scipion-pyworkflow 3.11.1__tar.gz → 3.11.2__tar.gz

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/CHANGES.txt

@@ -1,3 +1,21 @@
+V3.11.2
+ users:
+  Copy (Control-C) work in log viewers too
+  Pasting a copied workflow refreshes the graph
+  Bugfix: Protocol with very fast (almost notime) steps work instead of end up finished with pending steps.
+  templates can be fetched from urls having ".json" and not json.template only.
+  Double click in a protocol in "list mode" opens the protocol
+  Double click in a collapsed node, expands it.
+
+ developers:
+  new icon
+  Executor.getGpuListStr(): Returns the assigned gpus for the step as a string (accepts sep --> separator, defaults to " ")
+  Executor.setCudaVisibleDevices(): Sets the variable CUDA_VISIBLE_DEVICES with owned information.
+  Protocol.getExecutor: returns the executor. Useful to aske for gpu information inside a step
+  __debug__ allowed: By default Project load is with -O (optimized) so __debug__ is false.
+       asserts removed, swap to if + raise AssertionError
+       if optimized, shown in project window header
+
 V3.11.1 fix packaging
 V3.11.0
 users:

{scipion_pyworkflow-3.11.1/scipion_pyworkflow.egg-info → scipion_pyworkflow-3.11.2}/PKG-INFO

@@ -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 → scipion_pyworkflow-3.11.2}/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):

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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)))

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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)

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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.

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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']
 

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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)

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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)

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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:

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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)

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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.

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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):
 

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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()

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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)

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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):

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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):

{scipion_pyworkflow-3.11.1 → scipion_pyworkflow-3.11.2}/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