Merge pull request #47 from mesoscope/fix/dependencies

Updating dependencies via uv lock --upgrade && uv sync

Author: mogres

.github/dependabot.yml

@@ -0,0 +1,17 @@
+version: 2
+
+updates:
+  - package-ecosystem: "uv"
+    directory: "/"
+
+    schedule:
+      interval: "monthly"
+
+    # Group *all* Python dependency updates into a single PR
+    groups:
+      python-all:
+        patterns:
+          - "*"
+
+    # Ensure Dependabot never opens more than one PR at a time
+    open-pull-requests-limit: 1

cellpack_analysis/lib/distance.py

@@ -512,7 +512,7 @@ def get_ks_test_df(
                 logger.warning(f"Missing distances for {mode}, {cell_id}, skipping KS test")
                 continue
             ks_result = ks_2samp(distances_1, distances_2)
-            ks_stat, p_value = ks_result.statistic, ks_result.pvalue  # type:ignore
+            ks_stat, p_value = ks_result.statistic, ks_result.pvalue  # type: ignore
             record_list.append(
                 {
                     "distance_measure": distance_measure,
@@ -946,7 +946,7 @@ def get_scaled_structure_radius(
             else 1 / PIXEL_SIZE_IN_UM
         )
         scaled_radius_list.append(
-            df_struct_stats.loc[cell_id, "radius"] / normalization_factor  # type:ignore
+            df_struct_stats.loc[cell_id, "radius"] / normalization_factor  # type: ignore
         )
 
     avg_radius = np.mean(scaled_radius_list).item()

cellpack_analysis/lib/occupancy.py

@@ -306,7 +306,7 @@ def get_occupancy_ks_test_df(
             occupancy_1 = occupancy_dict[baseline_mode]["individual"][cell_id]["occupancy"]
             occupancy_2 = occupancy_dict[mode]["individual"][cell_id]["occupancy"]
             ks_result = ks_2samp(occupancy_1, occupancy_2)
-            ks_stat, p_value = ks_result.statistic, ks_result.pvalue  # type:ignore
+            ks_stat, p_value = ks_result.statistic, ks_result.pvalue  # type: ignore
             record_list.append(
                 {
                     "distance_measure": distance_measure,

cellpack_analysis/preprocessing/calculate_available_space.py

@@ -9,6 +9,7 @@
 distances are saved in a grid directory for each cell_id.
 Distances are normalized by the cell diameter and saved in the grid directory.
 """
+
 import argparse
 import logging
 from concurrent.futures import ProcessPoolExecutor, as_completed