Merge branch 'dev'

byemaxx · Dec 16, 2024 · 5518141 · 5518141
2 parents e2fb407 + 8b0ddab
commit 5518141
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diff --git 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'<img (.*?)>', r'<div style="text-align: center;"><img \1 class="img-fluid" style="max-width: 60%; min-width: 300px; height: auto; display: inline-block;"></div>', html_content)
             html_content = re.sub(r'<table>', r'<div class="table-responsive"><table class="table table-striped table-bordered">', html_content)
             html_content = re.sub(r'</table>', r'</table></div>', 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('''
             <!DOCTYPE html>

diff --git 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
@@ -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):
@@ -1519,16 +1602,20 @@ 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:
                         # save settings.ini only
                         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
@@ -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
@@ -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()
diff --git 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'
diff --git 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" }