From 9beae2bc2b370b0a9eca6e472dd1f6b9e331775a Mon Sep 17 00:00:00 2001
From: GuyTeichman <48219633+GuyTeichman@users.noreply.github.com>
Date: Fri, 6 Sep 2024 18:46:40 +0300
Subject: [PATCH] transitioned RNAlysis to Qt6
---
pytest.ini | 2 +-
requirements.txt | 6 +-
rnalysis/gui/gui.py | 216 ++++++++++----------
rnalysis/gui/gui_graphics.py | 4 +-
rnalysis/gui/gui_quickstart.py | 24 +--
rnalysis/gui/gui_style.py | 2 +-
rnalysis/gui/gui_widgets.py | 50 ++---
rnalysis/gui/gui_windows.py | 350 ++++++++-------------------------
tests/test_gui.py | 52 ++---
tests/test_gui_graphics.py | 6 +-
tests/test_gui_quickstart.py | 44 ++---
tests/test_gui_widgets.py | 10 +-
tests/test_gui_windows.py | 71 +------
13 files changed, 301 insertions(+), 536 deletions(-)
diff --git a/pytest.ini b/pytest.ini
index 608ad155f..ddae59950 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -2,4 +2,4 @@
testpaths = tests/
python_files = *.py
python_functions = test_*
-qt_api=pyqt5
+qt_api=pyqt6
diff --git a/requirements.txt b/requirements.txt
index 76d2bdd33..5af48976d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -15,8 +15,8 @@ joblib>=1.4.2
tqdm>=4.65
appdirs>=1.4.0
typing_extensions>=4.5
-PyQt5>=5.15.9
-qdarkstyle
+PyQt6>=6.7
+qdarkstyle>=3
defusedxml>=0.7.1
aiohttp>=3.8.4, <3.10
aiodns>=3.0.0
@@ -26,5 +26,5 @@ tenacity>=8.2.3
mslex>=1.1.0
nest-asyncio>=1.6.0
kmedoids>=0.5.1
-polars[async,numpy,pyarrow,pandas]>=1.5.0
+polars[async,numpy,pyarrow,pandas]>=1.6.0,<1.7
pandas[performance,parquet]
diff --git a/rnalysis/gui/gui.py b/rnalysis/gui/gui.py
index 62400629a..841d0f6f3 100644
--- a/rnalysis/gui/gui.py
+++ b/rnalysis/gui/gui.py
@@ -20,7 +20,7 @@
import numpy as np
import polars as pl
import yaml
-from PyQt5 import QtCore, QtWidgets, QtGui
+from PyQt6 import QtCore, QtWidgets, QtGui
from rnalysis import fastq, filtering, enrichment, __version__
from rnalysis.gui import gui_style, gui_widgets, gui_windows, gui_graphics, gui_quickstart
@@ -512,7 +512,7 @@ def init_setups_ui(self):
self.setups_grid.addWidget(self.stack, 1, 0)
self.setups_widgets['list'] = gui_widgets.MultiChoiceListWithDelete(list(), parent=self.setups_group)
self.setups_widgets['list'].itemDeleted.connect(self.remove_clustering_setup)
- self.setups_grid.addWidget(QtWidgets.QLabel('Added setups'), 0, 1, QtCore.Qt.AlignCenter)
+ self.setups_grid.addWidget(QtWidgets.QLabel('Added setups'), 0, 1, QtCore.Qt.AlignmentFlag.AlignCenter)
self.setups_grid.addWidget(self.setups_widgets['list'], 1, 1, 2, 1)
self.setups_widgets['add_button'] = QtWidgets.QPushButton('Add setup')
@@ -622,10 +622,10 @@ def init_basic_ui(self):
self.plot_group.setVisible(False)
self.stats_group.setVisible(False)
- self.scroll.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+ self.scroll.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarPolicy.ScrollBarAlwaysOff)
self.scroll.setWidgetResizable(True)
self.scroll.setWidget(self.scroll_widget)
- self.scroll_layout.setSizeConstraint(QtWidgets.QLayout.SetMinAndMaxSize)
+ self.scroll_layout.setSizeConstraint(QtWidgets.QLayout.SizeConstraint.SetMinAndMaxSize)
self.scroll_layout.addWidget(self.list_group)
self.scroll_layout.addWidget(self.stats_group)
@@ -994,7 +994,7 @@ def init_ui(self):
self.setWindowTitle('Set Operations')
self.setGeometry(600, 50, 1050, 800)
self.setLayout(self.layout)
- self.widgets['splitter'] = QtWidgets.QSplitter(QtCore.Qt.Horizontal)
+ self.widgets['splitter'] = QtWidgets.QSplitter(QtCore.Qt.Orientation.Horizontal)
self.layout.addWidget(self.widgets['splitter'])
self.widgets['splitter'].addWidget(self.list_group)
self.widgets['splitter'].addWidget(self.operations_group)
@@ -1223,7 +1223,7 @@ def init_ui(self):
self.setWindowTitle('Gene Set Visualization')
self.setGeometry(600, 50, 1050, 800)
self.setLayout(self.layout)
- self.widgets['splitter'] = QtWidgets.QSplitter(QtCore.Qt.Horizontal)
+ self.widgets['splitter'] = QtWidgets.QSplitter(QtCore.Qt.Orientation.Horizontal)
self.layout.addWidget(self.widgets['splitter'])
self.widgets['splitter'].addWidget(self.list_group)
self.widgets['splitter'].addWidget(self.visualization_group)
@@ -1398,18 +1398,25 @@ class TabPage(QtWidgets.QWidget):
GENERAL_FUNCS = ()
THREADED_FUNCS = set()
- def __init__(self, parent=None, undo_stack: QtWidgets.QUndoStack = None, tab_id: int = None):
+ def __init__(self, parent=None, undo_stack: QtGui.QUndoStack = None, tab_id: int = None):
super().__init__(parent)
self.tab_id = tab_id
self.undo_stack = undo_stack
self.sup_layout = QtWidgets.QVBoxLayout(self)
- self.container = QtWidgets.QWidget(self)
- self.layout = QtWidgets.QVBoxLayout(self.container)
+
+ self.splitter = QtWidgets.QSplitter(QtCore.Qt.Orientation.Vertical)
+ self.sup_layout.addWidget(self.splitter)
+
+ # initiate the splitter layout for the tab
self.scroll = QtWidgets.QScrollArea()
- self.scroll.setWidget(self.container)
- self.scroll.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOn)
- self.scroll.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+ self.scroll.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarPolicy.ScrollBarAlwaysOn)
+ self.scroll.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarPolicy.ScrollBarAlwaysOff)
self.scroll.setWidgetResizable(True)
+ self.splitter.addWidget(self.scroll)
+
+ self.container = QtWidgets.QWidget()
+ self.layout = QtWidgets.QVBoxLayout(self.container)
+ self.scroll.setWidget(self.container)
self.name = None
self.creation_time = time.time()
@@ -1429,7 +1436,7 @@ def __init__(self, parent=None, undo_stack: QtWidgets.QUndoStack = None, tab_id:
self.function_group = QtWidgets.QGroupBox('Apply functions')
self.function_grid = QtWidgets.QGridLayout(self.function_group)
self.function_widgets = {}
- self.layout.insertWidget(2, self.function_group)
+ self.layout.addWidget(self.function_group)
self.function_group.setVisible(False)
self.stdout_group = QtWidgets.QGroupBox('Log')
@@ -1439,13 +1446,9 @@ def __init__(self, parent=None, undo_stack: QtWidgets.QUndoStack = None, tab_id:
# initiate apply button
self.apply_button = QtWidgets.QPushButton('Apply')
self.apply_button.clicked.connect(self.apply_function)
- self.layout.insertWidget(3, self.apply_button)
+ self.layout.addWidget(self.apply_button)
self.apply_button.setVisible(False)
- # initiate the splitter layout for the tab
- self.splitter = QtWidgets.QSplitter(QtCore.Qt.Vertical)
- self.sup_layout.addWidget(self.splitter)
- self.splitter.addWidget(self.scroll)
self.splitter.addWidget(self.stdout_group)
self.splitter.setStretchFactor(0, 1)
@@ -1670,7 +1673,7 @@ class SetTabPage(TabPage):
}
def __init__(self, set_name: str, gene_set: typing.Union[set, enrichment.FeatureSet] = None, parent=None,
- undo_stack: QtWidgets.QUndoStack = None, tab_id: int = None):
+ undo_stack: QtGui.QUndoStack = None, tab_id: int = None):
super().__init__(parent, undo_stack, tab_id)
if gene_set is None:
gene_set = enrichment.FeatureSet(set(), set_name)
@@ -1971,7 +1974,7 @@ class FilterTabPage(TabPage):
startedClustering = QtCore.pyqtSignal(object, object, object)
widthChanged = QtCore.pyqtSignal()
- def __init__(self, parent=None, undo_stack: QtWidgets.QUndoStack = None, tab_id: int = None):
+ def __init__(self, parent=None, undo_stack: QtGui.QUndoStack = None, tab_id: int = None):
super().__init__(parent, undo_stack, tab_id)
self.filter_obj = None
@@ -2051,8 +2054,8 @@ def init_overview_ui(self):
self.overview_widgets['table_name_label'].setWordWrap(True)
self.overview_widgets['preview'] = gui_widgets.ReactiveTableView()
- self.overview_widgets['preview'].setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
- self.overview_widgets['preview'].setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+ self.overview_widgets['preview'].setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarPolicy.ScrollBarAlwaysOff)
+ self.overview_widgets['preview'].setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarPolicy.ScrollBarAlwaysOff)
self.overview_grid.addWidget(self.overview_widgets['table_name_label'], this_row, 0, 1, 4)
this_row += 1
@@ -2158,7 +2161,7 @@ def init_basic_ui(self):
self.basic_grid.setRowStretch(4, 1)
self.basic_grid.setColumnStretch(4, 1)
- def _check_for_special_functions(self, is_selected: bool):
+ def _check_for_special_functions(self, is_selected: bool=True):
if not is_selected:
return
this_stack: FuncTypeStack = self.stack.currentWidget()
@@ -2513,7 +2516,7 @@ def remove_last_function(self):
err = QtWidgets.QMessageBox(self)
err.setWindowTitle('Pipeline is already empty!')
err.setText('Cannot remove functions from the Pipeline - it is already empty!')
- err.setIcon(err.Warning)
+ err.setIcon(err.Icon.Warning)
err.exec()
def _get_pipeline_name(self):
@@ -2536,9 +2539,10 @@ def closeEvent(self, event): # pragma: no cover
"All unsaved progress will be lost"
reply = QtWidgets.QMessageBox.question(self, "Close 'Create Pipeline' window?",
- quit_msg, QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.Yes)
+ quit_msg, QtWidgets.QMessageBox.StandardButton.No,
+ QtWidgets.QMessageBox.StandardButton.Yes)
- if reply == QtWidgets.QMessageBox.Yes:
+ if reply == QtWidgets.QMessageBox.StandardButton.Yes:
event.accept()
else:
event.ignore()
@@ -2577,7 +2581,8 @@ def __init__(self, objs: List[Union[filtering.Filter, enrichment.FeatureSet]], j
self.objs[key] = obj
self.files = list(self.objs.keys())
- self.button_box = QtWidgets.QDialogButtonBox(QtWidgets.QDialogButtonBox.Ok | QtWidgets.QDialogButtonBox.Cancel)
+ self.button_box = QtWidgets.QDialogButtonBox(
+ QtWidgets.QDialogButtonBox.StandardButton.Ok | QtWidgets.QDialogButtonBox.StandardButton.Cancel)
self.labels = dict()
self.keep_marks = dict()
self.names = dict()
@@ -2596,7 +2601,7 @@ def init_ui(self):
self.scroll.setWidgetResizable(True)
self.scroll.setWidget(self.scroll_widget)
self.scroll_widget.setLayout(self.scroll_layout)
- self.scroll_layout.setSizeConstraint(QtWidgets.QLayout.SetMinAndMaxSize)
+ self.scroll_layout.setSizeConstraint(QtWidgets.QLayout.SizeConstraint.SetMinAndMaxSize)
self.select_all.clicked.connect(self.change_all)
self.button_box.accepted.connect(self.accept)
@@ -2658,7 +2663,8 @@ class MultiOpenWindow(QtWidgets.QDialog):
def __init__(self, files: List[str], parent=None):
super().__init__(parent)
self.files = files
- self.button_box = QtWidgets.QDialogButtonBox(QtWidgets.QDialogButtonBox.Ok | QtWidgets.QDialogButtonBox.Cancel)
+ self.button_box = QtWidgets.QDialogButtonBox(
+ QtWidgets.QDialogButtonBox.StandardButton.Ok | QtWidgets.QDialogButtonBox.StandardButton.Cancel)
self.all_types_combo = QtWidgets.QComboBox(self)
self.paths = dict()
self.table_types = dict()
@@ -2679,7 +2685,7 @@ def init_ui(self):
self.scroll.setWidgetResizable(True)
self.scroll.setWidget(self.scroll_widget)
self.scroll_widget.setLayout(self.scroll_layout)
- self.scroll_layout.setSizeConstraint(QtWidgets.QLayout.SetMinAndMaxSize)
+ self.scroll_layout.setSizeConstraint(QtWidgets.QLayout.SizeConstraint.SetMinAndMaxSize)
self.button_box.accepted.connect(self.accept)
self.button_box.rejected.connect(self.reject)
@@ -2770,9 +2776,9 @@ def __init__(self, parent=None):
self.setElideMode(QtCore.Qt.TextElideMode.ElideMiddle)
def mousePressEvent(self, event: QtGui.QMouseEvent):
- if event.button() == QtCore.Qt.LeftButton:
+ if event.button() == QtCore.Qt.MouseButton.LeftButton:
super().mousePressEvent(event)
- elif event.button() == QtCore.Qt.RightButton:
+ elif event.button() == QtCore.Qt.MouseButton.RightButton:
point = event.pos()
if point.isNull():
return
@@ -2810,7 +2816,7 @@ def widget(self, index: int) -> Union[FilterTabPage, SetTabPage]:
return super().widget(index)
-class RenameCommand(QtWidgets.QUndoCommand):
+class RenameCommand(QtGui.QUndoCommand):
__slots__ = {'prev_name': 'previous name of the tab',
'new_name': 'new name of the tab',
'prev_id': 'previous ID',
@@ -2835,7 +2841,7 @@ def redo(self):
self.tab._rename(self.new_name, self.job_id)
-class CloseTabCommand(QtWidgets.QUndoCommand):
+class CloseTabCommand(QtGui.QUndoCommand):
__slots__ = {'tab_container': 'ReactiveTabWidget containing the tabs',
'tab_index': 'index of the tab to be closed',
'tab_icon': 'icon of the tab',
@@ -2868,7 +2874,7 @@ def redo(self):
self.tab_container.removeTab(self.tab_index)
-class InplaceCommand(QtWidgets.QUndoCommand):
+class InplaceCommand(QtGui.QUndoCommand):
__slots__ = {'tab': 'tab widget',
'prev_job_id': 'previous job ID',
'new_job_id': 'new job ID',
@@ -2965,7 +2971,7 @@ def redo(self):
self.tab.itemSpawned.emit(f"'{source_name}'\noutput", new_spawn_id, self.new_job_id, self.tab.obj())
-class PipelineInplaceCommand(QtWidgets.QUndoCommand):
+class PipelineInplaceCommand(QtGui.QUndoCommand):
__slots__ = {'tab': 'tab object',
'pipeline': 'Pipeline to apply',
'pipeline_name': 'Pipeline name',
@@ -3016,8 +3022,8 @@ def __init__(self, gather_stdout: bool = True):
self.report = None
self.tabs = ReactiveTabWidget(self)
- self.closed_tabs_stack = QtWidgets.QUndoStack(self)
- self.undo_group = QtWidgets.QUndoGroup(self)
+ self.closed_tabs_stack = QtGui.QUndoStack(self)
+ self.undo_group = QtGui.QUndoGroup(self)
self.tabs.currentChanged.connect(self._change_undo_stack)
self.undo_view = QtWidgets.QUndoView(self.undo_group)
@@ -3150,12 +3156,12 @@ def init_ui(self):
self.command_history_dock.setWidget(self.undo_view)
self.command_history_dock.setFloating(False)
- self.addDockWidget(QtCore.Qt.RightDockWidgetArea, self.command_history_dock)
+ self.addDockWidget(QtCore.Qt.DockWidgetArea.RightDockWidgetArea, self.command_history_dock)
self.setStatusBar(self.status_bar)
self.task_queue_window.cancelRequested.connect(self.cancel_job)
- self.tabs.setCornerWidget(self.add_tab_button, QtCore.Qt.TopRightCorner)
+ self.tabs.setCornerWidget(self.add_tab_button, QtCore.Qt.Corner.TopRightCorner)
self.setCentralWidget(self.tabs)
@QtCore.pyqtSlot()
@@ -3164,11 +3170,12 @@ def clear_history(self, confirm_action: bool = True):
clear_msg = """Are you sure you want to clear all command history?
This cannot be undone!"""
reply = QtWidgets.QMessageBox.question(self, 'Clear history',
- clear_msg, QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.Yes)
+ clear_msg, QtWidgets.QMessageBox.StandardButton.No,
+ QtWidgets.QMessageBox.StandardButton.Yes)
else:
- reply = QtWidgets.QMessageBox.Yes
+ reply = QtWidgets.QMessageBox.StandardButton.Yes
- if reply == QtWidgets.QMessageBox.Yes:
+ if reply == QtWidgets.QMessageBox.StandardButton.Yes:
for stack in self.undo_group.stacks():
stack.clear()
self.closed_tabs_stack.clear()
@@ -3177,7 +3184,7 @@ def clear_history(self, confirm_action: bool = True):
def init_tab_contextmenu(self, ind: int):
self.tab_contextmenu = QtWidgets.QMenu(self)
- new_to_right_action = QtWidgets.QAction("New tab to the right")
+ new_to_right_action = QtGui.QAction("New tab to the right")
new_to_right_action.triggered.connect(
functools.partial(self.add_new_tab_at, index=ind + 1, name=None, is_set=False))
self.tab_contextmenu.addAction(new_to_right_action)
@@ -3186,36 +3193,36 @@ def init_tab_contextmenu(self, ind: int):
color_menu = self.tab_contextmenu.addMenu("Change tab &color")
actions = []
for color in gui_graphics.COLOR_ICONS:
- this_action = QtWidgets.QAction(color.capitalize())
+ this_action = QtGui.QAction(color.capitalize())
this_action.setIcon(gui_graphics.get_icon(color))
this_action.triggered.connect(functools.partial(self.set_tab_icon, ind, icon_name=color))
actions.append(this_action)
color_menu.addAction(this_action)
- reset_action = QtWidgets.QAction("Reset color")
+ reset_action = QtGui.QAction("Reset color")
reset_action.triggered.connect(functools.partial(self.set_tab_icon, ind, icon_name=None))
color_menu.addAction(reset_action)
self.tab_contextmenu.addSeparator()
# sort_menu = self.tab_contextmenu.addMenu("Sort tabs")
- sort_by_name = QtWidgets.QAction("Sort by tab &name")
+ sort_by_name = QtGui.QAction("Sort by tab &name")
sort_by_name.triggered.connect(self.sort_tabs_by_name)
- sort_by_time = QtWidgets.QAction("Sort by creation &time")
+ sort_by_time = QtGui.QAction("Sort by creation &time")
sort_by_time.triggered.connect(self.sort_tabs_by_creation_time)
- sort_by_type = QtWidgets.QAction("Sort by tab type")
+ sort_by_type = QtGui.QAction("Sort by tab type")
sort_by_type.triggered.connect(self.sort_tabs_by_type)
- sort_by_size = QtWidgets.QAction("Sort by number of features")
+ sort_by_size = QtGui.QAction("Sort by number of features")
sort_by_size.triggered.connect(self.sort_tabs_by_n_features)
- reverse = QtWidgets.QAction("Reverse tab order")
+ reverse = QtGui.QAction("Reverse tab order")
reverse.triggered.connect(self.sort_reverse)
self.tab_contextmenu.addActions([sort_by_name, sort_by_time, sort_by_type, sort_by_size, reverse])
self.tab_contextmenu.addSeparator()
- close_this_action = QtWidgets.QAction("Close")
+ close_this_action = QtGui.QAction("Close")
close_this_action.triggered.connect(functools.partial(self.close_tab, ind))
- close_others_action = QtWidgets.QAction("Close other tabs")
+ close_others_action = QtGui.QAction("Close other tabs")
close_others_action.triggered.connect(functools.partial(self.close_other_tabs, ind))
- close_right_action = QtWidgets.QAction("Close tabs to the right")
+ close_right_action = QtGui.QAction("Close tabs to the right")
close_right_action.triggered.connect(functools.partial(self.close_tabs_to_the_right, ind))
- close_left_action = QtWidgets.QAction("Close tabs to the left")
+ close_left_action = QtGui.QAction("Close tabs to the left")
close_left_action.triggered.connect(functools.partial(self.close_tabs_to_the_left, ind))
self.tab_contextmenu.addActions([close_this_action, close_others_action, close_right_action, close_left_action])
@@ -3306,7 +3313,7 @@ def add_new_tab_at(self, index: int, name: str = None, is_set: bool = False):
self.tabs.tabBar().moveTab(self.tabs.currentIndex(), index)
def add_new_tab(self, name: str = None, is_set: bool = False):
- new_undo_stack = QtWidgets.QUndoStack()
+ new_undo_stack = QtGui.QUndoStack()
self.undo_group.addStack(new_undo_stack)
if name is None:
name = 'New Table'
@@ -3354,7 +3361,7 @@ def remove_tab_asterisk(self):
self.tabs.setTabText(self.tab.currentIndex(), current_name.rstrip('*'))
def new_table_from_folder(self):
- folder_name = QtWidgets.QFileDialog.getExistingDirectory(self, "Choose directory", str(Path.home()))
+ folder_name = QtWidgets.QFileDialog.getExistingDirectory(self, "Choose directory")
if folder_name:
filter_obj = filtering.CountFilter.from_folder(folder_name)
if self.tabs.currentWidget().is_empty():
@@ -3362,13 +3369,13 @@ def new_table_from_folder(self):
self.new_tab_from_filter_obj(filter_obj, JOB_COUNTER.get_id())
def new_table_from_folder_htseqcount(self):
- folder_name = QtWidgets.QFileDialog.getExistingDirectory(self, "Choose directory", str(Path.home()))
+ folder_name = QtWidgets.QFileDialog.getExistingDirectory(self, "Choose directory")
if folder_name:
normalize_answer = QtWidgets.QMessageBox.question(self, 'Normalize values?',
"Do you want to normalize your count table to "
"reads-per-million (RPM)?",
- QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No)
- to_normalize = normalize_answer == QtWidgets.QMessageBox.Yes
+ QtWidgets.QMessageBox.StandardButton.Yes | QtWidgets.QMessageBox.StandardButton.No)
+ to_normalize = normalize_answer == QtWidgets.QMessageBox.StandardButton.Yes
filter_obj = filtering.CountFilter.from_folder_htseqcount(folder_name, norm_to_rpm=to_normalize)
if self.tabs.currentWidget().is_empty():
@@ -3376,10 +3383,8 @@ def new_table_from_folder_htseqcount(self):
self.new_tab_from_filter_obj(filter_obj, JOB_COUNTER.get_id())
def load_multiple_files(self):
- dialog = gui_windows.MultiFileSelectionDialog()
- accepted = dialog.exec()
- if accepted == QtWidgets.QDialog.Accepted:
- filenames = dialog.result()
+ filenames, _ = QtWidgets.QFileDialog.getOpenFileNames(self, "Choose files")
+ if filenames:
if len(filenames) > 0:
window = MultiOpenWindow(filenames, self)
accepted = window.exec()
@@ -3574,8 +3579,8 @@ def delete_pipeline(self):
reply = QtWidgets.QMessageBox.question(self, 'Delete Pipeline?',
"Are you sure you want to delete this Pipeline? "
"This action cannot be undone!",
- QtWidgets.QMessageBox.No | QtWidgets.QMessageBox.Yes)
- if reply == QtWidgets.QMessageBox.Yes:
+ QtWidgets.QMessageBox.StandardButton.No | QtWidgets.QMessageBox.StandardButton.Yes)
+ if reply == QtWidgets.QMessageBox.StandardButton.Yes:
self.pipelines.pop(pipeline_name)
print(f"Pipeline '{pipeline_name}' deleted successfully")
@@ -3626,7 +3631,7 @@ def import_pipeline(self):
def import_multiple_gene_sets(self):
dialog = gui_windows.MultiFileSelectionDialog()
accepted = dialog.exec()
- if accepted == QtWidgets.QDialog.Accepted:
+ if accepted == QtWidgets.QDialog.DialogCode.Accepted:
filenames = dialog.result()
tabs_to_close = None
if len(filenames) > 0 and self.tabs.currentWidget().is_empty():
@@ -3638,11 +3643,11 @@ def import_multiple_gene_sets(self):
self.tabs.removeTab(tabs_to_close)
def import_gene_set(self):
- filename, _ = QtWidgets.QFileDialog.getOpenFileName(self, "Choose a file", str(Path.home()),
- "Text Document (*.txt);;"
- "Comma-Separated Values (*.csv);;"
- "Tab-Separated Values (*.tsv);;"
- "All Files (*)")
+ filename, _ = QtWidgets.QFileDialog.getOpenFileName(self, "Choose a file", filter=
+ "Text Document (*.txt);;"
+ "Comma-Separated Values (*.csv);;"
+ "Tab-Separated Values (*.tsv);;"
+ "All Files (*)")
if filename:
tabs_to_close = None
if self.tabs.currentWidget().is_empty():
@@ -3733,13 +3738,13 @@ def save_pipeline(self, pipeline_name: str, pipeline: filtering.Pipeline):
response = QtWidgets.QMessageBox.question(self, 'Overwrite Pipeline?',
'A Pipeline with this name already exists. '
'Are you sure you want to overwrite it?',
- defaultButton=QtWidgets.QMessageBox.No)
+ defaultButton=QtWidgets.QMessageBox.StandardButton.No)
else:
is_new = True
- response = QtWidgets.QMessageBox.Yes
+ response = QtWidgets.QMessageBox.StandardButton.Yes
- if response == QtWidgets.QMessageBox.Yes:
+ if response == QtWidgets.QMessageBox.StandardButton.Yes:
new_pipeline_id = JOB_COUNTER.get_id()
if self._generate_report:
if is_new:
@@ -3754,7 +3759,7 @@ def settings(self):
self.settings_window.exec()
def create_action(self, name, triggered_func, checkable=False, checked=False, enabled=True, shortcut=None):
- action = QtWidgets.QAction(name, self)
+ action = QtGui.QAction(name, self)
action.triggered.connect(triggered_func)
action.setCheckable(checkable)
action.setChecked(checked)
@@ -3923,8 +3928,8 @@ def clear_cache(self):
reply = QtWidgets.QMessageBox.question(self, 'Clear cache?',
'Are you sure you want to clear the RNAlysis cache? '
'This cannot be undone!',
- defaultButton=QtWidgets.QMessageBox.No)
- if reply == QtWidgets.QMessageBox.Yes:
+ defaultButton=QtWidgets.QMessageBox.StandardButton.No)
+ if reply == QtWidgets.QMessageBox.StandardButton.Yes:
io.clear_gui_cache()
io.clear_cache()
@@ -3936,16 +3941,16 @@ def check_for_updates(self, confirm_updated: bool = True): # pragma: no cover
reply = QtWidgets.QMessageBox.question(self, 'A new version is available',
'A new version of RNAlysis is available! '
'Do you wish to download it?')
- if reply == QtWidgets.QMessageBox.Yes:
+ if reply == QtWidgets.QMessageBox.StandardButton.Yes:
url = QtCore.QUrl('https://github.com/GuyTeichman/RNAlysis/releases/latest')
if not QtGui.QDesktopServices.openUrl(url):
- QtGui.QMessageBox.warning(self, 'Connection failed', 'Could not download new version')
+ QtWidgets.QMessageBox.warning(self, 'Connection failed', 'Could not download new version')
return
reply = QtWidgets.QMessageBox.question(self, 'A new version is available',
'A new version of RNAlysis is available! '
'Do you wish to update?')
- if reply == QtWidgets.QMessageBox.Yes:
+ if reply == QtWidgets.QMessageBox.StandardButton.Yes:
io.update_rnalysis()
QtCore.QCoreApplication.quit()
self.deleteLater()
@@ -4187,7 +4192,7 @@ def _populate_pipelines(self, menu: QtWidgets.QMenu, func: Callable, pipeline_ar
# Dynamically create the actions
actions = []
for name, (pipeline, pipeline_id) in self.pipelines.items():
- action = QtWidgets.QAction(name, self)
+ action = QtGui.QAction(name, self)
args = []
if pipeline_arg:
args.append(pipeline)
@@ -4225,11 +4230,11 @@ def _apply_table_pipeline(self, pipeline: filtering.Pipeline, pipeline_name: str
apply_msg = f"Do you want to apply Pipeline '{pipeline_name}' inplace?"
reply = QtWidgets.QMessageBox.question(self, f"Apply Pipeline '{pipeline_name}'",
apply_msg,
- QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No |
- QtWidgets.QMessageBox.Cancel)
- if reply == QtWidgets.QMessageBox.Cancel:
+ QtWidgets.QMessageBox.StandardButton.Yes | QtWidgets.QMessageBox.StandardButton.No |
+ QtWidgets.QMessageBox.StandardButton.Cancel)
+ if reply == QtWidgets.QMessageBox.StandardButton.Cancel:
return
- inplace = reply == QtWidgets.QMessageBox.Yes
+ inplace = reply == QtWidgets.QMessageBox.StandardButton.Yes
available_objs = self.get_available_objects()
filtered_available_objs = {}
@@ -4254,11 +4259,11 @@ def clear_session(self, confirm_action: bool = True) -> bool:
response = QtWidgets.QMessageBox.question(self, 'Clear session?',
'Are you sure you want to clear your session? '
'All unsaved changes will be lost!',
- defaultButton=QtWidgets.QMessageBox.No)
+ defaultButton=QtWidgets.QMessageBox.StandardButton.No)
else:
- response = QtWidgets.QMessageBox.Yes
+ response = QtWidgets.QMessageBox.StandardButton.Yes
- if response == QtWidgets.QMessageBox.Yes:
+ if response == QtWidgets.QMessageBox.StandardButton.Yes:
self.close_figs_action.trigger()
self.close_external_windows()
while self.tabs.count() > 1:
@@ -4270,13 +4275,12 @@ def clear_session(self, confirm_action: bool = True) -> bool:
self._change_undo_stack(0)
self._reset_reporting()
- return response == QtWidgets.QMessageBox.Yes
+ return response == QtWidgets.QMessageBox.StandardButton.Yes
def load_session(self):
session_filename, _ = QtWidgets.QFileDialog.getOpenFileName(self, "Load session",
- str(Path.home()),
- "RNAlysis session files (*.rnal);;"
- "All Files (*)")
+ filter="RNAlysis session files (*.rnal);;"
+ "All Files (*)")
if session_filename:
self._load_session_from(session_filename)
@@ -4290,7 +4294,7 @@ def _load_session_from(self, session_filename: Union[str, Path]):
load_report = QtWidgets.QMessageBox.question(self, 'Resume previous session report?',
'Do you want to resume the previous session report?\n'
'This will clear the current session and replace it. ',
- defaultButton=QtWidgets.QMessageBox.Yes) == QtWidgets.QMessageBox.Yes
+ defaultButton=QtWidgets.QMessageBox.StandardButton.Yes) == QtWidgets.QMessageBox.StandardButton.Yes
if load_report:
self.clear_session(confirm_action=False)
self._toggle_reporting(True)
@@ -4387,9 +4391,10 @@ def closeEvent(self, event): # pragma: no cover
"All unsaved progress will be lost"
reply = QtWidgets.QMessageBox.question(self, 'Close program',
- quit_msg, QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.Yes)
+ quit_msg, QtWidgets.QMessageBox.StandardButton.No,
+ QtWidgets.QMessageBox.StandardButton.Yes)
- if reply == QtWidgets.QMessageBox.Yes:
+ if reply == QtWidgets.QMessageBox.StandardButton.Yes:
plt.close('all')
# quit job and STDOUT listener threads
try:
@@ -4675,25 +4680,34 @@ async def run(): # pragma: no cover
app.setDesktopFileName('RNAlysis')
icon_pth = str(Path(__file__).parent.parent.joinpath('favicon.ico').absolute())
app.setWindowIcon(QtGui.QIcon(icon_pth))
- matplotlib.use('Qt5Agg')
+ matplotlib.use('QtAgg')
if show_app:
splash = gui_windows.splash_screen()
app.processEvents()
base_message = f"RNAlysis version {__version__}:\t"
- splash.showMessage(base_message + 'loading dependencies', QtCore.Qt.AlignBottom | QtCore.Qt.AlignHCenter)
+ splash.showMessage(base_message + 'loading dependencies',
+ QtCore.Qt.AlignmentFlag.AlignBottom | QtCore.Qt.AlignmentFlag.AlignHCenter)
gui_widgets.init_color_map_pixmap_cache()
if io.check_changed_version():
video_files = gui_quickstart.QuickStartWizard.VIDEO_FILES
splash.showMessage(base_message + 'validating tutorial videos',
- QtCore.Qt.AlignBottom | QtCore.Qt.AlignHCenter)
+ QtCore.Qt.AlignmentFlag.AlignBottom | QtCore.Qt.AlignmentFlag.AlignHCenter)
async for i in io.get_gui_videos(video_files):
splash.showMessage(base_message + f'getting tutorial videos {i + 1}/{len(video_files)}',
- QtCore.Qt.AlignBottom | QtCore.Qt.AlignHCenter)
+ QtCore.Qt.AlignmentFlag.AlignBottom | QtCore.Qt.AlignmentFlag.AlignHCenter)
+
+ splash.showMessage(base_message + 'loading application',
+ QtCore.Qt.AlignmentFlag.AlignBottom | QtCore.Qt.AlignmentFlag.AlignHCenter)
+
+ # set taskbar icon on Windows
+ if platform.system() == 'Windows':
+ import ctypes
+ myappid = u'RNAlysis.{version}'.format(version=__version__) # arbitrary string
+ ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
- splash.showMessage(base_message + 'loading application', QtCore.Qt.AlignBottom | QtCore.Qt.AlignHCenter)
window = MainWindow()
sys.excepthook = window.excepthook
builtins.input = window.input
diff --git a/rnalysis/gui/gui_graphics.py b/rnalysis/gui/gui_graphics.py
index ce0893216..2d9aa5245 100644
--- a/rnalysis/gui/gui_graphics.py
+++ b/rnalysis/gui/gui_graphics.py
@@ -7,7 +7,7 @@
import matplotlib
import matplotlib_venn
import upsetplot
-from PyQt5 import QtCore, QtGui
+from PyQt6 import QtCore, QtGui
from matplotlib import pyplot as plt
from matplotlib.backends.backend_qtagg import FigureCanvasQTAgg, NavigationToolbar2QT
@@ -473,6 +473,6 @@ def get_icon(name: str):
return icon
elif name == 'blank':
pixmap = QtGui.QPixmap(32, 32)
- pixmap.fill(QtCore.Qt.transparent)
+ pixmap.fill(QtCore.Qt.GlobalColor.transparent)
return QtGui.QIcon(pixmap)
return None
diff --git a/rnalysis/gui/gui_quickstart.py b/rnalysis/gui/gui_quickstart.py
index 46683855e..01590f587 100644
--- a/rnalysis/gui/gui_quickstart.py
+++ b/rnalysis/gui/gui_quickstart.py
@@ -1,6 +1,6 @@
from pathlib import Path
-from PyQt5 import QtCore, QtWidgets, QtGui
+from PyQt6 import QtCore, QtWidgets, QtGui
from rnalysis.utils import settings, io
@@ -134,9 +134,9 @@ def __init__(self, parent=None):
self.currentIdChanged.connect(self.play_tutorial)
- self.setWizardStyle(QtWidgets.QWizard.ModernStyle)
+ self.setWizardStyle(QtWidgets.QWizard.WizardStyle.ModernStyle)
self.setWindowTitle('Welcome to RNAlysis!')
- self.setPixmap(self.LogoPixmap,
+ self.setPixmap(self.WizardPixmap.LogoPixmap,
QtGui.QPixmap(Path.cwd().parent.parent.joinpath('docs/source/favicon.ico').as_posix()))
self.setField('dont_show_again', not settings.get_show_tutorial_settings())
@@ -223,22 +223,22 @@ def __init__(self, video_path: Path, parent=None):
self.layout = QtWidgets.QGridLayout(self)
self.label = QtWidgets.QLabel(self)
self.video = QtGui.QMovie(full_video_path)
- self.video.setCacheMode(self.video.CacheAll)
+ self.video.setCacheMode(self.video.CacheMode.CacheAll)
self.label.setMovie(self.video)
self.play_button = QtWidgets.QToolButton()
self.play_button.clicked.connect(self.change_play_state)
self.stop_button = QtWidgets.QToolButton()
- self.stop_button.setIcon(self.style().standardIcon(QtWidgets.QStyle.SP_MediaStop))
+ self.stop_button.setIcon(self.style().standardIcon(QtWidgets.QStyle.StandardPixmap.SP_MediaStop))
self.stop_button.clicked.connect(self.stop)
self.speed_button = QtWidgets.QToolButton()
- self.speed_button.setIcon(self.style().standardIcon(QtWidgets.QStyle.SP_MediaSeekForward))
+ self.speed_button.setIcon(self.style().standardIcon(QtWidgets.QStyle.StandardPixmap.SP_MediaSeekForward))
self.speed_button.setCheckable(True)
self.speed_button.clicked.connect(self.change_speed)
- self.position_slider = QtWidgets.QSlider(QtCore.Qt.Horizontal)
+ self.position_slider = QtWidgets.QSlider(QtCore.Qt.Orientation.Horizontal)
self.position_slider.setRange(0, self.video.frameCount())
self.position_slider.valueChanged.connect(self.set_frame)
self.position_slider.setTracking(False)
@@ -256,7 +256,7 @@ def __init__(self, video_path: Path, parent=None):
pixmap = QtGui.QPixmap(full_video_path)
size = pixmap.size()
- size.scale(750, 750, QtCore.Qt.KeepAspectRatio)
+ size.scale(750, 750, QtCore.Qt.AspectRatioMode.KeepAspectRatio)
self.video.setScaledSize(size)
self.layout.addWidget(self.label, 0, 0, 4, 8)
@@ -279,19 +279,19 @@ def change_play_state(self):
def update_play_button(self):
if self.paused:
- self.play_button.setIcon(self.style().standardIcon(QtWidgets.QStyle.SP_MediaPlay))
+ self.play_button.setIcon(self.style().standardIcon(QtWidgets.QStyle.StandardPixmap.SP_MediaPlay))
else:
- self.play_button.setIcon(self.style().standardIcon(QtWidgets.QStyle.SP_MediaPause))
+ self.play_button.setIcon(self.style().standardIcon(QtWidgets.QStyle.StandardPixmap.SP_MediaPause))
QtWidgets.QApplication.processEvents()
def mousePressEvent(self, event):
- if event.button() == QtCore.Qt.LeftButton:
+ if event.button() == QtCore.Qt.MouseButton.LeftButton:
self.press_pos = event.pos()
def mouseReleaseEvent(self, event):
# ensure that the left button was pressed *and* released within the
# geometry of the widget; if so, emit the signal;
- if self.press_pos is not None and event.button() == QtCore.Qt.LeftButton and event.pos() in self.rect():
+ if self.press_pos is not None and event.button() == QtCore.Qt.MouseButton.LeftButton and event.pos() in self.rect():
self.clicked.emit()
self.press_pos = None
diff --git a/rnalysis/gui/gui_style.py b/rnalysis/gui/gui_style.py
index a5a43eaf7..3696304ba 100644
--- a/rnalysis/gui/gui_style.py
+++ b/rnalysis/gui/gui_style.py
@@ -43,5 +43,5 @@ def get_stylesheet():
QSplitter::handle:hover { background-color: #788D9C; }
"""
else:
- other_stylesheet = qdarkstyle.load_stylesheet(qt_api='pyqt5', palette=palette)
+ other_stylesheet = qdarkstyle.load_stylesheet(qt_api='pyqt6', palette=palette)
return param_stylesheet + '\n' + other_stylesheet
diff --git a/rnalysis/gui/gui_widgets.py b/rnalysis/gui/gui_widgets.py
index 6a148b9e6..0cea4c6b2 100644
--- a/rnalysis/gui/gui_widgets.py
+++ b/rnalysis/gui/gui_widgets.py
@@ -14,7 +14,7 @@
import numpy as np
import polars as pl
import polars.selectors as cs
-from PyQt5 import QtCore, QtWidgets, QtGui
+from PyQt6 import QtCore, QtWidgets, QtGui
from joblib import Parallel, parallel_backend
from tqdm.auto import tqdm
from typing_extensions import get_origin, get_args
@@ -93,13 +93,13 @@ def value(self):
return picked_cols
def _update_window_size(self):
- self.dialog_table.setSizePolicy(QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Minimum)
- # self.dialog_table.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
- self.dialog_table.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+ self.dialog_table.setSizePolicy(QtWidgets.QSizePolicy.Policy.Minimum, QtWidgets.QSizePolicy.Policy.Minimum)
+ # self.dialog_table.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarPolicy.ScrollBarAlwaysOff)
+ self.dialog_table.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarPolicy.ScrollBarAlwaysOff)
self.dialog_table.resizeRowsToContents()
self.dialog_table.resizeColumnsToContents()
- self.dialog_table.horizontalHeader().setSectionResizeMode(QtWidgets.QHeaderView.ResizeToContents)
- self.dialog_table.horizontalHeader().setSectionResizeMode(0, QtWidgets.QHeaderView.Stretch)
+ self.dialog_table.horizontalHeader().setSectionResizeMode(QtWidgets.QHeaderView.ResizeMode.ResizeToContents)
+ self.dialog_table.horizontalHeader().setSectionResizeMode(0, QtWidgets.QHeaderView.ResizeMode.Stretch)
screen_height = QtWidgets.QApplication.primaryScreen().size().height()
@@ -303,7 +303,7 @@ def __init__(self, message: str = "No prompt available", parent=None):
super().__init__(parent)
self.message = message
self.layout = QtWidgets.QVBoxLayout(self)
- self.button_box = QtWidgets.QDialogButtonBox(QtWidgets.QDialogButtonBox.Ok)
+ self.button_box = QtWidgets.QDialogButtonBox(QtWidgets.QDialogButtonBox.StandardButton.Ok)
self.path = PathLineEdit(parent=self)
self.init_ui()
@@ -480,7 +480,7 @@ def create_colormap_pixmap(map_name: str):
fig.canvas.draw()
data = np.frombuffer(fig.canvas.tostring_rgb(), dtype=np.uint8)
data = data.reshape(fig.canvas.get_width_height()[::-1] + (3,))
- image = QtGui.QImage(data, data.shape[1], data.shape[0], QtGui.QImage.Format_RGB888)
+ image = QtGui.QImage(data, data.shape[1], data.shape[0], QtGui.QImage.Format.Format_RGB888)
pixmap = QtGui.QPixmap.fromImage(image)
plt.close(fig)
@@ -530,7 +530,7 @@ def init_ui(self):
def copy_to_clipboard(self):
cb = QtWidgets.QApplication.clipboard()
- cb.clear(mode=cb.Clipboard)
+ cb.clear(mode=QtGui.QClipboard.Mode.Clipboard)
cb.setText(self.text_edit.toPlainText())
self.copied_label.setText('Copied to clipboard')
@@ -570,7 +570,7 @@ def paintEvent(self, event):
self.setMinimumHeight((radius + self.BORDER) * 2)
painter = QtGui.QPainter(self)
- painter.setRenderHint(QtGui.QPainter.Antialiasing)
+ painter.setRenderHint(QtGui.QPainter.RenderHint.Antialiasing)
painter.translate(center)
painter.setBrush(QtGui.QColor("#cccccc"))
@@ -584,7 +584,7 @@ def paintEvent(self, event):
if not self.isChecked():
sw_rect.moveLeft(-width)
painter.drawRoundedRect(sw_rect, radius, radius)
- painter.drawText(sw_rect, QtCore.Qt.AlignCenter, label)
+ painter.drawText(sw_rect, QtCore.Qt.AlignmentFlag.AlignCenter, label)
class ToggleSwitch(QtWidgets.QWidget):
@@ -664,7 +664,7 @@ class HelpButton(QtWidgets.QToolButton):
def __init__(self, parent=None):
super().__init__(parent)
- self.setIcon(self.style().standardIcon(QtWidgets.QStyle.SP_MessageBoxQuestion))
+ self.setIcon(self.style().standardIcon(QtWidgets.QStyle.StandardPixmap.SP_MessageBoxQuestion))
self.param_name = ''
self.desc = ''
@@ -679,7 +679,7 @@ def set_param_help(self, param_name: str, desc: str):
def mouseReleaseEvent(self, event: QtGui.QMouseEvent):
super().mouseReleaseEvent(event)
- help_event = QtGui.QHelpEvent(QtCore.QEvent.Type.ToolTip, event.pos(), event.globalPos())
+ help_event = QtGui.QHelpEvent(QtCore.QEvent.Type.ToolTip, event.pos(), event.globalPosition().toPoint())
self.event(help_event)
@@ -752,7 +752,7 @@ def __init__(self, items: Sequence, icons: Sequence = None, parent=None):
self.items = []
self.list_items = []
self.list = QtWidgets.QListWidget(self)
- self.list.setSelectionMode(QtWidgets.QAbstractItemView.MultiSelection)
+ self.list.setSelectionMode(QtWidgets.QAbstractItemView.SelectionMode.MultiSelection)
self.layout.addWidget(self.list, 1, 1, 4, 1)
self.select_all_button = QtWidgets.QPushButton('Select all', self)
@@ -831,8 +831,8 @@ def delete_selected(self):
def delete_all(self):
accepted = QtWidgets.QMessageBox.question(self, f"{self.delete_text.capitalize()} all items?",
f"Are you sure you want to {self.delete_text} all items?",
- QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No)
- if accepted == QtWidgets.QMessageBox.Yes:
+ QtWidgets.QMessageBox.StandardButton.Yes | QtWidgets.QMessageBox.StandardButton.No)
+ if accepted == QtWidgets.QMessageBox.StandardButton.Yes:
for n_item in reversed(range(len(self.items))):
self.itemDeleted.emit(n_item)
self.delete_all_quietly()
@@ -1055,7 +1055,7 @@ class MinMaxDialog(QtWidgets.QDialog):
def __init__(self, parent=None):
super().__init__(parent)
- self.setWindowFlag(QtCore.Qt.WindowMinMaxButtonsHint)
+ self.setWindowFlag(QtCore.Qt.WindowType.WindowMinMaxButtonsHint)
class TrueFalseBoth(QtWidgets.QWidget):
@@ -1796,7 +1796,7 @@ def __init__(self, parent=None):
@QtCore.pyqtSlot(str)
def append_text(self, text: str):
- self.moveCursor(QtGui.QTextCursor.End)
+ self.moveCursor(QtGui.QTextCursor.MoveOperation.End)
if text == '\n':
return
text = text.replace("<", "<").replace(">", ">")
@@ -1805,8 +1805,8 @@ def append_text(self, text: str):
self.carriage = False
diff = self.document().characterCount() - self.prev_coord
cursor = self.textCursor()
- cursor.movePosition(QtGui.QTextCursor.PreviousCharacter, QtGui.QTextCursor.MoveAnchor, n=diff)
- cursor.movePosition(QtGui.QTextCursor.End, QtGui.QTextCursor.KeepAnchor)
+ cursor.movePosition(QtGui.QTextCursor.MoveOperation.PreviousCharacter, QtGui.QTextCursor.MoveMode.MoveAnchor, n=diff)
+ cursor.movePosition(QtGui.QTextCursor.MoveOperation.End, QtGui.QTextCursor.MoveMode.KeepAnchor)
cursor.removeSelectedText()
if text.endswith('\r'):
@@ -2180,7 +2180,7 @@ def __init__(self, *args, **kwargs):
def contextMenu(self, value: str):
self.context_menu = QtWidgets.QMenu(self)
- copy_action = QtWidgets.QAction(f'Copy "{value}"')
+ copy_action = QtGui.QAction(f'Copy "{value}"')
copy_action.triggered.connect(functools.partial(QtWidgets.QApplication.clipboard().setText, value))
self.context_menu.addAction(copy_action)
@@ -2189,7 +2189,7 @@ def contextMenu(self, value: str):
self.db_actions = []
for name in settings.get_databases_settings():
- action = QtWidgets.QAction(f'Search "{value}" on {name}')
+ action = QtGui.QAction(f'Search "{value}" on {name}')
self.db_actions.append(action)
open_url_partial = functools.partial(QtGui.QDesktopServices.openUrl,
QtCore.QUrl(f'{databases[name]}{value}'))
@@ -2225,7 +2225,7 @@ def __init__(self, *args, **kwargs):
def contextMenu(self, value: str):
self.context_menu = QtWidgets.QMenu(self)
- copy_action = QtWidgets.QAction(f'Copy "{value}"')
+ copy_action = QtGui.QAction(f'Copy "{value}"')
copy_action.triggered.connect(functools.partial(QtWidgets.QApplication.clipboard().setText, value))
self.context_menu.addAction(copy_action)
@@ -2234,7 +2234,7 @@ def contextMenu(self, value: str):
self.db_actions = []
for name in settings.get_databases_settings():
- action = QtWidgets.QAction(f'Search "{value}" on {name}')
+ action = QtGui.QAction(f'Search "{value}" on {name}')
self.db_actions.append(action)
open_url_partial = functools.partial(QtGui.QDesktopServices.openUrl,
QtCore.QUrl(f'{databases[name]}{value}'))
@@ -2268,7 +2268,7 @@ def __init__(self, *args, **kwargs):
def contextMenu(self, value: str):
self.context_menu = QtWidgets.QMenu(self)
- copy_action = QtWidgets.QAction(f'Copy "{value}"')
+ copy_action = QtGui.QAction(f'Copy "{value}"')
copy_action.triggered.connect(functools.partial(QtWidgets.QApplication.clipboard().setText, value))
self.context_menu.addAction(copy_action)
diff --git a/rnalysis/gui/gui_windows.py b/rnalysis/gui/gui_windows.py
index 0f2af4fdb..1a9539225 100644
--- a/rnalysis/gui/gui_windows.py
+++ b/rnalysis/gui/gui_windows.py
@@ -1,223 +1,26 @@
import functools
-import itertools
import json
import time
import traceback
-import warnings
from pathlib import Path
-from queue import Queue
from typing import Callable, Union, Tuple
import polars as pl
import yaml
-from PyQt5 import QtCore, QtWidgets, QtGui
+from PyQt6 import QtCore, QtWidgets, QtGui
from rnalysis import __version__
from rnalysis.gui import gui_style, gui_widgets
from rnalysis.utils import settings, io, generic, parsing
-class CheckableFileSystemModel(QtWidgets.QFileSystemModel):
- checkStateChanged = QtCore.pyqtSignal(str, bool)
- finishedDataChange = QtCore.pyqtSignal()
-
- def __init__(self):
- super().__init__()
- self.checkStates = {}
- self.rowsInserted.connect(self.checkAdded)
- self.rowsRemoved.connect(self.checkParent)
- self.rowsAboutToBeRemoved.connect(self.checkRemoved)
-
- def checkState(self, index):
- return self.checkStates.get(self.filePath(index), QtCore.Qt.Unchecked)
-
- def setCheckState(self, index, state, emitStateChange=True):
- path = self.filePath(index)
- if self.checkStates.get(path) == state:
- return
- self.checkStates[path] = state
- if emitStateChange:
- self.checkStateChanged.emit(path, bool(state))
-
- def checkAdded(self, parent, first, last):
- # if a file/directory is added, ensure it follows the parent state as long
- # as the parent is already tracked; note that this happens also when
- # expanding a directory that has not been previously loaded
- if not parent.isValid():
- return
- if self.filePath(parent) in self.checkStates:
- state = self.checkState(parent)
- for row in range(first, last + 1):
- index = self.index(row, 0, parent)
- path = self.filePath(index)
- if path not in self.checkStates:
- self.checkStates[path] = state
- self.checkParent(parent)
-
- def checkRemoved(self, parent, first, last):
- # remove items from the internal dictionary when a file is deleted;
- # note that this *has* to happen *before* the model actually updates,
- # that's the reason this function is connected to rowsAboutToBeRemoved
- for row in range(first, last + 1):
- path = self.filePath(self.index(row, 0, parent))
- if path in self.checkStates:
- self.checkStates.pop(path)
-
- def checkParent(self, parent):
- # verify the state of the parent according to the children states
- if not parent.isValid():
- self.finishedDataChange.emit()
- return
- childStates = [self.checkState(self.index(r, 0, parent)) for r in range(self.rowCount(parent))]
- newState = QtCore.Qt.Checked if all(childStates) else QtCore.Qt.Unchecked
- oldState = self.checkState(parent)
- if newState != oldState:
- self.setCheckState(parent, newState)
- self.dataChanged.emit(parent, parent)
- self.checkParent(parent.parent())
-
- def flags(self, index):
- return super().flags(index) | QtCore.Qt.ItemIsUserCheckable
-
- def data(self, index, role=QtCore.Qt.DisplayRole):
- if role == QtCore.Qt.CheckStateRole and index.column() == 0:
- return self.checkState(index)
- return super().data(index, role)
-
- def setData(self, index, value, role, checkParent=True, emitStateChange=True):
- if role == QtCore.Qt.CheckStateRole and index.column() == 0:
- self.setCheckState(index, value, emitStateChange)
- for row in range(self.rowCount(index)):
- # set the data for the children, but do not emit the state change,
- # and don't check the parent state (to avoid recursion)
- self.setData(index.child(row, 0), value, QtCore.Qt.CheckStateRole,
- checkParent=False, emitStateChange=False)
- self.dataChanged.emit(index, index)
- if checkParent:
- self.checkParent(index.parent())
- return True
-
- return super().setData(index, value, role)
-
-
-class FilterProxy(QtCore.QSortFilterProxyModel):
- '''
- Based on StackOverflow answer by user ekhumoro:
- https://stackoverflow.com/questions/72587813/how-to-filter-by-no-extension-in-qfilesystemmodel
- '''
-
- def __init__(self, disables=False, parent=None):
- super().__init__(parent)
- self._disables = bool(disables)
-
- def filterAcceptsRow(self, row, parent):
- index = self.sourceModel().index(row, 0, parent)
- if not self._disables:
- return self.matchIndex(index)
- return index.isValid()
-
- def matchIndex(self, index):
- return (super().filterAcceptsRow(index.row(), index.parent()))
-
- def flags(self, index):
- flags = super().flags(index)
- if (self._disables and
- not self.matchIndex(self.mapToSource(index))):
- flags &= ~QtCore.Qt.ItemIsEnabled
- return flags
-
-
-class MultiFileSelectionDialog(gui_widgets.MinMaxDialog):
- '''
- Based on a Stack Overflow answer by user 'musicamante':
- https://stackoverflow.com/questions/63309406/qfilesystemmodel-with-checkboxes
- '''
-
- def __init__(self):
- super().__init__()
- self.layout = QtWidgets.QGridLayout(self)
- self.tree_mycomputer = QtWidgets.QTreeView()
- self.tree_home = QtWidgets.QTreeView()
- self.open_button = QtWidgets.QPushButton('Open')
- self.cancel_button = QtWidgets.QPushButton('Cancel')
- self.logger = QtWidgets.QPlainTextEdit()
- self.init_models()
- self.init_ui()
-
- def init_models(self):
- model_mycomputer = CheckableFileSystemModel()
- model_mycomputer.setRootPath('')
- model_home = CheckableFileSystemModel()
- model_home.setRootPath('.')
- proxy = FilterProxy(False, self)
- proxy.setFilterRegularExpression(r'^(?![.])(?!.*[-_.]$).+')
- proxy.setSourceModel(model_home)
- self.tree_mycomputer.setModel(model_mycomputer)
- self.tree_mycomputer.setRootIndex(model_mycomputer.index(model_mycomputer.myComputer()))
- self.tree_home.setModel(proxy)
- self.tree_home.setRootIndex(proxy.mapFromSource(
- model_home.index(QtCore.QStandardPaths.standardLocations(QtCore.QStandardPaths.HomeLocation)[0])))
- model_mycomputer.finishedDataChange.connect(self.update_log)
- model_home.finishedDataChange.connect(self.update_log)
-
- def init_ui(self):
- self.setWindowTitle('Choose files:')
- self.resize(1000, 750)
-
- self.tree_mycomputer.setSortingEnabled(True)
- self.tree_home.setSortingEnabled(True)
- self.tree_mycomputer.header().setSectionResizeMode(QtWidgets.QHeaderView.Stretch)
- self.tree_home.header().setSectionResizeMode(QtWidgets.QHeaderView.Stretch)
-
- self.layout.addWidget(self.tree_mycomputer, 0, 0, 4, 8)
- self.layout.addWidget(self.tree_home, 4, 0, 4, 8)
- self.layout.setRowStretch(3, 2)
- self.layout.setRowStretch(7, 2)
-
- self.layout.addWidget(self.open_button, 8, 7)
- self.layout.addWidget(self.cancel_button, 9, 7)
-
- self.layout.addWidget(self.logger, 8, 0, 2, 7)
- self.logger.setReadOnly(True)
-
- self.open_button.clicked.connect(self.accept)
- self.cancel_button.clicked.connect(self.reject)
-
- self.update_log()
-
- def update_log(self):
- self.logger.setPlainText("\n".join(self.result()))
- self.logger.verticalScrollBar().setValue(
- self.logger.verticalScrollBar().maximum())
-
- def result(self):
- files_to_open = []
- queue = Queue()
- for pth, state in itertools.chain(self.tree_mycomputer.model().checkStates.items(),
- self.tree_home.model().sourceModel().checkStates.items()):
- if state:
- queue.put(pth)
-
- while not queue.empty():
- this_path = Path(queue.get())
- if this_path.is_file():
- files_to_open.append(str(this_path))
- else:
- try:
- for item in this_path.iterdir():
- queue.put(item)
- except PermissionError:
- warnings.warn(f'Cannot access items under {this_path} - permission denied. ')
- return files_to_open
-
-
class DataFrameModel(QtCore.QAbstractTableModel):
"""
Based upon:
https://stackoverflow.com/a/44605011
"""
- DtypeRole = QtCore.Qt.UserRole + 1000
- ValueRole = QtCore.Qt.UserRole + 1001
+ DtypeRole = QtCore.Qt.ItemDataRole.UserRole + 1000
+ ValueRole = QtCore.Qt.ItemDataRole.UserRole + 1001
def __init__(self, df=pl.DataFrame(), parent=None):
super().__init__(parent)
@@ -236,9 +39,10 @@ def dataFrame(self):
dataFrame = QtCore.pyqtProperty(pl.DataFrame, fget=dataFrame, fset=setDataFrame)
@QtCore.pyqtSlot(int, QtCore.Qt.Orientation, result=str)
- def headerData(self, section: int, orientation: QtCore.Qt.Orientation, role: int = QtCore.Qt.DisplayRole):
- if role == QtCore.Qt.DisplayRole:
- if orientation == QtCore.Qt.Horizontal:
+ def headerData(self, section: int, orientation: QtCore.Qt.Orientation,
+ role: int = QtCore.Qt.ItemDataRole.DisplayRole):
+ if role == QtCore.Qt.ItemDataRole.DisplayRole:
+ if orientation == QtCore.Qt.Orientation.Horizontal:
return self._dataframe.columns[section + 1]
else:
return str(self._dataframe.row(section)[0])
@@ -254,7 +58,7 @@ def columnCount(self, parent=QtCore.QModelIndex()):
return 0
return max(0, self._dataframe.width - 1)
- def data(self, index, role=QtCore.Qt.DisplayRole):
+ def data(self, index, role=QtCore.Qt.ItemDataRole.DisplayRole):
if not index.isValid() or not (0 <= index.row() < self.rowCount()
and 0 <= index.column() < self.columnCount()):
return QtCore.QVariant()
@@ -267,7 +71,7 @@ def data(self, index, role=QtCore.Qt.DisplayRole):
val = self._dataframe[row, col]
except IndexError:
print(row, col, self._dataframe.shape)
- if role == QtCore.Qt.DisplayRole:
+ if role == QtCore.Qt.ItemDataRole.DisplayRole:
return str(val)
elif role == DataFrameModel.ValueRole:
return val
@@ -277,7 +81,7 @@ def data(self, index, role=QtCore.Qt.DisplayRole):
def roleNames(self):
roles = {
- QtCore.Qt.DisplayRole: b'display',
+ QtCore.Qt.ItemDataRole.DisplayRole: b'display',
DataFrameModel.DtypeRole: b'dtype',
DataFrameModel.ValueRole: b'value'
}
@@ -409,7 +213,7 @@ def __init__(self, exc_type, exc_value, exc_tb, parent=None):
def init_ui(self):
self.setWindowTitle("Error")
- self.setWindowIcon(self.style().standardIcon(QtWidgets.QStyle.SP_MessageBoxCritical))
+ self.setWindowIcon(self.style().standardIcon(QtWidgets.QStyle.StandardPixmap.SP_MessageBoxCritical))
self.widgets['error_label'] = QtWidgets.QLabel('RNAlysis has encountered the following error:')
self.layout.addWidget(self.widgets['error_label'])
@@ -442,8 +246,8 @@ def init_ui(self):
def copy_to_clipboard(self):
cb = QtWidgets.QApplication.clipboard()
- cb.clear(mode=cb.Clipboard)
- cb.setText("".join(traceback.format_exception(*self.exception)), mode=cb.Clipboard)
+ cb.clear(mode=QtGui.QClipboard.Mode.Clipboard)
+ cb.setText("".join(traceback.format_exception(*self.exception)), mode=QtGui.QClipboard.Mode.Clipboard)
self.widgets['copied_label'].setText('Copied to clipboard')
@@ -464,12 +268,12 @@ def __init__(self, parent=None):
self.text.setTextFormat(QtCore.Qt.TextFormat.MarkdownText)
self.text.setText(text)
self.text.setWordWrap(True)
- self.scroll_layout.addWidget( self.text)
+ self.scroll_layout.addWidget(self.text)
self.layout().addWidget(self.scroll, 0, 0, 1, self.layout().columnCount())
self.setWindowTitle(f"What's new in version {__version__}")
self.setStyleSheet("QScrollArea{min-width:900 px; min-height: 600px}"
"QScrollBar:vertical {width: 40;}")
- self.setStandardButtons(QtWidgets.QMessageBox.Ok)
+ self.setStandardButtons(QtWidgets.QMessageBox.StandardButton.Ok)
self.buttonClicked.connect(self.close)
@@ -490,7 +294,7 @@ def __init__(self, parent=None):
"""
self.setText(text)
self.setWindowTitle("About RNAlysis")
- self.setStandardButtons(QtWidgets.QMessageBox.Ok)
+ self.setStandardButtons(QtWidgets.QMessageBox.StandardButton.Ok)
self.buttonClicked.connect(self.close)
@@ -516,8 +320,8 @@ def __init__(self, parent=None):
self.tables_widgets = {}
self.button_box = QtWidgets.QDialogButtonBox(
- QtWidgets.QDialogButtonBox.Ok | QtWidgets.QDialogButtonBox.Cancel |
- QtWidgets.QDialogButtonBox.Apply | QtWidgets.QDialogButtonBox.RestoreDefaults)
+ QtWidgets.QDialogButtonBox.StandardButton.Ok | QtWidgets.QDialogButtonBox.StandardButton.Cancel |
+ QtWidgets.QDialogButtonBox.StandardButton.Apply | QtWidgets.QDialogButtonBox.StandardButton.RestoreDefaults)
self.layout.addWidget(self.appearance_group)
self.layout.addWidget(self.tables_group)
@@ -552,7 +356,7 @@ def set_choices(self):
for i in range(self.appearance_widgets['databases'].count()):
item = self.appearance_widgets['databases'].item(i)
if item.text() in current_dbs:
- item.setCheckState(QtCore.Qt.Checked)
+ item.setCheckState(QtCore.Qt.CheckState.Checked)
attr_ref_path = settings.get_attr_ref_path('predefined') if settings.is_setting_in_file(
settings.__attr_file_key__) else 'No file chosen'
@@ -567,10 +371,11 @@ def init_appearance_ui(self):
self.appearance_widgets['app_theme'].addItems(self.THEMES.keys())
self.appearance_widgets['app_font'] = QtWidgets.QFontComboBox(self.appearance_group)
- self.appearance_widgets['app_font'].setFontFilters(QtWidgets.QFontComboBox.ScalableFonts)
+ self.appearance_widgets['app_font'].setFontFilters(QtWidgets.QFontComboBox.FontFilter.ScalableFonts)
self.appearance_widgets['app_font'].setEditable(True)
- self.appearance_widgets['app_font'].completer().setCompletionMode(QtWidgets.QCompleter.PopupCompletion)
- self.appearance_widgets['app_font'].setInsertPolicy(QtWidgets.QComboBox.NoInsert)
+ self.appearance_widgets['app_font'].completer().setCompletionMode(
+ QtWidgets.QCompleter.CompletionMode.PopupCompletion)
+ self.appearance_widgets['app_font'].setInsertPolicy(QtWidgets.QComboBox.InsertPolicy.NoInsert)
self.appearance_widgets['app_font_size'] = QtWidgets.QComboBox(self.appearance_group)
self.appearance_widgets['app_font_size'].addItems(self.FONT_SIZES)
@@ -579,13 +384,13 @@ def init_appearance_ui(self):
with open(self.LOOKUP_DATABASES_PATH) as f:
for key in json.load(f).keys():
item = QtWidgets.QListWidgetItem(key)
- item.setCheckState(QtCore.Qt.Unchecked)
+ item.setCheckState(QtCore.Qt.CheckState.Unchecked)
self.appearance_widgets['databases'].addItem(item)
self.appearance_widgets['show_tutorial'] = QtWidgets.QCheckBox("Show tutorial page on startup")
self.appearance_widgets['report_gen'] = QtWidgets.QComboBox()
self.appearance_widgets['report_gen'].addItems(self.REPORT_GEN_OPTIONS.keys())
- self.appearance_widgets['report_gen'].setInsertPolicy(QtWidgets.QComboBox.NoInsert)
+ self.appearance_widgets['report_gen'].setInsertPolicy(QtWidgets.QComboBox.InsertPolicy.NoInsert)
for widget_name in ['app_theme', 'app_font', 'app_font_size', 'report_gen']:
self.appearance_widgets[widget_name].currentIndexChanged.connect(self._trigger_settings_changed)
@@ -659,9 +464,9 @@ def init_buttons(self):
def handle_button_click(self, button):
role = self.button_box.buttonRole(button)
- if role == QtWidgets.QDialogButtonBox.ApplyRole:
+ if role == QtWidgets.QDialogButtonBox.ButtonRole.ApplyRole:
self.save_settings()
- elif role == QtWidgets.QDialogButtonBox.ResetRole:
+ elif role == QtWidgets.QDialogButtonBox.ButtonRole.ResetRole:
self.reset_settings()
def closeEvent(self, event):
@@ -670,8 +475,9 @@ def closeEvent(self, event):
quit_msg = "Are you sure you want to close settings without saving?"
reply = QtWidgets.QMessageBox.question(self, 'Close settings without saving?',
- quit_msg, QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.Yes)
- to_exit = reply == QtWidgets.QMessageBox.Yes
+ quit_msg, QtWidgets.QMessageBox.StandardButton.No,
+ QtWidgets.QMessageBox.StandardButton.Yes)
+ to_exit = reply == QtWidgets.QMessageBox.StandardButton.Yes
if to_exit:
event.accept()
@@ -681,49 +487,49 @@ def closeEvent(self, event):
class HowToCiteWindow(gui_widgets.MinMaxDialog):
CITATION_RNALYSIS = """
- Teichman, G., Cohen, D., Ganon, O., Dunsky, N., Shani, S., Gingold, H., and Rechavi, O. (2022).
- RNAlysis: analyze your RNA sequencing data without writing a single line of code. BioRxiv 2022.11.25.517851.
-
- doi.org/10.1101/2022.11.25.517851
- """
+ Teichman, G., Cohen, D., Ganon, O., Dunsky, N., Shani, S., Gingold, H., and Rechavi, O. (2022).
+ RNAlysis: analyze your RNA sequencing data without writing a single line of code. BioRxiv 2022.11.25.517851.
+
+ doi.org/10.1101/2022.11.25.517851
+ """
CITATION_CUTADAPT = """
- Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads.
- EMBnet.journal, 17(1), pp. 10-12.
-
- doi.org/10.14806/ej.17.1.200
- """
+ Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads.
+ EMBnet.journal, 17(1), pp. 10-12.
+
+ doi.org/10.14806/ej.17.1.200
+ """
CITATION_KALLISTO = """
- Bray, N., Pimentel, H., Melsted, P. et al.
- Near-optimal probabilistic RNA-seq quantification.
- Nat Biotechnol 34, 525–527 (2016).
-
- doi.org/10.1038/nbt.3519
- """
+ Bray, N., Pimentel, H., Melsted, P. et al.
+ Near-optimal probabilistic RNA-seq quantification.
+ Nat Biotechnol 34, 525–527 (2016).
+
+ doi.org/10.1038/nbt.3519
+ """
CITATION_DESEQ2 = """
- Love MI, Huber W, Anders S (2014).
- “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.”
- Genome Biology, 15, 550.
-
- doi.org/10.1186/s13059-014-0550-8
- """
+ Love MI, Huber W, Anders S (2014).
+ “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.”
+ Genome Biology, 15, 550.
+
+ doi.org/10.1186/s13059-014-0550-8
+ """
CITATION_HDBSCAN = """
- L. McInnes, J. Healy, S. Astels, hdbscan:
- Hierarchical density based clustering In:
- Journal of Open Source Software, The Open Journal, volume 2, number 11. 2017
-
- doi.org/10.1371/journal.pcbi.0030039"""
+ L. McInnes, J. Healy, S. Astels, hdbscan:
+ Hierarchical density based clustering In:
+ Journal of Open Source Software, The Open Journal, volume 2, number 11. 2017
+
+ doi.org/10.1371/journal.pcbi.0030039"""
CITATION_XLMHG = """
-
- Eden, E., Lipson, D., Yogev, S., and Yakhini, Z. (2007).
- Discovering Motifs in Ranked Lists of DNA Sequences. PLOS Comput. Biol. 3, e39.
-
- doi.org/10.1371/journal.pcbi.0030039
-
-
- Wagner, F. (2017). The XL-mHG test for gene set enrichment. ArXiv.
-
- doi.org/10.48550/arXiv.1507.07905
-
"""
+
+ Eden, E., Lipson, D., Yogev, S., and Yakhini, Z. (2007).
+ Discovering Motifs in Ranked Lists of DNA Sequences. PLOS Comput. Biol. 3, e39.
+
+ doi.org/10.1371/journal.pcbi.0030039
+
+
+ Wagner, F. (2017). The XL-mHG test for gene set enrichment. ArXiv.
+
+ doi.org/10.48550/arXiv.1507.07905
+
"""
CITATION_FILE_PATH = Path(__file__).parent.parent.joinpath('data_files/tool_citations.json')
def __init__(self, parent=None):
@@ -753,10 +559,10 @@ def __init__(self, parent=None):
self.init_ui()
def init_ui(self):
- self.scroll.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+ self.scroll.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarPolicy.ScrollBarAlwaysOff)
self.scroll.setWidgetResizable(True)
self.scroll.setWidget(self.scroll_widget)
- self.layout.setSizeConstraint(QtWidgets.QLayout.SetMinAndMaxSize)
+ self.layout.setSizeConstraint(QtWidgets.QLayout.SizeConstraint.SetMinAndMaxSize)
self.main_layout.addWidget(self.scroll)
@@ -777,7 +583,8 @@ def splash_screen():
splash_font = QtGui.QFont('Calibri', 16)
splash = QtWidgets.QSplashScreen(splash_pixmap)
splash.setFont(splash_font)
- splash.showMessage(f"RNAlysis version {__version__}", QtCore.Qt.AlignBottom | QtCore.Qt.AlignHCenter)
+ splash.showMessage(f"RNAlysis version {__version__}",
+ QtCore.Qt.AlignmentFlag.AlignBottom | QtCore.Qt.AlignmentFlag.AlignHCenter)
splash.show()
return splash
@@ -834,10 +641,10 @@ def __init__(self, func_name: str, func: Callable, help_link: Union[None, str],
self.close_button = QtWidgets.QPushButton('Close')
def init_ui(self):
- self.scroll.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+ self.scroll.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarPolicy.ScrollBarAlwaysOff)
self.scroll.setWidgetResizable(True)
self.scroll.setWidget(self.scroll_widget)
- self.scroll_layout.setSizeConstraint(QtWidgets.QLayout.SetMinAndMaxSize)
+ self.scroll_layout.setSizeConstraint(QtWidgets.QLayout.SizeConstraint.SetMinAndMaxSize)
self.main_layout.addWidget(self.scroll)
@@ -1131,7 +938,8 @@ def __init__(self, available_objects: dict, parent=None):
self.available_objects = available_objects
self.layout = QtWidgets.QVBoxLayout(self)
self.label = QtWidgets.QLabel('Choose the tables you wish to apply your Pipeline to', self)
- self.button_box = QtWidgets.QDialogButtonBox(QtWidgets.QDialogButtonBox.Ok | QtWidgets.QDialogButtonBox.Cancel)
+ self.button_box = QtWidgets.QDialogButtonBox(
+ QtWidgets.QDialogButtonBox.StandardButton.Ok | QtWidgets.QDialogButtonBox.StandardButton.Cancel)
self.list = gui_widgets.MultipleChoiceList(self.available_objects,
[val[1] for val in self.available_objects.values()],
self)
@@ -1144,7 +952,7 @@ def init_ui(self):
self.button_box.rejected.connect(self.reject)
self.layout.addWidget(self.label)
self.layout.addWidget(self.list)
- self.layout.addWidget(self.button_box, QtCore.Qt.AlignCenter)
+ self.layout.addWidget(self.button_box, QtCore.Qt.AlignmentFlag.AlignCenter)
def result(self):
return [item.text() for item in self.list.get_sorted_selection()]
@@ -1157,8 +965,8 @@ def __init__(self, parent=None):
self.setText("Do you want to enable report generation for this session?\n"
"(this will slow down the program slightly)")
- self.yes_button = self.addButton(QtWidgets.QPushButton("Yes"), QtWidgets.QMessageBox.YesRole)
- self.no_button = self.addButton(QtWidgets.QPushButton("No"), QtWidgets.QMessageBox.NoRole)
+ self.yes_button = self.addButton(QtWidgets.QPushButton("Yes"), QtWidgets.QMessageBox.ButtonRole.YesRole)
+ self.no_button = self.addButton(QtWidgets.QPushButton("No"), QtWidgets.QMessageBox.ButtonRole.NoRole)
self.checkbox = QtWidgets.QCheckBox("Don't ask me again")
self.setCheckBox(self.checkbox)
diff --git a/tests/test_gui.py b/tests/test_gui.py
index cdb0ab18a..15df0631c 100644
--- a/tests/test_gui.py
+++ b/tests/test_gui.py
@@ -11,8 +11,8 @@
matplotlib.use('Agg')
from rnalysis.gui.gui import *
-LEFT_CLICK = QtCore.Qt.LeftButton
-RIGHT_CLICK = QtCore.Qt.RightButton
+LEFT_CLICK = QtCore.Qt.MouseButton.LeftButton
+RIGHT_CLICK = QtCore.Qt.MouseButton.RightButton
def _pytestqt_graceful_shutdown():
@@ -27,7 +27,7 @@ def _pytestqt_graceful_shutdown():
@pytest.fixture(autouse=True)
def mainwindow_setup(monkeypatch):
- monkeypatch.setattr(QtWidgets.QMessageBox, 'question', lambda *args, **kwargs: QtWidgets.QMessageBox.Yes)
+ monkeypatch.setattr(QtWidgets.QMessageBox, 'question', lambda *args, **kwargs: QtWidgets.QMessageBox.StandardButton.Yes)
monkeypatch.setattr(gui_widgets.ThreadStdOutStreamTextQueueReceiver, 'run', lambda self: None)
monkeypatch.setattr(gui_quickstart.QuickStartWizard, '__init__', lambda *args, **kwargs: None)
@@ -35,21 +35,21 @@ def mainwindow_setup(monkeypatch):
@pytest.fixture
def blank_icon():
pixmap = QtGui.QPixmap(32, 32)
- pixmap.fill(QtCore.Qt.transparent)
+ pixmap.fill(QtCore.Qt.GlobalColor.transparent)
return QtGui.QIcon(pixmap)
@pytest.fixture
def red_icon():
pixmap = QtGui.QPixmap(32, 32)
- pixmap.fill(QtCore.Qt.red)
+ pixmap.fill(QtCore.Qt.GlobalColor.red)
return QtGui.QIcon(pixmap)
@pytest.fixture
def green_icon():
pixmap = QtGui.QPixmap(32, 32)
- pixmap.fill(QtCore.Qt.green)
+ pixmap.fill(QtCore.Qt.GlobalColor.green)
return QtGui.QIcon(pixmap)
@@ -72,11 +72,11 @@ def available_objects(qtbot, red_icon, green_icon):
qtbot, first = widget_setup(qtbot, SetTabPage, 'first tab',
{'WBGene00000002', 'WBGene00000006', 'WBGene00000015', 'WBGene00000017'})
- qtbot, second = widget_setup(qtbot, FilterTabPage, undo_stack=QtWidgets.QUndoStack())
+ qtbot, second = widget_setup(qtbot, FilterTabPage, undo_stack=QtGui.QUndoStack())
second.start_from_filter_obj(filtering.DESeqFilter('tests/test_files/test_deseq.csv'), 1)
second.rename('second tab')
- qtbot, third = widget_setup(qtbot, FilterTabPage, undo_stack=QtWidgets.QUndoStack())
+ qtbot, third = widget_setup(qtbot, FilterTabPage, undo_stack=QtGui.QUndoStack())
third.start_from_filter_obj(filtering.CountFilter('tests/test_files/counted.tsv'), 2)
third.rename('third tab')
@@ -89,19 +89,19 @@ def four_available_objects_and_empty(qtbot, red_icon, green_icon, blank_icon):
qtbot, first = widget_setup(qtbot, SetTabPage, 'first tab',
{'WBGene00008447', 'WBGene00044258', 'WBGene00045410', 'WBGene00010100'})
- qtbot, second = widget_setup(qtbot, FilterTabPage, undo_stack=QtWidgets.QUndoStack())
+ qtbot, second = widget_setup(qtbot, FilterTabPage, undo_stack=QtGui.QUndoStack())
second.start_from_filter_obj(filtering.DESeqFilter('tests/test_files/test_deseq_set_ops_1.csv'), 2)
second.rename('second tab')
- qtbot, third = widget_setup(qtbot, FilterTabPage, undo_stack=QtWidgets.QUndoStack())
+ qtbot, third = widget_setup(qtbot, FilterTabPage, undo_stack=QtGui.QUndoStack())
third.start_from_filter_obj(filtering.DESeqFilter('tests/test_files/test_deseq_set_ops_2.csv'), 3)
third.rename('third tab')
- qtbot, fourth = widget_setup(qtbot, FilterTabPage, undo_stack=QtWidgets.QUndoStack())
+ qtbot, fourth = widget_setup(qtbot, FilterTabPage, undo_stack=QtGui.QUndoStack())
fourth.start_from_filter_obj(filtering.CountFilter('tests/test_files/counted.tsv'), 4)
fourth.rename('fourth tab')
- qtbot, empty = widget_setup(qtbot, FilterTabPage, undo_stack=QtWidgets.QUndoStack())
+ qtbot, empty = widget_setup(qtbot, FilterTabPage, undo_stack=QtGui.QUndoStack())
yield {'first tab': (first, red_icon), 'second tab': (second, red_icon), 'third tab': (third, red_icon),
'fourth tab': (fourth, green_icon), 'empty tab': (empty, blank_icon)}
@@ -160,7 +160,7 @@ def filtertabpage(qtbot):
@pytest.fixture
def filtertabpage_with_undo_stack(qtbot):
- stack = QtWidgets.QUndoStack()
+ stack = QtGui.QUndoStack()
qtbot, window = widget_setup(qtbot, FilterTabPage, undo_stack=stack)
window.start_from_filter_obj(filtering.DESeqFilter('tests/test_files/test_deseq_sig.csv'), 1)
yield window, stack
@@ -169,7 +169,7 @@ def filtertabpage_with_undo_stack(qtbot):
@pytest.fixture
def countfiltertabpage_with_undo_stack(qtbot):
- stack = QtWidgets.QUndoStack()
+ stack = QtGui.QUndoStack()
qtbot, window = widget_setup(qtbot, FilterTabPage, undo_stack=stack)
window.start_from_filter_obj(filtering.CountFilter('tests/test_files/counted.csv'), 1)
yield window, stack
@@ -178,7 +178,7 @@ def countfiltertabpage_with_undo_stack(qtbot):
@pytest.fixture
def settabpage_with_undo_stack(qtbot):
- stack = QtWidgets.QUndoStack()
+ stack = QtGui.QUndoStack()
qtbot, window = widget_setup(qtbot, SetTabPage, 'my set name', {'a', 'b', 'c', 'd'}, undo_stack=stack)
yield window, stack
_pytestqt_graceful_shutdown()
@@ -627,7 +627,7 @@ def test_ClicomWindow_add_setup(qtbot, clicom_window):
def test_ClicomWindow_remove_setup(qtbot, monkeypatch, clicom_window):
- monkeypatch.setattr(QtWidgets.QMessageBox, 'question', lambda *args: QtWidgets.QMessageBox.Yes)
+ monkeypatch.setattr(QtWidgets.QMessageBox, 'question', lambda *args: QtWidgets.QMessageBox.StandardButton.Yes)
qtbot.keyClicks(clicom_window.stack.func_combo, filtering.CountFilter.split_kmeans.readable_name)
clicom_window.stack.parameter_widgets['n_clusters'].other.setValue(3)
qtbot.mouseClick(clicom_window.setups_widgets['add_button'], LEFT_CLICK)
@@ -1631,7 +1631,7 @@ def mock_show_multikeep(self):
self.select_all.setChecked(True)
self.change_all()
self.accept()
- self.button_box.button(QtWidgets.QDialogButtonBox.Ok).click()
+ self.button_box.button(QtWidgets.QDialogButtonBox.StandardButton.Ok).click()
monkeypatch.setattr(MultiKeepWindow, 'exec', mock_show_multikeep)
@@ -1943,7 +1943,7 @@ def test_CreatePipelineWindow_from_pipeline(qtbot):
('Sequence files (paired-end)', fastq.PairedEndPipeline, False)
])
def test_CreatePipelineWindow_create_pipeline(qtbot, monkeypatch, pipeline_type, exp_pipeline, exp_filter_type):
- monkeypatch.setattr(QtWidgets.QMessageBox, "question", lambda *args: QtWidgets.QMessageBox.Yes)
+ monkeypatch.setattr(QtWidgets.QMessageBox, "question", lambda *args: QtWidgets.QMessageBox.StandardButton.Yes)
pipeline_name = 'my pipeline name'
qtbot, window = widget_setup(qtbot, CreatePipelineWindow)
window.basic_widgets['pipeline_name'].clear()
@@ -1962,7 +1962,7 @@ def test_CreatePipelineWindow_add_function(qtbot, monkeypatch):
pipeline_truth = filtering.Pipeline('DESeqFilter')
pipeline_truth.add_function('split_fold_change_direction')
- monkeypatch.setattr(QtWidgets.QMessageBox, "question", lambda *args: QtWidgets.QMessageBox.Yes)
+ monkeypatch.setattr(QtWidgets.QMessageBox, "question", lambda *args: QtWidgets.QMessageBox.StandardButton.Yes)
qtbot, window = widget_setup(qtbot, CreatePipelineWindow)
window.basic_widgets['pipeline_name'].clear()
@@ -1980,7 +1980,7 @@ def test_CreatePipelineWindow_add_function(qtbot, monkeypatch):
def test_CreatePipelineWindow_remove_function(qtbot, monkeypatch):
warned = []
- monkeypatch.setattr(QtWidgets.QMessageBox, "question", lambda *args: QtWidgets.QMessageBox.Yes)
+ monkeypatch.setattr(QtWidgets.QMessageBox, "question", lambda *args: QtWidgets.QMessageBox.StandardButton.Yes)
monkeypatch.setattr(QtWidgets.QMessageBox, 'exec', lambda *args, **kwargs: warned.append(True))
qtbot, window = widget_setup(qtbot, CreatePipelineWindow)
@@ -2009,7 +2009,7 @@ def test_CreatePipelineWindow_add_function_with_args(qtbot, monkeypatch):
pipeline_truth = filtering.Pipeline('DESeqFilter')
pipeline_truth.add_function('filter_significant', alpha=0.01, opposite=True)
- monkeypatch.setattr(QtWidgets.QMessageBox, "question", lambda *args: QtWidgets.QMessageBox.Yes)
+ monkeypatch.setattr(QtWidgets.QMessageBox, "question", lambda *args: QtWidgets.QMessageBox.StandardButton.Yes)
qtbot, window = widget_setup(qtbot, CreatePipelineWindow)
window.basic_widgets['pipeline_name'].clear()
@@ -2039,7 +2039,7 @@ def test_CreatePipelineWindow_save_pipeline(qtbot, monkeypatch):
pipeline_truth.add_function('describe', percentiles=[0.01, 0.25, 0.5, 0.75, 0.99])
pipeline_name = 'my pipeline name'
- monkeypatch.setattr(QtWidgets.QMessageBox, "question", lambda *args: QtWidgets.QMessageBox.Yes)
+ monkeypatch.setattr(QtWidgets.QMessageBox, "question", lambda *args: QtWidgets.QMessageBox.StandardButton.Yes)
qtbot, window = widget_setup(qtbot, CreatePipelineWindow)
window.basic_widgets['pipeline_name'].clear()
@@ -2062,7 +2062,7 @@ def test_CreatePipelineWindow_export_pipeline(qtbot, monkeypatch):
pipeline_truth.add_function('describe', percentiles=[0.01, 0.25, 0.5, 0.75, 0.99])
pipeline_name = 'my pipeline name'
- monkeypatch.setattr(QtWidgets.QMessageBox, "question", lambda *args: QtWidgets.QMessageBox.Yes)
+ monkeypatch.setattr(QtWidgets.QMessageBox, "question", lambda *args: QtWidgets.QMessageBox.StandardButton.Yes)
qtbot, window = widget_setup(qtbot, CreatePipelineWindow)
window.basic_widgets['pipeline_name'].clear()
@@ -2212,7 +2212,7 @@ def __init__(self, parent=None):
def test_ReactiveTabWidget_remove_tab(qtbot, tab_widget):
qtbot, widget = widget_setup(qtbot, MockTab)
- tab_widget.setCornerWidget(widget, QtCore.Qt.TopRightCorner)
+ tab_widget.setCornerWidget(widget, QtCore.Qt.Corner.TopRightCorner)
for i in range(3):
qtbot, widget = widget_setup(qtbot, MockTab)
tab_widget.addTab(widget, 'name')
@@ -2405,8 +2405,8 @@ def mock_get_dir(*args, **kwargs):
def mock_question(*args, **kwargs):
if args[1] == 'Close program':
- return QtWidgets.QMessageBox.Yes
- return QtWidgets.QMessageBox.Yes if normalize else QtWidgets.QMessageBox.No
+ return QtWidgets.QMessageBox.StandardButton.Yes
+ return QtWidgets.QMessageBox.StandardButton.Yes if normalize else QtWidgets.QMessageBox.StandardButton.No
monkeypatch.setattr(QtWidgets.QFileDialog, 'getExistingDirectory', mock_get_dir)
monkeypatch.setattr(QtWidgets.QMessageBox, 'question', mock_question)
diff --git a/tests/test_gui_graphics.py b/tests/test_gui_graphics.py
index 2228195d8..e0717f907 100644
--- a/tests/test_gui_graphics.py
+++ b/tests/test_gui_graphics.py
@@ -3,8 +3,8 @@
from rnalysis.gui.gui_graphics import *
-LEFT_CLICK = QtCore.Qt.LeftButton
-RIGHT_CLICK = QtCore.Qt.RightButton
+LEFT_CLICK = QtCore.Qt.MouseButton.LeftButton
+RIGHT_CLICK = QtCore.Qt.MouseButton.RightButton
class MockEvent:
@@ -47,7 +47,7 @@ def test_get_icon_invalid(qtbot):
def test_get_icon_blank(qtbot):
pixmap = QtGui.QPixmap(32, 32)
- pixmap.fill(QtCore.Qt.transparent)
+ pixmap.fill(QtCore.Qt.GlobalColor.transparent)
truth = pixmap.toImage()
icon = get_icon('blank')
diff --git a/tests/test_gui_quickstart.py b/tests/test_gui_quickstart.py
index b89ce268c..2a9a4538b 100644
--- a/tests/test_gui_quickstart.py
+++ b/tests/test_gui_quickstart.py
@@ -2,8 +2,8 @@
from rnalysis.gui.gui_quickstart import *
-LEFT_CLICK = QtCore.Qt.LeftButton
-RIGHT_CLICK = QtCore.Qt.RightButton
+LEFT_CLICK = QtCore.Qt.MouseButton.LeftButton
+RIGHT_CLICK = QtCore.Qt.MouseButton.RightButton
def widget_setup(qtbot, widget_class, *args, **kwargs):
@@ -23,69 +23,69 @@ def test_TutorialMovie_set_frame(qtbot):
window.video.start()
window.pause()
window.set_frame(17)
- assert window.video.state() == QtGui.QMovie.Paused
+ assert window.video.state() == QtGui.QMovie.MovieState.Paused
assert window.video.currentFrameNumber() == 17
window.set_frame(19)
- assert window.video.state() == QtGui.QMovie.Paused
+ assert window.video.state() == QtGui.QMovie.MovieState.Paused
assert window.video.currentFrameNumber() == 19
window.set_frame(19)
- assert window.video.state() == QtGui.QMovie.Paused
+ assert window.video.state() == QtGui.QMovie.MovieState.Paused
assert window.video.currentFrameNumber() == 19
window.set_frame(1)
- assert window.video.state() == QtGui.QMovie.Paused
+ assert window.video.state() == QtGui.QMovie.MovieState.Paused
assert window.video.currentFrameNumber() == 1
def test_TutorialMovie_start(qtbot):
qtbot, window = widget_setup(qtbot, QuickStartMovie, Path('tests/test_files/test_video.webp'))
- assert window.video.state() == QtGui.QMovie.NotRunning
+ assert window.video.state() == QtGui.QMovie.MovieState.NotRunning
window.start()
- assert window.video.state() == QtGui.QMovie.Running
+ assert window.video.state() == QtGui.QMovie.MovieState.Running
def test_TutorialMovie_restart(qtbot):
qtbot, window = widget_setup(qtbot, QuickStartMovie, Path('tests/test_files/test_video.webp'))
window.restart()
assert window.video.currentFrameNumber() in {0, 1}
- assert window.video.state() == QtGui.QMovie.Running
+ assert window.video.state() == QtGui.QMovie.MovieState.Running
def test_TutorialMovie_stop(qtbot):
qtbot, window = widget_setup(qtbot, QuickStartMovie, Path('tests/test_files/test_video.webp'))
window.video.start()
window.stop()
- assert window.video.state() == QtGui.QMovie.NotRunning
+ assert window.video.state() == QtGui.QMovie.MovieState.NotRunning
def test_TutorialMovie_pause(qtbot):
qtbot, window = widget_setup(qtbot, QuickStartMovie, Path('tests/test_files/test_video.webp'))
window.video.start()
window.pause()
- assert window.video.state() == QtGui.QMovie.Paused
+ assert window.video.state() == QtGui.QMovie.MovieState.Paused
def test_TutorialMovie_stop_button(qtbot):
qtbot, window = widget_setup(qtbot, QuickStartMovie, Path('tests/test_files/test_video.webp'))
qtbot.mouseClick(window.stop_button, LEFT_CLICK)
- assert window.video.state() == QtGui.QMovie.NotRunning
+ assert window.video.state() == QtGui.QMovie.MovieState.NotRunning
def test_TutorialMovie_pause_button(qtbot):
qtbot, window = widget_setup(qtbot, QuickStartMovie, Path('tests/test_files/test_video.webp'))
window.video.start()
qtbot.mouseClick(window.play_button, LEFT_CLICK)
- assert window.video.state() == QtGui.QMovie.Paused
+ assert window.video.state() == QtGui.QMovie.MovieState.Paused
qtbot.mouseClick(window.play_button, LEFT_CLICK)
- assert window.video.state() == QtGui.QMovie.Running
+ assert window.video.state() == QtGui.QMovie.MovieState.Running
def test_TutorialMovie_pause_click_video(qtbot):
qtbot, window = widget_setup(qtbot, QuickStartMovie, Path('tests/test_files/test_video.webp'))
window.video.start()
qtbot.mouseClick(window, LEFT_CLICK)
- assert window.video.state() == QtGui.QMovie.Paused
+ assert window.video.state() == QtGui.QMovie.MovieState.Paused
qtbot.mouseClick(window, LEFT_CLICK)
- assert window.video.state() == QtGui.QMovie.Running
+ assert window.video.state() == QtGui.QMovie.MovieState.Running
def test_TutorialMovie_speed_button(qtbot):
@@ -101,16 +101,16 @@ def test_TutorialMovie_speed_button(qtbot):
def test_WelcomeWizard_init(qtbot):
qtbot, window = widget_setup(qtbot, QuickStartWizard)
for i in range(len(window.TITLES) + 1):
- qtbot.mouseClick(window.button(QtWidgets.QWizard.NextButton), LEFT_CLICK)
- qtbot.mouseClick(window.button(QtWidgets.QWizard.FinishButton), LEFT_CLICK)
+ qtbot.mouseClick(window.button(QtWidgets.QWizard.WizardButton.NextButton), LEFT_CLICK)
+ qtbot.mouseClick(window.button(QtWidgets.QWizard.WizardButton.FinishButton), LEFT_CLICK)
@pytest.mark.parametrize('n_next', [0, 1, len(QuickStartWizard.TITLES)])
def test_WelcomeWizard_cancel(qtbot, n_next):
qtbot, window = widget_setup(qtbot, QuickStartWizard)
for i in range(n_next):
- qtbot.mouseClick(window.button(QtWidgets.QWizard.NextButton), LEFT_CLICK)
- qtbot.mouseClick(window.button(QtWidgets.QWizard.CancelButton), LEFT_CLICK)
+ qtbot.mouseClick(window.button(QtWidgets.QWizard.WizardButton.NextButton), LEFT_CLICK)
+ qtbot.mouseClick(window.button(QtWidgets.QWizard.WizardButton.CancelButton), LEFT_CLICK)
def test_WelcomeWizard_do_not_show_again_finish(qtbot, monkeypatch):
@@ -125,7 +125,7 @@ def save_func(show_tutorial):
qtbot, window = widget_setup(qtbot, QuickStartWizard)
assert not window.currentPage().dont_show_again.isChecked()
window.currentPage().dont_show_again.setChecked(True)
- qtbot.mouseClick(window.button(QtWidgets.QWizard.FinishButton), LEFT_CLICK)
+ qtbot.mouseClick(window.button(QtWidgets.QWizard.WizardButton.FinishButton), LEFT_CLICK)
assert saved[0]
@@ -143,5 +143,5 @@ def save_func(show_tutorial):
qtbot, window = widget_setup(qtbot, QuickStartWizard)
assert window.currentPage().dont_show_again.isChecked() != show
window.currentPage().dont_show_again.setChecked(show)
- qtbot.mouseClick(window.button(QtWidgets.QWizard.CancelButton), LEFT_CLICK)
+ qtbot.mouseClick(window.button(QtWidgets.QWizard.WizardButton.CancelButton), LEFT_CLICK)
assert saved[0]
diff --git a/tests/test_gui_widgets.py b/tests/test_gui_widgets.py
index e917b03fc..8793b9e6d 100644
--- a/tests/test_gui_widgets.py
+++ b/tests/test_gui_widgets.py
@@ -7,8 +7,8 @@
from rnalysis.gui.gui_widgets import *
from rnalysis.utils import io
-LEFT_CLICK = QtCore.Qt.LeftButton
-RIGHT_CLICK = QtCore.Qt.RightButton
+LEFT_CLICK = QtCore.Qt.MouseButton.LeftButton
+RIGHT_CLICK = QtCore.Qt.MouseButton.RightButton
def widget_setup(qtbot, widget_class, *args, **kwargs):
@@ -443,11 +443,11 @@ def selection_changed_slot(*args, **kwargs):
def test_MultipleChoiceList_icons(qtbot):
pixmap = QtGui.QPixmap(32, 32)
- pixmap.fill(QtCore.Qt.transparent)
+ pixmap.fill(QtCore.Qt.GlobalColor.transparent)
icon = QtGui.QIcon(pixmap)
pixmap2 = QtGui.QPixmap(34, 34)
- pixmap2.fill(QtCore.Qt.white)
+ pixmap2.fill(QtCore.Qt.GlobalColor.white)
icon2 = QtGui.QIcon(pixmap2)
items = ['item1', 'item2', 'item3']
icons = [icon, icon2, icon2]
@@ -622,7 +622,7 @@ def test_ToggleSwitchCore(qtbot):
def test_MultiChoiceListWithDelete_delete_all(qtbot, monkeypatch):
- monkeypatch.setattr(QtWidgets.QMessageBox, "question", lambda *args: QtWidgets.QMessageBox.Yes)
+ monkeypatch.setattr(QtWidgets.QMessageBox, "question", lambda *args: QtWidgets.QMessageBox.StandardButton.Yes)
items = ['item1', 'item2', 'item3']
qtbot, widget = widget_setup(qtbot, MultiChoiceListWithDelete, items)
diff --git a/tests/test_gui_windows.py b/tests/test_gui_windows.py
index 25f770718..07f9b4718 100644
--- a/tests/test_gui_windows.py
+++ b/tests/test_gui_windows.py
@@ -5,8 +5,8 @@
from rnalysis.gui.gui_windows import *
-LEFT_CLICK = QtCore.Qt.LeftButton
-RIGHT_CLICK = QtCore.Qt.RightButton
+LEFT_CLICK = QtCore.Qt.MouseButton.LeftButton
+RIGHT_CLICK = QtCore.Qt.MouseButton.RightButton
@pytest.fixture
@@ -205,8 +205,8 @@ def test_SettingsWindow_get_defaults(qtbot, use_temp_settings_file):
for i in range(dialog.appearance_widgets['databases'].count()):
item = dialog.appearance_widgets['databases'].item(i)
- assert bool(item.checkState()) == (item.text() in dbs_truth)
- if item.checkState():
+ assert (item.checkState() == QtCore.Qt.CheckState.Checked) == (item.text() in dbs_truth)
+ if item.checkState() == QtCore.Qt.CheckState.Checked:
dbs_matched.append(item.text())
assert sorted(dbs_matched) == sorted(dbs_truth)
@@ -227,7 +227,7 @@ def mock_reset():
monkeypatch.setattr(settings, 'reset_settings', mock_reset)
qtbot, dialog = widget_setup(qtbot, SettingsWindow)
- qtbot.mouseClick(dialog.button_box.button(QtWidgets.QDialogButtonBox.RestoreDefaults), LEFT_CLICK)
+ qtbot.mouseClick(dialog.button_box.button(QtWidgets.QDialogButtonBox.StandardButton.RestoreDefaults), LEFT_CLICK)
assert len(reset_done) == 1
assert reset_done[0]
@@ -280,7 +280,7 @@ def mock_save_tables(attr, biotype):
qtbot.keyClicks(dialog.tables_widgets['attr_ref_path'].file_path, attr_truth)
qtbot.keyClicks(dialog.tables_widgets['biotype_ref_path'].file_path, biotype_truth)
- qtbot.mouseClick(dialog.button_box.button(QtWidgets.QDialogButtonBox.Apply), LEFT_CLICK)
+ qtbot.mouseClick(dialog.button_box.button(QtWidgets.QDialogButtonBox.StandardButton.Apply), LEFT_CLICK)
assert settings_saved[0]
assert settings_saved[1]
@@ -295,68 +295,11 @@ def mock_save():
monkeypatch.setattr(settings, 'set_table_settings', mock_save)
qtbot, dialog = widget_setup(qtbot, SettingsWindow)
dialog.appearance_widgets['app_font'].setCurrentText("David")
- qtbot.mouseClick(dialog.button_box.button(QtWidgets.QDialogButtonBox.Cancel), LEFT_CLICK)
+ qtbot.mouseClick(dialog.button_box.button(QtWidgets.QDialogButtonBox.StandardButton.Cancel), LEFT_CLICK)
assert len(save_done) == 0
-def test_MultiFileSelectionDialog_init(qtbot, use_temp_settings_file):
- _, _ = widget_setup(qtbot, MultiFileSelectionDialog)
-
-
-@pytest.mark.parametrize('pth', ['tests/test_files/test_deseq.csv', 'tests/test_files/test_fastqs'])
-def test_MultiFileSelectionDialog_selection_log(qtbot, use_temp_settings_file, pth):
- qtbot, dialog = widget_setup(qtbot, MultiFileSelectionDialog)
- model = dialog.tree_mycomputer.model()
-
- for parent in reversed(list(Path(pth).absolute().parents)):
- dialog.tree_mycomputer.expand(model.index(str(parent)))
-
- index = model.index(str(Path(pth).absolute()))
- model.setCheckState(index, True)
-
- dialog.update_log()
- txt = dialog.logger.toPlainText()
- assert str(Path(pth).name) in txt
-
- if Path(pth).is_dir():
- for item in Path(pth).rglob('*'):
- assert str(item.absolute()) in txt
-
-
-@pytest.mark.parametrize('pth', ['tests/test_files/test_deseq.csv', 'tests/test_files/counted.tsv'])
-def test_MultiFileSelectionDialog_selection_files(qtbot, use_temp_settings_file, pth):
- qtbot, dialog = widget_setup(qtbot, MultiFileSelectionDialog)
- model = dialog.tree_mycomputer.model()
-
- for parent in reversed(list(Path(pth).absolute().parents)):
- dialog.tree_mycomputer.expand(model.index(str(parent)))
-
- index = model.index(str(Path(pth).absolute()))
- model.setCheckState(index, True)
- assert dialog.result() == [str(Path(pth).absolute())]
-
-
-@pytest.mark.parametrize('pth', ['tests/test_files/test_count_from_folder', 'tests/test_files'])
-def test_MultiFileSelectionDialog_selection_folders(qtbot, use_temp_settings_file, pth):
- qtbot, dialog = widget_setup(qtbot, MultiFileSelectionDialog)
- model = dialog.tree_mycomputer.model()
-
- for parent in reversed(list(Path(pth).absolute().parents)):
- dialog.tree_mycomputer.expand(model.index(str(parent)))
-
- index = model.index(str(Path(pth).absolute()))
- model.setCheckState(index, True)
- assert sorted(dialog.result()) == sorted(
- [str(Path(child).absolute()) for child in Path(pth).rglob('*') if child.is_file()])
-
-
-def test_MultiFileSelectionDialog_no_selection(qtbot, use_temp_settings_file):
- qtbot, dialog = widget_setup(qtbot, MultiFileSelectionDialog)
-
- assert len(dialog.result()) == 0
-
-
def test_splash_screen(qtbot):
splash = splash_screen()
splash.show()