Minor polish

RamizGindullin-UU · web-flow · commit 5b579392826a · 2026-04-10T09:55:19.000+02:00
- (minor) transform_coordinate now returns a tuple instead of a list, preventing potential silent mutation of cached results via @lru_cache
- minor code quality fixes — corrected `Optional` return type annotation, replaced `raise e` with bare `raise`,  fixed some docstrings, and replaced hardcoded plate dimension magic numbers with constants
diff --git a/config/loader.py b/config/loader.py
@@ -16,8 +16,8 @@
 # Description:  Various supplementary utilities related to reading the config file
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 
diff --git a/controllers/csv_controller.py b/controllers/csv_controller.py
@@ -20,8 +20,8 @@
 # Coordinates file selection and writing through native dialog interfaces.
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 import logging
diff --git a/controllers/dzn_controller.py b/controllers/dzn_controller.py
@@ -17,8 +17,8 @@
 # Handles validation and generation of DZN files.
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 import logging
diff --git a/controllers/main_controller.py b/controllers/main_controller.py
@@ -17,8 +17,8 @@
 # Orchestrates main window operations and coordinates other controllers.
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 import logging
@@ -78,7 +78,7 @@ def parse_dzn_file(self, path: str) -> Tuple[str, str, str]:
             path: Path to DZN file
         
         Returns:
-            Tuple of (num_cols, num_rows, control_names) as strings
+            Tuple of (num_rows, num_cols, control_names) as strings (in this specific order)
         
         Raises:
             FileNotFoundError: If DZN file doesn't exist
@@ -91,15 +91,15 @@ def parse_dzn_file(self, path: str) -> Tuple[str, str, str]:
             self.state.num_cols = cols
             self.state.control_names = controls
             self.state.dzn_file_path = path
-            return (cols, rows, controls)
+            return (rows, cols, controls)
         except FileNotFoundError as e:
             logger.error(f"DZN file not found: {path}")
             raise
         except Exception as e:
             logger.error(f"Failed to parse DZN file: {e}")
             raise ValueError(f"Invalid DZN file format: {e}") from e
     
-    def load_csv_file(self, path: str) -> CsvDiagnostics:
+    def load_csv_file(self, path: str) -> Optional[CsvDiagnostics]:
         """
         Load CSV file and update application state, and return consistency diagnostics.
         
@@ -109,6 +109,9 @@ def load_csv_file(self, path: str) -> CsvDiagnostics:
         
         Args:
             path: Path to CSV file to load
+        
+        Returns:
+            CsvDiagnostics or None
             
         Raises:
             FileNotFoundError: If CSV file doesn't exist
diff --git a/controllers/minizinc_controller.py b/controllers/minizinc_controller.py
@@ -17,8 +17,8 @@
 # Handles running constraint programming models and processing output.
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 import logging
diff --git a/controllers/viz_controller.py b/controllers/viz_controller.py
@@ -17,8 +17,8 @@
 # Orchestrates data preparation and figure generation for plate layouts.
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 import logging
@@ -32,7 +32,7 @@
 from core.io_utils import read_csv_file
 from core.layout_utils import find_all_plates_concentrations
 from core.layout_utils import transform_concentrations_to_alphas
-from models.constants import Visualization, Performance, FigureProperties
+from models.constants import PlateDefaults, Visualization, Performance, FigureProperties
 
 logger = logging.getLogger(__name__)
 
@@ -228,9 +228,9 @@ def plot_plate_wells(self, ax, plate_data: List, viz_state: VisualizationState)
         
             for well in materials[material]:
                 if is_switched:
-                    [y_coord, x_coord] = transform_coordinate(well[0])
+                    y_coord, x_coord = transform_coordinate(well[0])
                 else:
-                    [x_coord, y_coord] = transform_coordinate(well[0])
+                    x_coord, y_coord = transform_coordinate(well[0])
             
                 x_coords.append(x_coord + Visualization.WELL_COORDINATE_OFFSET)
                 y_coords.append(y_coord + Visualization.WELL_COORDINATE_OFFSET)
@@ -361,10 +361,11 @@ def _concentration_to_size(
         """
         from core.layout_utils import to_number_if_possible
         
-        # if the plate differs from 16x24 then we need to readjust the size ranges
+        # if the plate differs from 24x16 then we need to readjust the size ranges
         # We do not increase more than 1 / 0.7 to keep the marker size reasonable
+        # NOTE: we use the reoriented grid, thus PlateDefaults.COLS and PlateDefaults.ROWS are swapped
         plate_num_rows, plate_num_cols, _ = self._resolve_orientation(plate_num_rows, plate_num_cols)
-        ratio = max(0.7, plate_num_rows / 24, plate_num_cols / 16)
+        ratio = max(0.7, plate_num_rows / int(PlateDefaults.COLS), plate_num_cols / int(PlateDefaults.ROWS))
         
         # Get size range from constants
         size_min = math.floor(Visualization.CONCENTRATION_SIZE_MIN / ratio)
@@ -451,7 +452,7 @@ def _generate_colors(self, concentrations_list: Dict[str, List[Any]]) -> Dict[st
         return material_colors
     
     def _resolve_orientation(self, num_rows: int, num_cols: int) -> Tuple[int, int, bool]:
-        """Return (effective_rows, effective_cols, is_switched).
+        """Return (num_rows, num_cols, is_switched).
     
         MPLACE convention: wider dimension is always horizontal (x-axis).
         If num_cols > num_rows the axes are swapped for display.
diff --git a/core/csv_validator.py b/core/csv_validator.py
@@ -16,8 +16,8 @@
 # Description:  Validation of CSV files on loading
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 import logging
 from typing import List, Optional
diff --git a/core/dzn_parser.py b/core/dzn_parser.py
@@ -16,8 +16,8 @@
 # Description:  Various supplementary utilities related to DZN parsing
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 import re
diff --git a/core/dzn_writer.py b/core/dzn_writer.py
@@ -16,8 +16,8 @@
 # Description:  DZN text generation logic
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 from models.dto import DznBuildParams, ValidationVerdict
diff --git a/core/io_utils.py b/core/io_utils.py
@@ -16,8 +16,8 @@
 # Description:  Various supplementary utilities related to I/O operations
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 
@@ -140,7 +140,7 @@ def read_csv_file(file_path: str) -> List[str]:
         return layout_text_array
     except (ValueError) as e:
         logger.error(f"Failed to read CSV file: {file_path}, error: {e}")
-        raise e
+        raise
     except (FileNotFoundError, IOError) as e:
         logger.error(f"Failed to read CSV file: {file_path}, error: {e}")
         raise FileNotFoundError(f"Could not read CSV file: {file_path}") from e
@@ -279,7 +279,7 @@ def scan_csv_plater_matrices(layout_text_array: List[str]) -> Tuple[int, int, Li
         logger.info('Concentrations:')
         for line in concentrations_matrix:
             logger.info(line)
-        raise ValueError(f'Drug and concentration layouts of Plater file have mismatched number of rows: {rows} and {len(concentrations_matrix)}')
+        raise ValueError(f'Drug and concentration layouts of Plater file have mismatched number of rows: {len(rows)} and {len(concentrations_matrix)}')
     
     return rows, cols, drugs_matrix, concentrations_matrix
 
@@ -361,7 +361,7 @@ def convert_pharmbio_to_plater_plate(input_data: CSVConversionRequest) -> str:
         input_data: CSVConversionRequest() object containing all input data
         
     Returns:
-        List of CSV lines compatible with Plater R-package
+        CSV rows compatible with Plater R-package as a single string
     """
     rows = int(input_data.rows)
     cols = int(input_data.cols)
@@ -382,7 +382,7 @@ def convert_pharmbio_to_plater_plate(input_data: CSVConversionRequest) -> str:
         concentration_matrix[0][i] = str(i)
     
     for line in lines:
-        x,y = transform_coordinate(line[0])
+        x, y = transform_coordinate(line[0])
         drugs_matrix[x+1][y+1] = line[1]
         concentration_matrix[x+1][y+1] = line[2]
         
diff --git a/core/layout_utils.py b/core/layout_utils.py
@@ -16,8 +16,8 @@
 # Description:  Various supplementary utilities related to visualization of layouts
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 import logging
@@ -33,7 +33,7 @@
 
 
 @lru_cache(maxsize=Performance.COORDINATE_CACHE_SIZE)
-def transform_coordinate(well: str) -> List[int]:
+def transform_coordinate(well: str) -> Tuple[int, int]:
     """Transform coordinates from standard csv-file format.
     
     Args:
@@ -43,9 +43,9 @@ def transform_coordinate(well: str) -> List[int]:
         List of [row, col] coordinates (0-indexed)
         
     Example:
-        transform_coordinate('A1') returns [0, 0]
-        transform_coordinate('B3') returns [1, 2]
-        transform_coordinate('Aa14')returns [26,14]
+        transform_coordinate('A1') returns (0, 0)
+        transform_coordinate('B3') returns (1, 2)
+        transform_coordinate('Aa14')returns (26,14)
     
     Note:
         This function is cached for performance when processing repeated well coordinates.
@@ -60,7 +60,7 @@ def transform_coordinate(well: str) -> List[int]:
         else:
             col = int(well[i:]) - 1
             logger.debug(f"Coordinate transform: {well} -> [{row}, {col}]")
-            return [row, col]
+            return (row, col)
     error_msg = f'Coordinates {well} can not be transformed.'
     logger.debug(error_msg)
     raise ValueError(error_msg)
diff --git a/core/minizinc_runner.py b/core/minizinc_runner.py
@@ -16,8 +16,8 @@
 # Description:  Various supplementary utilities related to running MiniZinc models
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 
diff --git a/core/model_validator.py b/core/model_validator.py
@@ -19,8 +19,8 @@
 #               assert or derived constraint in the respective .mzn model.
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 # MAINTENANCE NOTE:
 #   Quantity computations in _plaid_quantities() and _compd_quantities() must
diff --git a/core/validators.py b/core/validators.py
@@ -16,8 +16,8 @@
 # Description:  Various supplementary utilities related to validating material dictionaries
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 import ast
diff --git a/models/application_state.py b/models/application_state.py
@@ -17,8 +17,8 @@
 # Centralizes all application state that was previously scattered across tk.StringVar variables.
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 import os
diff --git a/models/constants.py b/models/constants.py
@@ -16,8 +16,8 @@
 # Description: Constants for the MPLACE application
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 
diff --git a/models/dto.py b/models/dto.py
@@ -16,8 +16,8 @@
 # Description: Data Transfer Objects for MPLACE application
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 
diff --git a/mplace.py b/mplace.py
@@ -16,8 +16,8 @@
 # Main application entry point with MVC architecture.
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 
 import tkinter as tk
 from tkinter import messagebox
diff --git a/ui/ui_utils.py b/ui/ui_utils.py
@@ -16,8 +16,8 @@
 # Description:  Utilities related to UI manipulations that can be used with multiple views
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 import logging
diff --git a/views/dzn_view.py b/views/dzn_view.py
@@ -17,8 +17,8 @@
 # Pure view layer - handles only UI display and user input.
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 import tkinter as tk
diff --git a/views/main_view.py b/views/main_view.py
@@ -17,8 +17,8 @@
 # Pure view layer - handles only UI display and user input.
 #
 # Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)
-# Version: 1.3.4
-# Last Revision: March 2026
+# Version: 1.3.5
+# Last Revision: April 2026
 #
 
 import logging
@@ -351,7 +351,7 @@ def _on_load_dzn(self) -> None:
             try:
                 path_show(path, self.label_dzn_loaded)
                 self.dzn_file_path.set(path)
-                cols, rows, controls = self.controller.parse_dzn_file(path)
+                rows, cols, controls = self.controller.parse_dzn_file(path)
                 self.num_cols.set(cols)
                 self.num_rows.set(rows)
                 self.control_names.set(controls)
@@ -533,7 +533,7 @@ def _open_recent_file(self, path: str, is_dzn: bool) -> None:
             self.dzn_file_path.set(path)
             path_show(path, self.label_dzn_loaded)
             try:
-                cols, rows, controls = self.controller.parse_dzn_file(path)
+                rows, cols, controls = self.controller.parse_dzn_file(path)
                 self.num_cols.set(cols)
                 self.num_rows.set(rows)
                 self.control_names.set(controls)
diff --git a/views/viz_view.py b/views/viz_view.py

Original file line number	Diff line number	Diff line change
`@@ -16,8 +16,8 @@`
`16`	`16`	`# Description: Various supplementary utilities related to reading the config file`
`17`	`17`	`#`
`18`	`18`	`# Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)`
`19`		`-# Version: 1.3.4`
`20`		`-# Last Revision: March 2026`
	`19`	`+# Version: 1.3.5`
	`20`	`+# Last Revision: April 2026`
`21`	`21`	`#`
`22`	`22`
`23`	`23`
Original file line number	Diff line number	Diff line change
`@@ -20,8 +20,8 @@`
`20`	`20`	`# Coordinates file selection and writing through native dialog interfaces.`
`21`	`21`	`#`
`22`	`22`	`# Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)`
`23`		`-# Version: 1.3.4`
`24`		`-# Last Revision: March 2026`
	`23`	`+# Version: 1.3.5`
	`24`	`+# Last Revision: April 2026`
`25`	`25`	`#`
`26`	`26`
`27`	`27`	`import logging`
Original file line number	Diff line number	Diff line change
`@@ -17,8 +17,8 @@`
`17`	`17`	`# Handles validation and generation of DZN files.`
`18`	`18`	`#`
`19`	`19`	`# Authors: Ramiz GINDULLIN (ramiz.gindullin@it.uu.se)`
`20`		`-# Version: 1.3.4`
`21`		`-# Last Revision: March 2026`
	`20`	`+# Version: 1.3.5`
	`21`	`+# Last Revision: April 2026`
`22`	`22`	`#`
`23`	`23`
`24`	`24`	`import logging`