Minor polish

Minor editing of comments, indentation, a duplicated call. No bugs fixed, just cleaning up the codebase

Author: RamizGindullin-UU

controllers/main_controller.py

@@ -86,9 +86,9 @@ def parse_dzn_file(self, path: str) -> Tuple[str, str, str]:
         """
         logger.debug(f"Parsing DZN file: {path}")
         try:
-            cols, rows, controls = scan_dzn(path)
-            self.state.num_cols = cols
+            rows, cols, controls = scan_dzn(path)
             self.state.num_rows = rows
+            self.state.num_cols = cols
             self.state.control_names = controls
             self.state.dzn_file_path = path
             return (cols, rows, controls)

core/csv_validator.py

@@ -114,4 +114,4 @@ def check_csv_consistency(
         csv_rows=max_row,
         csv_cols=max_col,
         warnings=warnings
-    )
+    )

core/dzn_parser.py

@@ -70,7 +70,7 @@ def scan_dzn(file_path: str) -> Tuple[str, str, str]:
     if rows.isnumeric() and cols.isnumeric():
         controls = str(__parse_control_string__(ctrs))
         logger.info(f"DZN parsed: {cols}x{rows} plate, controls: {controls}")
-        return cols, rows, controls
+        return rows, cols, controls
     else:
         logger.error(f"Invalid DZN file - non-numeric dimensions: rows={rows}, cols={cols}")
         raise ValueError('Corrupt dzn file - invalid numeric values')

core/io_utils.py

@@ -176,6 +176,7 @@ def convert_to_pharmbio_format(layout_text_array: List[str]) -> List[str]:
             for i in range(rows):
                 for j in range(1,cols):
                     if drugs_matrix[i][j] != '':
+                        # VOLuL column always empty as we do not store VOLuL column in Plater format
                         plater_layout_text_array.append(''.join(['plate_1',
                                                                  ',',
                                                                  drugs_matrix[i][0] + "{:02d}".format(j),

models/dto.py

@@ -35,7 +35,7 @@
 
 @dataclass(frozen=True)
 class AppConfig:
-    """Contains all all configuration fields (paths) the app relies on
+    """Contains all configuration fields (paths) the app relies on
     """
     minizinc_path: str
     plaid_path: str

views/dzn_view.py

@@ -298,82 +298,82 @@ def _on_replicates_same_changed(self) -> None:
             self.flag_replicates_on_different_plates.set(False)
 
     def _on_generate(self) -> None:
-            """Handle generate button click."""
-            logger.info("Generate DZN button clicked")
-    
-            # Collect form data
-            form_data = DznFormData(
-                num_rows=self.num_rows.get(),
-                num_cols=self.num_cols.get(),
-                inner_empty_edge=self.inner_empty_edge.get(),
-                size_empty_edge=self.size_empty_edge.get(),
-                size_corner_empty_wells=self.size_corner_empty_wells.get(),
-                horizontal_cell_lines=self.horizontal_cell_lines.get(),
-                vertical_cell_lines=self.vertical_cell_lines.get(),
-                flag_allow_empty_wells=self.flag_allow_empty_wells.get(),
-                flag_concentrations_on_different_rows=self.flag_concentrations_on_different_rows.get(),
-                flag_concentrations_on_different_columns=self.flag_concentrations_on_different_columns.get(),
-                flag_replicates_on_different_plates=self.flag_replicates_on_different_plates.get(),
-                flag_replicates_on_same_plate=self.flag_replicates_on_same_plate.get(),
-                compounds_dict=self.drugs.get(),
-                controls_dict=self.controls.get()
-            )
-            self.button_generate.config(state=tk.DISABLED, text='Generating...')
-            self.window.update_idletasks()
+        """Handle generate button click."""
+        logger.info("Generate DZN button clicked")
 
-            try:
-                # Step 1: UI-level validation
-                errors = self.controller.validate_form_data(form_data)
-                if errors:
-                    logger.warning(f"DZN validation failed: {len(errors)} errors")
-                    error_message = '\n'.join([f"{i+1}. {err}" for i, err in enumerate(errors)])
-                    messagebox.showerror("Input Validation Error", error_message)
-                    return
+        # Collect form data
+        form_data = DznFormData(
+            num_rows=self.num_rows.get(),
+            num_cols=self.num_cols.get(),
+            inner_empty_edge=self.inner_empty_edge.get(),
+            size_empty_edge=self.size_empty_edge.get(),
+            size_corner_empty_wells=self.size_corner_empty_wells.get(),
+            horizontal_cell_lines=self.horizontal_cell_lines.get(),
+            vertical_cell_lines=self.vertical_cell_lines.get(),
+            flag_allow_empty_wells=self.flag_allow_empty_wells.get(),
+            flag_concentrations_on_different_rows=self.flag_concentrations_on_different_rows.get(),
+            flag_concentrations_on_different_columns=self.flag_concentrations_on_different_columns.get(),
+            flag_replicates_on_different_plates=self.flag_replicates_on_different_plates.get(),
+            flag_replicates_on_same_plate=self.flag_replicates_on_same_plate.get(),
+            compounds_dict=self.drugs.get(),
+            controls_dict=self.controls.get()
+        )
+        self.button_generate.config(state=tk.DISABLED, text='Generating...')
+        self.window.update_idletasks()
 
-                # Step 2: Model compatibility validation
-                verdict = self.controller.validate_model_compat(form_data)
+        try:
+            # Step 1: UI-level validation
+            errors = self.controller.validate_form_data(form_data)
+            if errors:
+                logger.warning(f"DZN validation failed: {len(errors)} errors")
+                error_message = '\n'.join([f"{i+1}. {err}" for i, err in enumerate(errors)])
+                messagebox.showerror("Input Validation Error", error_message)
+                return
 
-                if verdict.both_blocked():
-                    msg = _format_verdict_message(verdict)
-                    messagebox.showerror("Incompatible with All Models", msg)
-                    return
+            # Step 2: Model compatibility validation
+            verdict = self.controller.validate_model_compat(form_data)
 
-                if verdict.any_issues():
-                    msg = _format_verdict_message(verdict)
-                    proceed = messagebox.askokcancel("Model Compatibility Warnings", msg +
-                                                     "\n\nProceed with file generation?")
-                    if not proceed:
-                        return
+            if verdict.both_blocked():
+                msg = _format_verdict_message(verdict)
+                messagebox.showerror("Incompatible with All Models", msg)
+                return
 
-                # Step 3: Generate and save
-                dzn_content, control_names = self.controller.generate_dzn_content(form_data, verdict)
-                logger.info(f"DZN content generated: {len(dzn_content)} characters")
-        
-                # Save via controller
-                file_path = self.controller.save_dzn_file(dzn_content)
+            if verdict.any_issues():
+                msg = _format_verdict_message(verdict)
+                proceed = messagebox.askokcancel("Model Compatibility Warnings", msg +
+                                                 "\n\nProceed with file generation?")
+                if not proceed:
+                    return
+
+            # Step 3: Generate and save
+            dzn_content, control_names = self.controller.generate_dzn_content(form_data, verdict)
+            logger.info(f"DZN content generated: {len(dzn_content)} characters")
+    
+            # Save via controller
+            file_path = self.controller.save_dzn_file(dzn_content)
+    
+            if file_path:
+                logger.info(f"DZN saved successfully: {file_path}")
 
-                if file_path:
-                    logger.info(f"DZN saved successfully: {file_path}")
-            
-                    # Notify callback
-                    self.on_generation_complete(
-                        file_path,
-                        form_data.num_rows,
-                        form_data.num_cols,
-                        str(control_names)
-                    )
-            
-                    # Hide window
-                    self.hide()
-                    self.parent.focus_force()
-                else:
-                    logger.info("DZN save cancelled by user")
+                # Notify callback
+                self.on_generation_complete(
+                    file_path,
+                    form_data.num_rows,
+                    form_data.num_cols,
+                    str(control_names)
+                )
 
-            except Exception as e:
-                logger.error(f"DZN generation failed: {e}")
-                messagebox.showerror("Error", f"DZN generation failed:\n{str(e)}")
-            finally:
-                self.button_generate.config(state=tk.NORMAL, text='Generate *.dzn file')
+                # Hide window
+                self.hide()
+                self.parent.focus_force()
+            else:
+                logger.info("DZN save cancelled by user")
+    
+        except Exception as e:
+            logger.error(f"DZN generation failed: {e}")
+            messagebox.showerror("Error", f"DZN generation failed:\n{str(e)}")
+        finally:
+            self.button_generate.config(state=tk.NORMAL, text='Generate *.dzn file')
 
     def _on_close(self) -> None:
         """Handle window close button."""

views/main_view.py

@@ -601,7 +601,6 @@ def _load_csv_into_ui(self, path: str) -> None:
             warning_text = "\n\n".join(diagnostics.warnings)
             messagebox.showwarning("CSV Consistency Warning", warning_text)
 
-        self.controller.load_csv_file(path)
         path_show(path, self.label_csv_loaded)
         self.csv_file_path.set(path)
         self.button_visualize.config(state=tk.NORMAL)