numpy as np
 import math
-from pyworkflow.constants import StrColors
+from pyworkflow.constants import StrColors, TRUE_YES_ON_
 from pyworkflow import Config
 
 
@@ -705,7 +706,7 @@ def envVarOn(varName, env=None):
 
 def strToBoolean(string):
     """ Converts a string into a Boolean if the string is on of true, yes, on, 1. Case insensitive."""
-    return string is not None and string.lower() in ['true', 'yes', 'on', '1']
+    return string is not None and string.lower() in TRUE_YES_ON_
 
 def strToDuration(durationStr):
     """ Converts a string representing an elapsed time to seconds

pyworkflow/viewer.py

@@ -133,6 +133,22 @@ class Viewer(object):
         self._keyPressed = args.get('keyPressed', None)
         self._tkRoot = self.formWindow.root if self.formWindow else None
 
+    @classmethod
+    def can_handle_this(cls, classHierarchy, instance=None):
+        """ Returns none if it cannot handle the instance, otherwise returns which of the
+        classes of the hierarchy it targets (used for establishing priority"""
+
+        for t in cls._targets:
+            if t in classHierarchy:
+
+                if instance is not None and not cls.can_handle_this_instance(instance):
+                    return None
+                else:
+                    return t
+
+    @classmethod
+    def can_handle_this_instance(cls, instance):
+        return True
     def getKeyPressed(self):
         return self._keyPressed
 
@@ -222,6 +238,8 @@ class ProtocolViewer(Viewer, pwprot.Protocol):
     If should provide a mapping between form params and the corresponding
     functions that will return the corresponding Views.
     """
+
+    _label ="Protocol viewer"
     def __init__(self, **kwargs):
         # Here we are going to intercept the original _defineParams function
         # and replace by an empty one, this is to postpone the definition of 
@@ -241,7 +259,11 @@ class ProtocolViewer(Viewer, pwprot.Protocol):
         
     def getWindow(self):
         return self.formWindow
-    
+
+    @classmethod
+    def getName(cls):
+        return cls._label
+
     def getTkRoot(self):
         return self._tkRoot
     

pyworkflow/webservices/config.py

@@ -1,9 +1,6 @@
 # Variable related to the online services (workflow stats and repository) that Scipion reports to or communicate.
 # These variables may change between Scipion versions but do not depend on the user or system
 
-# Web that gathers protocol usage
-SCIPION_STATS_SERVER = 'https://scipion.i2pc.es'
-SCIPION_STATS_WORKFLOW_APP = SCIPION_STATS_SERVER + '/report_protocols/api/workflow/workflow/'
 
 # Web that handles workflows
 WORKFLOW_REPOSITORY_SERVER = 'https://workflows.scipion.i2pc.es/'

pyworkflow/webservices/notifier.py

@@ -34,9 +34,9 @@ from datetime import timedelta, datetime
 from urllib.parse import urlencode
 from urllib.request import build_opener, HTTPHandler
 
-import pyworkflow
 import pyworkflow.utils as pwutils
-from . import config
+from pyworkflow import Config
+
 
 
 class ProjectWorkflowNotifier(object):
@@ -79,18 +79,32 @@ class ProjectWorkflowNotifier(object):
 
         return delta < timedelta(seconds=seconds)
 
-    def _sendData(self, url, dataDict=None):
+    def _sendData(self, url, project_workflow):
         try:
             # then connect to webserver a send json
             # set debuglevel=0 for no messages
+
+            dataDict = {'project_uuid': self._getUuid(),
+                        'project_workflow': project_workflow}
+
             opener = build_opener(HTTPHandler(debuglevel=0))
             data = urlencode(dataDict).encode()
-            content = opener.open(url, data=data).read()
+            opener.open(url, data=data).read()
+
+            # Store file time stamp with last time it was sent
             now = time.time()
             os.utime(self._getUuidFileName(), (now, now))
+
+            # Write what was sent in a file for _modifiedBefore to check file TS and avoid resending stats
+            dataFile = self._getDataFileName()
+            # create the folder of the file path if not exists
+            pwutils.makeFilePath(dataFile)
+            with open(dataFile, 'w') as f:
+                f.write(project_workflow)
+
         except Exception as e:
+            # Tolerate errors
             pass
-            # print("Could not notify, maybe there is not internet connection.")
 
     def _dataModified(self, projectWorfklow):
         try:
@@ -106,12 +120,13 @@ class ProjectWorkflowNotifier(object):
 
         try:
             # check if environment exists otherwise abort
-            if not pyworkflow.Config.SCIPION_NOTIFY:
+            if not Config.SCIPION_NOTIFY:
                 return
 
             # if project specifies not to send stats
             if self._isProjectMuted():
                 return
+
             # Check the seconds range of the notify, by default one day
             seconds = int(os.environ.get('SCIPION_NOTIFY_SECONDS', '86400'))
 
@@ -120,28 +135,11 @@ class ProjectWorkflowNotifier(object):
 
             # INFO: now we are only sending the protocols names in the project.
             # We could pass namesOnly=False to get the full workflow template
-            projectWorfklow = self.project.getProtocolsJson(namesOnly=True)
-
-            # if list with workflow has not been altered do not sent it
-            if not self._dataModified(projectWorfklow):
-                return
-            else:
-                # For compatibility with version 1.0 check
-                # if Log directory exists. If it does not
-                # create it
-                # TODO: REMOVE this check in scipion 1.3
-                dataFile = self._getDataFileName()
-                # create the folder of the file path if not exists
-                pwutils.makeFilePath(dataFile)
-                with open(dataFile, 'w') as f:
-                    f.write(projectWorfklow)
-            dataDict = {'project_uuid': self._getUuid(),
-                        'project_workflow': projectWorfklow}
+            project_workflow = self.project.getProjectUsage().toJSON()  # self.project.getProtocolsJson(namesOnly=True)
 
-            urlName = os.environ.get('SCIPION_NOTIFY_URL',
-                                     config.SCIPION_STATS_WORKFLOW_APP).strip()
+            urlName = Config.SCIPION_STATS_WORKFLOW_APP.strip()
             urlName += "addOrUpdateWorkflow/"
-            t = threading.Thread(name="notifier", target=lambda: self._sendData(urlName, dataDict))
+            t = threading.Thread(name="notifier", target=lambda: self._sendData(urlName, project_workflow))
             t.start()  # will execute function in a separate thread
         except Exception as e:
             print("Can't report usage: ", e)
@@ -152,11 +150,3 @@ class ProjectWorkflowNotifier(object):
         a test and therefore no statistics will be sent"""
         return os.path.basename(self.project.name).startswith("Test")
 
-    def getEntryFromWebservice(self, uuid):
-        if not pyworkflow.Config.SCIPION_NOTIFY:
-            return
-        urlName = os.environ.get('SCIPION_NOTIFY_URL').strip()
-        # remove last directory
-        urlName = os.path.split(urlName)[0]
-        url = urlName + "/?project_uuid=" + uuid
-        resultDict = self._sendData(url)

pyworkflowtests/protocols.py

@@ -69,9 +69,7 @@ class ParallelSleepingProtocol(SleepingProtocol):
 class ConcurrencyProtocol(SleepingProtocol):
     """ Protocol to test concurrency access to sets"""
 
-    def __init__(self, **kwargs):
-        super().__init__(**kwargs)
-        self.stepsExecutionMode = pwprot.STEPS_PARALLEL
+    stepsExecutionMode = pwprot.STEPS_PARALLEL
 
     def _defineParams(self, form):
         form.addParallelSection(threads=2, mpi=0)

pyworkflowtests/tests/test_protocol_execution.py

@@ -98,6 +98,10 @@ class TestProtocolExecution(pwtests.BaseTest):
 
 
         currThread = threading.currentThread()
+        def needForGPU():
+            return True
+
+        currThread.needsGPU =needForGPU
         currThread.thId = 1
         self.assertEqual(stepExecutor.getGpuList(),[], "Gpu list should be empty")
 

{scipion_pyworkflow-3.10.6.dist-info → scipion_pyworkflow-3.11.1.dist-info}/METADATA

@@ -1,22 +1,15 @@
 Metadata-Version: 2.4
 Name: scipion-pyworkflow
-Version: 3.10.6
-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
-Author-email: delarosatrevin@scilifelab.se, roberto@cnb.csic.es, gsharov@mrc-lmb.cam.ac.uk, josue.gomez-blanco@mcgill.ca, pconesa@cnb.csic.es, fonsecareyna@cnb.csic.es
-Project-URL: Bug Reports, https://github.com/scipion-em/scipion-pyworkflow/issues
-Project-URL: Source, https://github.com/scipion-em/scipion-pyworkflow/
-Keywords: workflows science electron-microscopy cryo-em structural-biology image-processing scipion
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Topic :: Scientific/Engineering
+Version: 3.11.1
+Summary: Workflow platform used in scientific applications, initially developed within the Scipion framework for image processing in Electron Microscopy but generic by design to be applied to any domain.
+Author-email: Pablo Conesa <pconesa@cnb.csic.es>, Yunior Fonseca <cfonseca@cnb.csic.es>, "J.M. De la Rosa Trevin" <josemiguel.delarosatrevin@stjude.org>, Roberto Marabini <roberto@cnb.csic.es>, Grigory Sharov <sharov.grigory@gmail.com>, Josue Gomez Blanco <josue.gomez-blanco@mcgill.ca>
+License: GNU General Public License v3 (GPLv3)
+Project-URL: Homepage, https://scipion.i2pc.es
+Project-URL: Repository, https://github.com/scipion-em/scipion-pyworkflow
+Project-URL: Issues, https://github.com/scipion-em/scipion-pyworkflow/issues
+Keywords: scipion,electron-microscopy,cryo-em,structural-biology,generic-workflow-engine,image-processing,scipion-3.0
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
 License-File: LICENSE.txt
 Requires-Dist: bibtexparser<=1.4.1
 Requires-Dist: psutil<=5.9.6
@@ -27,19 +20,12 @@ Requires-Dist: pillow==10.1.0; python_version >= "3.8"
 Requires-Dist: numpy==1.24.4; python_version == "3.8"
 Requires-Dist: numpy==1.26.1; python_version >= "3.9"
 Requires-Dist: requests==2.31.0; python_version >= "3.8"
-Requires-Dist: tkcolorpicker
+Requires-Dist: tkcolorpicker2
 Requires-Dist: distro<=1.8
 Requires-Dist: importlib-metadata<=6.8.0
-Dynamic: author
-Dynamic: author-email
-Dynamic: classifier
-Dynamic: description
-Dynamic: home-page
-Dynamic: keywords
+Requires-Dist: setuptools>=62.6
+Requires-Dist: pyperclip==1.9.0
 Dynamic: license-file
-Dynamic: project-url
-Dynamic: requires-dist
-Dynamic: summary
 
 .. image:: https://img.shields.io/pypi/v/scipion-pyworkflow.svg
         :target: https://pypi.python.org/pypi/scipion-pyworkflow