Merge pull request #284 from etetoolkit/qt5

add Qt5 support

.travis.yml

@@ -5,14 +5,14 @@ python:
   - "2.7"
   - "3.4"
   - "3.5"
-
+  - "3.6"
 
 cache:
   directories:
   - test_tmp
 
 install:
-  - ./run_tests.sh --setup-only -sv "$TRAVIS_PYTHON_VERSION"
+  - ./run_tests.sh -s --setup-only -v "$TRAVIS_PYTHON_VERSION"
 
 before_script:
   # Ensure tags are available on the cloned repository
@@ -24,6 +24,7 @@ before_script:
 
 script:
   - ./run_tests.sh --test-only -sv "$TRAVIS_PYTHON_VERSION"
+  - if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then ./run_tests.sh --qt4 -sv "$TRAVIS_PYTHON_VERSION" ; fi 
   #- coverage run -m ete3.test.test_api
   #- coverage run -a -m ete3.test.test_ete_evol   # too heavy for travis
   #- coverage run -a -m ete3.test.test_ete_build  # too heavy for travis

ete3/test/test_treeview/item_faces.py

@@ -1,21 +1,20 @@
-# We will need to create Qt4 items
-from PyQt4 import QtCore
-from PyQt4.QtGui import QGraphicsRectItem, QGraphicsSimpleTextItem, \
-    QGraphicsEllipseItem, QColor, QPen, QBrush
-
-from ... import Tree, faces, TreeStyle, NodeStyle
-
 # To play with random colors
 import colorsys
 import random
 
+from ... import Tree, faces, TreeStyle, NodeStyle, Face
+
+# We will need to create Qt4 items
+from ...treeview.qt import QtCore, Qt
+from ...treeview.qt import QGraphicsRectItem, QGraphicsSimpleTextItem, \
+    QGraphicsEllipseItem, QColor, QPen, QBrush
+
 class InteractiveItem(QGraphicsRectItem):
     def __init__(self, *arg, **karg):
         QGraphicsRectItem.__init__(self, *arg, **karg)
         self.node = None
         self.label = None
         self.setCursor(QtCore.Qt.PointingHandCursor)
-        self.setAcceptsHoverEvents(True)
 
     def hoverEnterEvent (self, e):
         # There are many ways of adding interactive elements. With the
@@ -39,6 +38,7 @@ def hoverLeaveEvent(self, e):
         if self.label:
             self.label.setVisible(False)
 
+
 def random_color(h=None):
     """Generates a random color in RGB format."""
     if not h:
@@ -58,17 +58,19 @@ def ugly_name_face(node, *args, **kargs):
 
     # receive an arbitrary number of arguments, in this case width and
     # height of the faces
-    width = args[0][0]
-    height = args[0][1]
+    width = args[0]
+    height = args[1]
 
     ## Creates a main master Item that will contain all other elements
     ## Items can be standard QGraphicsItem
     # masterItem = QGraphicsRectItem(0, 0, width, height)
 
     # Or your custom Items, in which you can re-implement interactive
     # functions, etc. Check QGraphicsItem doc for details.
-    masterItem = InteractiveItem(0, 0, width, height)
 
+    masterItem = InteractiveItem(0, 0, width, height)
+    masterItem.setAcceptHoverEvents(True)
+
     # Keep a link within the item to access node info
     masterItem.node = node
 

ete3/test/test_treeview/new_seq_face.py

@@ -1,9 +1,9 @@
 # We will need to create Qt4 items
-from PyQt4       import QtCore
-from PyQt4.QtGui import QGraphicsRectItem, QColor, QPen, QBrush
-from PyQt4.QtGui import QGraphicsSimpleTextItem, QFont
+from ...treeview.qt import QtCore
+from ...treeview.qt import QGraphicsRectItem, QColor, QPen, QBrush
+from ...treeview.qt import QGraphicsSimpleTextItem, QFont
 
-from ... import faces, TreeStyle, PhyloTree, TextFace
+from ... import faces, TreeStyle, PhyloTree, TextFace, SequenceFace
 from random import random
 
 _aafgcolors = {
@@ -87,130 +87,6 @@
 }
 
 
-class MySequenceFace(faces.StaticItemFace):
-    """ Creates a new molecular sequence face object.
-
-
-    :argument seq:  Sequence string to be drawn
-    :argument seqtype: Type of sequence: "nt" or "aa"
-    :argument fsize:   Font size,  (default=10)
-
-    You can set custom colors for amino-acids or nucleotides:
-
-    :argument None  codon       : a string that corresponds to the reverse translation of the amino-acid sequence
-    :argument 11    col_w       : width of the column (if col_w is lower than font size, letter wont be displayed)
-    :argument None  fg_colors   : dictionary of colors for foreground, with as keys each possible character in sequences, and as value the colors
-    :argument None  bg_colors   : dictionary of colors for background, with as keys each possible character in sequences, and as value the colors
-    :argument 3     alt_col_w   : works together with special_col option, defines the width of given columns
-    :argument None  special_col : list of lists containing the bounds of columns to be displayed with alt_col_w as width
-    :argument False interactive : more info can be displayed when mouse over sequence
-
-    """
-    def __init__(self, seq, seqtype="aa", fsize=10,
-                 fg_colors=None, bg_colors=None,
-                 codon=None, col_w=11, alt_col_w=3,
-                 special_col=None, interactive=False):
-        self.seq         = seq
-        self.codon       = codon
-        self.fsize       = fsize
-        self.style       = seqtype
-        self.col_w       = float(col_w)
-        self.alt_col_w   = float(alt_col_w)
-        self.special_col = special_col if special_col else []
-        self.width       = 0 # will store the width of the whole sequence
-        self.interact    = interactive
-
-        if self.style == "aa":
-            if not fg_colors:
-                fg_colors = _aafgcolors
-            if not bg_colors:
-                bg_colors = _aabgcolors
-        else:
-            if not fg_colors:
-                fg_colors = _ntfgcolors
-            if not bg_colors:
-                bg_colors = _ntbgcolors
-
-        self.fg_col = self.__init_col(fg_colors)
-        self.bg_col = self.__init_col(bg_colors)
-
-        # for future?
-        self.row_h       = 13.0
-
-        super(MySequenceFace,
-              self).__init__(QGraphicsRectItem(0, 0, self.width, self.row_h))
-
-    def __init_col(self, color_dic):
-        """to speed up the drawing of colored rectangles and characters"""
-        new_color_dic = {}
-        for car in color_dic:
-            new_color_dic[car] = QBrush(QColor(color_dic[car]))
-        return new_color_dic
-
-    def update_items(self):
-        #self.item = QGraphicsRectItem(0,0,self._total_w, self.row_h)
-        seq_width = 0
-        nopen = QPen(QtCore.Qt.NoPen)
-        font = QFont("Courier", self.fsize)
-        rect_cls = self.InteractiveLetterItem if self.interact else QGraphicsRectItem
-        for i, letter in enumerate(self.seq):
-            width = self.col_w
-            for m in self.special_col:
-                if m[0] < i <= m[1]:
-                    width = self.alt_col_w
-                    break
-            #load interactive item if called correspondingly
-            rectItem = rect_cls(0, 0, width, self.row_h, parent=self.item)
-            rectItem.setX(seq_width) # to give correct X to children item
-            rectItem.setBrush(self.bg_col[letter])
-            rectItem.setPen(nopen)
-            if self.interact:
-                if self.codon:
-                    rectItem.codon = '%s, %d: %s' % (self.seq[i], i,
-                                                     self.codon[i*3:i*3+3])
-                else:
-                    rectItem.codon = '%s, %d' % (self.seq[i], i)
-            # write letter if enough space
-            if width >= self.fsize:
-                text = QGraphicsSimpleTextItem(letter, parent=rectItem)
-                text.setFont(font)
-                text.setBrush(self.fg_col[letter])
-                # Center text according to rectItem size
-                tw = text.boundingRect().width()
-                th = text.boundingRect().height()
-                text.setPos((width - tw)/2, (self.row_h - th)/2)
-            seq_width += width
-        self.width = seq_width
-
-    class InteractiveLetterItem(QGraphicsRectItem):
-        """This is a class"""
-        def __init__(self, *arg, **karg):
-            QGraphicsRectItem.__init__(self, *arg, **karg)
-            self.codon = None
-            self.label = None
-            self.setAcceptsHoverEvents(True)
-
-        def hoverEnterEvent (self, e):
-            """ when mouse is over"""
-            if not self.label:
-                self.label = QGraphicsRectItem(parent=self)
-                #self.label.setY(-18)
-                self.label.setX(11)
-                self.label.setBrush(QBrush(QColor("white")))
-                self.label.text = QGraphicsSimpleTextItem(parent=self.label)
-
-            self.setZValue(1)
-            self.label.text.setText(self.codon)
-            self.label.setRect(self.label.text.boundingRect())
-            self.label.setVisible(True)
-
-        def hoverLeaveEvent(self, e):
-            """when mouse leaves area"""
-            if self.label:
-                self.label.setVisible(False)
-                self.setZValue(0)
-
-
 
 def test_layout_evol(node):
     '''
@@ -221,7 +97,7 @@ def test_layout_evol(node):
             node.img_style["draw_descendants"]= False
     if node.is_leaf():
         if hasattr (node, "sequence"):
-            seqface =  MySequenceFace(node.sequence, "aa",
+            seqface =  SequenceFace(node.sequence, "aa",
                                       codon=node.nt_sequence, fsize=10,
                                       col_w=11, interactive=True)
             faces.add_face_to_node(seqface, node, 1, aligned=True)
@@ -235,7 +111,7 @@ def test_layout_phylo_aa(node):
             node.img_style["draw_descendants"]= False
     if node.is_leaf():
         if hasattr (node, "sequence"):
-            seqface =  MySequenceFace(node.sequence, "aa",
+            seqface = SequenceFace(node.sequence, "aa",
                                       fsize=10,
                                       col_w=11, interactive=False)
             faces.add_face_to_node(seqface, node, 1, aligned=True)
@@ -251,7 +127,7 @@ def test_layout_phylo_aa_motif(node):
     special_col = [[10,100],[150,1000],[1000,2000],[3000,4990]]
     if node.is_leaf():
         if hasattr (node, "sequence"):
-            seqface =  MySequenceFace(node.sequence, "aa",
+            seqface = SequenceFace(node.sequence, "aa",
                                       fsize=10,special_col=special_col,
                                       alt_col_w=3,
                                       col_w=11, interactive=True)
@@ -267,7 +143,7 @@ def test_layout_phylo_nt(node):
             node.img_style["draw_descendants"]= False
     if node.is_leaf():
         if hasattr (node, "sequence"):
-            seqface =  MySequenceFace(node.sequence, "nt",
+            seqface =  SequenceFace(node.sequence, "nt",
                                       fsize=10,
                                       col_w=11, interactive=True)
             faces.add_face_to_node(seqface, node, 1, aligned=True)

ete3/treeview/_about.py

@@ -45,38 +45,38 @@
 #      by: PyQt4 UI code generator 4.7.2
 #
 # WARNING! All changes made in this file will be lost!
-
-from PyQt4 import QtCore, QtGui
+from __future__ import absolute_import
+from .qt import *
 
 class Ui_About(object):
     def setupUi(self, About):
         About.setObjectName("About")
         About.resize(462, 249)
-        self.verticalLayoutWidget = QtGui.QWidget(About)
+        self.verticalLayoutWidget = QWidget(About)
         self.verticalLayoutWidget.setGeometry(QtCore.QRect(10, 0, 441, 208))
         self.verticalLayoutWidget.setObjectName("verticalLayoutWidget")
-        self.verticalLayout = QtGui.QVBoxLayout(self.verticalLayoutWidget)
+        self.verticalLayout = QVBoxLayout(self.verticalLayoutWidget)
         self.verticalLayout.setObjectName("verticalLayout")
-        self.label = QtGui.QLabel(self.verticalLayoutWidget)
+        self.label = QLabel(self.verticalLayoutWidget)
         self.label.setObjectName("label")
         self.verticalLayout.addWidget(self.label)
-        self.version = QtGui.QLabel(self.verticalLayoutWidget)
+        self.version = QLabel(self.verticalLayoutWidget)
         self.version.setObjectName("version")
         self.verticalLayout.addWidget(self.version)
 
         self.retranslateUi(About)
         QtCore.QMetaObject.connectSlotsByName(About)
 
     def retranslateUi(self, About):
-        About.setWindowTitle(QtGui.QApplication.translate("About", "Dialog", None, QtGui.QApplication.UnicodeUTF8))
-        self.label.setText(QtGui.QApplication.translate("About", "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0//EN\" \"http://www.w3.org/TR/REC-html40/strict.dtd\">\n"
+        About.setWindowTitle(QApplication.translate("About", "Dialog", None))
+        self.label.setText(QApplication.translate("About", "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.0//EN\" \"http://www.w3.org/TR/REC-html40/strict.dtd\">\n"
 "<html><head><meta name=\"qrichtext\" content=\"1\" /><style type=\"text/css\">\n"
 "p, li { white-space: pre-wrap; }\n"
 "</style></head><body style=\" font-family:\'DejaVu Sans\'; font-size:10pt; font-weight:400; font-style:normal;\">\n"
 "<p align=\"center\" style=\" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;\"><img src=\":/ete icons/ete_logo.png\" /></p>\n"
-"<p align=\"center\" style=\" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-weight:600;\"><span style=\" font-size:11pt;\">ETE: a python Environment for Tree Exploration</span></p>\n"
+                                                        "<p align=\"center\" style=\" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-weight:600;\"><span style=\" font-size:11pt;\">ETE3: Reconstruction and Analysis Phylogenomics Data</span></p>\n"
 "<p align=\"center\" style=\" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:11pt; font-weight:600;\"><a href=\"http://etetoolkit.org\"><span style=\" text-decoration: underline; color:#0057ae;\">http://etetoolkit.org</span></a></p>\n"
-"<p align=\"center\" style=\"-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;\"></p></body></html>", None, QtGui.QApplication.UnicodeUTF8))
-        self.version.setText(QtGui.QApplication.translate("About", "VERSION", None, QtGui.QApplication.UnicodeUTF8))
+"<p align=\"center\" style=\"-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;\"></p></body></html>", None))
+        self.version.setText(QApplication.translate("About", "VERSION", None))
 
 from . import ete_resources_rc