offtracker 2.14.0__zip → 2.14.2__zip

{offtracker-2.14.0/offtracker.egg-info → offtracker-2.14.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.14.0
+Version: 2.14.2
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu

{offtracker-2.14.0 → offtracker-2.14.2}/offtracker/_version.py

@@ -1,4 +1,4 @@
-__version__ = "2.14.0"
+__version__ = "2.14.2"
 # 2023.08.11. v1.1.0	adding a option for not normalizing the bw file
 # 2023.10.26. v1.9.0	prerelease for v2.0
 # 2023.10.27. v2.0.0	大更新，还没微调
@@ -46,3 +46,5 @@ __version__ = "2.14.0"
 # 2025.08.09. v2.13.1	测试 correction 功能
 # 2025.08.09. v2.13.2	chromap + trim 参数
 # 2025.10.05. v2.14.0	添加 threads 监控，在 offtracker_config.py 中添加 --cpu_help 选项进入互动模式，推荐 CPU 参数。
+# 2025.10.05. v2.14.1	修正小问题。
+# 2025.10.06. v2.14.2	修正依赖。

{offtracker-2.14.0 → offtracker-2.14.2/offtracker.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: offtracker
-Version: 2.14.0
+Version: 2.14.2
 Summary: Tracking-seq data analysis
 Home-page: https://github.com/Lan-lab/offtracker
 Author: Runda Xu

offtracker-2.14.2/offtracker.egg-info/requires.txt

@@ -0,0 +1,20 @@
+pandas
+polars>=1.19.0
+numpy
+scipy
+matplotlib
+biopython<=1.85
+pybedtools
+pyyaml
+psutil
+os
+sys
+re
+glob
+time
+itertools
+argparse
+multiprocessing
+shutil
+yaml
+math

{offtracker-2.14.0 → offtracker-2.14.2}/scripts/offtracker_config.py

@@ -83,23 +83,35 @@ def main():
     #####################
     import psutil
     if args.cpu_help:
+        # CPU 相关信息
         cpu_count_total = psutil.cpu_count(logical=True)  # 逻辑 CPU 总数（包括超线程）
+        cpu_percent = psutil.cpu_percent(interval=1)  # 1秒内的 CPU 使用率（百分比）
+        cpu_idle_percent = 100 - cpu_percent
+        cpu_available = int(cpu_count_total*cpu_idle_percent/100)
+
+        # 内存相关信息
         memory = psutil.virtual_memory()
+        memory_total = round(memory.total/1024/1024/1024, 2)        # 总内存
         memory_available = round(memory.available/1024/1024/1024, 2)  # 可用内存 GB
-        print('Total available memory:', memory_available, 'GB')
+
+        print('\n')
+        print('Total memory:', memory_total, 'GB')
         print('Total CPU threads:', cpu_count_total)
+        print('Available memory:', memory_available, 'GB')
+        print('Available CPU threads:', cpu_available)
         n_sample = len(sample_names)
         print('Total samples:', n_sample)
+        print('\n')
         # 用户输入分配的最大内存和CPU线程数
-        max_memory_gb = float(input(f"Please input the maximum memory for the program (GB): 25 - {memory_available}"))
-        max_cpu_threads = int(input(f"Please input the maximum CPU threads for the program: 1 - {cpu_count_total}"))
+        max_memory_gb = float(input(rf"Please input the maximum memory for the program (GB): 25 - {memory_available}\n"))
+        max_cpu_threads = int(input(rf"Please input the maximum CPU threads for the program: 1 - {cpu_available}\n"))
         assert (max_memory_gb < memory_available)&(max_memory_gb >= 25), f'max memory must be < available memory ({memory_available} GB) and >= 25 GB, current input: {max_memory_gb} GB'
-        assert (max_cpu_threads <= cpu_count_total)&(max_cpu_threads >= 1), f'max cpu threads must be <= total cpu threads ({cpu_count_total}) and >= 1, current input: {max_cpu_threads}'
+        assert (max_cpu_threads <= cpu_available)&(max_cpu_threads >= 1), f'max CPU threads must be <= available CPU threads ({cpu_available}) and >= 1, current input: {max_cpu_threads}'
         # 计算推荐的 cpu 参数
         max_task = min(int(max(max_memory_gb,30)/30), n_sample)
         max_cpu_per_task = int(max_cpu_threads/max_task)
         total_cpu = max_task*max_cpu_per_task
-
+        print('\n')
         print('Assigning', max_cpu_per_task, f'CPU threads to each task. (i.e., -t {max_cpu_per_task})')
         print('Number of parallel tasks:', max_task)
         print(f'Please specify "--cores {total_cpu}" when formally running snakemake.')

{offtracker-2.14.0 → offtracker-2.14.2}/setup.py

@@ -26,7 +26,8 @@ with open(os.path.join(here, package_folder, '_version.py'),'r',encoding='utf-8'
 
 # requirements
 REQUIRED = [
-   'pandas', 'polars>=1.19.0', 'numpy', 'biopython<=1.85', 'pybedtools', 'pyyaml', 'psutil'
+   'pandas', 'polars>=1.19.0', 'numpy', 'scipy', 'matplotlib', 'biopython<=1.85', 'pybedtools', 'pyyaml', 'psutil',
+   'os','sys','re', 'glob', 'time','itertools','argparse', 'multiprocessing', 'shutil', 'yaml', 'math'
 ]
 ## pybedtools may be not supported in Windows
 

offtracker-2.14.0/offtracker.egg-info/requires.txt

@@ -1,7 +0,0 @@
-pandas
-polars>=1.19.0
-numpy
-biopython<=1.85
-pybedtools
-pyyaml
-psutil