FunVIP 0.3.20__py3-none-any.whl

src/patch.py

@@ -0,0 +1,261 @@
+# ete3 patch
+# After using ete3 3.1.3, we don't need this anymore
+from __future__ import absolute_import
+from __future__ import print_function
+import ete3
+from copy import deepcopy
+
+
+# Patch for ete3 3.1.2 colliding with higher version PyQt5
+def save(scene, imgName, w=None, h=None, dpi=90, take_region=False, units="px"):
+    import colorsys
+    import random
+    import re
+    import types
+    from sys import stderr
+
+    from PyQt5 import QtGui, QtCore
+    from PyQt5.QtCore import (
+        Qt,
+        QPointF,
+        QRect,
+        QRectF,
+        QBuffer,
+        QByteArray,
+        QThread,
+        QIODevice,
+        QMetaObject,
+        QModelIndex,
+        QObject,
+        QRegExp,
+        QSize,
+        QSizeF,
+        QVariant,
+    )  # QString
+    from PyQt5.QtSvg import QGraphicsSvgItem, QSvgGenerator
+    from PyQt5.QtOpenGL import QGLFormat, QGLWidget
+    from PyQt5.QtPrintSupport import QPrinter
+    from PyQt5.QtWidgets import (
+        QAction,
+        QApplication,
+        QCheckBox,
+        QWidget,
+        QColorDialog,
+        QComboBox,
+        QDialog,
+        QDialogButtonBox,
+        QFileDialog,
+        QGraphicsEllipseItem,
+        QGraphicsItem,
+        QGraphicsItemGroup,
+        QGraphicsLineItem,
+        QGraphicsPathItem,
+        QGraphicsPixmapItem,
+        QGraphicsPolygonItem,
+        QGraphicsRectItem,
+        QGraphicsScene,
+        QGraphicsSimpleTextItem,
+        QGraphicsTextItem,
+        QGraphicsView,
+        QInputDialog,
+        QItemDelegate,
+        QLabel,
+        QLineEdit,
+        QListWidget,
+        QMainWindow,
+        QMenu,
+        QMenuBar,
+        QMessageBox,
+        QPushButton,
+        QSplitter,
+        QStatusBar,
+        QTableView,
+        QTextEdit,
+        QToolBar,
+        QVBoxLayout,
+        QWidget,
+    )
+
+    from PyQt5.QtGui import (
+        QBrush,
+        QColor,
+        QCursor,
+        QFont,
+        QFontMetrics,
+        QIcon,
+        QImage,
+        QPainter,
+        QPainterPath,
+        QPen,
+        QPixmap,
+        QPolygonF,
+        QRadialGradient,
+        QRegExpValidator,
+        QStandardItemModel,
+        QTransform,
+    )
+
+    QtCore.pyqtSignature = QtCore.pyqtSlot
+
+    from ete3.treeview.svg_colors import SVG_COLORS, COLOR_SCHEMES
+
+    import time
+
+    ipython_inline = False
+    if imgName == "%%inline":
+        ipython_inline = True
+        ext = "PNG"
+    elif imgName == "%%inlineSVG":
+        ipython_inline = True
+        ext = "SVG"
+    elif imgName.startswith("%%return"):
+        try:
+            ext = imgName.split(".")[1].upper()
+        except IndexError:
+            ext = "SVG"
+        imgName = "%%return"
+    else:
+        ext = imgName.split(".")[-1].upper()
+
+    main_rect = scene.sceneRect()
+    aspect_ratio = main_rect.height() / main_rect.width()
+
+    # auto adjust size
+    if not w and not h:
+        units = "px"
+        w = main_rect.width()
+        h = main_rect.height()
+        ratio_mode = Qt.KeepAspectRatio
+    elif w and h:
+        ratio_mode = Qt.IgnoreAspectRatio
+    elif h is None:
+        h = w * aspect_ratio
+        ratio_mode = Qt.KeepAspectRatio
+    elif w is None:
+        w = h / aspect_ratio
+        ratio_mode = Qt.KeepAspectRatio
+
+    # Adjust to resolution
+    if units == "mm":
+        if w:
+            w = w * 0.0393700787 * dpi
+        if h:
+            h = h * 0.0393700787 * dpi
+    elif units == "in":
+        if w:
+            w = w * dpi
+        if h:
+            h = h * dpi
+    elif units == "px":
+        pass
+    else:
+        raise Exception("wrong unit format")
+
+    x_scale, y_scale = w / main_rect.width(), h / main_rect.height()
+
+    if ext == "SVG":
+        svg = QSvgGenerator()
+        targetRect = QRectF(0, 0, w, h)
+        # print(f"DEBUG {w} {h}")
+        svg.setSize(QSize(int(w), int(h)))
+        svg.setViewBox(targetRect)
+        svg.setTitle("Generated with ETE http://etetoolkit.org")
+        svg.setDescription("Generated with ETE http://etetoolkit.org")
+
+        if imgName == "%%return":
+            ba = QByteArray()
+            buf = QBuffer(ba)
+            buf.open(QIODevice.WriteOnly)
+            svg.setOutputDevice(buf)
+        else:
+            svg.setFileName(imgName)
+
+        pp = QPainter()
+        pp.begin(svg)
+        scene.render(pp, targetRect, scene.sceneRect(), ratio_mode)
+        pp.end()
+        if imgName == "%%return":
+            compatible_code = str(ba)
+            print("from memory")
+        else:
+            compatible_code = open(imgName).read()
+        # Fix a very annoying problem with Radial gradients in
+        # inkscape and browsers...
+        compatible_code = compatible_code.replace("xml:id=", "id=")
+        compatible_code = re.sub(
+            'font-size="(\d+)"', 'font-size="\\1pt"', compatible_code
+        )
+        compatible_code = compatible_code.replace("\n", " ")
+        compatible_code = re.sub("<g [^>]+>\s*</g>", "", compatible_code)
+        # End of fix
+        if ipython_inline:
+            from IPython.core.display import SVG
+
+            return SVG(compatible_code)
+
+        elif imgName == "%%return":
+            return x_scale, y_scale, compatible_code
+        else:
+            open(imgName, "w").write(compatible_code)
+
+    elif ext == "PDF" or ext == "PS":
+        if ext == "PS":
+            format = QPrinter.PostScriptFormat
+        else:
+            format = QPrinter.PdfFormat
+
+        printer = QPrinter(QPrinter.HighResolution)
+        printer.setResolution(dpi)
+        printer.setOutputFormat(format)
+        printer.setPageSize(QPrinter.A4)
+        printer.setPaperSize(QSizeF(int(w), int(h)), QPrinter.DevicePixel)
+        printer.setPageMargins(0, 0, 0, 0, QPrinter.DevicePixel)
+
+        # pageTopLeft = printer.pageRect().topLeft()
+        # paperTopLeft = printer.paperRect().topLeft()
+        # For PS -> problems with margins
+        # print paperTopLeft.x(), paperTopLeft.y()
+        # print pageTopLeft.x(), pageTopLeft.y()
+        # print  printer.paperRect().height(),  printer.pageRect().height()
+        # topleft =  pageTopLeft - paperTopLeft
+
+        printer.setFullPage(True)
+        printer.setOutputFileName(imgName)
+        pp = QPainter(printer)
+        targetRect = QRectF(0, 0, w, h)
+        scene.render(pp, targetRect, scene.sceneRect(), ratio_mode)
+    else:
+        targetRect = QRectF(0, 0, w, h)
+        ii = QImage(w, h, QImage.Format_ARGB32)
+        ii.fill(QColor(Qt.white).rgb())
+        ii.setDotsPerMeterX(dpi / 0.0254)  # Convert inches to meters
+        ii.setDotsPerMeterY(dpi / 0.0254)
+        pp = QPainter(ii)
+        pp.setRenderHint(QPainter.Antialiasing)
+        pp.setRenderHint(QPainter.TextAntialiasing)
+        pp.setRenderHint(QPainter.SmoothPixmapTransform)
+
+        scene.render(pp, targetRect, scene.sceneRect(), ratio_mode)
+        pp.end()
+        if ipython_inline:
+            ba = QByteArray()
+            buf = QBuffer(ba)
+            buf.open(QIODevice.WriteOnly)
+            ii.save(buf, "PNG")
+            from IPython.core.display import Image
+
+            return Image(ba.data())
+        elif imgName == "%%return":
+            ba = QByteArray()
+            buf = QBuffer(ba)
+            buf.open(QIODevice.WriteOnly)
+            ii.save(buf, "PNG")
+            return x_scale, y_scale, ba.toBase64()
+        else:
+            ii.save(imgName)
+
+    return w / main_rect.width(), h / main_rect.height()
+
+
+def patch():
+    ete3.treeview.main.save = deepcopy(save)