sciv 0.0.101__tar.gz → 0.0.102__tar.gz

{sciv-0.0.101 → sciv-0.0.102}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sciv
-Version: 0.0.101
+Version: 0.0.102
 Summary: Unveiling the pivotal cell types involved in variant function regulation at a single-cell resolution
 Project-URL: github, https://github.com/YuZhengM/sciv
 Author-email: Zheng-Min Yu <yuzmbio@163.com>
@@ -48,6 +48,7 @@ Requires-Dist: numba==0.60.0
 Requires-Dist: numpy==1.26.4
 Requires-Dist: palettable==3.3.3
 Requires-Dist: pandas==1.5.3
+Requires-Dist: psutil==7.2.1
 Requires-Dist: pycomplexheatmap==1.6.1
 Requires-Dist: pynndescent==0.5.13
 Requires-Dist: scanpy==1.11.5

{sciv-0.0.101 → sciv-0.0.102}/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 [project]
 name = "sciv"
-version = "0.0.101"
+version = "0.0.102"
 authors = [
     { name = "Zheng-Min Yu", email = "yuzmbio@163.com" },
 ]
@@ -48,7 +48,8 @@ dependencies = [
     "louvain==0.8.2",
     "numba==0.60.0",
     "pynndescent==0.5.13",
-    "fa2-modified==0.4"
+    "fa2-modified==0.4",
+    "psutil==7.2.1"
 ]
 classifiers = [
     "Programming Language :: Python :: 3",

{sciv-0.0.101 → sciv-0.0.102}/requirements.txt

@@ -28,4 +28,5 @@ louvain==0.8.2
 snapatac2==2.7.1
 numba==0.60.0
 pynndescent==0.5.13
-fa2-modified==0.4
+fa2-modified==0.4
+psutil==7.2.1

{sciv-0.0.101 → sciv-0.0.102}/src/sciv/model/_core_.py

@@ -21,7 +21,7 @@ __name__: str = "model_core"
 
 
 def _run_random_walk_(random_walk: RandomWalk, is_ablation: bool, is_simple: bool) -> AnnData:
-    start_time = time.time()
+    start_time = time.perf_counter()
 
     if not random_walk.is_run_core:
         random_walk.run_core()
@@ -57,7 +57,7 @@ def _run_random_walk_(random_walk: RandomWalk, is_ablation: bool, is_simple: boo
         if not random_walk.is_run_en_ablation_m_knn:
             random_walk.run_en_ablation_m_knn()
 
-    random_walk.elapsed_time += time.time() - start_time
+    random_walk.elapsed_time += time.perf_counter() - start_time
 
     return random_walk.trs_adata
 
@@ -181,7 +181,7 @@ def core(
     """
 
     # start time
-    start_time = time.time()
+    start_time = time.perf_counter()
 
     if len(variants.keys()) == 0:
         ul.log(__name__).error("The number of mutations is empty.")
@@ -591,7 +591,7 @@ def core(
     random_walk_time = random_walk.elapsed_time
 
     # end time
-    elapsed_time = time.time() - start_time
+    elapsed_time = time.perf_counter() - start_time
     step_time = poisson_vi_time + overlap_time + init_score_time + smknn_time + random_walk_time
 
     if elapsed_time < step_time:

{sciv-0.0.101 → sciv-0.0.102}/src/sciv/plot/_pie_.py

@@ -115,6 +115,7 @@ def pie_label(
         startangle=90,
         labeldistance=label_distance,
         pctdistance=pct_distance,
+        wedgeprops=dict(linewidth=0),
         **kwargs
     )
     ax.pie(
@@ -122,7 +123,7 @@ def pie_label(
         colors=['white'],
         radius=radius,
         startangle=90,
-        wedgeprops=dict(width=radius, edgecolor='w'),
+        wedgeprops=dict(width=radius, edgecolor='w', linewidth=0),
         **kwargs
     )
     ax.text(0, 0, "{:.2f}%".format(top_x[0] / top_sum * 100), ha='center', va='center', fontsize=fontsize)

{sciv-0.0.101 → sciv-0.0.102}/src/sciv/preprocessing/_scanpy_.py

@@ -1,4 +1,5 @@
 # -*- coding: UTF-8 -*-
+
 import time
 import warnings
 from typing import Optional, Literal
@@ -47,7 +48,7 @@ def filter_data(
     """
 
     # start time
-    start_time = time.time()
+    start_time = time.perf_counter()
 
     import scanpy as sc
 
@@ -109,7 +110,7 @@ def filter_data(
     )
     ul.log(__name__).info(f"Size of filtered scATAC-seq data: {filter_adata.shape}")
     filter_adata.uns["step"] = 0
-    filter_adata.uns["elapsed_time"] = time.time() - start_time
+    filter_adata.uns["elapsed_time"] = time.perf_counter() - start_time
 
     return filter_adata
 

{sciv-0.0.101 → sciv-0.0.102}/src/sciv/preprocessing/_scvi_.py

@@ -50,7 +50,7 @@ def poisson_vi(
     """
     ul.log(__name__).info("Start PoissonVI")
 
-    start_time = time.time()
+    start_time = time.perf_counter()
 
     import scvi
     import scanpy as sc
@@ -241,7 +241,7 @@ def poisson_vi(
     da_peaks_adata.layers["emp_prob1"] = matrix_ep1
     da_peaks_adata.uns["latent_name"] = latent_name
     da_peaks_adata.uns["dp_delta"] = dp_delta
-    da_peaks_adata.uns["elapsed_time"] = time.time() - start_time
+    da_peaks_adata.uns["elapsed_time"] = time.perf_counter() - start_time
 
     adata.uns["step"] = 1
 

{sciv-0.0.101 → sciv-0.0.102}/src/sciv/tool/_algorithm_.py

@@ -913,7 +913,7 @@ def overlap_sum(regions: AnnData, variants: dict, trait_info: DataFrame, n_jobs:
     :return: overlap data
     """
 
-    start_time = time.time()
+    start_time = time.perf_counter()
 
     # Unique feature set
     label_all = regions.var.index.tolist()
@@ -1025,7 +1025,7 @@ def overlap_sum(regions: AnnData, variants: dict, trait_info: DataFrame, n_jobs:
 
     overlap_adata = AnnData(overlap_sparse, var=trait_info, obs=regions.var)
     overlap_adata.uns["is_overlap"] = True
-    overlap_adata.uns["elapsed_time"] = time.time() - start_time
+    overlap_adata.uns["elapsed_time"] = time.perf_counter() - start_time
 
     return overlap_adata
 
@@ -1129,7 +1129,7 @@ def calculate_init_score_weight(
     :return: Initial TRS with weight.
     """
 
-    start_time = time.time()
+    start_time = time.perf_counter()
 
     if "is_overlap" not in overlap_adata.uns:
         ul.log(__name__).warning(
@@ -1258,7 +1258,7 @@ def calculate_init_score_weight(
     del _init_trs_ncw_, _cell_type_weight_
 
     init_trs_adata.uns["is_sample"] = is_simple
-    init_trs_adata.uns["elapsed_time"] = time.time() - start_time
+    init_trs_adata.uns["elapsed_time"] = time.perf_counter() - start_time
     return init_trs_adata
 
 
@@ -1314,7 +1314,7 @@ def obtain_cell_cell_network(
     :return: Cell similarity data.
     """
 
-    start_time = time.time()
+    start_time = time.perf_counter()
 
     from sklearn.metrics.pairwise import laplacian_kernel, rbf_kernel
 
@@ -1373,7 +1373,7 @@ def obtain_cell_cell_network(
     if not is_simple:
         cc_data.layers["cell_mutual_knn"] = to_sparse(cell_mutual_knn)
 
-    cc_data.uns["elapsed_time"] = time.time() - start_time
+    cc_data.uns["elapsed_time"] = time.perf_counter() - start_time
 
     return cc_data
 

{sciv-0.0.101 → sciv-0.0.102}/src/sciv/tool/_random_walk_.py

@@ -282,7 +282,7 @@ class RandomWalk:
         """
         ul.log(__name__).info("Random walk with weighted seed cells.")
 
-        start_time = time.time()
+        start_time = time.perf_counter()
 
         # judge length
         if cc_adata.shape[0] != init_status.shape[0]:
@@ -459,7 +459,7 @@ class RandomWalk:
         del self.cell_affinity
         del init_status
 
-        self.elapsed_time = time.time() - start_time
+        self.elapsed_time = time.perf_counter() - start_time
 
     def _random_walk_(
         self,

{sciv-0.0.101 → sciv-0.0.102}/src/sciv/util/__init__.py

@@ -29,6 +29,7 @@ from ._constant_ import (
 from ._core_ import (
     file_method,
     log,
+    track_with_memory,
     to_dense,
     to_sparse,
     sum_min_max,
@@ -58,6 +59,7 @@ __all__ = [
     "log_file_path",
     "file_method",
     "log",
+    "track_with_memory",
     "path",
     "plot_color_types",
     "sparse_array",

{sciv-0.0.101 → sciv-0.0.102}/src/sciv/util/_core_.py

@@ -4,7 +4,11 @@ import math
 import os
 import random
 import string
-from typing import Tuple, Union, Literal
+import threading
+import time
+from functools import wraps
+from typing import Tuple, Union, Literal, Callable, Any
+import psutil
 
 import numpy as np
 import pandas as pd
@@ -35,6 +39,71 @@ def log(name: str = None) -> Logger:
     return Logger(name, log_path=os.path.join(ul.log_file_path, name), is_form_file=ul.is_form_log_file)
 
 
+def track_with_memory(is_monitor: bool = False , interval: float = 60) -> Callable:
+    """
+    Decorator: Records memory usage at fixed intervals during function execution and returns the result, elapsed time, and memory list.
+
+    Parameters
+    ----------
+    is_monitor : bool, optional
+        Whether to enable memory monitoring, default is False.
+    interval : float, optional
+        Sampling interval (seconds), default is 60 seconds.
+
+    Returns
+    -------
+    Callable
+        Decorator function; when the wrapped function is called, it returns a dictionary containing:
+        - 'result': the original function's return value
+        - 'time': function execution time (seconds) if is_monitor is True, otherwise None.
+        - 'memory': list of sampled memory usage (bytes) if is_monitor is True, otherwise None.
+    """
+
+    def decorator(func) -> Callable:
+        @wraps(func)
+        def wrapper(*args, **kwargs) -> Union[Any, dict]:
+
+            if not is_monitor:
+                return func(*args, **kwargs)
+
+            process = psutil.Process(os.getpid())
+
+            stop_monitor = False
+
+            mem_list = []
+
+            def monitor():
+                nonlocal stop_monitor
+
+                while not stop_monitor:
+                    current_mem = process.memory_info().rss
+                    mem_list.append(current_mem)
+
+                    time.sleep(interval)
+
+            t = threading.Thread(target=monitor, daemon=True)
+            t.start()
+
+            start_time = time.perf_counter()
+            _result_ = func(*args, **kwargs)
+            end_time = time.perf_counter()
+
+            stop_monitor = True
+            t.join()
+
+            exec_time = end_time - start_time
+
+            return {
+                'result': _result_,
+                'time': exec_time,
+                'memory': mem_list
+            }
+
+        return wrapper
+
+    return decorator
+
+
 def to_dense(sm: matrix_data, is_array: bool = False) -> dense_data:
     """
     Convert sparse matrix to dense matrix