Merge pull request #559 from scipion-em/devel

release 3.9

CHANGES.txt

@@ -1,3 +1,21 @@
+V3.9.0
+  - Project can have a comment (tooltip over the project name and click will edit it). Will be populated with templates description.
+  - Project Color modes:
+       size color mode removed: Problematic in slow setups or huge projects.
+       labels color mode merged with status color mode.
+  - Manual subsets works when SCIPION_USE_QUEUE is active. For now this execution is not sent to the QUEUE: Might need to ask for the queue parameters.
+  - Step details show it step needs a GPU
+  - Folder size not showing in protocol's tooltip: poor performance in some setups
+  - Threads field and help improved: Distinguish between "Scipion threads" and "Threads" (program threads)
+  - create script accepts a comment (location optional as -)
+  - GPU "queue":
+      Basic GPU queue implemented for a more robust GPU specification in combination with threads. See threadmpigpu help page in the doc. Linked in the help.
+      Tests added
+  - Tolerate non exisiting SCIPION_SPRITES_FILE falling back to default value.
+  - Scroll and zoom gestures swap to more standard usage: Control + scroll = zoom, Shift + Scroll = Horizontal scroll.
+
+developers:
+  - New constants for "id" and "_objId": ID_COLUMN='id', ID_ATTRIBUTE='_objId'
 V3.8.0
 users:
   - Inform when a plugin does not import properly

pyworkflow/config.py

@@ -198,6 +198,7 @@ def join(self, *path):
 
     # Internal cached variables, use __ so they are not returned in getVars
     __activeColor = None
+    __defaultSpritesFile = _join(getResourcesPath(),'sprites.png')
 
     CONDA_ACTIVATION_CMD = _get(CONDA_ACTIVATION_CMD_VAR,'',
     "str: Command to activate/initialize conda itself. Do not confuse it with 'conda activate'. It should be defined at installation time. It looks like this: eval \"$(/extra/miniconda3/bin/conda shell.bash hook)\"")
@@ -299,7 +300,7 @@ def join(self, *path):
     SCIPION_CONTRAST_COLOR = _get('SCIPION_CONTRAST_COLOR', 'cyan',
     "Color used to highlight features over grayscaled images.", caster=validColor)
 
-    SCIPION_SPRITES_FILE = _get('SCIPION_SPRITES_FILE', _join(getResourcesPath(),'sprites.png'),
+    SCIPION_SPRITES_FILE = _get('SCIPION_SPRITES_FILE', __defaultSpritesFile,
     "File (png) with the icons in a collage. Default is found at pyworkflow/resources/sprites.png. And a GIMP file could be found at the same folder in the github repo.")
 
     SCIPION_SHOW_TEXT_IN_TOOLBAR = _get('SCIPION_SHOW_TEXT_IN_TOOLBAR', TRUE_STR,
@@ -544,7 +545,12 @@ def isCondaInstallation(cls):
             condaExe = os.path.join(envFolder, "bin", "python")
             return condaExe == getPython()
 
-
+    @classmethod
+    def getSpritesFile(cls):
+        if not os.path.exists(Config.SCIPION_SPRITES_FILE):
+            return cls.__defaultSpritesFile
+        else:
+            return Config.SCIPION_SPRITES_FILE
 
 
 # Add bindings folder to sys.path

pyworkflow/constants.py

@@ -43,7 +43,7 @@
 VERSION_1_1 = '1.1.0'
 VERSION_1_2 = '1.2.0'
 VERSION_2_0 = '2.0.0'
-VERSION_3_0 = '3.8.0'
+VERSION_3_0 = '3.9.0'
 
 # For a new release, define a new constant and assign it to LAST_VERSION
 # The existing one has to be added to OLD_VERSIONS list.
@@ -192,6 +192,7 @@ class DOCSITEURLS:
     WAIT_FOR = GUI + '#waiting-for-other-protocols'
     PLUGIN_MANAGER = USER + 'plugin-manager.html'
     HOST_CONFIG = DOCS + "scipion-modes/host-configuration.html"
+    THREADS_MPIS_AND_GPUS = USER + 'threads-mpi-gpus.html'
 
 
 # tkinter bind constants
@@ -211,3 +212,7 @@ class TK:
 DEFAULT_EXECUTION_ACTION_SINGLE = 2
 DEFAULT_EXECUTION_ACTION_ALL = 3
 
+# Id field/attribute constants
+ID_COLUMN='id'
+ID_ATTRIBUTE='_objId'
+

pyworkflow/gui/canvas.py

@@ -82,8 +82,8 @@ def __init__(self, parent, tooltipCallback=None, tooltipDelay=1500, **kwargs):
         self.bind("<Control-1>", self.onControlClick)
         # self.bind("<MouseWheel>", self.onScroll)
         # Scroll bindings in Linux
-        self.bind("<Shift-Button-4>", self.zoomerP)
-        self.bind("<Shift-Button-5>", self.zoomerM)
+        self.bind("<Control-Button-4>", self.zoomerP)
+        self.bind("<Control-Button-5>", self.zoomerM)
 
         self._tooltipId = None
         self._tooltipOn = False  # True if the tooltip is displayed
@@ -475,7 +475,7 @@ def _drawNodes(self, node, visitedDict={}):
             self.addItem(item)
 
             if getattr(node, 'expanded', True):
-                for child in node.getChilds():
+                for child in node.getChildren():
                     if self.nodeList is None:
                         self._drawNodes(child, visitedDict)
                     elif self.nodeList.getNode(child.run.getObjId()).isVisible():
@@ -512,7 +512,7 @@ def _visibleParents(self, node, parentlist):
         """
         Return a list with the visible parents of the node's children
         """
-        for child in node.getChilds():
+        for child in node.getChildren():
             parents = child.getParents()
             for parent in parents:
                 parentNode = self.nodeList.getNode(parent.run.getObjId())
@@ -525,7 +525,7 @@ def _setupParentProperties(self, node, visitedDict):
         the properties (width, height, x and y) is propagated
         to the hidden childs.
         """
-        for child in node.getChilds():
+        for child in node.getChildren():
             if child.getName() not in visitedDict:
                 child.width = node.width
                 child.height = node.height
@@ -544,7 +544,7 @@ def _updatePositions(self, node, visitedDict=None, createEdges=True):
             item.moveTo(node.x, node.y)
 
             if getattr(node, 'expanded', True):
-                for child in node.getChilds():
+                for child in node.getChildren():
                     if self.nodeList is None:
                         self.createEdge(item, child.item)
                         self._updatePositions(child, visitedDict, createEdges)

pyworkflow/gui/dialog.py

@@ -35,7 +35,7 @@
 from pyworkflow import Config
 from pyworkflow.exceptions import PyworkflowException
 from pyworkflow.utils import Message, Icon, Color
-from . import gui, Window, widgets, configureWeigths, LIST_TREEVIEW, defineStyle, ToolTip
+from . import gui, Window, widgets, configureWeigths, LIST_TREEVIEW, defineStyle, ToolTip, getDefaultFont
 from .tree import BoundTree, Tree
 from .text import Text, TaggedText
 
@@ -443,7 +443,8 @@ def body(self, bodyFrame):
         label = tk.Label(bodyFrame, text=self.entryLabel, bg=Config.SCIPION_BG_COLOR, bd=0)
         label.grid(row=row, column=0, sticky='nw', padx=(15, 10), pady=15)
         self.entry = tk.Entry(bodyFrame, bg=gui.cfgEntryBgColor,
-                              width=self.entryWidth, textvariable=self.tkvalue)
+                              width=self.entryWidth, textvariable=self.tkvalue,
+                              font=getDefaultFont())
         self.entry.grid(row=row, column=1, sticky='new', padx=(0, 15), pady=15)
         self.initial_focus = self.entry
 

pyworkflow/gui/form.py

@@ -1698,14 +1698,19 @@ def _createParallel(self, runFrame, r):
                 c2 = 0
                 sticky = 'e'
 
+                helpMessage = pwutils.Message.HELP_PARALLEL_HEADER
+
                 if mode == pwprot.STEPS_PARALLEL:
                     if allowThreads and numberOfThreads > 0:
                         prot.numberOfMpi.set(1)
-                        self._createHeaderLabel(procFrame, pwutils.Message.LABEL_THREADS,
+                        self._createHeaderLabel(procFrame, pwutils.Message.LABEL_SCIPION_THREADS,
                                                 sticky=sticky, row=r2, column=c2,
                                                 pady=0)
                         entry = self._createBoundEntry(procFrame,
                                                        pwutils.Message.VAR_THREADS)
+
+                        helpMessage += pwutils.Message.HELP_SCIPION_THREADS
+
                         entry.grid(row=r2, column=c2 + 1, padx=(0, 5), sticky='w')
                     elif allowMpi and numberOfMpi > 1:
                         self.showError("MPI parameter is deprecated for protocols "
@@ -1728,6 +1733,8 @@ def _createParallel(self, runFrame, r):
                         # Modify values to be used in MPI entry
                         c2 += 2
                         sticky = 'w'
+
+                        helpMessage += pwutils.Message.HELP_PARALLEL_THREADS
                     # ---- MPI ----
                     if allowMpi:
                         self._createHeaderLabel(procFrame, pwutils.Message.LABEL_MPI,
@@ -1736,11 +1743,14 @@ def _createParallel(self, runFrame, r):
                         entry = self._createBoundEntry(procFrame, pwutils.Message.VAR_MPI)
                         entry.grid(row=r2, column=c2 + 1, padx=(0, 5), sticky='w')
 
+                        helpMessage += pwutils.Message.HELP_PARALLEL_MPI
+
+
                 btnHelp = IconButton(procFrame, pwutils.Message.TITLE_COMMENT,
                                      pwutils.Icon.ACTION_HELP,
                                      highlightthickness=0,
                                      command=self._createHelpCommand(
-                                         pwutils.Message.HELP_MPI_THREADS))
+                                         helpMessage))
                 btnHelp.grid(row=0, column=4, padx=(5, 0), pady=2, sticky='e')
 
                 procFrame.columnconfigure(0, minsize=60)

pyworkflow/gui/graph.py

@@ -85,7 +85,7 @@ def _setLevel(self, node, level, parent):
         nextLevel = level + 1
         if nextLevel > self.maxLevel:
             return
-        for child in node.getChilds():
+        for child in node.getChildren():
             if nextLevel > getattr(child, 'level', 0):
                 self._setLevel(child, nextLevel, node)
 
@@ -97,7 +97,7 @@ def _paintNodeWithChilds(self, node, level):
         if level > self.maxLevel:
             return
 
-        childs = [c for c in node.getChilds() if c.parent is node]
+        childs = [c for c in node.getChildren() if c.parent is node]
         n = len(childs)
 
         if n > 0:
@@ -174,7 +174,7 @@ def _getHLimits(self, node):
         for each level of the tree
         """
         node.hLimits = [[-node.half, node.half]]
-        childs = [c for c in node.getChilds() if c.parent is node]
+        childs = [c for c in node.getChildren() if c.parent is node]
         for child in childs:
             count = 1
             if not hasattr(child, 'hLimits'):
@@ -221,7 +221,7 @@ def _createEdges(self, node, x):
         if node.level == self.maxLevel:
             return
 
-        for c in node.getChilds():
+        for c in node.getChildren():
             if c.parent is node:
                 self._createEdges(c, nx)
             self.createEdge(node.item, c.item)
@@ -230,7 +230,7 @@ def _paintNodeWithPosition(self, node):
         """ Paint nodes using its position. """
         self._paintNode(node, None)
 
-        for child in node.getChilds():
+        for child in node.getChildren():
             # parent = None for nodes that have been not traversed
             parent = getattr(child, 'parent', None)
             if parent is None:
@@ -241,7 +241,7 @@ def _paintEdges(self, node):
         """ Paint only the edges between nodes, assuming they are
         already well positioned. 
         """
-        for child in node.getChilds():
+        for child in node.getChildren():
             if child.parent is node:
                 self._paintEdges(child)
             self.createEdge(node.item, child.item)

pyworkflow/gui/graph_layout.py

@@ -132,7 +132,7 @@ def _setLayoutLevel(self, node, level, parent,  ancestors=[]):
 
             if self.__isNodeExpanded(node):
                 ancestors.append(node.getName())
-                for child in node.getChilds():
+                for child in node.getChildren():
                     if child.getName() in ancestors:
                         logger.warning("WARNING: There might be a cyclic redundancy error in this protocol: %s (%s)" %(child.getLabel(),
                                                                                                                        child.getName()))
@@ -155,7 +155,7 @@ def __getNodeChilds(self, node):
         visited by this node first (its 'parent')
         """
         if self.__isNodeExpanded(node):
-            return [c for c in node.getChilds() if c._layout['parent'] is node]
+            return [c for c in node.getChildren() if c._layout['parent'] is node]
         else:
             return []  # treat collapsed nodes as if they have no childs
 

pyworkflow/gui/project/base.py

@@ -28,7 +28,7 @@
 import tkinter as tk
 
 import pyworkflow as pw
-from pyworkflow.gui import Window, Message, Color, getBigFont, defineStyle
+from pyworkflow.gui import Window, Message, Color, getBigFont, defineStyle, ToolTip
 from pyworkflow.gui.widgets import GradientFrame
 from pyworkflow.utils.properties import Icon
 from pyworkflow.gui.project.variables import VariablesDialog
@@ -98,18 +98,18 @@ def createHeaderFrame(self, parent):
                                 bg=pw.Config.SCIPION_BG_COLOR)
         versionLabel.grid(row=0, column=1, sticky='sw', pady=20)
 
-        # Create the Project Name label
-        projName = getattr(self, 'projName', '')
-        projLabel = tk.Label(header, text=projName, font=getBigFont(),
-                             borderwidth=0, anchor='nw', bg=pw.Config.SCIPION_BG_COLOR,
-                             fg=Color.ALT_COLOR_DARK)
-        projLabel.grid(row=0, column=2, sticky='sw', padx=(20, 5), pady=10)
+        self.customizeheader(header)
+
         # Create gradient
         GradientFrame(header, height=8, borderwidth=0).grid(row=1, column=0,
                                                             columnspan=3,
                                                             sticky='new')
         return header
 
+    def customizeheader(self, headerFrame):
+        """ Implement in children classes to customize it: e.g.: Project name in project window"""
+        pass
+
     def addViewList(self, header):
         """Create the view selection frame (Protocols|Data) in the header.
         """