cytocommunity2 0.1.2__tar.gz → 0.1.3__tar.gz

{cytocommunity2-0.1.2/src/cytocommunity2.egg-info → cytocommunity2-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cytocommunity2
-Version: 0.1.2
+Version: 0.1.3
 Summary: Weakly supervised cellular-neighborhood learning for spatial omics
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
@@ -81,7 +81,6 @@ conda create -n cytocommunity2 python=3.10
 conda activate cytocommunity2
 ```
 
-Install PyTorch for your compute platform before installing CytoCommunity2.
 For an NVIDIA GPU on Windows or Linux, first install the appropriate
 CUDA-enabled PyTorch build from the
 [official PyTorch installation page](https://pytorch.org/get-started/locally/).

{cytocommunity2-0.1.2 → cytocommunity2-0.1.3}/README.md

@@ -60,7 +60,6 @@ conda create -n cytocommunity2 python=3.10
 conda activate cytocommunity2
 ```
 
-Install PyTorch for your compute platform before installing CytoCommunity2.
 For an NVIDIA GPU on Windows or Linux, first install the appropriate
 CUDA-enabled PyTorch build from the
 [official PyTorch installation page](https://pytorch.org/get-started/locally/).

{cytocommunity2-0.1.2 → cytocommunity2-0.1.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cytocommunity2"
-version = "0.1.2"
+version = "0.1.3"
 description = "Weakly supervised cellular-neighborhood learning for spatial omics"
 readme = "README.md"
 requires-python = ">=3.10"

{cytocommunity2-0.1.2 → cytocommunity2-0.1.3}/src/cytocommunity2/downstream/plotting/recurrence.py

@@ -62,7 +62,7 @@ def plot_recurrence_results(config):
     output_dir.mkdir(parents=True, exist_ok=True)
     real = pd.read_csv(overlap_dir / "RealDistribution_sameCN.csv")
     background = pd.read_csv(overlap_dir / "BackgroundDistribution_randomCN.csv")
-    tests = pd.read_csv(overlap_dir / "KSTest_Results.csv")
+    tests = pd.read_csv(overlap_dir / "TTest_Results.csv")
     real["CN"] = real["CN"].astype(str).str.strip()
     real["OverlapCoefficient"] = pd.to_numeric(real["OverlapCoefficient"], errors="coerce")
     background["OverlapCoefficient"] = pd.to_numeric(

{cytocommunity2-0.1.2 → cytocommunity2-0.1.3}/src/cytocommunity2/learning/api.py

@@ -7,8 +7,9 @@ import shutil
 
 import pandas as pd
 
-from ..config import CytoCommunityConfig
-from ..ensemble import ensemble_cn
+from ..config import CytoCommunityConfig
+from ..ensemble import ensemble_cn
+from ..paths import build_paths
 from .dataset import SpatialGraphDataset
 from .model import TrainingConfig
 from .selection import evaluate_cn_num, select_cn_num
@@ -33,11 +34,9 @@ class LearningResult:
 def load_learning_result(
     dataset: SpatialGraphDataset,
     config: CytoCommunityConfig,
-    *,
-    output_dir,
 ) -> LearningResult:
     """Restore a :class:`LearningResult` from a completed learning run."""
-    output_dir = Path(output_dir).expanduser().resolve()
+    output_dir = build_paths(config).learning_output
     paths = {
         "selected CN number": output_dir / "SelectedCNNum.txt",
         "cell-type list": output_dir / "UniqueCellTypeList.txt",
@@ -86,13 +85,11 @@ def _training_config(config, num_cn, num_class):
 
 
 def run_learning(
-    dataset: SpatialGraphDataset,
-    config: CytoCommunityConfig,
-    *,
-    output_dir,
+    dataset: SpatialGraphDataset,
+    config: CytoCommunityConfig,
 ) -> LearningResult:
     """Select the CN number, train final runs, and export consensus labels."""
-    output_dir = Path(output_dir).expanduser().resolve()
+    output_dir = build_paths(config).learning_output
     input_dir = config.input_dir
     unique_celltypes_file = output_dir / "UniqueCellTypeList.txt"
     selected_model_dir = output_dir / "SelectedModel"

{cytocommunity2-0.1.2 → cytocommunity2-0.1.3}/src/cytocommunity2/learning/dataset.py

@@ -5,9 +5,11 @@ from pathlib import Path
 import numpy as np
 from scipy.sparse import csr_matrix
 from sklearn.neighbors import NearestNeighbors
-import torch
-from torch_geometric.data import Data
-
+import torch
+from torch_geometric.data import Data
+
+from ..config import CytoCommunityConfig
+
 
 class SpatialGraphDataset(torch.utils.data.Dataset):
     """In-memory collection of real spatial graphs."""
@@ -64,9 +66,9 @@ def _build_knn_edge_index(coordinates, knn_k):
     ).contiguous()
 
 
-def build_spatial_graphs(input_dir, *, knn_k):
-    """Read real samples and construct their coordinate-based KNN graphs once."""
-    input_folder = Path(input_dir)
+def build_spatial_graphs(config: CytoCommunityConfig):
+    """Build spatial graphs from the input folder associated with ``config``."""
+    input_folder = config.input_dir
     sample_names = _read_lines(input_folder / "ImageNameList.txt")
     labels_by_sample = {
         sample: _read_lines(input_folder / f"{sample}_CellTypeLabel.txt")
@@ -125,7 +127,7 @@ def build_spatial_graphs(input_dir, *, knn_k):
         data_list.append(Data(
             x=x,
             y=torch.tensor([training_label], dtype=torch.long),
-            edge_index=_build_knn_edge_index(coordinates, knn_k),
+            edge_index=_build_knn_edge_index(coordinates, config.main.knn_k),
         ))
 
     return SpatialGraphDataset(

{cytocommunity2-0.1.2 → cytocommunity2-0.1.3}/src/cytocommunity2/learning/selection.py

@@ -5,8 +5,10 @@ from pathlib import Path
 
 import numpy as np
 import pandas as pd
-from scipy.stats import hypergeom, ttest_ind
-
+from scipy.stats import hypergeom, ttest_ind
+
+from ..paths import build_paths
+
 
 MIN_FLOAT_P = np.finfo(np.float64).tiny
 
@@ -419,7 +421,30 @@ def evaluate_cn_num(
     return result, per_cn.copy()
 
 
-def select_cn_num(results):
+def evaluate_selected_cn(result, config):
+    """Evaluate the selected model using the configured project layout."""
+    paths = build_paths(config)
+    metrics, recurrence = evaluate_cn_num(
+        num_cn=result.selected_cn,
+        dataset=result.input_dir,
+        cn_label_dir=result.hard_assignment_dir,
+        celltype_file=result.unique_celltypes_file,
+        output_dir=paths.downstream_data,
+        enrichment_p_threshold=config.enrichment.p_value_threshold,
+        minimum_adjusted_p=config.enrichment.minimum_adjusted_p,
+        recurrence_p_threshold=config.recurrence.recurrence_p_threshold,
+        n_random=config.recurrence.null_draws,
+        seed=config.random_seed,
+    )
+    export_enrichment_long(
+        dataset=result.input_dir,
+        enrichment_dir=paths.enrichment,
+        output_file=paths.communication_config / "EnrichScoreMatrix_long.csv",
+    )
+    return metrics, recurrence
+
+
+def select_cn_num(results):
     """Select maximum score, using smaller K as the deterministic tie-break."""
     if not results:
         raise ValueError("No CN-number results were supplied")

{cytocommunity2-0.1.2 → cytocommunity2-0.1.3/src/cytocommunity2.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cytocommunity2
-Version: 0.1.2
+Version: 0.1.3
 Summary: Weakly supervised cellular-neighborhood learning for spatial omics
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
@@ -81,7 +81,6 @@ conda create -n cytocommunity2 python=3.10
 conda activate cytocommunity2
 ```
 
-Install PyTorch for your compute platform before installing CytoCommunity2.
 For an NVIDIA GPU on Windows or Linux, first install the appropriate
 CUDA-enabled PyTorch build from the
 [official PyTorch installation page](https://pytorch.org/get-started/locally/).