chore: apply CodeRabbit quick fixes

.github/workflows/ci-auto-fix.yml

@@ -0,0 +1,83 @@
+name: CI Auto-Fix
+
+on:
+  workflow_run:
+    workflows: ["CI"]
+    types: [completed]
+
+jobs:
+  auto_fix:
+    if: github.event.workflow_run.conclusion == 'failure'
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+
+      - name: Install dev deps
+        run: python -m pip install -e '.[dev]'
+
+      - name: Run ruff and black auto-fixes
+        run: |
+          set -e
+          ruff format --quiet --fix . || true
+          black --quiet . || true
+
+      - name: Check for formatting changes
+        id: git-check
+        run: |
+          git config user.name "GitHub Actions"
+          git config user.email "actions@github.com"
+          if [ -n "$(git status --porcelain)" ]; then echo "changed=true" >> $GITHUB_OUTPUT; else echo "changed=false" >> $GITHUB_OUTPUT; fi
+
+      - name: Create branch and PR for formatting fixes
+        if: steps.git-check.outputs.changed == 'true'
+        env:
+          BRANCH_NAME: auto/ci-fix/format-${{ github.run_id }}
+        run: |
+          git checkout -b "$BRANCH_NAME"
+          git add -A
+          git commit -m "style: apply ruff/black fixes from CI auto-fix"
+          git push origin "$BRANCH_NAME"
+          # Ensure auto-fix label exists then create PR and enable auto-merge so formatting fixes are merged automatically when checks pass
+          gh label create "auto-fix" --color ffcc00 --description "Automated formatting fixes from CI" || true
+          gh pr create --title "style: apply ruff/black fixes (auto)" --body "Automated formatting fixes (ruff/black) applied by CI Auto-Fix workflow. This PR will be auto-merged when checks pass." --base main --head "$BRANCH_NAME" --label "auto-fix" --auto || true
+
+      - name: Run tests to check if fixes pass
+        run: python -m pytest -q || true
+
+      - name: Create PR on other failures (diagnostic)
+        if: steps.git-check.outputs.changed == 'false'
+        run: |
+          echo "Opening PR for CI failure diagnostics"
+          BRANCH=auto/ci-fix/failure-${{ github.run_id }}
+          git checkout -b "$BRANCH"
+          # Add a short diagnostic file for human triage
+          echo "CI failure triggered by workflow_run id: ${{ github.event.workflow_run.id }}" > CI_FAILURE.md
+          git add CI_FAILURE.md
+          git commit -m "ci: record CI failure for diagnostics"
+          git push origin "$BRANCH"
+          # Ensure ci-fail label exists and create a non-draft PR for triage
+          gh label create "ci-fail" --color ee0000 --description "CI failure requires human triage" || true
+          gh pr create --title "ci: investigate failing CI run #${{ github.event.workflow_run.id }}" --body "PR created automatically to investigate CI failure (workflow_run id: ${{ github.event.workflow_run.id }}). Please see workflow run logs for details." --base main --head "$BRANCH" --label "ci-fail" --web || true
+
+      - name: Comment on original run
+        uses: actions/github-script@v7
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            const runId = context.payload.workflow_run.id
+            const owner = context.repo.owner
+            const repo = context.repo.repo
+            await github.rest.actions.createWorkflowRunComment({
+              owner, repo, run_id: runId, body: 'CI Auto-Fix ran: formatting fixes applied or diagnostic PR created.'
+            })

app/config.py

@@ -155,7 +155,7 @@ class ValidationConfig:
     def __post_init__(self):
         """Initialize validation sets."""
         if self.valid_group_types is None:
-            self.valid_group_types = {0, 1, 2, 3}
+            self.valid_group_types = frozenset({0, 1, 2, 3})
 
 
 @dataclass

app/logger.py

@@ -31,16 +31,9 @@
         file_handler.setLevel(logging.DEBUG)
         file_handler.setFormatter(formatter)
         logger.addHandler(file_handler)
-    except Exception:
-        # If can't create logs directory, just use console
-        pass
-
-
-def get_logger(name: str = None):
-    """Get a logger instance.
-
-    Parameters
-    ----------
+    except OSError as e:
+        # If can't create logs directory, log a warning and continue using console
+        logger.warning(f"Could not create log directory '{log_dir}': {e!s}")
     name : str, optional
         Logger name (typically __name__). If None, returns root app logger.
 

app/pages/ecopath.py

@@ -732,7 +732,7 @@ def _handle_model_params_edit():
                         duration=5
                     )
 
-            except (ValueError, TypeError) as e:
+            except (ValueError, TypeError):
                 ui.notification_show(
                     f"Invalid numeric value for {col_name}: '{new_value}'",
                     type="error",
@@ -785,7 +785,7 @@ def _handle_diet_matrix_edit():
                     duration=2
                 )
 
-            except (ValueError, TypeError) as e:
+            except (ValueError, TypeError):
                 ui.notification_show(
                     f"Invalid numeric value for diet: '{new_value}'",
                     type="error",
@@ -952,9 +952,10 @@ def model_results_table():
 
         # Add special styling for calculated columns (EE, GE, TL)
         calculated_cols = ['EE', 'GE', 'TL']
+        col_positions = {c: i for i, c in enumerate(formatted_df.columns)}
         for col in calculated_cols:
             if col in formatted_df.columns:
-                col_idx = list(formatted_df.columns).index(col)
+                col_idx = col_positions[col]
                 for row_idx in range(len(formatted_df)):
                     is_no_data = bool(no_data_mask.iloc[row_idx][col]) if col in no_data_mask.columns else False
                     is_stanza = bool(stanza_mask.iloc[row_idx][col]) if (stanza_mask is not None and col in stanza_mask.columns) else False

app/pages/ecospace.py

@@ -234,7 +234,7 @@ def create_hexagon(center_x: float, center_y: float, radius: float) -> "Polygon"
     angles = np.linspace(0, 2 * np.pi, 7) + np.pi / 6  # Rotate by 30 degrees
     x_coords = center_x + radius * np.cos(angles)
     y_coords = center_y + radius * np.sin(angles)
-    return Polygon(zip(x_coords, y_coords))
+    return Polygon(zip(x_coords, y_coords, strict=True))
 
 
 def ecospace_ui():
@@ -578,14 +578,14 @@ def ecospace_ui():
     )
 
 
-def ecospace_server(input: Inputs, output: Outputs, session: Session, model_data: reactive.Value, sim_results: reactive.Value):
+def ecospace_server(input: Inputs, _output: Outputs, _session: Session, _model_data: reactive.Value, _sim_results: reactive.Value):
     """Server logic for ECOSPACE page."""
 
     # Reactive values for spatial state
     grid = reactive.Value(None)
     boundary_polygon = reactive.Value(None)  # Store uploaded boundary for visualization
-    ecospace_params = reactive.Value(None)
-    spatial_results = reactive.Value(None)
+    ecospace_params = reactive.Value(None)  # TODO: reserved for future use  # noqa: F841
+    spatial_results = reactive.Value(None)  # TODO: reserved for future use  # noqa: F841
 
     # Load and display boundary polygon immediately on file upload
     @reactive.effect
@@ -655,9 +655,9 @@ def load_boundary_on_upload():
                 # Clean up temporary directory
                 shutil.rmtree(temp_dir, ignore_errors=True)
 
-        except Exception as e:
+        except (ValueError, IOError, OSError, zipfile.BadZipFile) as e:
             ui.notification_show(
-                f"Error loading boundary: {str(e)}",
+                f"Error loading boundary: {e!s}",
                 type="warning",
                 duration=5
             )
@@ -838,9 +838,9 @@ def create_spatial_grid():
                         # Clean up temporary directory
                         shutil.rmtree(temp_dir, ignore_errors=True)
 
-                except Exception as e:
+                except (ValueError, IOError, OSError, zipfile.BadZipFile) as e:
                     ui.notification_show(
-                        f"Error processing spatial file: {str(e)}",
+                        f"Error processing spatial file: {e!s}",
                         type="error",
                         duration=6
                     )
@@ -849,9 +849,9 @@ def create_spatial_grid():
             # Enable run button
             ui.update_action_button("run_spatial_sim", disabled=False)
 
-        except Exception as e:
+        except (ValueError, OSError) as e:
             ui.notification_show(
-                f"Error creating grid: {str(e)}",
+                f"Error creating grid: {e!s}",
                 type="error",
                 duration=5
             )
@@ -929,7 +929,7 @@ def grid_plot():
             folium.GeoJson(
                 boundary_geojson,
                 name='Boundary',
-                style_function=lambda x: {
+                style_function=lambda _x: {
                     'fillColor': 'red',
                     'color': 'red',
                     'weight': 2.5,
@@ -971,7 +971,7 @@ def grid_plot():
                     folium.GeoJson(
                         geojson_data,
                         name='Grid Patches',
-                        style_function=lambda x: {
+                        style_function=lambda _x: {
                             'fillColor': 'lightblue',
                             'color': 'steelblue',
                             'weight': 0.5,  # Thinner lines for large grids
@@ -1003,7 +1003,7 @@ def grid_plot():
                             # Add polygon to map
                             folium.GeoJson(
                                 geojson_data,
-                                style_function=lambda x: {
+                                style_function=lambda _x: {
                                     'fillColor': 'lightblue',
                                     'color': 'steelblue',
                                     'weight': 1.5,
@@ -1284,7 +1284,7 @@ def habitat_plot():
                     x, y = geom.exterior.xy
                     color = cmap(norm(habitat[idx]))
                     polygon = MplPolygon(
-                        list(zip(x, y)),
+                        list(zip(x, y, strict=True)),
                         facecolor=color,
                         edgecolor='darkgreen',
                         linewidth=1.2,

src/pypath/analysis/prebalance.py

@@ -46,7 +46,7 @@ def _calculate_trophic_levels(model: RpathParams) -> pd.Series:
     # Iteratively calculate TL for consumers
     # TL = 1 + weighted average of prey TLs
     max_iterations = 50
-    for iteration in range(max_iterations):
+    for _iteration in range(max_iterations):
         tl_old = tl.copy()
 
         for i, group in enumerate(groups):
@@ -313,7 +313,7 @@ def plot_biomass_vs_trophic_level(
 
     # Add group labels (sample if too many)
     if len(df) <= 30:
-        for idx, row in df.iterrows():
+        for _idx, row in df.iterrows():
             ax.annotate(
                 row['Group'],
                 (row['TL'], row['Biomass']),
@@ -379,7 +379,7 @@ def plot_vital_rate_vs_trophic_level(
 
     # Add labels for interesting points
     if len(df) <= 20:
-        for idx, row in df.iterrows():
+        for _idx, row in df.iterrows():
             ax.annotate(
                 row['Group'],
                 (row['TL'], row[rate_name]),