Merge remote-tracking branch 'biolab/master'

Revert "Fix for crash on empty data, better handling on sparcisity changes" This reverts commit 246795b9bc2c343d4214cf42a986f2a6be40b732. Fix for empty data crash, better handling of sparse data Merge remote-tracking branch 'origin/owsave' into owsave
biolab · Oct 25, 2018 · 9045f49ce259b184fec3b23fe284bc13065b089f · 9045f49
1 parent 371a193
commit 9045f49ce259b184fec3b23fe284bc13065b089f
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,66 @@ Change Log
 * ...
+  
+[3.16.0] - 2018-09-14
+  
+--------------------
+  
+##### Enhancements
+  
+* ROC analysis: show thresholds ([#3172](../../pull/3172))
+  
+* Edit Domain: Record transformations ([#3231](../../pull/3231))
+  
+* Data Table: Enable deselection ([#3189](../../pull/3189))
+  
+* Empty helper pane message ([#3210](../../pull/3210))
+  
+* Matplotlib output for Scatter plot ([#3134](../../pull/3134))
+  
+* Scatterplot: indicate overlap of points. ([#3177](../../pull/3177))
+  
+* Selection of format and compression in save data widget ([#3147](../../pull/3147))
+  
+* OWBoxPlot: add option to sort discrete distributions by size ([#3156](../../pull/3156))
+  
+* Table: speed-up computation of basic stats of given columns. ([#3166](../../pull/3166))
+  
+* Canvas: 'Window Groups' continued ([#3085](../../pull/3085))
+  
+* Combo Box Search Filter ([#3014](../../pull/3014))
+  
+* Widget Insertion ([#3179](../../pull/3179))
+  
+
+  
+##### Bugfixes
+  
+* Documentation fetching with redirects ([#3248](../../pull/3248))
+  
+* DiscreteVariable reconstruction ([#3242](../../pull/3242))
+  
+* io: Handle mismatched number of header/data values ([#3237](../../pull/3237))
+  
+* OWNeuralNetwork model pickling ([#3230](../../pull/3230))
+  
+* Variable: Prevent hashing of Values of DiscreteVariable. ([#3217](../../pull/3217))
+  
+
+  
+
+  
+[3.15.0] - 2018-08-06
+  
+--------------------
+  
+##### Enhancements
+  
+* Silhouette Plot: Add cosine distance ([#3176](../../pull/3176))
+  
+* Add pandas_compat.table_to_frame(tab) ([#3180](../../pull/3180))
+  
+* OWSelectByDataIndex: New widget (move from Prototypes) ([#3181](../../pull/3181))
+  
+* Make filters available in Orange.data namespace. ([#3170](../../pull/3170))
+  
+* Move Louvain clustering from prototypes to core ([#3111](../../pull/3111))
+  
+* OWWidget: Collapse/expand the widget on control area toggle ([#3146](../../pull/3146))
+  
+* Rank: SklScorer should use the faster SklImputer. ([#3164](../../pull/3164))
+  
+* RecentFiles: Check for missing file in workflow dir ([#3064](../../pull/3064))
+  
+* Smart widget suggestions ([#3112](../../pull/3112))
+  
+* Match Keywords in Widget Search ([#3117](../../pull/3117))
+  
+* io: Speedup write_data ([#3115](../../pull/3115))
+  
+* OWEditDomain: Enable reordering of discrete variables ([#3119](../../pull/3119))
+  
+
+  
+##### Bugfixes
+  
+* oweditdomain: Fix an IndexError when all rows are deselected ([#3183](../../pull/3183))
+  
+* OWFreeViz: fix class density size ([#3158](../../pull/3158))
+  
+* OWBoxPlot: Fix empty continuous contingency check ([#3165](../../pull/3165))
+  
+* OWSql: enforce data download for non PostgreSQL databases ([#3178](../../pull/3178))
+  
+* owlouvainclustering: Make the task completion handler a single slot ([#3182](../../pull/3182))
+  
+* OWReport: disable save and print on empty report ([#3175](../../pull/3175))
+  
+* RemoveConstant: remove constant NaN features. ([#3163](../../pull/3163))
+  
+* utils/concurrent: Switch default thread pool ([#3138](../../pull/3138))
+  
+* OWBoxPlot: Fix quartiles computation ([#3159](../../pull/3159))
+  
+* OWBoxPlot: Plot axis labels and quartiles label layout ([#3162](../../pull/3162))
+  
+* [RFC] OWHeatMap: remove empty clusters from visualization ([#3155](../../pull/3155))
+  
+* report: Fix the number of hidden rows. ([#3150](../../pull/3150))
+  
+* [RFC] KMeans upgrade sparse support ([#3140](../../pull/3140))
+  
+* WebView fixes ([#3148](../../pull/3148))
+  
+* ci/appveyor: Update test dependencies ([#3139](../../pull/3139))
+  
+* Replace use of obsolete QStyle.standardPixmap ([#3127](../../pull/3127))
+  
+* BoxPlot: Hide groups with no instances ([#3122](../../pull/3122))
+  
+
+  
+
 [3.14.0] - 2018-07-04
 --------------------
 ##### Enhancements
@@ -865,7 +925,9 @@ Change Log
 * Initial version based on Python 1.5.2 and Qt 2.3
-  
-[next]: https://github.com/biolab/orange3/compare/3.14.0...HEAD
+  
+[next]: https://github.com/biolab/orange3/compare/3.16.0...HEAD
+  
+[3.16.0]: https://github.com/biolab/orange3/compare/3.15.0...3.16.0
+  
+[3.15.0]: https://github.com/biolab/orange3/compare/3.14.0...3.15.0
 [3.14.0]: https://github.com/biolab/orange3/compare/3.13.0...3.14.0
 [3.13.0]: https://github.com/biolab/orange3/compare/3.12.0...3.13.0
 [3.12.0]: https://github.com/biolab/orange3/compare/3.11.0...3.12.0

diff --git a/Orange/canvas/application/canvasmain.py b/Orange/canvas/application/canvasmain.py
@@ -273,6 +273,12 @@ def touch():
        self.dock_help = canvas_tool_dock.help
        self.dock_help.setMaximumHeight(150)
        self.dock_help.document().setDefaultStyleSheet("h3, a {color: orange;}")
+  
+        default_help = "Select a widget to show its description." \
+  
+                       "<br><br>" \
+  
+                       "See <a href='orange://examples'>workflow examples</a>, " \
+  
+                       "<a href='orange://tutorials'>YouTube tutorials</a>, " \
+  
+                       "or open the <a href='orange://welcome'>welcome screen</a>."
+  
+        self.dock_help.setDefaultText(default_help)
        self.dock_help_action = canvas_tool_dock.toogleQuickHelpAction()
        self.dock_help_action.setText(self.tr("Show Help"))
@@ -460,15 +466,15 @@ def setup_actions(self):
                    )
        self.tutorials_action = \
-  
-            QAction(self.tr("Tutorials"), self,
+  
+            QAction(self.tr("YouTube Tutorials"), self,
                    objectName="tutorials-action",
                    toolTip=self.tr("View YouTube tutorials."),
                    triggered=self.tutorials,
                    icon=canvas_icons("YouTube.svg")
                    )
        self.examples_action = \
-  
-            QAction(self.tr("Examples"), self,
+  
+            QAction(self.tr("Workflow Examples"), self,
                    objectName="tutorial-action",
                    toolTip=self.tr("Browse example workflows."),
                    triggered=self.tutorial_scheme,
@@ -688,7 +694,7 @@ def setup_menu(self):
        window_groups = self.scheme_widget.findChild(
            QAction, "window-groups-action"
        )
-  
-        if isinstance(window_groups, QAction):
+  
+        if window_groups is not None:
            self.view_menu.addAction(window_groups)
        self.view_menu.addSeparator()
@@ -704,6 +710,12 @@ def setup_menu(self):
        self.view_menu.addSeparator()
        self.view_menu.addAction(self.toogle_margins_action)
+  
+        raise_widgets_action = self.scheme_widget.findChild(
+  
+            QAction, "bring-widgets-to-front-action"
+  
+        )
+  
+        if raise_widgets_action is not None:
+  
+            self.view_menu.addAction(raise_widgets_action)
+  
+
        self.view_menu.addAction(self.float_widgets_on_top_action)
        menu_bar.addMenu(self.view_menu)
@@ -1099,6 +1111,9 @@ def load_scheme(self, filename):
            scheme_doc_widget.setPath(filename)
            self.add_recent_scheme(new_scheme.title, filename)
+  
+            if not self.freeze_action.isChecked():
+  
+                # activate the default window group.
+  
+                scheme_doc_widget.activateDefaultWindowGroup()
    def load_scheme_xml(self, xml):
        new_scheme = widgetsscheme.WidgetsScheme(parent=self)
@@ -1316,6 +1331,7 @@ def save_scheme_to(self, scheme, filename):
        # existing scheme file if `scheme.save_to` raises an error.
        buffer = BytesIO()
        try:
+  
+            scheme.set_runtime_env("basedir", dirname)
            scheme.save_to(buffer, pretty=True, pickle_fallback=True)
        except Exception:
            log.error("Error saving %r to %r", scheme, filename, exc_info=True)
@@ -1331,7 +1347,6 @@ def save_scheme_to(self, scheme, filename):
        try:
            with open(filename, "wb") as f:
                f.write(buffer.getvalue())
-  
-            scheme.set_runtime_env("basedir", dirname)
            return True
        except (IOError, OSError) as ex:
            log.error("%s saving '%s'", type(ex).__name__, filename,
@@ -1522,12 +1537,13 @@ def open_examples():
                    )
        examples_action = \
-  
-            QAction(self.examples_action.text(), dialog,
-  
-                    icon=self.examples_action.icon(),
-  
-                    toolTip=self.examples_action.toolTip(),
-  
-                    whatsThis=self.examples_action.whatsThis(),
-  
-                    triggered=open_examples,
+  
+            QAction(self.tr("Examples"), self,
+  
+                    icon=canvas_icons("Examples.svg"),
+  
+                    toolTip=self.tr("Browse example workflows."),
+  
+                    objectName="tutorial-action",
+  
+                    triggered=open_examples
                    )
+  
+
        tutorials_action = \
            QAction(self.tr("Tutorials"), self,
                    objectName="tutorials-action",
@@ -1913,16 +1929,22 @@ def event(self, event):
            if url.scheme() == "help" and url.authority() == "search":
                try:
                    url = self.help.search(url)
+  
+                    self.show_help(url)
                except KeyError:
-  
-                    url = None
                    log.info("No help topic found for %r", url)
-  
-
-  
-            if url:
-  
-                self.show_help(url)
-  
-            else:
-  
-                message_information(
-  
-                    self.tr("There is no documentation for this widget yet."),
-  
-                    parent=self)
+  
+                    message_information(
+  
+                        self.tr("There is no documentation for this widget yet."),
+  
+                        parent=self)
+  
+            elif url.scheme() == "orange":
+  
+                target = url.host()
+  
+                if target == "examples":
+  
+                    self.tutorial_scheme()
+  
+                elif target == "tutorials":
+  
+                    self.tutorials()
+  
+                elif target == "welcome":
+  
+                    self.welcome_dialog()
+  
+                else:
+  
+                    log.error("No target found for %r", url)
            return True

diff --git a/Orange/canvas/application/widgettoolbox.py b/Orange/canvas/application/widgettoolbox.py
@@ -419,7 +419,7 @@ def __on_rowsInserted(self, parent, start, end):
        Items have been inserted in the model.
        """
        # Only the top level items (categories) are handled here.
-  
-        if not parent is not None:
+  
+        if parent is None:
            root = self.__model.invisibleRootItem()
            for i in range(start, end + 1):
                item = root.child(i)
@@ -430,6 +430,6 @@ def __on_rowsRemoved(self, parent, start, end):
        Rows have been removed from the model.
        """
        # Only the top level items (categories) are handled here.
-  
-        if not parent is not None:
+  
+        if parent is None:
            for i in range(end, start - 1, -1):
                self.removeItem(i)
diff --git a/Orange/canvas/canvas/items/annotationitem.py b/Orange/canvas/canvas/items/annotationitem.py
@@ -4,7 +4,6 @@
 from xml.sax.saxutils import escape
 import docutils.core
-  
-import CommonMark
 from AnyQt.QtWidgets import (
    QGraphicsItem, QGraphicsPathItem, QGraphicsWidget, QGraphicsTextItem,
@@ -175,22 +174,6 @@ def render_html(content):
    return content
-  
-def render_markdown(content):
-  
-    """
-  
-    Return a html fragment from markdown text content
-  
-
-  
-    Parameters
-  
-    ----------
-  
-    content : str
-  
-        A markdown formatted text
-  
-
-  
-    Returns
-  
-    -------
-  
-    html : str
-  
-    """
-  
-    return CommonMark.commonmark(content)
-  
-
-  
-
 def render_rst(content):
    """
    Return a html fragment from a RST text content
@@ -236,7 +219,6 @@ class TextAnnotation(Annotation):
    ContentRenderer = OrderedDict([
        ("text/plain", render_plain),
        ("text/rst", render_rst),
-  
-        ("text/markdown", render_markdown),
        ("text/html", render_html),
    ])  # type: Dict[str, Callable[[str], [str]]]

diff --git a/Orange/canvas/document/commands.py b/Orange/canvas/document/commands.py
@@ -69,6 +69,27 @@ def undo(self):
        self.scheme.add_link(self.link)
+  
+class InsertNodeCommand(QUndoCommand):
+  
+    def __init__(self, scheme, new_node, old_link, new_links, parent=None):
+  
+        QUndoCommand.__init__(self, "Insert widget into link", parent)
+  
+        self.scheme = scheme
+  
+        self.inserted_widget = new_node
+  
+        self.original_link = old_link
+  
+        self.new_links = new_links
+  
+
+  
+    def redo(self):
+  
+        self.scheme.add_node(self.inserted_widget)
+  
+        self.scheme.remove_link(self.original_link)
+  
+        self.scheme.add_link(self.new_links[0])
+  
+        self.scheme.add_link(self.new_links[1])
+  
+
+  
+    def undo(self):
+  
+        self.scheme.remove_link(self.new_links[0])
+  
+        self.scheme.remove_link(self.new_links[1])
+  
+        self.scheme.add_link(self.original_link)
+  
+        self.scheme.remove_node(self.inserted_widget)
+  
+
+  
+
 class AddAnnotationCommand(QUndoCommand):
    def __init__(self, scheme, annotation, parent=None):
        QUndoCommand.__init__(self, "Add annotation", parent)

diff --git a/Orange/canvas/document/interactions.py b/Orange/canvas/document/interactions.py
@@ -80,6 +80,7 @@ def __init__(self, document, parent=None, deleteOnEnd=True):
        self.document = document
        self.scene = document.scene()
        self.scheme = document.scheme()
+  
+        self.suggestions = document.suggestions()
        self.deleteOnEnd = deleteOnEnd
        self.cancelOnEsc = False
@@ -428,6 +429,7 @@ def mouseReleaseEvent(self, event):
                else:
                    source_node = node
                    sink_node = self.scene.node_for_item(self.sink_item)
+  
+                self.suggestions.set_direction(self.direction)
                self.connect_nodes(source_node, sink_node)
                if not self.isCanceled() or not self.isFinished() and \
@@ -458,6 +460,15 @@ def is_compatible(source, sink):
        if self.direction == self.FROM_SINK:
            # Reverse the argument order.
            is_compatible = reversed_arguments(is_compatible)
+  
+            suggestion_sort = self.suggestions.get_source_suggestions(from_desc.name)
+  
+        else:
+  
+            suggestion_sort = self.suggestions.get_sink_suggestions(from_desc.name)
+  
+
+  
+        def sort(left, right):
+  
+            # list stores frequencies, so sign is flipped
+  
+            return suggestion_sort[left] > suggestion_sort[right]
+  
+
+  
+        menu.setSortingFunc(sort)
        def filter(index):
            desc = index.data(QtWidgetRegistry.WIDGET_DESC_ROLE)
@@ -776,6 +787,15 @@ def create_new(self, pos, search_text=""):
        menu = self.document.quickMenu()
        menu.setFilterFunc(None)
+  
+        # compares probability of the user needing the widget as a source
+  
+        def defaultSort(left, right):
+  
+            default_suggestions = self.suggestions.get_default_suggestions()
+  
+            left_frequency = sum(default_suggestions[left].values())
+  
+            right_frequency = sum(default_suggestions[right].values())
+  
+            return left_frequency > right_frequency
+  
+
+  
+        menu.setSortingFunc(defaultSort)
+  
+
        action = menu.exec_(pos, search_text)
        if action:
            item = action.property("item")