Strong refactoring, trying to disentangle imports from models views and controllers

Author: PaulJonasJost

src/petab_gui/controllers/mother_controller.py

@@ -42,7 +42,7 @@
     process_file,
 )
 from ..views import TaskBar
-from ..views.other_views import NextStepsPanel
+from ..views.dialogs import NextStepsPanel
 from .logger_controller import LoggerController
 from .sbml_controller import SbmlController
 from .table_controllers import (

src/petab_gui/controllers/sbml_controller.py

@@ -9,7 +9,7 @@
 
 from ..C import DEFAULT_ANTIMONY_TEXT
 from ..models.sbml_model import SbmlViewerModel
-from ..utils import sbmlToAntimony
+from ..models.sbml_utils import sbml_to_antimony
 from ..views.sbml_view import SbmlViewer
 
 
@@ -67,7 +67,7 @@ def reset_to_original_model(self):
         self.model.sbml_text = libsbml.writeSBMLToString(
             self.model._sbml_model_original.sbml_model.getSBMLDocument()
         )
-        self.model.antimony_text = sbmlToAntimony(self.model.sbml_text)
+        self.model.antimony_text = sbml_to_antimony(self.model.sbml_text)
         self.view.sbml_text_edit.setPlainText(self.model.sbml_text)
         self.view.antimony_text_edit.setPlainText(self.model.antimony_text)
 

src/petab_gui/controllers/table_controllers.py

@@ -23,22 +23,21 @@
     PandasTableFilterProxy,
     PandasTableModel,
 )
+from ..resources.whats_this import WHATS_THIS
 from ..settings_manager import settings_manager
 from ..utils import (
     CaptureLogHandler,
-    ConditionInputDialog,
     get_selected,
     process_file,
 )
-from ..views.other_views import DoseTimeDialog
+from ..views.dialogs import ConditionInputDialog, DoseTimeDialog
 from ..views.table_view import (
     ColumnSuggestionDelegate,
     ComboBoxDelegate,
     ParameterIdSuggestionDelegate,
     SingleSuggestionDelegate,
     TableViewer,
 )
-from ..views.whats_this import WHATS_THIS
 from .utils import linter_wrapper, prompt_overwrite_or_append, save_petab_table
 
 

…petab_gui/controllers/default_handler.py src/petab_gui/models/default_handler.pysrc/petab_gui/controllers/default_handler.py renamed to src/petab_gui/models/default_handler.py src/petab_gui/controllers/default_handler.py renamed to src/petab_gui/models/default_handler.py

@@ -10,7 +10,6 @@
     Signal,
 )
 from PySide6.QtGui import QBrush, QColor, QPalette
-from PySide6.QtWidgets import QApplication
 
 from ..C import COLUMNS
 from ..commands import (
@@ -19,16 +18,42 @@
     ModifyRowCommand,
     RenameIndexCommand,
 )
-from ..controllers.default_handler import DefaultHandlerModel
+from ..resources.whats_this import column_whats_this
 from ..settings_manager import settings_manager
 from ..utils import (
     create_empty_dataframe,
     get_selected,
-    is_invalid,
-    validate_value,
 )
-from ..views.whats_this import column_whats_this
+from .default_handler import DefaultHandlerModel
 from .tooltips import cell_tip, header_tip
+from .validators import is_invalid, validate_value
+
+
+def _get_system_palette_color(role):
+    """Get system palette color, with fallback if Qt is not available.
+
+    Args:
+        role: QPalette color role (e.g., QPalette.Highlight)
+
+    Returns:
+        QColor: The system color or a fallback color
+    """
+    try:
+        # Try to get system palette from QApplication
+        from PySide6.QtWidgets import QApplication
+
+        app = QApplication.instance()
+        if app:
+            return app.palette().color(role)
+    except (ImportError, RuntimeError):
+        pass
+
+    # Fallback colors when Qt is not available or no QApplication
+    fallback_colors = {
+        QPalette.Highlight: QColor(51, 153, 255, 100),  # Light blue
+        QPalette.HighlightedText: QColor(255, 255, 255),  # White
+    }
+    return fallback_colors.get(role, QColor(0, 0, 0))
 
 
 class PandasTableModel(QAbstractTableModel):
@@ -88,6 +113,13 @@ def __init__(
         self.config = settings_manager.get_table_defaults(table_type)
         self.default_handler = DefaultHandlerModel(self, self.config)
         self.undo_stack = undo_stack
+        # Cache colors to avoid runtime dependency on QApplication
+        self._highlight_bg_color = _get_system_palette_color(
+            QPalette.Highlight
+        )
+        self._highlight_fg_color = _get_system_palette_color(
+            QPalette.HighlightedText
+        )
 
     def rowCount(self, parent=None):
         """Return the number of rows in the model.
@@ -159,9 +191,9 @@ def data(self, index, role=Qt.DisplayRole):
         if role == Qt.BackgroundRole:
             return self.determine_background_color(row, column)
         if role == Qt.ForegroundRole:
-            # Return yellow text if this cell is a match
+            # Return highlighted text color if this cell is a match
             if (row, column) in self.highlighted_cells:
-                return QApplication.palette().color(QPalette.HighlightedText)
+                return self._highlight_fg_color
             return QBrush(QColor(0, 0, 0))  # Default black text
         if role == Qt.ToolTipRole:
             if row == self._data_frame.shape[0]:
@@ -880,7 +912,7 @@ def determine_background_color(self, row, column):
         if (row, column) == (self._data_frame.shape[0], 0):
             return QColor(144, 238, 144, 150)
         if (row, column) in self.highlighted_cells:
-            return QApplication.palette().color(QPalette.Highlight)
+            return self._highlight_bg_color
         if (row, column) in self._invalid_cells:
             return QColor(255, 100, 100, 150)
         if row % 2 == 0:

src/petab_gui/models/pandas_table_model.py

@@ -7,7 +7,7 @@
 from PySide6.QtCore import QObject, QSignalBlocker, Signal
 
 from ..C import DEFAULT_ANTIMONY_TEXT
-from ..utils import antimonyToSBML, sbmlToAntimony
+from .sbml_utils import antimony_to_sbml, sbml_to_antimony
 
 
 class SbmlViewerModel(QObject):
@@ -30,20 +30,20 @@ def __init__(self, sbml_model: petab.models.Model, parent=None):
             self.sbml_text = libsbml.writeSBMLToString(
                 self._sbml_model_original.sbml_model.getSBMLDocument()
             )
-            self.antimony_text = sbmlToAntimony(self.sbml_text)
+            self.antimony_text = sbml_to_antimony(self.sbml_text)
         else:
             self.antimony_text = DEFAULT_ANTIMONY_TEXT
             with QSignalBlocker(self):
                 self.convert_antimony_to_sbml()
         self.model_id = self._get_model_id()
 
     def convert_sbml_to_antimony(self):
-        self.antimony_text = sbmlToAntimony(self.sbml_text)
+        self.antimony_text = sbml_to_antimony(self.sbml_text)
         self.model_id = self._get_model_id()
         self.something_changed.emit(True)
 
     def convert_antimony_to_sbml(self):
-        self.sbml_text = antimonyToSBML(self.antimony_text)
+        self.sbml_text = antimony_to_sbml(self.antimony_text)
         self.model_id = self._get_model_id()
         self.something_changed.emit(True)
 

src/petab_gui/models/sbml_model.py

@@ -0,0 +1,70 @@
+"""SBML and Antimony conversion utilities."""
+
+import logging
+import os
+
+import antimony
+
+
+def _check_antimony_return_code(code):
+    """Helper for checking the antimony response code.
+
+    Raises Exception if error in antimony.
+
+    Args:
+        code: antimony response code
+
+    Raises:
+        Exception: If antimony encountered an error
+    """
+    if code < 0:
+        raise Exception(f"Antimony: {antimony.getLastError()}")
+
+
+def sbml_to_antimony(sbml):
+    """Convert SBML to antimony string.
+
+    Args:
+        sbml: SBML string or file path
+
+    Returns:
+        str: Antimony representation
+    """
+    antimony.clearPreviousLoads()
+    antimony.freeAll()
+    isfile = False
+    try:
+        isfile = os.path.isfile(sbml)
+    except Exception as e:
+        logging.warning(f"Error checking if {sbml} is a file: {str(e)}")
+        isfile = False
+    if isfile:
+        code = antimony.loadSBMLFile(sbml)
+    else:
+        code = antimony.loadSBMLString(str(sbml))
+    _check_antimony_return_code(code)
+    return antimony.getAntimonyString(None)
+
+
+def antimony_to_sbml(ant):
+    """Convert Antimony to SBML string.
+
+    Args:
+        ant: Antimony string or file path
+
+    Returns:
+        str: SBML representation
+    """
+    antimony.clearPreviousLoads()
+    antimony.freeAll()
+    try:
+        isfile = os.path.isfile(ant)
+    except ValueError:
+        isfile = False
+    if isfile:
+        code = antimony.loadAntimonyFile(ant)
+    else:
+        code = antimony.loadAntimonyString(ant)
+    _check_antimony_return_code(code)
+    mid = antimony.getMainModuleName()
+    return antimony.getSBMLString(mid)

src/petab_gui/models/sbml_utils.py

@@ -0,0 +1,46 @@
+"""Validation utilities for PEtab data."""
+
+import math
+
+import numpy as np
+
+
+def validate_value(value, expected_type):
+    """Validate and convert a value to the expected type.
+
+    Args:
+        value: The value to validate and convert
+        expected_type: The numpy type to convert the value to
+
+    Returns:
+        tuple: A tuple containing:
+            - The converted value, or None if conversion failed
+            - An error message if conversion failed, or None if successful
+    """
+    try:
+        if expected_type == np.object_:
+            value = str(value)
+        elif expected_type == np.float64:
+            value = float(value)
+    except ValueError as e:
+        return None, str(e)
+    return value, None
+
+
+def is_invalid(value):
+    """Check if a value is invalid.
+
+    Args:
+        value: The value to check
+
+    Returns:
+        bool: True if the value is invalid (None, NaN, or infinity)
+    """
+    if value is None:  # None values are invalid
+        return True
+    if isinstance(value, str):  # Strings can always be displayed
+        return False
+    try:
+        return not math.isfinite(value)
+    except TypeError:
+        return True