Various Fixes (#83)

* Added application Icon (not visible in MacOS)

* Fixed typesetting in copy/paste

* Removed superfluous line

Author: PaulJonasJost

pyproject.toml

@@ -50,3 +50,9 @@ petab_gui="petab_gui:main"
 
 [project.scripts]
 petab_gui_cli="petab_gui:main"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.package-data]
+"petab_gui.assets" = ["PEtab.png"]

src/petab_gui/C.py

@@ -38,7 +38,7 @@
         "conditionId": {"type": np.object_, "optional": False},
         "conditionName": {"type": np.object_, "optional": False},
     }
-    }
+}
 
 CONFIG = {
     'window_title': 'My Application',

src/petab_gui/app.py

@@ -1,6 +1,7 @@
 from PySide6.QtWidgets import QApplication
-from PySide6.QtGui import QFileOpenEvent
+from PySide6.QtGui import QFileOpenEvent, QIcon
 from PySide6.QtCore import QEvent
+from importlib.resources import files
 import sys
 import os
 import petab.v1 as petab
@@ -21,6 +22,15 @@ def find_example(path: Path) -> Path:
     raise FileNotFoundError("Could not find examples directory")
 
 
+def get_icon() -> QIcon:
+    """Get the Icon for the Window"""
+    icon_path = files("petab_gui.assets").joinpath("PEtab.png")
+    if not icon_path.is_file():
+        raise FileNotFoundError(f"Icon file not found: {icon_path}")
+    icon = QIcon(str(icon_path))
+    return icon
+
+
 class PEtabGuiApp(QApplication):
     def __init__(self):
         super().__init__(sys.argv)
@@ -29,6 +39,7 @@ def __init__(self):
         # self.apply_stylesheet()
         self.model = PEtabModel()
         self.view = MainWindow()
+        self.view.setWindowIcon(get_icon())
         self.controller = MainController(self.view, self.model)
 
         # hack to be discussed

src/petab_gui/assets/PEtab.png

@@ -180,10 +180,17 @@ def _set_data_single(self, index, value):
         column_name = self._data_frame.columns[column - col_setoff]
         old_value = self._data_frame.iloc[row, column - col_setoff]
         # cast to numeric if necessary
-        if not self._data_frame[column_name].dtype == "object":
-            try:
-                value = float(value)
-            except ValueError:
+        expected_type = self._allowed_columns.get(column_name, None)
+        if is_invalid(value):
+            if not expected_type["optional"]:
+                return False
+            self._data_frame.iloc[row, column - col_setoff] = None
+            self.dataChanged.emit(index, index, [Qt.DisplayRole])
+            return True
+        if expected_type:
+            expected_type = expected_type["type"]
+            value, error_message = validate_value(value, expected_type)
+            if error_message:
                 self.new_log_message.emit(
                     f"Column '{column_name}' expects a numeric value",
                     "red"

src/petab_gui/models/pandas_table_model.py

@@ -488,12 +488,10 @@ def highlightBlock(self, text):
 
 def validate_value(value, expected_type):
     try:
-        if expected_type == "STRING":
+        if expected_type == np.object_:
             value = str(value)
-        elif expected_type == "NUMERIC":
+        elif expected_type == np.float64:
             value = float(value)
-        elif expected_type == "BOOLEAN":
-            value = bool(value)
     except ValueError as e:
         return None, str(e)
     return value, None
@@ -599,6 +597,12 @@ def get_selected_rectangles(table_view: QTableView) -> np.array:
     selected = get_selected(table_view, mode=INDEX)
     if not selected:
         return None
+
+    model = table_view.model()
+    if hasattr(model, "mapToSource"):
+        # map all indices to source
+        selected = [model.mapToSource(index) for index in selected]
+
     rows = [index.row() for index in selected]
     cols = [index.column() for index in selected]
     min_row, max_row = min(rows), max(rows)
@@ -609,6 +613,7 @@ def get_selected_rectangles(table_view: QTableView) -> np.array:
     )
     for index in selected:
         selected_rect[index.row() - min_row, index.column() - min_col] = True
+
     return selected_rect, rect_start
 
 

src/petab_gui/utils.py

@@ -41,33 +41,43 @@ def paste_from_clipboard(self):
         text = clipboard.text()
         if not text:
             return
+
+        # Get the proxy and source models
+        proxy_model = self.table_view.model()
+        source_model = proxy_model.sourceModel()
+
+        # Get the start index from the current selection
         start_index = self.table_view.selectionModel().currentIndex()
         if not start_index.isValid():
             return
-        model = self.table_view.model()
-        row_start, col_start = start_index.row(), start_index.column()
-        # identify which invalid cells are being pasted into
+
+        # Map the start index to the source model
+        source_index = proxy_model.mapToSource(start_index)
+        row_start, col_start = source_index.row(), source_index.column()
+
+        # Parse clipboard data
         pasted_data = [line.split("\t") for line in text.split("\n") if
                        line.strip()]
         num_rows = len(pasted_data)
-        num_cols = max([len(line) for line in pasted_data])
+        num_cols = max(len(line) for line in pasted_data)
+
+        # Identify which cells are being overridden
         overridden_cells = {
             (row_start + r, col_start + c)
             for r in range(num_rows)
             for c in range(num_cols)
-            if model.index(row_start + r, col_start + c).isValid()
+            if source_model.index(row_start + r, col_start + c).isValid()
         }
-        invalid_overridden_cells = overridden_cells.intersection(
-            model._invalid_cells
-        )
-        if invalid_overridden_cells:
+
+        # Handle invalid cells
+        if hasattr(source_model, "_invalid_cells"):
+            invalid_overridden_cells = overridden_cells.intersection(
+                source_model._invalid_cells)
             for row_invalid, col_invalid in invalid_overridden_cells:
-                model.discard_invalid_cell(row_invalid, col_invalid)
+                source_model.discard_invalid_cell(row_invalid, col_invalid)
 
-        model.setDataFromText(
-            text, start_index.row(),
-            start_index.column()
-        )
+        # Paste the data into the source model
+        source_model.setDataFromText(text, row_start, col_start)
 
 
 class ComboBoxDelegate(QStyledItemDelegate):