diff --git a/.github/workflows/jekyll-gh-pages.yml b/.github/workflows/jekyll-gh-pages.yml
index a2fbff7..ec25460 100644
--- a/.github/workflows/jekyll-gh-pages.yml
+++ b/.github/workflows/jekyll-gh-pages.yml
@@ -61,7 +61,7 @@ jobs:
for heading in headings:
level = len(heading[0])
title = heading[1]
- anchor = re.sub(r'\W+', '-', title.lower()).strip('-')
+ anchor = re.sub(r'[^a-zA-Z0-9]+', '-', title.strip()).lower().strip('-')
toc_items.append((level, title, anchor))
# Convert markdown to HTML
@@ -71,7 +71,11 @@ jobs:
html_content = re.sub(r'![]()
', r'', html_content)
html_content = re.sub(r'', r'', html_content)
html_content = re.sub(r'
', r'
', html_content)
-
+ html_content = re.sub(
+ r'href="##([^"]+)"', # 匹配类似 ##Module-4.-Peptide-Annotator 的链接
+ lambda match: f'href="#{re.sub(r"[^a-zA-Z0-9]+", "-", match.group(1).strip()).lower().strip("-")}"',
+ html_content
+ )
# Jinja2 template for HTML output
template = Template('''
diff --git a/Docs/ChangeLog.md b/Docs/ChangeLog.md
index 9adee17..274cf37 100644
--- a/Docs/ChangeLog.md
+++ b/Docs/ChangeLog.md
@@ -1,3 +1,13 @@
+# Version: 1.120.1
+## Date: 2024-12-16
+### Changes:
+- Fix: font size change was not work for some widgets.
+
+# Version: 1.120.0
+## Date: 2024-12-15
+### Changes:
+- New: 1.Using dynamic font size for lables of GUI by the scaling DPI of the screen. 2. New option in Theme menue to set the font size of the GUI.
+
# Version: 1.119.11
## Date: 2024-12-10
### Changes:
diff --git a/metax/gui/main_gui.py b/metax/gui/main_gui.py
index 3ef8125..285d334 100644
--- a/metax/gui/main_gui.py
+++ b/metax/gui/main_gui.py
@@ -137,7 +137,7 @@
from .metax_gui.ui_lca_help import UiLcaHelpDialog
from .metax_gui.ui_func_threshold_help import UifuncHelpDialog
from .metax_gui.generic_thread import FunctionExecutor
- from .metax.gui.metax_gui.resources import icon_rc
+ from .metax_gui.resources import icon_rc # noqa: F401
from ..peptide_annotator.metalab2otf import MetaLab2OTF
from ..peptide_annotator.peptable_annotator import PeptideAnnotator
@@ -161,6 +161,8 @@ def __init__(self, MainWindow):
self.MainWindow.resize(1200, 800)
self.MainWindow.setWindowTitle("MetaX v" + __version__)
+ self.font_size = 12
+ self.current_theme = 'light_blue'
self.logger = LoggerManager()
@@ -261,7 +263,7 @@ def __init__(self, MainWindow):
self.actionCheck_Update.triggered.connect(lambda: self.check_update(show_message=True, manual_check_trigger=True))
self.actionSettings.triggered.connect(self.show_settings_window)
- self.screen = self.screen = QApplication.screenAt(QCursor.pos()).geometry()
+ self.screen = QApplication.screenAt(QCursor.pos()).geometry()
self.screen_width = self.screen.width()
self.screen_height = self.screen.height()
@@ -922,37 +924,81 @@ def hide_plot_setting_groupbox(self):
############### basic function End ###############
-
-
-
+
def init_theme_menu(self):
# Create a menu for themes
theme_menu = QMenu("Themes", self.MainWindow)
# Fetch all available themes
themes = list_themes()
- # replace the .xml suffix
+ # Replace the .xml suffix
themes = [theme.replace('.xml', '') for theme in themes]
- # reordering the themes , light theme first
+ # Reorder the themes, light themes first
light_themes = [theme for theme in themes if "light_" in theme]
dark_themes = [theme for theme in themes if "dark_" in theme]
themes = light_themes + dark_themes
+ # Add themes to the menu
for theme in themes:
theme_action = QAction(theme, self.MainWindow)
- theme_action.triggered.connect(lambda checked, theme=theme: self.change_theme(theme))
+ theme_action.triggered.connect(lambda checked, theme=theme: self.change_theme(theme, silent=False, is_load_font_size_from_settings=False))
theme_menu.addAction(theme_action)
- # Add theme menu to menu bar
+ # Add a font size submenu
+ font_size_menu = QMenu("Font Size", self.MainWindow)
+
+ # Predefined font size options
+ predefined_sizes = [10, 12, 14, 16, 18, 20]
+
+ for size in predefined_sizes:
+ size_action = QAction(f"{size} pt", self.MainWindow)
+ size_action.triggered.connect(lambda checked, size=size: self.set_font_size(size))
+ font_size_menu.addAction(size_action)
+
+ # Add an option for custom font size
+ custom_size_action = QAction("Custom...", self.MainWindow)
+ custom_size_action.triggered.connect(self.set_custom_font_size)
+ font_size_menu.addAction(custom_size_action)
+
+ # Add the font size menu to the theme menu
+ theme_menu.addMenu(font_size_menu)
+
+ # Add theme menu to the menu bar
self.MainWindow.menuBar().addMenu(theme_menu)
+
+ def set_font_size(self, size):
+ """
+ Set the font size and apply the current theme.
+ """
+ self.font_size = size
+ self.change_theme(self.current_theme, silent=False, is_load_font_size_from_settings=False)
+
+ def set_custom_font_size(self):
+ """
+ Open a dialog for the user to input a custom font size.
+ """
+ from PyQt5.QtWidgets import QInputDialog
+
+ size, ok = QInputDialog.getInt(
+ self.MainWindow,
+ "Custom Font Size",
+ "Enter font size (pt):",
+ value=self.font_size,
+ min=8,
+ max=72
+ )
+ if ok:
+ self.set_font_size(size)
+
def init_theme(self):
if self.settings.contains("theme"):
theme = self.settings.value("theme", type=str)
- print(f"Loading theme {theme}...")
+ theme = theme if theme != "" else "light_blue"
else:
theme = "light_blue"
print(f"Loading default theme {theme}...")
+ self.current_theme = theme
self.change_theme(theme, silent=True)
# restore the window size
@@ -967,11 +1013,13 @@ def init_theme(self):
- def change_theme(self, theme, silent=False):
+ def change_theme(self, theme, silent=False, is_load_font_size_from_settings=True):
if not silent:
- self.show_message(f"Changing theme to {theme}...")
+ text = f"Changing theme to {theme}...\n\nTheme: {theme}\nFont size: {self.font_size}"
+ self.show_message(text)
# save the theme to settings
self.settings.setValue("theme", theme)
+ self.current_theme = theme
#! Deprecated, switch to manual change in Settings
## save the theme mode to GUI attribute (dark or light)
@@ -1000,8 +1048,22 @@ def change_theme(self, theme, silent=False):
combobox = getattr(self, attribute_name)
combobox.clear()
############### avoid the window size change when change theme ###############
-
-
+ if is_load_font_size_from_settings:
+ screen = QApplication.screenAt(QCursor.pos())
+ logical_dpi = screen.logicalDotsPerInch()
+ scaling_factor = logical_dpi / 96.0
+ # read if setting has font size and height
+ if self.settings.contains("font_size"):
+ self.font_size = self.settings.value("font_size", type=int)
+ print(f"Reading font size from settings file: {self.font_size}")
+ else:
+ self.font_size = int(12 * scaling_factor)
+ print(f"Setting default font size: {self.font_size}")
+
+
+ font_size = self.font_size
+ height = self.font_size + 8
+
custom_css = '''
QGroupBox {{
text-transform: none;
@@ -1017,36 +1079,36 @@ def change_theme(self, theme, silent=False):
text-transform: none;
}}
QLineEdit {{
- font-size: 12px;
+ font-size: setted_font_size;
}}
QLabel {{
- font-size: 12px;
+ font-size: setted_font_size;
}}
QComboBox {{
- font-size: 12px;
- height: 20px;
+ font-size: setted_font_size;
+ height: setted_height;
}}
QSpinBox {{
- font-size: 12px;
- height: 20px;
+ font-size: setted_font_size;
+ height: setted_height;
}}
QListWidget {{
- font-size: 12px;
+ font-size: setted_font_size;
}}
QDoubleSpinBox {{
- font-size: 12px;
- height: 20px;
+ font-size: setted_font_size;
+ height: setted_height;
}}
QCheckBox {{
- font-size: 12px;
- height: 20px;
+ font-size: setted_font_size;
+ height: setted_height;
}}
QRadioButton {{
- font-size: 12px;
- height: 20px;
+ font-size: setted_font_size;
+ height: setted_height;
}}
QToolBox {{
- font-size: 12px;
+ font-size: setted_font_size;
font-weight: bold;
}}
QPushButton {{
@@ -1055,13 +1117,31 @@ def change_theme(self, theme, silent=False):
background-color: {QTMATERIAL_SECONDARYCOLOR};
border: 1px solid {QTMATERIAL_PRIMARYCOLOR};
border-radius: 2px;
- font-size: 12px;
+ font-size: setted_font_size;
padding: 5px;
margin: 2px;
- height: 20px;
+ height: setted_height;
}}
-
- '''
+ QTabBar {{
+ font-size: setted_font_size;
+ }}
+ QMenuBar {{
+ font-size: setted_font_size;
+ }}
+ QMenuBar::item {{
+ font-size: setted_font_size;
+ }}
+ QTextBrowser {{
+ font-size: setted_font_size;
+ }}
+ QTableWidget {{
+ font-size: setted_font_size;
+ }}
+ QHeaderView::section {{
+ font-size: setted_font_size;
+ }}
+
+ '''.replace('setted_font_size', f'{font_size}px').replace('setted_height', f'{height}px')
current_app = QtWidgets.QApplication.instance()
extra = {
@@ -1070,10 +1150,10 @@ def change_theme(self, theme, silent=False):
# Apply the selected theme
if "light" in theme:
- self.msgbox_style = "QLabel{min-width: 400px; color: black; font-size: 12px;} QMessageBox{background-color: white;}"
+ self.msgbox_style = "QLabel{min-width: 400px; color: black; font-size: setted_font_size;} QMessageBox{background-color: white;}".replace('setted_font_size', f'{font_size}px')
apply_stylesheet(current_app, theme=theme, invert_secondary=True, extra=extra)
else:
- self.msgbox_style = "QLabel{min-width: 400px; color: white; font-size: 12px;} QMessageBox{background-color: #333;}"
+ self.msgbox_style = "QLabel{min-width: 400px; color: white; font-size: setted_font_size;} QMessageBox{background-color: #333;}".replace('setted_font_size', f'{font_size}px')
# set text color to white of QComboBox , QSpinBox and QDoubleSpinBox , lineEdit
custom_css += '''
QComboBox {{
@@ -1288,6 +1368,9 @@ def save_basic_settings(self, line_edit_name: str | None = None):
# save current window size
self.settings.setValue("window_size", self.MainWindow.size())
+
+ # save font_size
+ self.settings.setValue("font_size", self.font_size)
def save_set_multi_table_settings(self):
@@ -1519,8 +1602,9 @@ def closeEvent(self, event):
msgBox.addButton(do_not_close_button, QMessageBox.RejectRole)
reply = msgBox.exec()
- if reply == 0 or reply == 1:
+ if reply == 0 or reply == 1: # 0 is save and close, 1 is close without saving
try:
+
if reply == 0:
self.show_message("Saving settings...", "Closing...")
if getattr(self, 'tfa', None) is None:
@@ -1528,7 +1612,10 @@ def closeEvent(self, event):
self.save_basic_settings()
else:
self.save_metax_obj_to_file(save_path=self.metax_home_path, no_message=True)
-
+ else: # close without saving
+ # save settings.ini only
+ self.save_basic_settings()
+
# 关闭 self.web_list 中的所有窗口
for web_window in self.web_list:
web_window.close()
@@ -1751,8 +1838,6 @@ def show_message(self,message,title='Information'):
self.msg.setWindowModality(Qt.NonModal)
self.msg.setWindowTitle(title)
- if not hasattr(self, 'msgbox_style'):
- self.msgbox_style = "QLabel{min-width: 400px; color: black; font-size: 12px;} QMessageBox{background-color: white;}"
self.msg.setStyleSheet(self.msgbox_style)
self.msg.setText(message)
diff --git a/metax/taxafunc_ploter/basic_plot.py b/metax/taxafunc_ploter/basic_plot.py
index 92ca6ba..1625aaf 100644
--- a/metax/taxafunc_ploter/basic_plot.py
+++ b/metax/taxafunc_ploter/basic_plot.py
@@ -694,7 +694,7 @@ def plot_upset(self, df, title_name='Table', width=12, height=6, font_size=10,
plt.rcParams.update({'font.size': font_size})
upset_plot(upset_data, fig = fig, show_counts=show_label,
show_percentages=show_percentages if show_label else False,
- element_size=None, sort_categories_by ='input',
+ element_size=None, sort_categories_by ='-input',
min_subset_size=min_subset_size if min_subset_size != 0 else None,
max_subset_rank=max_subset_rank if max_subset_rank != 0 else None)
diff --git a/metax/tests/test_metax.py b/metax/tests/test_metax.py
index e69de29..56e80fb 100644
--- a/metax/tests/test_metax.py
+++ b/metax/tests/test_metax.py
@@ -0,0 +1,11 @@
+import sys
+import os
+script_dir = os.path.dirname(__file__) #<-- absolute dir the script is in
+parentDir = os.path.abspath(os.path.join(script_dir, os.pardir))
+grandParentDir = os.path.abspath(os.path.join(parentDir, os.pardir))
+sys.path.append(grandParentDir)
+
+
+from metax.gui.main_gui import runGUI
+
+runGUI()
\ No newline at end of file
diff --git a/metax/utils/version.py b/metax/utils/version.py
index 5118493..dd68a74 100644
--- a/metax/utils/version.py
+++ b/metax/utils/version.py
@@ -1,2 +1,2 @@
-__version__ = '1.119.11'
+__version__ = '1.120.1'
API_version = '4'
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 058dd95..48287e9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
[project]
name = "MetaXTools"
-version = "1.119.11"
+version = "1.120.1"
description = "MetaXTools is a novel tool for linking peptide sequences with taxonomic and functional information in Metaproteomics."
readme = "README_PyPi.md"
license = { text = "NorthOmics" }