cytocommunity2 0.1.7__tar.gz → 0.1.8__tar.gz

{cytocommunity2-0.1.7/src/cytocommunity2.egg-info → cytocommunity2-0.1.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cytocommunity2
-Version: 0.1.7
+Version: 0.1.8
 Summary: Weakly supervised cellular-neighborhood learning for spatial omics
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown

{cytocommunity2-0.1.7 → cytocommunity2-0.1.8}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cytocommunity2"
-version = "0.1.7"
+version = "0.1.8"
 description = "Weakly supervised cellular-neighborhood learning for spatial omics"
 readme = "README.md"
 requires-python = ">=3.10"

{cytocommunity2-0.1.7 → cytocommunity2-0.1.8}/src/cytocommunity2/__init__.py

@@ -10,7 +10,7 @@ from .learning import (
 )
 from .visualization import visualize_results
 
-__version__ = "0.1.7"
+__version__ = "0.1.8"
 
 __all__ = [
     "CytoCommunityConfig",

{cytocommunity2-0.1.7 → cytocommunity2-0.1.8}/src/cytocommunity2/config.py

@@ -29,6 +29,7 @@ FIXED_DOWNSTREAM = {
         "cca_minimum_abs_rho": 0.0,
         "cca_sd_epsilon": 1e-8,
         "cca_max_iterations": 1000,
+        "cca_canonical_components": 2,
     },
 }
 

{cytocommunity2-0.1.7 → cytocommunity2-0.1.8}/src/cytocommunity2/downstream/communication/cca.py

@@ -107,7 +107,7 @@ def run_cca_for_scores(
             extreme = 0
             valid_count = 0
             invalid_count = 0
-            for _ in range(communication_params["cca_n_bootstrap"]):
+            for _ in range(communication_params["cca_n_permutations"]):
                 shuffled_y = rng.permutation(y_matrix)
                 permutation_model = CCA(
                     n_components=min(

{cytocommunity2-0.1.7 → cytocommunity2-0.1.8}/src/cytocommunity2/downstream/communication/within.py

@@ -245,7 +245,7 @@ def run_within_cn_analysis(config, *, input_file=None, output_dir=None):
             cn_order=cn_order,
             celltype_order=celltype_order,
             min_samples=params["minimum_samples"],
-            n_permutations=params["n_permutations"],
+            n_permutations=params["within_cn_n_permutations"],
             max_attempt_multiplier=params["permutation_max_attempt_multiplier"],
             base_seed=config.random_seed,
         )

{cytocommunity2-0.1.7 → cytocommunity2-0.1.8}/src/cytocommunity2/downstream/moran.py

@@ -56,9 +56,7 @@ def build_distance_weights(coordinates, distance_threshold):
     return weights
 
 
-def calculate_celltype_moran(
-    cell_type_series, weights, minimum_positive_count, permutations
-):
+def calculate_celltype_moran(cell_type_series, weights, minimum_positive_count):
     """Calculate Moran's I for every eligible cell type in one CN."""
     try:
         from esda.moran import Moran
@@ -75,7 +73,7 @@ def calculate_celltype_moran(
         positive_count = int(indicator.sum())
         if positive_count < minimum_positive_count or positive_count == n_cells:
             continue
-        moran = Moran(indicator, weights, permutations=permutations)
+        moran = Moran(indicator, weights, permutations=0)
         rows.append(
             {
                 "CellType": cell_type,
@@ -116,12 +114,11 @@ def calculate_sample_moran_frame(
         )
         if weights.sparse.nnz == 0:
             continue
-        for result in calculate_celltype_moran(
-            cn_frame["Cell_Type"],
-            weights,
-            moran_params["minimum_positive_count"],
-            moran_params["permutations"],
-        ):
+        for result in calculate_celltype_moran(
+            cn_frame["Cell_Type"],
+            weights,
+            moran_params["minimum_positive_count"],
+        ):
             rows.append(
                 {
                     "Sample": str(sample_name),

{cytocommunity2-0.1.7 → cytocommunity2-0.1.8/src/cytocommunity2.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cytocommunity2
-Version: 0.1.7
+Version: 0.1.8
 Summary: Weakly supervised cellular-neighborhood learning for spatial omics
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown