scipion-pyworkflow 3.11.1__py3-none-any.whl → 3.11.2__py3-none-any.whl

pyworkflow/apps/pw_project.py

@@ -30,8 +30,9 @@ Launch main project window
 
 import sys
 import os
+from subprocess import Popen
 
-from pyworkflow import Config
+from pyworkflow import Config, PYTHON
 from pyworkflow.project import Manager
 from pyworkflow.gui.project import ProjectWindow
 import pyworkflow.utils as pwutils
@@ -89,12 +90,28 @@ def openProject(projectName):
     projPath = manager.getProjectPath(projName)
 
     if os.path.exists(projPath):
-        projWindow = ProjectWindow(projPath)
-        projWindow.show()
+
+        # This opens the project in the same process as the launcher. This is good for directly debugging code
+        # but  does not allow -O or not execution (usage of __debug__ flag).
+        # All we can do is to go straight to loading the project if debug is active or running optimized.
+        if Config.debugOn() or not __debug__:
+
+
+            # This may or may not be run Optimized (-O). It depends on the call to scipion last (launcher)
+            print("Launching project in debug or optimized...")
+            projWindow = ProjectWindow(projPath)
+            projWindow.show()
+        else:
+
+            # Run this same  script optimized: Defined in scipion module under scipion-app: Circular definition. To fix! Bad design.
+            print("Launching project optimized...")
+            Popen([PYTHON, "-O", "-m","scipion", "project", projectName])
+
+
     else:
         print("Can't open project %s. It does not exist" % projPath)
 
-        #Show the list of projects
+        # Show the list of projects
         showProjectList(manager)
 
 def showProjectList(manager):

pyworkflow/apps/pw_run_tests.py

@@ -166,7 +166,8 @@ class Tester:
         """ Show the list of tests available """
         mode = self.mode
 
-        assert mode in ['modules', 'classes', 'onlyclasses', 'all'], 'Unknown mode %s' % mode
+        if mode not in ['modules', 'classes', 'onlyclasses', 'all']:
+            raise AssertionError('Unknown mode %s' % mode)
 
         # First flatten the list of tests.
         # testsFlat = list(iter(self.__iterTests(tests)))

pyworkflow/apps/pw_sync_data.py

@@ -278,8 +278,8 @@ def download(dataset, destination=None, url=None, verbose=False):
                 urlopen('%s/%s/%s' % (url, dataset, fname)))
 
             md5 = md5sum(fpath)
-            assert md5 == md5Remote, \
-                "Bad md5. Expected: %s Computed: %s" % (md5Remote, md5)
+            if md5 != md5Remote:
+                raise AssertionError("Bad md5. Expected: %s Computed: %s" % (md5Remote, md5))
 
             done += inc
             if verbose:
@@ -315,7 +315,8 @@ def update(dataset, workingCopy=None, url=None, verbose=False):
     try:
         last = max(os.stat(join(datasetFolder, x)).st_mtime for x in md5sRemote)
         t_manifest = os.stat(join(datasetFolder, 'MANIFEST')).st_mtime
-        assert t_manifest > last and time.time() - t_manifest < 60*60*24*7
+        if not (t_manifest > last and time.time() - t_manifest < 60*60*24*7):
+            raise AssertionError("Manifest times seems to be wrong.")
     except (OSError, IOError, AssertionError) as e:
         logger.info("Regenerating local MANIFEST...")
         createMANIFEST(datasetFolder)

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 = '3.11.1'
+VERSION_3_0 = '3.11.2'
 
 # 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/gui/browser.py

@@ -72,6 +72,10 @@ class ObjectBrowser(tk.Frame):
         p.grid(row=0, column=0, sticky='news')
 
         leftPanel = tk.Frame(p)
+
+        # Optional, widget to get the focus
+        self.initial_focus=None
+
         self._fillLeftPanel(leftPanel)
         p.add(leftPanel, padx=5, pady=5)
         p.paneconfig(leftPanel, minsize=300)
@@ -88,6 +92,7 @@ class ObjectBrowser(tk.Frame):
     def _fillLeftPanel(self, frame):
         gui.configureWeigths(frame)
         self.tree = BoundTree(frame, self.treeProvider, style=LIST_TREEVIEW)
+        self.initial_focus=self.tree
         self.tree.grid(row=0, column=0, sticky='news')
         self.itemConfig = self.tree.itemConfig
         self.getImage = self.tree.getImage
@@ -489,6 +494,7 @@ class FileBrowser(ObjectBrowser):
         pathLabel.grid(row=0, column=0, padx=0, pady=3)
         pathEntry = tk.Entry(pathFrame, bg='white', width=65,
                              textvariable=self.pathVar, font=gui.getDefaultFont())
+        self.initial_focus=pathEntry
         pathEntry.grid(row=0, column=1, sticky='new', pady=3)
         pathEntry.bind("<Return>", self._onEnterPath)
         pathEntry.bind("<KP_Enter>", self._onEnterPath)
@@ -711,6 +717,8 @@ class BrowserWindow(gui.Window):
         browser.grid(row=row, column=column, sticky='news')
         self.itemConfig = browser.tree.itemConfig
 
+        if browser.initial_focus is not None:
+            self.initial_focus = browser.initial_focus
 
 STANDARD_IMAGE_EXTENSIONS = ['.png', '.jpg', '.jpeg']
 

pyworkflow/gui/dialog.py

@@ -644,7 +644,7 @@ class ListDialog(Dialog):
             label = tk.Label(bodyFrame, text=self.message, compound=tk.LEFT,
                              image=self.getImage(Icon.LIGHTBULB))
             label.grid(row=2, column=0, sticky='nw', padx=5, pady=5)
-        self.initial_focus = self.tree
+        # CAncel this, now focus is set to the search box. self.initial_focus = self.tree
 
     def _createTree(self, parent):
         self.tree = BoundTree(parent, self.provider, selectmode=self._selectmode, style=LIST_TREEVIEW)
@@ -677,6 +677,7 @@ class ListDialog(Dialog):
         self.entry.bind('<KeyRelease>', self._onSearch)
         self.entry.focus_set()
         self.entry.grid(row=0, column=1, sticky='news')
+        self.initial_focus=self.entry
         self.searchBoxframe.grid(row=0, column=0, sticky='news', padx=5,
                                  pady=(10, 5))
 
@@ -910,6 +911,7 @@ class SearchBaseWindow(Window):
         entry.bind(TK.ENTER, self._onSearchClick)
         entry.focus_set()
         entry.grid(row=0, column=1, sticky='nw')
+        self.initial_focus=entry
         btn = widgets.IconButton(frame, "Search",
                                  imagePath=Icon.ACTION_SEARCH,
                                  command=self._onSearchClick)

pyworkflow/gui/form.py

@@ -1937,6 +1937,7 @@ class FormWindow(Window):
         self.waitForVar.set(', '.join(self.protocol.getPrerequisites()))
         entryWf = tk.Entry(runFrame, font=self.font, width=25,
                            textvariable=self.waitForVar)
+        self.initial_focus = entryWf
         entryWf.grid(row=r, column=c + 1, padx=(0, 5), pady=5, sticky='ew')
 
         self.waitForVar.trace('w', self._setWaitFor)

pyworkflow/gui/gui.py

@@ -371,6 +371,8 @@ class Window:
         self.master = masterWindow
         setCommonFonts(self)
 
+        self.initial_focus = None
+
         if kwargs.get('enableQueue', False):
             self.queue = queue.Queue(maxsize=0)
         else:
@@ -451,6 +453,9 @@ class Window:
         if self.queue is not None:
             self._queueTimer = self.root.after(1000, self.__processQueue)
 
+        if self.initial_focus is not None:
+            self.initial_focus.focus_set()
+
         if modal:
             self.root.wait_window(self.root)
         else:

pyworkflow/gui/project/base.py

@@ -92,7 +92,8 @@ class ProjectBaseWindow(Window):
         logoLabel = tk.Label(header, image=logoImg, 
                              borderwidth=0, anchor='nw', bg=pw.Config.SCIPION_BG_COLOR)
         logoLabel.grid(row=0, column=0, sticky='nw', padx=(5, 0), pady=5)
-        version = "%s - %s (core)" % (os.environ.get('SCIPION_VERSION', ""), pw.LAST_VERSION)
+
+        version = "%s - %s (core%s)" % (os.environ.get('SCIPION_VERSION', ""), pw.LAST_VERSION, ' optimized'if not __debug__ else '')
 
         versionLabel = tk.Label(header, text=version,
                                 bg=pw.Config.SCIPION_BG_COLOR)

pyworkflow/gui/project/searchprotocol.py

@@ -24,6 +24,8 @@
 # **************************************************************************
 """ This module contains the provider and dialog to search for a protocol"""
 import tkinter as tk
+import logging
+logger = logging.getLogger(__name__)
 from pyworkflow import Config
 import pyworkflow.gui as pwgui
 import pyworkflow.object as pwobj
@@ -35,12 +37,9 @@ from pyworkflow.project.usage import getNextProtocolSuggestions
 from pyworkflow.utils import Icon
 
 UPDATED = "updated"
-
 NEW = "new"
-
 BETA = "beta"
 
-
 class ProtocolTreeProvider(pwgui.tree.ObjectTreeProvider):
     """Create the tree elements for a Protocol run"""
 
@@ -81,6 +80,7 @@ class SearchProtocolWindow(SearchBaseWindow):
                          title="Add a protocol" + posStr)
 
         self.root.bind("<FocusIn>", self._onWindowFocusIn)
+        self.root.focus()
 
     def _onWindowFocusIn(self, event):
         """
@@ -92,6 +92,8 @@ class SearchProtocolWindow(SearchBaseWindow):
             self.selectedProtocol = self.selectionGetter()
             if self._isSuggestionActive():
                 self._onSearchClick()
+        self.initial_focus.focus_set()
+
     def _isSuggestionActive(self):
         """
         :return: Returns true if current mode is suggestion mode.

pyworkflow/gui/project/viewprojects.py

@@ -220,7 +220,16 @@ class ProjectsView(tk.Frame):
     def openProject(self, projName):
         from subprocess import Popen
         script = pw.join(pw.APPS, 'pw_project.py')
-        Popen([pw.PYTHON, script, projName])
+        args=[pw.PYTHON, "-O", script, projName]
+
+        # Launcher is the ona calling this process. Since launcher does not deal
+        # with __debug__ we should use the variable in the config
+        if pw.Config.debugOn():
+            # If not optimizing code, remove -O
+            logger.warning(f"Launching project {projName} in debug mode.")
+            del args[1]
+
+        Popen(args)
 
     def deleteProject(self, projInfo):
 

pyworkflow/gui/project/viewprotocols.py

@@ -85,10 +85,23 @@ class ProtocolsView(tk.Frame):
                     SIZE_1GB: "orange",
                     SIZE_1TB: "red"}
 
+    _actionList = [
+        ACTION_NEW, ACTION_EDIT, ACTION_RENAME, ACTION_DUPLICATE, ACTION_COPY, ACTION_PASTE, ACTION_DELETE,
+        ACTION_BROWSE,
+        ACTION_STOP, ACTION_STOP_WORKFLOW, ACTION_CONTINUE, ACTION_CONTINUE_WORKFLOW, ACTION_RESTART_WORKFLOW,
+        ACTION_RESET_WORKFLOW,
+        ACTION_RESULTS,
+        ACTION_EXPORT, ACTION_EXPORT_UPLOAD,
+        ACTION_COLLAPSE, ACTION_EXPAND,
+        ACTION_LABELS, ACTION_SEARCH,
+        ACTION_SELECT_FROM, ACTION_SELECT_TO,
+        ACTION_STEPS, ACTION_DB
+    ]
     _protocolViews = None
 
     def __init__(self, parent, window, **args):
         tk.Frame.__init__(self, parent, **args)
+
         # Load global configuration
         self.window = window
         self.project = window.project
@@ -110,6 +123,8 @@ class ProtocolsView(tk.Frame):
         self.root.bind("<Control-t>", self._toggleColorScheme)
         self.root.bind("<Control-D>", self._toggleDebug)
         self.root.bind("<Control-l>", self._locateProtocol)
+        # Bind to root "focus in"
+        self.root.bind("<FocusIn>", self._onWindowFocusIn)
 
         if Config.debugOn():
             self.root.bind("<Control-i>", self._inspectProtocols)
@@ -295,6 +310,11 @@ class ProtocolsView(tk.Frame):
 
         return p
 
+    def _onWindowFocusIn(self, event):
+        """ Refresh on windows get focus """
+        if event.widget == self.root:
+            self.runsGraphCanvas.focus_set()
+
     def _viewObject(self, objId):
         """ Call appropriate viewer for objId. """
         proj = self.project
@@ -442,17 +462,6 @@ class ProtocolsView(tk.Frame):
         """ Prepare the buttons that will be available for protocol actions. """
 
         self.actionButtons = {}
-        actionList = [
-            ACTION_NEW, ACTION_EDIT, ACTION_RENAME, ACTION_DUPLICATE, ACTION_COPY, ACTION_PASTE,  ACTION_DELETE,
-            ACTION_BROWSE,
-            ACTION_STOP, ACTION_STOP_WORKFLOW, ACTION_CONTINUE, ACTION_CONTINUE_WORKFLOW, ACTION_RESTART_WORKFLOW, ACTION_RESET_WORKFLOW,
-            ACTION_RESULTS,
-            ACTION_EXPORT, ACTION_EXPORT_UPLOAD,
-            ACTION_COLLAPSE, ACTION_EXPAND,
-            ACTION_LABELS, ACTION_SEARCH,
-            ACTION_SELECT_FROM, ACTION_SELECT_TO,
-            ACTION_STEPS, ACTION_DB
-        ]
 
         def addButton(action, text, toolbar):
 
@@ -464,17 +473,16 @@ class ProtocolsView(tk.Frame):
             callback = lambda e: self._runActionClicked(action, event=e)
             btn.bind(TK.LEFT_CLICK, callback)
 
-            # Shortcuts:
+            # Shortcuts, these are bind later!!
             shortCut = ActionShortCuts.get(action, None)
             if shortCut:
                 text += " (%s)" % shortCut
-                self.root.bind(shortCut, callback)
 
             ToolTip(btn, text, 500)
 
             return btn
 
-        for action in actionList:
+        for action in self._actionList:
             self.actionButtons[action] = addButton(action, action,
                                                    self.runsToolbar)
 
@@ -745,6 +753,17 @@ class ProtocolsView(tk.Frame):
 
         self.updateRunsGraph()
 
+        # Shortcuts for actions
+        for action in self._actionList:
+
+            # prevent "late binding closure" by passing action as a default value for the lambda param.
+            callback = lambda e, my_action=action: self._runActionClicked(my_action, event=e)
+
+            # Shortcuts:
+            shortCut = ActionShortCuts.get(action, None)
+            if shortCut:
+                self.runsGraphCanvas.bind(shortCut, callback)
+
     def updateRunsGraph(self, refresh=False, checkPids=False, position=None):
 
         self.runsGraph = self.project.getRunsGraph(refresh=refresh,
@@ -1215,9 +1234,15 @@ class ProtocolsView(tk.Frame):
         self._selectItemProtocol(prot)
 
     def _runItemDoubleClick(self, item=None, e=None):
-        if item.nodeInfo.isExpanded():
+
+        if self.runsView == VIEW_LIST:
             self._runActionClicked(ACTION_EDIT)
 
+        elif item.nodeInfo.isExpanded():
+            self._runActionClicked(ACTION_EDIT)
+        else:
+            self._runActionClicked(ACTION_EXPAND)
+
     def _runItemMiddleClick(self, e=None):
         self._runActionClicked(ACTION_SELECT_TO)
 
@@ -1612,7 +1637,7 @@ class ProtocolsView(tk.Frame):
 
             self.project.loadProtocols(jsonStr=self.clipboard_get())
             self.info("Clipboard content pasted successfully.")
-            self.updateRunsGraph(False)
+            self.updateRunsGraph(True)
         except Exception as e:
             self.info("Paste failed, maybe clipboard content is not valid content? See GUI log for details.")
             logger.error("Clipboard content couldn't be pasted." , exc_info=e)
@@ -1988,7 +2013,7 @@ class ProtocolsView(tk.Frame):
         if event is not None:
             # log Search box events are reaching here
             # Since this method is bound to the window events
-            if event.widget.widgetName == 'entry':
+            if event.widget.widgetName in ['text', 'entry']:
                 return
 
         # Following actions do not need a select run

pyworkflow/gui/text.py

@@ -170,6 +170,7 @@ class Text(tk.Text, Scrollable):
         # Associate with right click
         self.bind("<Button-1>", self.onClick)
         self.bind("<Button-3>", self.onRightClick)
+        self.bind("Control-c", self.copyToClipboard)
         
     def getDefaults(self):
         """This should be implemented in subclasses to provide defaults"""
@@ -234,6 +235,7 @@ class Text(tk.Text, Scrollable):
     def copyToClipboard(self, e=None):
         self.clipboard_clear()
         self.clipboard_append(self.selection)
+        return "break"
 
     def openFile(self):
         # What happens when you right-click and select "Open path"
@@ -508,7 +510,7 @@ class TextFileViewer(tk.Frame):
         self.maxSize = maxSize
         self.width = width
         self.height = height
-
+        self.searchEntry = None
         self.createWidgets(fileList)
         self.master = master
         self.addBinding()
@@ -755,6 +757,7 @@ def openTextFileEditor(filename, tkParent=None):
 def showTextFileViewer(title, filelist, parent=None, main=False):
     w = gui.Window(title, parent, minsize=(600, 400))
     viewer = TextFileViewer(w.root, filelist, maxSize=-1, font=w.font)
+    w.initial_focus=viewer.searchEntry
     viewer.grid(row=0, column=0, sticky='news')
     gui.configureWeigths(w.root)
     w.show()

pyworkflow/mapper/mapper.py

@@ -84,6 +84,10 @@ class Mapper:
 
         try:
             instance = self.dictClasses[className]()
+
+            if __debug__:
+                logger.debug("Object instantiated of class %s", className)
+
         except Exception as e:
             clazz = self.dictClasses._default
             logger.error('Class %s could not be created. Replacing it with %s ' % (className, clazz.__name__), exc_info=e)

pyworkflow/mapper/sqlite.py

@@ -187,6 +187,10 @@ class SqliteMapper(Mapper):
         """Build the object which id is objId"""
         if objId in self.objDict:
             obj = self.objDict[objId]
+
+            if __debug__:
+                # If not optimized code
+                logger.debug("Object with id %s already loaded: %s", objId, obj)
         else:
             objRow = self.db.selectObjectById(objId)
             if objRow is None:
@@ -211,10 +215,8 @@ class SqliteMapper(Mapper):
         rowName = self._getStrValue(objRow['name'])
 
         if not hasattr(obj, ID_ATTRIBUTE):
-            raise Exception("Entry '%s' (id=%s) in the database, stored as '%s'"
-                            ", is being mapped to %s object. " %
-                            (rowName, rowId,
-                             objRow['classname'], type(obj)))
+            raise Exception(f"Entry '{rowName}' (id={rowId}) in the database, stored as '{objRow['classname']}'"
+                            f", is being mapped to {type(obj)} object.")
 
         obj._objId = rowId
 
@@ -880,7 +882,7 @@ class SqliteFlatMapper(Mapper):
         self.db.deleteAll()
                 
     def delete(self, obj):
-        """Delete an object and all its childs"""
+        """Delete an object and all its children"""
         self.db.deleteObject(obj.getObjId())
     
     def updateTo(self, obj, level=1):

pyworkflow/object.py

@@ -1344,6 +1344,7 @@ class Set(Object):
         else:
             self._idCount = max(self._idCount, item.getObjId())
         self._insertItem(item)
+        # FIXME: Incrementing always!! When updating this is wrong.
         self._size.increment()
 
     def _insertItem(self, item):

pyworkflow/plugin.py

@@ -410,11 +410,11 @@ class Domain:
                                                           viewerClassName,
                                                           doRaise=True)
                         viewers.append(prefViewer)
-                    except Exception as e:
-                        logger.error("Couldn't load \"%s\" as preferred viewer for %s.\n"
+                    except Exception:
+                        logger.info("Couldn't load \"%s\" as preferred viewer for %s.\n"
                               "There might be a typo in your VIEWERS variable "
-                              "or an error in the viewer's plugin installation"
-                              % (prefViewerStr, className), exc_info=e)
+                              "or an error in the viewer's plugin installation or simply the plugin is not installed."
+                              % (prefViewerStr, target))
 
                 cls._preferred_viewers[target] = viewers
 

pyworkflow/protocol/executor.py

@@ -31,6 +31,7 @@ using different threads and the last one with MPI processes.
 """
 
 import logging
+
 logger = logging.getLogger(__name__)
 import time
 import datetime
@@ -47,6 +48,7 @@ from .launch import _submit, UNKNOWN_JOBID, _checkJobStatus
 
 class StepExecutor:
     """ Run a list of Protocol steps. """
+
     def __init__(self, hostConfig, **kwargs):
         self.hostConfig = hostConfig
         self.gpuList = kwargs.get(cts.GPU_LIST, None)
@@ -56,11 +58,22 @@ class StepExecutor:
         """ Return the GPU list assigned to current thread. """
         return self.gpuList
 
+    def getGpuListStr(self, sep=" "):
+        """ Returns the GPU list assigned to the current thread as string
+        :param sep: default ot space. Pass "," or other string to use a separator
+        """
+        return sep.join(map(str, self.getGpuList()))
+
+    def setCudaVisibleDevices(self):
+        """ sets CUDA_VISIBLE DEVICES in the environment to the available GPUs in turn"""
+        # https://developer.nvidia.com/blog/cuda-pro-tip-control-gpu-visibility-cuda_visible_devices/
+        os.environ["CUDA_VISIBLE_DEVICES"] = self.getGpuListStr(",")
+
     def setProtocol(self, protocol):
         """ Set protocol to append active jobs to its jobIds. """
         self.protocol = protocol
 
-    def runJob(self, log, programName, params,           
+    def runJob(self, log, programName, params,
                numberOfMpi=1, numberOfThreads=1,
                env=None, cwd=None, executable=None):
         """ This function is a wrapper around runJob, 
@@ -69,7 +82,8 @@ class StepExecutor:
         process.runJob(log, programName, params,
                        numberOfMpi, numberOfThreads,
                        self.hostConfig,
-                       env=env, cwd=cwd, gpuList=self._getGPUListForCommand(programName, params), executable=executable, context=self.protocol.getSubmitDict())
+                       env=env, cwd=cwd, gpuList=self._getGPUListForCommand(programName, params), executable=executable,
+                       context=self.protocol.getSubmitDict())
 
     def _getGPUListForCommand(self, program, params):
         """ Returns the list of GPUs if the program or the params have the GPU placeholder %(GPU)s """
@@ -86,13 +100,14 @@ class StepExecutor:
 
         for s in steps:
             if (s.getStatus() == cts.STATUS_NEW and
-                    all(steps[i-1].isFinished() for i in s._prerequisites)):
+                    all(steps[i - 1].isFinished() for i in s._prerequisites)):
 
                 if self._isStepRunnable(s):
                     rs.append(s)
                     if len(rs) == n:
                         break
         return rs
+
     def _isStepRunnable(self, step):
         """ Should be implemented by inherited classes to test extra conditions """
         return True
@@ -102,9 +117,9 @@ class StepExecutor:
         that can be done and thus enable other steps to be executed.
         """
         return any(s.isRunning() or s.isWaiting() for s in steps)
-    
-    def runSteps(self, steps, 
-                 stepStartedCallback, 
+
+    def runSteps(self, steps,
+                 stepStartedCallback,
                  stepFinishedCallback,
                  stepsCheckCallback,
                  stepsCheckSecs=3):
@@ -128,15 +143,15 @@ class StepExecutor:
                 stepStartedCallback(step)
                 step.run()
                 doContinue = stepFinishedCallback(step)
-            
+
                 if not doContinue:
                     break
 
             elif self._arePending(steps):
-                # We have not found any runnable step, but still there
+                # We have not found any runnable step, but still
                 # there are some running or waiting for dependencies
                 # So, let's wait a bit to check if something changes
-                time.sleep(0.5)
+                time.sleep(3)
             else:
                 # No steps to run, neither running or waiting
                 # So, we are done, either failed or finished :)
@@ -152,6 +167,7 @@ class StepExecutor:
 
 class StepThread(threading.Thread):
     """ Thread to run Steps in parallel. """
+
     def __init__(self, step, lock):
         threading.Thread.__init__(self)
         self.thId = step.getObjId()
@@ -167,7 +183,7 @@ class StepThread(threading.Thread):
             self.step._run()  # not self.step.run() , to avoid race conditions
         except Exception as e:
             error = str(e)
-            logger.error("Couldn't run the code in a thread." , exc_info=e)
+            logger.error("Couldn't run the code in a thread.", exc_info=e)
         finally:
             with self.lock:
                 if error is None:
@@ -178,6 +194,7 @@ class StepThread(threading.Thread):
 
 class ThreadStepExecutor(StepExecutor):
     """ Run steps in parallel using threads. """
+
     def __init__(self, hostConfig, nThreads, **kwargs):
         StepExecutor.__init__(self, hostConfig, **kwargs)
         self.numberOfProcs = nThreads
@@ -194,7 +211,7 @@ class ThreadStepExecutor(StepExecutor):
             nThreads = self.numberOfProcs
 
             # Nodes: each concurrent steps
-            nodes = range(1, nThreads+1)
+            nodes = range(1, nThreads + 1)
 
             # Number of GPUs
             nGpu = len(self.gpuList)
@@ -215,8 +232,8 @@ class ThreadStepExecutor(StepExecutor):
                     # Node 0 : GPU 0 1
                     # Node 1 : GPU 2
 
-                    extraGpu = 1 if spare>0 else 0
-                    toPos = fromPos + step +extraGpu
+                    extraGpu = 1 if spare > 0 else 0
+                    toPos = fromPos + step + extraGpu
                     gpusForNode = list(self.gpuList[fromPos:toPos])
 
                     newGpusForNode = self.cleanVoidGPUs(gpusForNode)
@@ -227,7 +244,7 @@ class ThreadStepExecutor(StepExecutor):
                         self.gpuDict[-node] = newGpusForNode
 
                     fromPos = toPos
-                    spare-=1
+                    spare -= 1
 
             else:
                 # Expand gpuList repeating until reach nThreads items
@@ -244,10 +261,10 @@ class ThreadStepExecutor(StepExecutor):
                     else:
                         logger.info("GPU slot for gpu %s." % gpu)
                         # Any negative number in the key means a free gpu slot. can't be 0!
-                        self.gpuDict[-index-1] = [gpu]
+                        self.gpuDict[-index - 1] = [gpu]
 
     def cleanVoidGPUs(self, gpuList):
-        newGPUList=[]
+        newGPUList = []
         for gpuid in gpuList:
             if gpuid == cts.VOID_GPU:
                 logger.info("Void GPU detected in %s" % gpuList)
@@ -280,10 +297,12 @@ class ThreadStepExecutor(StepExecutor):
 
                 gpus = self.getFreeGpuSlot(nodeId)
                 if gpus is None:
-                    logger.warning("Step on node %s is requesting GPUs but there isn't any available. Review configuration of threads/GPUs. Returning an empty list." % nodeId)
+                    logger.warning(
+                        "Step on node %s is requesting GPUs but there isn't any available. Review configuration of threads/GPUs. Returning an empty list." % nodeId)
                     return []
                 else:
                     return gpus
+
     def getFreeGpuSlot(self, stepId=None):
         """ Returns a free gpu slot available or None. If node is passed it also reserves it for that node
 
@@ -303,6 +322,7 @@ class ThreadStepExecutor(StepExecutor):
                 return gpus
 
         return None
+
     def freeGpusSlot(self, node):
         gpus = self.gpuDict.get(node, None)
 
@@ -323,8 +343,8 @@ class ThreadStepExecutor(StepExecutor):
 
         return True
 
-    def runSteps(self, steps, 
-                 stepStartedCallback, 
+    def runSteps(self, steps,
+                 stepStartedCallback,
                  stepFinishedCallback,
                  stepsCheckCallback,
                  stepsCheckSecs=5):
@@ -345,7 +365,7 @@ class ThreadStepExecutor(StepExecutor):
         sharedLock = threading.Lock()
 
         runningSteps = {}  # currently running step in each node ({node: step})
-        freeNodes = list(range(1, self.numberOfProcs+1))  # available nodes to send jobs
+        freeNodes = list(range(1, self.numberOfProcs + 1))  # available nodes to send jobs
         logger.info("Execution threads: %s" % freeNodes)
         logger.info("Running steps using %s threads. 1 thread is used for this main process." % self.numberOfProcs)
 
@@ -382,17 +402,21 @@ class ThreadStepExecutor(StepExecutor):
                         stepStartedCallback(step)
                         node = freeNodes.pop(0)  # take an available node
                         runningSteps[node] = step
-                        logger.debug("Running step %s on node %s" % (step, node))
+                        logger.info("Running step %s on node %s" % (step, node))
                         t = StepThread(step, sharedLock)
                         # won't keep process up if main thread ends
                         t.daemon = True
                         t.start()
+
                 anyPending = self._arePending(steps)
 
             if not anyLaunched:
+                logger.debug("Nothing launched in this loop")
                 if anyPending:  # nothing running
+                    logger.debug("There are steps pending. Waiting 3 secs")
                     time.sleep(3)
                 else:
+                    logger.info("Nothing pending. Breaking the loop.")
                     break  # yeah, we are done, either failed or finished :)
 
             now = datetime.datetime.now()
@@ -407,6 +431,15 @@ class ThreadStepExecutor(StepExecutor):
             if t is not threading.current_thread():
                 t.join()
 
+    def _arePending(self, steps):
+        """ Return True if there are pending steps (either running, waiting or new (not yet executed)
+        """
+        for s in steps:
+            if s.isRunning() or s.isWaiting() or s.isNew():
+                return True
+
+        return False
+
 
 class QueueStepExecutor(ThreadStepExecutor):
     def __init__(self, hostConfig, submitDict, nThreads, **kwargs):
@@ -429,7 +462,7 @@ class QueueStepExecutor(ThreadStepExecutor):
             for i in range(len(gpuList)):
                 self.gpuDict[threadId][i] = i
 
-        logger.debug("Updated gpus ids rebase starting from 0: %s per thread" %self.gpuDict)
+        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 """
@@ -457,7 +490,6 @@ class QueueStepExecutor(ThreadStepExecutor):
                                                             gpuList=self._getGPUListForCommand(programName, params),
                                                             context=submitDict)
 
-
         jobid = _submit(self.hostConfig, submitDict, cwd, env)
         self.protocol.appendJobId(jobid)  # append active jobs
         self.protocol._store(self.protocol._jobId)

pyworkflow/protocol/hosts.py

@@ -164,7 +164,8 @@ class HostConfig(Object):
         hosts = OrderedDict()
 
         try:
-            assert cp.read(hostsConf) != [], 'Missing file %s' % hostsConf
+            if not cp.read(hostsConf):
+                raise AssertionError('Missing file %s' % hostsConf)
 
             for hostName in cp.sections():
                 host = HostConfig(label=hostName, hostName=hostName)

pyworkflow/protocol/protocol.py

@@ -1795,6 +1795,11 @@ class Protocol(Step):
         self._stepsExecutor = executor
         self._stepsExecutor.setProtocol(self)  # executor needs the protocol to store the jobs Ids submitted to a queue
 
+    def getExecutor(self):
+        """Return the executor associated. This must be used only during protocol execution (steps code).
+         In "design/GUI time" is not set."""
+        return self._stepsExecutor
+
     def getFiles(self):
         resultFiles = set()
         for paramName, _ in self.getDefinition().iterPointerParams():

pyworkflow/template.py

@@ -101,7 +101,7 @@ class Template:
                     field.setValue(oldValue)
                     raise Exception("%s is not compatible with %s(%s) parameter." % (newValue, field.getTitle(), alias))
         if not paramsSetted:
-            raise Exception("Alias %s not recognized." % alias)
+            logger.warning('Argument "%s" not available in the template.' % alias)
         return paramsSetted
 
 class LocalTemplate(Template):

pyworkflow/tests/tests.py

@@ -61,7 +61,8 @@ class DataSet:
         """
         This method is called every time the dataset want to be retrieved
         """
-        assert name in cls._datasetDict, "Dataset: %s dataset doesn't exist." % name
+        if name not in cls._datasetDict:
+            raise AssertionError("Dataset: %s dataset doesn't exist." % name)
 
         ds = cls._datasetDict[name]
         folder = ds.folder

pyworkflow/utils/process.py

@@ -96,7 +96,8 @@ def buildRunCommand(programname, params, numberOfMpi, hostConfig=None,
     if numberOfMpi <= 1:
         return '%s %s %s' % (prepend, programname, params)
     else:
-        assert hostConfig is not None, 'hostConfig needed to launch MPI processes.'
+        if hostConfig is None:
+            raise AssertionError('hostConfig needed to launch MPI processes.')
 
         if programname.startswith('xmipp') and not programname.startswith('xmipp_mpi'):
             programname = programname.replace('xmipp', 'xmipp_mpi')

pyworkflow/utils/properties.py

@@ -519,6 +519,7 @@ class Icon:
     ACTION_FILAMENT_PICKING = SpriteImage(48, 176, 'filament.png')
     ACTION_GRID = SpriteImage(64, 160, 'grid.png')
     ACTION_CONTRAST = SpriteImage(80, 160, 'contrast.png')
+    ACTION_INTERPOLATE = SpriteImage(80, 144, 'interpolate.png')
 
 
     # Host template

pyworkflow/webservices/workflowhub.py

@@ -1,6 +1,8 @@
 import json
 from urllib.request import Request, urlopen
 from pyworkflow.template import Template
+import logging
+logger = logging.getLogger(__name__)
 
 
 class WHTemplate(Template):
@@ -12,24 +14,29 @@ class WHTemplate(Template):
     def loadContent(self):
         """ Download the file pointer by url and read the content"""
 
-        return make_request(self.url, asJson=False)
+        data = make_request(self.url, asJson=False)
 
+        # Clean all text up to the first [
+        data = data[data.index("["):]
+        return data
 
 def make_request(url, asJson=True):
     """ Makes a request to the url and returns the json as a dictionary"""
 
-    req = Request(url)
-    req.add_header("accept", "application/json")
-
-    with urlopen(req, timeout=1) as response:
-        if asJson:
-            data = json.load(response)
-        else:
-            html_response = response.read()
-            encoding = response.headers.get_content_charset('utf-8')
-            data = html_response.decode(encoding)
-        return data
-
+    try:
+        req = Request(url)
+        req.add_header("accept", "application/json")
+
+        with urlopen(req, timeout=1) as response:
+            if asJson:
+                data = json.load(response)
+            else:
+                html_response = response.read()
+                encoding = response.headers.get_content_charset('utf-8')
+                data = html_response.decode(encoding)
+            return data
+    except Exception as e:
+        logger.error(f"Couldn't get data from workflow hub at {url}: {str(e)}")
 
 def get_workflow_file_url(workflow_id, version):
     root_url = "https://workflowhub.eu/workflows/%s/git/%s/" % (workflow_id, version)
@@ -39,9 +46,12 @@ def get_workflow_file_url(workflow_id, version):
 
     for file in result["tree"]:
         path = (file["path"])
-        if path.endswith(".json.template"):
+        if ".json" in path:
             return root_url + 'raw/' + path
 
+    # Haven't found the workflow file
+    raise Exception(f"Couldn't find any path element at {url} containing .json in it")
+
 
 def get_wh_templates(template_id=None, organization="Scipion%20CNB"):
     """ Returns a list of scipion templates available in workflow hub"""
@@ -53,17 +63,19 @@ def get_wh_templates(template_id=None, organization="Scipion%20CNB"):
     template_list = []
 
     for workflow in response:
-        workflow_id = workflow["id"]
-        name = workflow["name"]
-        description = workflow['description']
-        version = workflow["versions"][-1]
-        version_id = version["id"]
-        template_url = get_workflow_file_url(workflow_id, version_id)
-
-        new_template = WHTemplate("Workflow hub", name, description, template_url)
-        if template_id is None or new_template.getObjId() == template_id:
-            template_list.append(new_template)
-
+        try:
+            workflow_id = workflow["id"]
+            name = workflow["name"]
+            description = workflow['description']
+            version = workflow["versions"][-1]
+            version_id = version["id"]
+            template_url = get_workflow_file_url(workflow_id, version_id)
+
+            new_template = WHTemplate("WH", name, description, template_url)
+            if template_id is None or new_template.getObjId() == template_id:
+                template_list.append(new_template)
+        except Exception as e:
+            logger.warning(f"Couldn't retrieve a data for {name} workflow hub template. ERROR: {e}" )
     return template_list
 
 

{scipion_pyworkflow-3.11.1.dist-info → scipion_pyworkflow-3.11.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scipion-pyworkflow
-Version: 3.11.1
+Version: 3.11.2
 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)

{scipion_pyworkflow-3.11.1.dist-info → scipion_pyworkflow-3.11.2.dist-info}/RECORD

@@ -1,54 +1,54 @@
 pyworkflow/__init__.py,sha256=Wr-MVKMQJy_Cy-rpPPB0-pyv8-8tx7GPPaLSNBrV1AI,1246
 pyworkflow/config.py,sha256=tvGMn6OlOrIUzZKCQwWFOA2oBSn85FTgPwNzA86oFn0,26291
-pyworkflow/constants.py,sha256=YGPhGk8-RijDCXrYi8bir3cM263wl-PcCz064moLdX0,7800
+pyworkflow/constants.py,sha256=CAAE2iM024hLj2jTKfItkX1galaOrognBEp2gQil6_U,7800
 pyworkflow/exceptions.py,sha256=3VFxuNJHcIWxRnLPR0vYg0RFAQMmxPBJZLZSi87VI8E,507
-pyworkflow/object.py,sha256=01nUr0Ud-EDVCULtElfC4patgxUYuUIbrI5qmCsC7BY,55149
-pyworkflow/plugin.py,sha256=VVUYkLvH_sBcqsrR3_WzTkogCUi9Zi-MkIgp5GGxRz8,30574
-pyworkflow/template.py,sha256=uScWMZCR3U6ishDlx7QGDDr8B_aLpKXoh8zOhqAirCY,10463
+pyworkflow/object.py,sha256=bMb6vohVw7O12xDXJOtjXhLqVVZviO8q_i83EYMCAt4,55217
+pyworkflow/plugin.py,sha256=guiGN2K38cMzRmhdaNcU4YNoY9MC89ywzlz4jnCFs7w,30592
+pyworkflow/template.py,sha256=KaF8VJjHHSHTiY5gmdbfMVoLlf_sav9SX3bf-khPRRk,10482
 pyworkflow/viewer.py,sha256=YCRoZaF0NYoBnSGhgBLQjCXuGKNWbKP6N1GWuALU_cQ,12053
 pyworkflow/wizard.py,sha256=nXuk_qMUVlQNa6nB6GCt0CoFQ_P2dnJbGWdwtpDG2tQ,2633
 pyworkflow/apps/__init__.py,sha256=doupoWHiPmpEwa7o7ro7suxYYjj7h-912kc-fxwnhfE,1187
 pyworkflow/apps/pw_manager.py,sha256=LqvNLqREsMN-O4QlxHr5mvG7XlKSYVvzgV1pGICV9rU,1356
 pyworkflow/apps/pw_plot.py,sha256=69L9_qbdaYuC8QbvE9MNOu4P2MYIna0II29PBu0HQdg,1829
-pyworkflow/apps/pw_project.py,sha256=1P6aGFxc-nDcWrTQ6SbtZSHZQkKHFHkGlnPkDLH0spk,3579
+pyworkflow/apps/pw_project.py,sha256=L7nfLC9Z1slA63f7Y-2XuOj9YPR68gzHenp6oSmJEvA,4415
 pyworkflow/apps/pw_protocol_list.py,sha256=bRC0W_M5Yx0KQ651S4HxB4AOqE4_P8hacc8qrS_3vPo,5193
 pyworkflow/apps/pw_protocol_run.py,sha256=Uboywq_pwIBAqa_YIsHtBg5iO9b134HEVwrhwkLMoNY,1916
-pyworkflow/apps/pw_run_tests.py,sha256=0rUeBXIMzq5sWC0BmNBA02zkQrqAkwkX0WJzIpvUdOs,10587
+pyworkflow/apps/pw_run_tests.py,sha256=0BNl_hmEJ5q-lqG3hDshwzYaBQjADLfaIZ_zrHqlD6E,10621
 pyworkflow/apps/pw_schedule_run.py,sha256=N3os7_wA-QIGnQGmnVoRWmM385idB0cH-h_sCxVy_14,12471
 pyworkflow/apps/pw_sleep.py,sha256=KhXjsmm04K_JMM13CMDI25sYEay7C2aJ_mTQlBH9n-I,1443
-pyworkflow/apps/pw_sync_data.py,sha256=rwAShzTuVlCDaLKMLeuY1cPSLyWSP9-1mNTgIgCX40A,17371
+pyworkflow/apps/pw_sync_data.py,sha256=rNoS_GnamoPI1jljvRI3E8qJ7FZCvuw2wmCauMaT24w,17460
 pyworkflow/apps/pw_viewer.py,sha256=dlvIPzBa_citucezBd0Cl0uCND4eXWYgXF-lZpXWzBc,2595
 pyworkflow/gui/__init__.py,sha256=D7PVYky81yTcqvkGEtw1CIxRkICpsn4TO5z5lJg84yM,1373
-pyworkflow/gui/browser.py,sha256=gFBvVYNw2tQW3-n8LqWazuzkKOvI-5FadR0h2aBVeHY,26716
+pyworkflow/gui/browser.py,sha256=Nq6itmAnVCbKXA-6WYpj36Py9ggRlhUTbZi4S9jhLCc,26969
 pyworkflow/gui/canvas.py,sha256=M_pD7QbqnYq9MY145WN6BYzeIAo0cIkbxLrZKNE80yg,42106
-pyworkflow/gui/dialog.py,sha256=PQQfS_bYevqBAAGOq1B7wGd9adabUk3KVTlyjiuddV4,35351
-pyworkflow/gui/form.py,sha256=bF8-y4LeXfV3n3B0Li81zwnzKq-4nyKXd55kOu0agsU,107449
+pyworkflow/gui/dialog.py,sha256=ZX0k_y-bhUUo84YLwbP1ab6qwkSaNMRbDbjVAqOc3to,35473
+pyworkflow/gui/form.py,sha256=g701xBE6wfpBevlZ9lppFkcCYZTlYRtVp3h7JxamO6M,107486
 pyworkflow/gui/graph.py,sha256=HSZ5PfFKkhv3tzl0o9UtSU_FfDevKR2M3L9HgU9_Gkc,8747
 pyworkflow/gui/graph_layout.py,sha256=R9uTc_Ei4oWAeCkZ3d78JjC1QKV7HPJaDLyhvSfK7NE,9520
-pyworkflow/gui/gui.py,sha256=c_KcuOZS7_Euu4Qu21KUJipdhzxI5a0XZjrqzzvk-u4,20619
+pyworkflow/gui/gui.py,sha256=b29zlbl74cu4Rg6elBZO6alZg37v7i4oyuv9Sq4YNKI,20741
 pyworkflow/gui/matplotlib_image.py,sha256=vGD5LKp-AZvu_kXa7Mf_jtOQfZ-QcRUoTMnicNrMqUk,7821
 pyworkflow/gui/plotter.py,sha256=E9ld43B-AzYhV1PIEPBy2TQWyzoia4y5lD5rqJOQlZY,8464
-pyworkflow/gui/text.py,sha256=cmAhCm_gCJMi5UDl9br8FoexHeDQjby8dplw9ZiUIgM,28576
+pyworkflow/gui/text.py,sha256=xQp-sZbqmWh1uK4uVS-Wk3FSWxJ9_awFpfHWsqCaCuo,28722
 pyworkflow/gui/tooltip.py,sha256=OceYHesQQ7vSH7FRJmbvDBXjVG1IKkX1A8vocb64ljE,8531
 pyworkflow/gui/tree.py,sha256=TglyZ-snZHp6hTIRRp4o5Fvzf8Z7hogpFaZ4DVgMGvo,23084
 pyworkflow/gui/widgets.py,sha256=mIG1AAFvfT_py_yjjgoYeikgIRz-IbD3VOfKAcknqY0,11115
 pyworkflow/gui/project/__init__.py,sha256=rZmTvqocYhsD2PH1owu7Dkgs7dMrGx7VbKOCpaqvLzM,1118
-pyworkflow/gui/project/base.py,sha256=N64UXy5ep7RFweyBWTDro9UESgKRRAIvlRuotWIaO_w,7871
+pyworkflow/gui/project/base.py,sha256=Sfc6lT-kgOj2GQXYNg4SDVJaulxQB8Wro5PL8Y4BT4A,7912
 pyworkflow/gui/project/constants.py,sha256=rORDaNCdAFRFcBmjRt2PJ1cXpSmYgDLfbvrbqZh1Bb0,4943
 pyworkflow/gui/project/labels.py,sha256=7m4heNcN3zXe0BHuFJyQrPD5hC8LiHnlu1sizRc8l_Y,7680
 pyworkflow/gui/project/project.py,sha256=2LdwlbPrCejKr_cdFALm_1kOx-Agk9KKIIS4mHOpTrk,18801
-pyworkflow/gui/project/searchprotocol.py,sha256=NchaO_JFQMGzZkYFyn5_D_BMS3NSbnLTuao6E5UTOfc,9338
+pyworkflow/gui/project/searchprotocol.py,sha256=Mkam8PwHOeJMjILBugwAaj_jNp-uDQ_mikN6OMrhFLg,9453
 pyworkflow/gui/project/searchrun.py,sha256=xCGxs7L9PMk48ei9Gi3HI2PAOYEM-zXR5vRfAQRLHKI,7269
 pyworkflow/gui/project/steps.py,sha256=fq0WhPBoByFs8Lr-qmGZ-aFC4lx3XCF2zM2DOBd_KAc,6053
 pyworkflow/gui/project/utils.py,sha256=H9oFPzz9lAjAI4PRYSYyYniTBn98Y6YSs0bE0qXpMEM,11923
 pyworkflow/gui/project/variables.py,sha256=UczW6yQqzssj3eETEKaae5GSpsWr04ItPrr5o2WBnu4,7496
 pyworkflow/gui/project/viewdata.py,sha256=DUpoF6HURNZagdOtI9M8QNMYcqSFRtXGFA5Ftmrw2P8,18172
-pyworkflow/gui/project/viewprojects.py,sha256=ZcWzfFLVeCKzVsFboxquzBsOagEoPW0CpVUQ8ZLpvQE,22516
-pyworkflow/gui/project/viewprotocols.py,sha256=6iq91LHtbHUtq0iQo6UsSuCe69X2mLWLHvjMbE3E64E,85391
+pyworkflow/gui/project/viewprojects.py,sha256=zLVSaoGerElTab3wT70VmhQKI8lAI42Egh46xEVSmXA,22868
+pyworkflow/gui/project/viewprotocols.py,sha256=UkDRh_sXYTe8X0-8MaqWYlHEcxjgaHl1aqC2SaqLsXs,86201
 pyworkflow/gui/project/viewprotocols_extra.py,sha256=_wHn4fa1Qy9zDhyHYJoluIEZtS6SxvF0s9fFmVA1mgc,21262
 pyworkflow/mapper/__init__.py,sha256=HM7tMMd1r2BZ8hbPGryUQ80E4evY46zIVjiZ3edg_Mg,1186
-pyworkflow/mapper/mapper.py,sha256=YGVlBK3btHL-jLID6v2jLy7Mb9Wu47lxfZjHdzz0hMg,7726
-pyworkflow/mapper/sqlite.py,sha256=Y8SGO2n71hfBiuES-oykTEpL08vtNpiQsyRc2qFPUIg,65460
+pyworkflow/mapper/mapper.py,sha256=tUP5L-B5m33bBjhp34fWgaIGSnuVSEjpYa8hf1tBLjQ,7829
+pyworkflow/mapper/sqlite.py,sha256=3DaJbZ6RJNkajVs3tfshM1SiBi4DITzyK7d3Oh7A_m0,65543
 pyworkflow/mapper/sqlite_db.py,sha256=HYSXe_fRX1NBKDs6l2zefdO4PMEajnoDMXPjmoFs8Kc,5602
 pyworkflow/project/__init__.py,sha256=05l9tvr3FfBNL3XNZSbFCs6yO-1HbFlmFu204w7yyKk,1369
 pyworkflow/project/config.py,sha256=F9H1vLJJ9vPyT6zeSqHX69o-wbaN8hWueOuDn53evjc,13692
@@ -68,12 +68,12 @@ 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=gyYtGFjfZbyAi2nDK6YpIRq6baZIJc_EdPD3oP2VdNM,3391
-pyworkflow/protocol/executor.py,sha256=pnUJr2sNu-Iqnf3-M3YWc4YTNmsUdyf7-v1Kg97rZBY,19108
-pyworkflow/protocol/hosts.py,sha256=fbuQjHsOL5zWeDuoLqOXZmVc1lfjS2Pb1uomXiC2ysc,10697
+pyworkflow/protocol/executor.py,sha256=_UCV9nxez7QVDMJUx-CiO-UpVENSAmsdATALIz1CrU8,20189
+pyworkflow/protocol/hosts.py,sha256=j6vC1ALRVwo8bSxLM9cFfnfWW5qGrzgrrAFJobvVnX0,10729
 pyworkflow/protocol/launch.py,sha256=Gls0WlLAkLtOxj4IWyKrDbmqaXXHsGd8oqBAcT61zEI,11731
 pyworkflow/protocol/package.py,sha256=L6x3HHKtbrhDQRJHD07SG3DQKNMGaRQ0ROoLEY3SuRQ,1444
 pyworkflow/protocol/params.py,sha256=kPXMPtPJrsSMJQQKIHIInPhity__lWYIVc1m3PXIywE,27947
-pyworkflow/protocol/protocol.py,sha256=KLqlm6KW4ITJ6TCvc972dUa3fZoTxtkr18CZAIHYG9I,103104
+pyworkflow/protocol/protocol.py,sha256=tJodpBU0PxKBOltQgVYyjzN00VqTuAsfr107Efry8BY,103318
 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
@@ -83,6 +83,7 @@ pyworkflow/resources/fa-times-circle_alert.png,sha256=pgTdYSR5s5tIt6i9ut2YTTMf0u
 pyworkflow/resources/file_vol.png,sha256=b_M_W5iXEnG5jEcGvlFAyOm8Nn_ngZcrJnDBq9_361g,961
 pyworkflow/resources/loading.gif,sha256=6Jktjiva7Z5W6tqxiQZJZI9zahpwmme_D5G-K9EwI1o,16824
 pyworkflow/resources/no-image128.png,sha256=AnPz8ehji-QTJiSSv0kwYh1QR1TMTLGEKRZg-dz0UKA,13217
+pyworkflow/resources/protlabels.xcf,sha256=djXjiVydmUoxtdrLxkgasycQtlBVY4Kp--kfYA8Wwlk,32512
 pyworkflow/resources/scipion_bn.png,sha256=0yVccw1PlBJaoJpIEsChGZH2dXEgphaqHnquaP2i-1c,113916
 pyworkflow/resources/scipion_icon.png,sha256=moMOOoaLmcWdPdOn_PUBoAQv79WlfxsKwx8nPmrLbzU,2674
 pyworkflow/resources/scipion_icon.svg,sha256=6CGXzBW6tlbwY0tywHcWxsKeEAhynKmzhvYxnIxN9qQ,126140
@@ -92,8 +93,8 @@ pyworkflow/resources/scipion_icon_prot.png,sha256=WOp8WTw54JPwlhXUzFDP75T1nEbIQy
 pyworkflow/resources/scipion_logo.png,sha256=NYxY7AxZmp7kb1So2uCDpkzoYRxKl-Fb-zmf59nBkBc,1999
 pyworkflow/resources/scipion_logo_normal.png,sha256=nrsdm4tI9r1WThlY7KoNtVRl48fZd8oSaGOSvMJdoKk,35151
 pyworkflow/resources/scipion_logo_small.png,sha256=lUUaMbJmCCewirp4SPc4LJrenMGSxz4243yuDYUaP2Q,7811
-pyworkflow/resources/sprites.png,sha256=mGbZqKApcnbITOBlH206FKTLcS7kVkrnwG1v9apiifQ,53903
-pyworkflow/resources/sprites.xcf,sha256=XImVzBax2VMQNNi1jnH78EhZfE9bb5cpVAUwUsYZFJ0,93331
+pyworkflow/resources/sprites.png,sha256=NG6lQivvgHAMvpEzX3NU3NOwgE8XPvDer8pW4JRwXSE,48542
+pyworkflow/resources/sprites.xcf,sha256=9Y4P7d7C-tJuAmTYazIVwqtiMXrWClUFvtL4ecqT_OE,97411
 pyworkflow/resources/wait.gif,sha256=H9UcWI4UbL9cpxrX_gZAtkmLhXHDAHFYirTRtZrn4q0,4035
 pyworkflow/resources/showj/arrowDown.png,sha256=qpePLXb2UKAWBL7EaHZChEpAFNwFm1mBiEfckNUwpus,268
 pyworkflow/resources/showj/arrowUp.png,sha256=1-rxZDyFUHVZ1SIO9at1_OhkvLnaJDlMx90r137RjGI,276
@@ -118,17 +119,17 @@ pyworkflow/resources/showj/volumeOff.png,sha256=LKMWEt8_xwA4tDBruP30Y22QqNebHtH3
 pyworkflow/resources/showj/volumeOn.png,sha256=SsZsmeTdIa0pfMcm0Kq8KzsTDG6A3nhi7jdWWk_7Qfk,614
 pyworkflow/tests/__init__.py,sha256=tCnNEVIyRLERuNkAd3stcKo23TxHUILonZM9UFEbUD0,1259
 pyworkflow/tests/test_utils.py,sha256=HmPVZ6UPu89u-x_aQmF5yyA4RwK55x4bhEhvWeNy1lY,493
-pyworkflow/tests/tests.py,sha256=KgBh_eNHrg3VcYHu-zGye7ot5DzGKFyH8ZI-xABjs98,11757
+pyworkflow/tests/tests.py,sha256=mnuaWUBCKWcau0j2YhxRqYnxYgY8aw81xxti8BqbUfQ,11791
 pyworkflow/utils/__init__.py,sha256=UEd4SxmVd9zv0JElz1J0Sva7klJw3HEKSzwf5a0c-Xc,1429
 pyworkflow/utils/dataset.py,sha256=141u2xb-FTe8nF6OVJBJtTNHWz7eDWd24veBWX7eoTI,14943
 pyworkflow/utils/echo.py,sha256=ZXJRrmxUaTT4Xxf7_pQwg7Th341iFafTs66VEKNOZmE,3442
 pyworkflow/utils/graph.py,sha256=z3Hcj0I38du97DQEqNT5gk--SCDTRPlKotaCszoZfX8,4981
 pyworkflow/utils/log.py,sha256=y7qLB1NKeHF43QhyWZq-32_5DtSJYR1uzrWjRxoSvWk,11096
 pyworkflow/utils/path.py,sha256=hDisc13HhfB6CxpBcI1JBd5er_S6yVTKw1MFSw1AR3U,16803
-pyworkflow/utils/process.py,sha256=6l4Mf6C3nyYMeLBQxbrGaAWWmJvf6zQuTLQzPYQVxPU,5790
+pyworkflow/utils/process.py,sha256=a2yixJxEQeZXI9dg2TKrfgaVmcDQocTQ2GUZ9d4rfQU,5816
 pyworkflow/utils/profiler.py,sha256=BC0KkAgfYqf-CV40zLcRxo5Td79f5jw1gzvaDH8iqt8,2218
 pyworkflow/utils/progressbar.py,sha256=VntEF_FTdQHjMKawfR1R4IoNgYNTEMmnLUIDvUXurxk,5903
-pyworkflow/utils/properties.py,sha256=EaTb7VTofsXuKZuOA4cK6ZmwfqmTSOwzd__TZwaL8Cc,23092
+pyworkflow/utils/properties.py,sha256=3hpTFoWEmH6bwSYIuwBFgbFY-OlATO8q19KBV0fjoiA,23157
 pyworkflow/utils/reflection.py,sha256=48cvIDO73JinBsFn3XMiVR56AcivfdJoiMXGM7ZwUDY,4429
 pyworkflow/utils/utils.py,sha256=6h1PthMyGc804PBqbNnVqzzr8upkJMZtaLKalIAELNc,26330
 pyworkflow/utils/which.py,sha256=KuyKYE4GnkwMpBJoKgOMnx-hNZjHf6OTyqxEsdHIftI,8627
@@ -136,7 +137,7 @@ pyworkflow/webservices/__init__.py,sha256=CfkvvoFQp2t2Tt5p7uOF_tpkZVWPHOl9TLlAtB
 pyworkflow/webservices/config.py,sha256=7XSkwUiVT71UuARNBQUcePARz8UevwlmxEdoKa_ZVlg,399
 pyworkflow/webservices/notifier.py,sha256=ntjmIxi2rO0Oc7RE6meuJZ6y5HG4NcrShRqfSUxM8eA,5601
 pyworkflow/webservices/repository.py,sha256=Hw2ZhvuJzKbN5ivTuN2gTNeJT49Q3-PuM9BdwayTYfU,2365
-pyworkflow/webservices/workflowhub.py,sha256=hA4RETMXmxUF-l605INS1TCT2nWnUwOIjrYKzRUZVLQ,2179
+pyworkflow/webservices/workflowhub.py,sha256=HBk0aEKklakhg-CPx9GkvexVs2LMnf82IwP--Xh_xCA,2768
 pyworkflowtests/__init__.py,sha256=RoXNgyShL7moVEXaimTDdfY1fU26dgGKtdjO4JfBQOk,1686
 pyworkflowtests/bibtex.py,sha256=1f9PjkRO937PB2b-ax-eKLwjU4YY11M5px3dk3xWQzw,2102
 pyworkflowtests/objects.py,sha256=uaD9THeybiCkUDbb_cpqEwqCpVG3RLyMsIjOKOX7oNQ,26688
@@ -153,9 +154,9 @@ 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-3.11.1.dist-info/licenses/LICENSE.txt,sha256=ixuiBLtpoK3iv89l7ylKkg9rs2GzF9ukPH7ynZYzK5s,35148
-scipion_pyworkflow-3.11.1.dist-info/METADATA,sha256=fj1k-LO55-QDXIxh7iGFe3sr_fxiphLt0EkSxd_o_lQ,4440
-scipion_pyworkflow-3.11.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-scipion_pyworkflow-3.11.1.dist-info/entry_points.txt,sha256=-P6GVocWl_NS8wS7lB-bTKf-tKANbw4n7DlXXh_VrWk,54
-scipion_pyworkflow-3.11.1.dist-info/top_level.txt,sha256=PzyJteyenJwLjAeSFP7oYrTN_U71GABQwET8oLZkh9k,27
-scipion_pyworkflow-3.11.1.dist-info/RECORD,,
+scipion_pyworkflow-3.11.2.dist-info/licenses/LICENSE.txt,sha256=ixuiBLtpoK3iv89l7ylKkg9rs2GzF9ukPH7ynZYzK5s,35148
+scipion_pyworkflow-3.11.2.dist-info/METADATA,sha256=ySnL_EiwGsdzu6T-r66WwCR1wntg80_xpvFeqchrrhA,4440
+scipion_pyworkflow-3.11.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+scipion_pyworkflow-3.11.2.dist-info/entry_points.txt,sha256=-P6GVocWl_NS8wS7lB-bTKf-tKANbw4n7DlXXh_VrWk,54
+scipion_pyworkflow-3.11.2.dist-info/top_level.txt,sha256=PzyJteyenJwLjAeSFP7oYrTN_U71GABQwET8oLZkh9k,27
+scipion_pyworkflow-3.11.2.dist-info/RECORD,,