bugfixes #259

Sierd · 2025-11-04T17:43:59Z

No description provided.

Co-authored-by: Sierd <[email protected]>

… variable dropdowns Co-authored-by: Sierd <[email protected]>

Copilot

Pull Request Overview

This PR refactors the GUI's plotting output functionality by splitting the single "Plot Output" tab into two separate tabs: "Plot Output 2D" and "Plot Output 1D". The changes introduce comprehensive support for 1D transect visualization and enhance the 2D plotting capabilities.

Key Changes:

Split the output plotting interface into separate 2D and 1D visualization tabs
Added variable selection dropdowns to both tabs for dynamic data exploration
Replaced button-based plotting with automatic plot updates when files are loaded
Introduced vegetation overlay checkbox for cleaner UI interaction
Refactored path handling to use os.pardir and os.sep for cross-platform compatibility

Comments suppressed due to low confidence (1)

aeolis/gui.py:41

The initialization sets overlay_veg_enabled to False, but this attribute is no longer used in the refactored code. The new implementation uses self.overlay_veg_var (a BooleanVar) instead. This unused attribute should be removed.

        self.nc_data_cache = None
        self.overlay_veg_enabled = False

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Copilot · 2025-11-04T21:44:38Z

aeolis/gui.py

+
+    def on_variable_changed(self, event):
+        """Update plot when variable selection changes"""
+        if hasattr(self, 'nc_data_cache_1d') and self.nc_data_cache_1d is not None:


The attribute nc_data_cache_1d is not initialized in __init__. Consider adding self.nc_data_cache_1d = None to the initialization to make the code's structure clearer and avoid potential AttributeError issues if code paths change.

Copilot · 2025-11-04T21:44:38Z

aeolis/gui.py

+        # Update plot if data is loaded
+        if hasattr(self, 'nc_data_cache_1d') and self.nc_data_cache_1d is not None:
+            # Reconfigure slider range based on new direction
+            first_var = list(self.nc_data_cache_1d['vars'].values())[0]


The code converts the entire dict_values object to a list just to get the first element. Use next(iter(self.nc_data_cache_1d['vars'].values())) instead for better performance, especially with large variable dictionaries.

Suggested change

first_var = list(self.nc_data_cache_1d['vars'].values())[0]

first_var = next(iter(self.nc_data_cache_1d['vars'].values()))

Copilot · 2025-11-04T21:44:39Z

aeolis/gui.py

+                coord_vars = {'x', 'y', 's', 'n', 'lat', 'lon', 'time', 'layers', 'fractions', 
+                             'x_bounds', 'y_bounds', 'lat_bounds', 'lon_bounds', 'time_bounds', 'crs', 'nv', 'nv2'}


The coordinate variables set is duplicated in both plot_1d_transect (lines 741-742) and plot_nc_2d (lines 1004-1005). Consider defining this as a class constant or module-level constant to avoid duplication and maintain consistency.

Copilot · 2025-11-04T21:44:39Z

aeolis/gui.py

+            # Use dict.values() directly instead of next(iter()) for clarity
+            first_var = list(var_data_dict.values())[0]


The code converts the entire dict_values object to a list just to get the first element. Use next(iter(var_data_dict.values())) instead for better performance.

Suggested change

# Use dict.values() directly instead of next(iter()) for clarity

first_var = list(var_data_dict.values())[0]

# Use next(iter(var_data_dict.values())) for better performance

first_var = next(iter(var_data_dict.values()))

Copilot · 2025-11-04T21:44:39Z

aeolis/gui.py

+            ylabel_dict = {
+                'zb': 'Bed Elevation (m)',
+                'ustar': 'Shear Velocity (m/s)',
+                'ustars': 'Shear Velocity S-component (m/s)',
+                'ustarn': 'Shear Velocity N-component (m/s)',
+                'zs': 'Surface Elevation (m)',
+                'zsep': 'Separation Elevation (m)',
+                'Ct': 'Sediment Concentration (kg/m²)',
+                'Cu': 'Equilibrium Concentration (kg/m²)',
+                'q': 'Sediment Flux (kg/m/s)',
+                'qs': 'Sediment Flux S-component (kg/m/s)',
+                'qn': 'Sediment Flux N-component (kg/m/s)',
+                'pickup': 'Sediment Entrainment (kg/m²)',
+                'uth': 'Threshold Shear Velocity (m/s)',
+                'w': 'Fraction Weight (-)',
+            }
+            ylabel = ylabel_dict.get(var_name, var_name)


The variable label/title dictionaries are duplicated across update_1d_plot, get_variable_label, and get_variable_title. Consider creating a single shared data structure (e.g., a class constant) that maps variables to both labels and titles to avoid inconsistencies and reduce duplication.

Suggested change

ylabel_dict = {

'zb': 'Bed Elevation (m)',

'ustar': 'Shear Velocity (m/s)',

'ustars': 'Shear Velocity S-component (m/s)',

'ustarn': 'Shear Velocity N-component (m/s)',

'zs': 'Surface Elevation (m)',

'zsep': 'Separation Elevation (m)',

'Ct': 'Sediment Concentration (kg/m²)',

'Cu': 'Equilibrium Concentration (kg/m²)',

'q': 'Sediment Flux (kg/m/s)',

'qs': 'Sediment Flux S-component (kg/m/s)',

'qn': 'Sediment Flux N-component (kg/m/s)',

'pickup': 'Sediment Entrainment (kg/m²)',

'uth': 'Threshold Shear Velocity (m/s)',

'w': 'Fraction Weight (-)',

}

ylabel = ylabel_dict.get(var_name, var_name)

ylabel = self.VARIABLE_LABELS.get(var_name, var_name)

Copilot · 2025-11-04T21:44:39Z

aeolis/gui.py

+                coord_vars = {'x', 'y', 's', 'n', 'lat', 'lon', 'time', 'layers', 'fractions', 
+                             'x_bounds', 'y_bounds', 'lat_bounds', 'lon_bounds', 'time_bounds', 'crs', 'nv', 'nv2'}


The coordinate variables set is duplicated from plot_1d_transect. This duplication violates the DRY principle. Consider defining this as a class constant or module-level constant.

Copilot · 2025-11-04T21:44:40Z

aeolis/gui.py

+
+        # Browse button for NC file
+        nc_browse_btn_1d = ttk.Button(file_frame_1d, text="Browse...", 
+                                       command=lambda: self.browse_nc_file_1d())


This 'lambda' is just a simple wrapper around a callable object. Use that object directly.

Suggested change

command=lambda: self.browse_nc_file_1d())

command=self.browse_nc_file_1d)

Copilot

Pull Request Overview

Copilot reviewed 1 out of 1 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (2)

aeolis/gui.py:1046

The comment states 'Need at least 3 dimensions: (time, n, s)' but does not mention the fractions dimension. This is inconsistent with the updated 1D plotting logic (line 778) which correctly documents '(time, n, s) or (time, n, s, fractions)'. The comment should be updated to include the fractions case for consistency.

                        # Need at least 3 dimensions: (time, n, s)
                        if var_data.ndim < 3:
                            continue  # Skip variables without spatial dimensions

aeolis/gui.py:1052

The 2D plotting function (plot_nc_2d) does not handle 3D variables without time dimension (n, s, fractions), unlike the 1D plotting function (plot_1d_transect) which correctly handles this case at lines 787-792. This inconsistency means 3D variables with fractions but no time dimension will be rejected in 2D plotting but accepted in 1D plotting. The logic should be updated to match the 1D implementation: check if var.ndim < 2 instead of != 2, and handle both 2D and 3D cases.

                        # Need exactly 2 spatial dimensions: (n, s)
                        if var.ndim != 2:
                            continue  # Skip variables without 2D spatial dimensions

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Copilot

Pull Request Overview

Copilot reviewed 1 out of 1 changed files in this pull request and generated 12 comments.

Comments suppressed due to low confidence (4)

aeolis/gui.py:1425

Except block directly handles BaseException.

                except:

aeolis/gui.py:1558

Except block directly handles BaseException.

                except:

aeolis/gui.py:1562

Except block directly handles BaseException.

                    except:

aeolis/gui.py:1645

Except block directly handles BaseException.

                except:

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Copilot · 2025-11-05T13:16:12Z

aeolis/gui.py

+    lz = math.sin(alt)
+
+    illum = np.clip(nx * lx + ny * ly + nz * lz, 0.0, 1.0)
+    shaded = 0.35 + (1.0 - 0.35) * illum  # ambient term


The magic number 0.35 appears twice in the calculation. Consider extracting it as a named constant (e.g., AMBIENT_TERM = 0.35) at the module level or as a function parameter to improve code clarity and maintainability.

Copilot · 2025-11-05T13:16:13Z

aeolis/gui.py

+                    try:
+                        self.plot_data('bed_file', 'Bed Elevation')
+                    except Exception as e:
+                        # Silently fail if plotting doesn't work (e.g., files don't exist)
+                        pass


The exception is caught but the variable 'e' is unused. Either remove the variable (use bare except Exception:) or log the error for debugging purposes instead of silently failing. Silent failures can make troubleshooting difficult.

Copilot · 2025-11-05T13:16:13Z

aeolis/gui.py

+                    self.output_colorbar.update_normal(im)
+                    cbar_label = self.get_variable_label(var_name)
+                    self.output_colorbar.set_label(cbar_label)
+                except:


Bare except: clause catches all exceptions including system exits and keyboard interrupts. Use except Exception: to catch only regular exceptions, or specify the expected exception types (e.g., except (AttributeError, ValueError):).

Suggested change

except:

except Exception:

Copilot · 2025-11-05T13:16:13Z

aeolis/gui.py

+                except:
+                    # If remove() fails, try removing from figure
+                    try:
+                        self.output_fig.delaxes(self.output_colorbar.ax)
+                    except:


Multiple bare except: clauses. Use except Exception: or specific exception types to avoid catching system exits and keyboard interrupts. This appears in nested try-except blocks.

Suggested change

except:

# If remove() fails, try removing from figure

try:

self.output_fig.delaxes(self.output_colorbar.ax)

except:

except Exception:

# If remove() fails, try removing from figure

try:

self.output_fig.delaxes(self.output_colorbar.ax)

except Exception:

Copilot · 2025-11-05T13:16:14Z

aeolis/gui.py

+                try:
+                    self.output_colorbar.update_normal(im)
+                    self.output_colorbar.set_label('Shear Velocity (m/s)')
+                except:


Bare except: clause. Use except Exception: or specify the expected exception types to avoid catching system exits and keyboard interrupts.

Suggested change

except:

except Exception:

Copilot · 2025-11-05T13:16:15Z

aeolis/gui.py

+                q = self.output_ax.quiver(X_plot, Y_plot, U_plot, V_plot,
+                                          color='black', scale=None, scale_units='xy',
+                                          angles='xy', pivot='mid', width=0.003)


The magic number 0.003 is used for quiver arrow width. Consider extracting this as a named constant (e.g., QUIVER_ARROW_WIDTH = 0.003) to improve maintainability.

Copilot · 2025-11-05T13:16:15Z

aeolis/gui.py

+                # Calculate reference vector magnitude for quiver key
+                magnitude_all = np.sqrt(U_plot**2 + V_plot**2)
+                if magnitude_all.max() > 0:
+                    ref_magnitude = magnitude_all.max() * 0.5


The magic number 0.5 is used to calculate reference magnitude for the quiver key. Consider extracting this as a named constant (e.g., QUIVER_KEY_SCALE_FACTOR = 0.5) to improve code clarity.

Copilot · 2025-11-05T13:16:15Z

aeolis/gui.py

+            # Apply ocean mask: zb < -0.5 and x < 200
+            if x_data is not None:
+                X2d, _ = np.meshgrid(x1d, y1d)
+                ocean_mask = (zb < -0.5) & (X2d < 200)


The magic numbers -0.5 and 200 are used for ocean masking criteria. Consider extracting these as named constants (e.g., OCEAN_DEPTH_THRESHOLD = -0.5, OCEAN_X_LIMIT = 200) to improve code clarity and maintainability.

Copilot · 2025-11-05T13:16:15Z

aeolis/gui.py

+                magnitude_all = np.sqrt(U_plot**2 + V_plot**2)
+                if magnitude_all.max() > 0:
+                    ref_magnitude = magnitude_all.max() * 0.5
+                    qk = self.output_ax.quiverkey(q, 0.9, 0.95, ref_magnitude,


Variable qk is not used.

Suggested change

qk = self.output_ax.quiverkey(q, 0.9, 0.95, ref_magnitude,

self.output_ax.quiverkey(q, 0.9, 0.95, ref_magnitude,

Copilot · 2025-11-05T13:16:16Z

aeolis/gui.py

+                    except:
+                        pass


'except' clause does nothing but pass and there is no explanatory comment.

Suggested change

except:

pass

except Exception as e:

# Failed to remove colorbar axes; log and continue

import traceback

print(f"Failed to remove colorbar axes: {e}")

traceback.print_exc()

* Initialisation of the GUI Including some overdue maintenance related to python 2-->3 in the write_configfile script. * Updated GUI structure using Class * updated gui * update gui branche with latest main (#255) * fixed dependencies for python 3.13 (#236) * test with timing function * Add devcontainer for use in codespaces (#240) * devcontainer added * Update Dockerfile * Update Dockerfile * Update devcontainer.json * Update Dockerfile * fixed dependencies for python 3.13 (#236) (#239) * Update Dockerfile * remove abundant stuff * Add devcontainer for use in codespaces (#240) (#242) * devcontainer added * Update Dockerfile * Update Dockerfile * Update devcontainer.json * Update Dockerfile * fixed dependencies for python 3.13 (#236) (#239) * Update Dockerfile * remove abundant stuff * Update Dockerfile (#243) This patch updates the dockerfile for the codespace to be compatible with developer mode. You need to manual install python in dev model after the docker is created. * Cleanup main (#245) * delete abundant files * deleted: aeolis/examples/vanWesten2024/blowout/figure_grid_initialization.png deleted: aeolis/examples/vanWesten2024/blowout/figure_params_initialization.png deleted: aeolis/examples/vanWesten2024/blowout/figure_timeseries_initialization.png * Update pyproject.toml * Update README.md * Update CITATION.cff * Update release info (#246) * Update pyproject.toml * Update CITATION.cff * Update README.md * Update Python version and dependencies in installation guide * Implement error message for missing ne_file Added error handling for missing 'ne_file' when using Avalanching. * Print message for aeolis installation in Dockerfile Add message indicating manual installation of aeolis * Update vegetation parameters in constants.py (#250) * Update vegetation parameters in constants.py Removes unused V_Lat parameter solves #120 Changes default for veg_min_elevation to -10 to avoid unwanted use of this functionality. * Update aeolis/constants.py Co-authored-by: Copilot <[email protected]> --------- Co-authored-by: Copilot <[email protected]> --------- Co-authored-by: Copilot <[email protected]> * input and output tab added improved domain plotting functionality * added functionality * Fix GUI crash when canceling file selection on startup (#256) * Initial plan * Fix GUI to handle cancel on startup gracefully Co-authored-by: Sierd <[email protected]> * Address code review feedback: move import to top and remove hardcoded path Co-authored-by: Sierd <[email protected]> * Remove placeholder path, set configfile to 'No file selected' when canceled Co-authored-by: Sierd <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: Sierd <[email protected]> * Add Plot Output 1D tab for transect visualization with unified interface (#257) * Initial plan * Add Plot Output 1D tab with transect plotting functionality Co-authored-by: Sierd <[email protected]> * Add variable change callback for 1D plot updates Co-authored-by: Sierd <[email protected]> * Fix code review issues: cross-platform paths and dimension validation Co-authored-by: Sierd <[email protected]> * Improve dimension validation and dictionary access robustness Co-authored-by: Sierd <[email protected]> * Fix transect direction bug and unify 2D/1D tab interface with dynamic variable dropdowns Co-authored-by: Sierd <[email protected]> --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: Sierd <[email protected]> * bugfixes (#259) * Initial plan * Add Plot Output 1D tab with transect plotting functionality Co-authored-by: Sierd <[email protected]> * Add variable change callback for 1D plot updates Co-authored-by: Sierd <[email protected]> * Fix code review issues: cross-platform paths and dimension validation Co-authored-by: Sierd <[email protected]> * Improve dimension validation and dictionary access robustness Co-authored-by: Sierd <[email protected]> * Fix transect direction bug and unify 2D/1D tab interface with dynamic variable dropdowns Co-authored-by: Sierd <[email protected]> * bugfixes * added functionality, colorbars, many small fixes. --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: Sierd <[email protected]> * domain overview added to 1D plot mode. * Delete aeolis/GUI.ipynb * Remove incompatible parameter checks for ne_file Removed error handling for missing ne_file when using Avalanching. --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Copilot <[email protected]> Co-authored-by: Sierd <[email protected]>

* Initialisation of the GUI Including some overdue maintenance related to python 2-->3 in the write_configfile script. * Updated GUI structure using Class * updated gui * update gui branche with latest main (#255) * fixed dependencies for python 3.13 (#236) * test with timing function * Add devcontainer for use in codespaces (#240) * devcontainer added * Update Dockerfile * Update Dockerfile * Update devcontainer.json * Update Dockerfile * fixed dependencies for python 3.13 (#236) (#239) * Update Dockerfile * remove abundant stuff * Add devcontainer for use in codespaces (#240) (#242) * devcontainer added * Update Dockerfile * Update Dockerfile * Update devcontainer.json * Update Dockerfile * fixed dependencies for python 3.13 (#236) (#239) * Update Dockerfile * remove abundant stuff * Update Dockerfile (#243) This patch updates the dockerfile for the codespace to be compatible with developer mode. You need to manual install python in dev model after the docker is created. * Cleanup main (#245) * delete abundant files * deleted: aeolis/examples/vanWesten2024/blowout/figure_grid_initialization.png deleted: aeolis/examples/vanWesten2024/blowout/figure_params_initialization.png deleted: aeolis/examples/vanWesten2024/blowout/figure_timeseries_initialization.png * Update pyproject.toml * Update README.md * Update CITATION.cff * Update release info (#246) * Update pyproject.toml * Update CITATION.cff * Update README.md * Update Python version and dependencies in installation guide * Implement error message for missing ne_file Added error handling for missing 'ne_file' when using Avalanching. * Print message for aeolis installation in Dockerfile Add message indicating manual installation of aeolis * Update vegetation parameters in constants.py (#250) * Update vegetation parameters in constants.py Removes unused V_Lat parameter solves #120 Changes default for veg_min_elevation to -10 to avoid unwanted use of this functionality. * Update aeolis/constants.py --------- --------- * input and output tab added improved domain plotting functionality * added functionality * Fix GUI crash when canceling file selection on startup (#256) * Initial plan * Fix GUI to handle cancel on startup gracefully * Address code review feedback: move import to top and remove hardcoded path * Remove placeholder path, set configfile to 'No file selected' when canceled --------- * Add Plot Output 1D tab for transect visualization with unified interface (#257) * Initial plan * Add Plot Output 1D tab with transect plotting functionality * Add variable change callback for 1D plot updates * Fix code review issues: cross-platform paths and dimension validation * Improve dimension validation and dictionary access robustness * Fix transect direction bug and unify 2D/1D tab interface with dynamic variable dropdowns --------- * bugfixes (#259) * Initial plan * Add Plot Output 1D tab with transect plotting functionality * Add variable change callback for 1D plot updates * Fix code review issues: cross-platform paths and dimension validation * Improve dimension validation and dictionary access robustness * Fix transect direction bug and unify 2D/1D tab interface with dynamic variable dropdowns * bugfixes * added functionality, colorbars, many small fixes. --------- * domain overview added to 1D plot mode. * Delete aeolis/GUI.ipynb * Remove incompatible parameter checks for ne_file Removed error handling for missing ne_file when using Avalanching. --------- Co-authored-by: Copilot <[email protected]> Co-authored-by: Copilot <[email protected]> Co-authored-by: Sierd <[email protected]>

Copilot AI and others added 7 commits November 4, 2025 11:43

Initial plan

2446d33

Add Plot Output 1D tab with transect plotting functionality

aa924f1

Co-authored-by: Sierd <[email protected]>

Add variable change callback for 1D plot updates

18d1429

Co-authored-by: Sierd <[email protected]>

Fix code review issues: cross-platform paths and dimension validation

68d3b13

Co-authored-by: Sierd <[email protected]>

Improve dimension validation and dictionary access robustness

5ead54f

Co-authored-by: Sierd <[email protected]>

Fix transect direction bug and unify 2D/1D tab interface with dynamic…

74edae0

… variable dropdowns Co-authored-by: Sierd <[email protected]>

bugfixes

74802c1

Sierd requested a review from Copilot November 4, 2025 21:42

Copilot AI reviewed Nov 4, 2025

View reviewed changes

Merge branch 'GUI_development' into copilot/add-plot-output-1d-tab

a5a1a7e

Sierd requested a review from Copilot November 5, 2025 06:09

Copilot AI reviewed Nov 5, 2025

View reviewed changes

added functionality, colorbars, many small fixes.

ed69eec

Sierd requested a review from Copilot November 5, 2025 13:12

Copilot AI reviewed Nov 5, 2025

View reviewed changes

Sierd merged commit 0f33713 into GUI_development Nov 5, 2025
6 checks passed

Sierd deleted the copilot/add-plot-output-1d-tab branch November 5, 2025 13:52

Sierd mentioned this pull request Nov 6, 2025

Gui v0.1 (#261) #262

Merged

	first_var = list(self.nc_data_cache_1d['vars'].values())[0]
	first_var = next(iter(self.nc_data_cache_1d['vars'].values()))

		coord_vars = {'x', 'y', 's', 'n', 'lat', 'lon', 'time', 'layers', 'fractions',
		'x_bounds', 'y_bounds', 'lat_bounds', 'lon_bounds', 'time_bounds', 'crs', 'nv', 'nv2'}

		# Use dict.values() directly instead of next(iter()) for clarity
		first_var = list(var_data_dict.values())[0]

	command=lambda: self.browse_nc_file_1d())
	command=self.browse_nc_file_1d)

	qk = self.output_ax.quiverkey(q, 0.9, 0.95, ref_magnitude,
	self.output_ax.quiverkey(q, 0.9, 0.95, ref_magnitude,

-                    except:
-                        pass
+                    except Exception as e:
+                        # Failed to remove colorbar axes; log and continue
+                        import traceback
+                        print(f"Failed to remove colorbar axes: {e}")
+                        traceback.print_exc()

bugfixes #259

bugfixes #259

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Pull Request Overview

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