0.1.161
This commit is contained in:
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@ -1,7 +1,7 @@
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[metadata]
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# replace with your username:
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name = guan
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version = 0.1.160
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version = 0.1.161
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author = guanjihuan
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author_email = guanjihuan@163.com
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description = An open source python package
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@ -1,6 +1,6 @@
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Metadata-Version: 2.2
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Name: guan
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Version: 0.1.160
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Version: 0.1.161
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Summary: An open source python package
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Home-page: https://py.guanjihuan.com
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Author: guanjihuan
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@ -86,6 +86,116 @@ def run(function_name, *args, **kwargs):
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pass
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return return_data
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# 获取运行的日期和时间并写入文件
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def statistics_with_day_and_time(content='', filename='time_logging', file_format='.txt'):
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import datetime
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datetime_today = str(datetime.date.today())
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datetime_time = datetime.datetime.now().strftime('%H:%M:%S')
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with open(filename+file_format, 'a', encoding="utf-8") as f2:
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if content == '':
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f2.write(datetime_today+' '+datetime_time+'\n')
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else:
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f2.write(datetime_today+' '+datetime_time+' '+content+'\n')
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# 创建一个sh文件用于提交任务（PBS）
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def make_sh_file_for_qsub(sh_filename='a', command_line='python a.py', cpu_num=1, task_name='task', cd_dir=0):
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sh_content = \
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'#!/bin/sh\n' \
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+'#PBS -N '+task_name+'\n' \
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+'#PBS -l nodes=1:ppn='+str(cpu_num)+'\n'
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if cd_dir==1:
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sh_content += 'cd $PBS_O_WORKDIR\n'
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sh_content += command_line
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with open(sh_filename+'.sh', 'w') as f:
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f.write(sh_content)
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# 创建一个sh文件用于提交任务（LSF）
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def make_sh_file_for_bsub(sh_filename='a', command_line='python a.py', cpu_num=1, task_name='task', queue_name='score', cd_dir=0):
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sh_content = \
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'#!/bin/sh\n' \
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+'#BSUB -J '+task_name+'\n' \
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+'#BSUB -q '+queue_name+'\n' \
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+'#BSUB -n '+str(cpu_num)+'\n'
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if cd_dir==1:
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sh_content += 'cd $PBS_O_WORKDIR\n'
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sh_content += command_line
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with open(sh_filename+'.sh', 'w') as f:
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f.write(sh_content)
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# 复制.py和.sh文件，然后提交任务，实现半手动并行（PBS）
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def copy_py_sh_file_and_qsub_task(parameter_array, py_filename='a', old_str_in_py='parameter = 0', new_str_in_py='parameter = ', sh_filename='a', qsub_task_name='task'):
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import os
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parameter_str_array = []
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for i0 in parameter_array:
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parameter_str_array.append(str(i0))
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index = 0
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for parameter_str in parameter_str_array:
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index += 1
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# copy python file
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old_file = py_filename+'.py'
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new_file = py_filename+'_'+str(index)+'.py'
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os.system('cp '+old_file+' '+new_file)
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with open(new_file, 'r') as f:
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content = f.read()
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old_str = old_str_in_py
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new_str = new_str_in_py+parameter_str
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content = content.replace(old_str, new_str)
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with open(py_filename+'_'+str(index)+'.py', 'w') as f:
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f.write(content)
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# copy sh file
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old_file = sh_filename+'.sh'
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new_file = sh_filename+'_'+str(index)+'.sh'
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os.system('cp '+old_file+' '+new_file)
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with open(new_file, 'r') as f:
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content = f.read()
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old_str = 'python '+py_filename+'.py'
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new_str = 'python '+py_filename+'_'+str(index)+'.py'
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content = content.replace(old_str, new_str)
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old_str = '#PBS -N '+qsub_task_name
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new_str = '#PBS -N '+qsub_task_name+'_'+str(index)
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content = content.replace(old_str, new_str)
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with open(sh_filename+'_'+str(index)+'.sh', 'w') as f:
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f.write(content)
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# qsub task
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os.system('qsub '+new_file)
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# 复制.py和.sh文件，然后提交任务，实现半手动并行（LSF）
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def copy_py_sh_file_and_bsub_task(parameter_array, py_filename='a', old_str_in_py='parameter = 0', new_str_in_py='parameter = ', sh_filename='a', bsub_task_name='task'):
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import os
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parameter_str_array = []
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for i0 in parameter_array:
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parameter_str_array.append(str(i0))
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index = 0
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for parameter_str in parameter_str_array:
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index += 1
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# copy python file
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old_file = py_filename+'.py'
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new_file = py_filename+'_'+str(index)+'.py'
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os.system('cp '+old_file+' '+new_file)
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with open(new_file, 'r') as f:
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content = f.read()
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old_str = old_str_in_py
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new_str = new_str_in_py+parameter_str
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content = content.replace(old_str, new_str)
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with open(py_filename+'_'+str(index)+'.py', 'w') as f:
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f.write(content)
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# copy sh file
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old_file = sh_filename+'.sh'
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new_file = sh_filename+'_'+str(index)+'.sh'
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os.system('cp '+old_file+' '+new_file)
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with open(new_file, 'r') as f:
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content = f.read()
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old_str = 'python '+py_filename+'.py'
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new_str = 'python '+py_filename+'_'+str(index)+'.py'
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content = content.replace(old_str, new_str)
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old_str = '#BSUB -J '+bsub_task_name
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new_str = '#BSUB -J '+bsub_task_name+'_'+str(index)
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content = content.replace(old_str, new_str)
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with open(sh_filename+'_'+str(index)+'.sh', 'w') as f:
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f.write(content)
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# bsub task
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os.system('bsub < '+new_file)
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# 获取矩阵的维度（考虑单一数值的矩阵维度为1）
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def dimension_of_array(array):
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import numpy as np
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@ -180,105 +290,6 @@ def preprocess_for_parallel_calculations(parameter_array_all, task_num=1, task_i
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parameter_array = parameter_array_all[task_index*num_parameter:num_all]
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return parameter_array
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# 创建一个sh文件用于提交任务（PBS）
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def make_sh_file_for_qsub(sh_filename='a', command_line='python a.py', cpu_num=1, task_name='task', cd_dir=0):
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sh_content = \
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'#!/bin/sh\n' \
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+'#PBS -N '+task_name+'\n' \
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+'#PBS -l nodes=1:ppn='+str(cpu_num)+'\n'
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if cd_dir==1:
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sh_content += 'cd $PBS_O_WORKDIR\n'
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sh_content += command_line
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with open(sh_filename+'.sh', 'w') as f:
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f.write(sh_content)
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# 创建一个sh文件用于提交任务（LSF）
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def make_sh_file_for_bsub(sh_filename='a', command_line='python a.py', cpu_num=1, task_name='task', queue_name='score', cd_dir=0):
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sh_content = \
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'#!/bin/sh\n' \
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+'#BSUB -J '+task_name+'\n' \
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+'#BSUB -q '+queue_name+'\n' \
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+'#BSUB -n '+str(cpu_num)+'\n'
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if cd_dir==1:
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sh_content += 'cd $PBS_O_WORKDIR\n'
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sh_content += command_line
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with open(sh_filename+'.sh', 'w') as f:
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f.write(sh_content)
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# 复制.py和.sh文件，然后提交任务，实现半手动并行（PBS）
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def copy_py_sh_file_and_qsub_task(parameter_array, py_filename='a', old_str_in_py='parameter=0', new_str_in_py='parameter=', sh_filename='a', qsub_task_name='task'):
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import os
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parameter_str_array = []
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for i0 in parameter_array:
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parameter_str_array.append(str(i0))
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index = 0
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for parameter_str in parameter_str_array:
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index += 1
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# copy python file
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old_file = py_filename+'.py'
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new_file = py_filename+'_'+str(index)+'.py'
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os.system('cp '+old_file+' '+new_file)
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with open(new_file, 'r') as f:
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content = f.read()
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old_str = old_str_in_py
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new_str = new_str_in_py+parameter_str
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content = content.replace(old_str, new_str)
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with open(py_filename+'_'+str(index)+'.py', 'w') as f:
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f.write(content)
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# copy sh file
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old_file = sh_filename+'.sh'
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new_file = sh_filename+'_'+str(index)+'.sh'
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os.system('cp '+old_file+' '+new_file)
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with open(new_file, 'r') as f:
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content = f.read()
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old_str = 'python '+py_filename+'.py'
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new_str = 'python '+py_filename+'_'+str(index)+'.py'
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content = content.replace(old_str, new_str)
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old_str = qsub_task_name
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new_str = qsub_task_name+'_'+str(index)
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content = content.replace(old_str, new_str)
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with open(sh_filename+'_'+str(index)+'.sh', 'w') as f:
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f.write(content)
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# qsub task
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os.system('qsub '+new_file)
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# 复制.py和.sh文件，然后提交任务，实现半手动并行（LSF）
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def copy_py_sh_file_and_bsub_task(parameter_array, py_filename='a', old_str_in_py='parameter=0', new_str_in_py='parameter=', sh_filename='a', bsub_task_name='task'):
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import os
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parameter_str_array = []
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for i0 in parameter_array:
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parameter_str_array.append(str(i0))
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index = 0
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for parameter_str in parameter_str_array:
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index += 1
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# copy python file
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old_file = py_filename+'.py'
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new_file = py_filename+'_'+str(index)+'.py'
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os.system('cp '+old_file+' '+new_file)
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with open(new_file, 'r') as f:
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content = f.read()
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old_str = old_str_in_py
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new_str = new_str_in_py+parameter_str
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content = content.replace(old_str, new_str)
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with open(py_filename+'_'+str(index)+'.py', 'w') as f:
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f.write(content)
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# copy sh file
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old_file = sh_filename+'.sh'
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new_file = sh_filename+'_'+str(index)+'.sh'
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os.system('cp '+old_file+' '+new_file)
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with open(new_file, 'r') as f:
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content = f.read()
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old_str = 'python '+py_filename+'.py'
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new_str = 'python '+py_filename+'_'+str(index)+'.py'
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content = content.replace(old_str, new_str)
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old_str = bsub_task_name
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new_str = bsub_task_name+'_'+str(index)
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content = content.replace(old_str, new_str)
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with open(sh_filename+'_'+str(index)+'.sh', 'w') as f:
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f.write(content)
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# bsub task
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os.system('bsub < '+new_file)
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# 自动先后运行程序
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def run_programs_sequentially(program_files=['./a.py', './b.py'], execute='python ', show_time=0):
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import os
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@ -457,8 +468,8 @@ def combine_two_pdf_files(input_file_1='a.pdf', input_file_2='b.pdf', output_fil
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with open(output_file, 'wb') as combined_file:
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output_pdf.write(combined_file)
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# 将PDF文件转成文本
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def pdf_to_text(pdf_path):
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# 使用pdfminer3k将PDF文件转成文本
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def pdf_to_text_with_pdfminer3k(pdf_path):
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from pdfminer.pdfparser import PDFParser, PDFDocument
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from pdfminer.pdfinterp import PDFResourceManager, PDFPageInterpreter
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from pdfminer.converter import PDFPageAggregator
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@ -488,6 +499,16 @@ def pdf_to_text(pdf_path):
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content = content + x.get_text().strip()
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return content
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# 使用PyPDF2将PDF文件转成文本
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def pdf_to_text_with_PyPDF2_for_all_pages(pdf_path):
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import guan
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num_pages = guan.get_pdf_page_number(pdf_path)
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content = ''
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for i0 in range(num_pages):
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page_text = guan.pdf_to_txt_for_a_specific_page(pdf_path, page_num=i0+1)
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content += page_text + '\n\n'
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return content
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# 获取PDF文件页数
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def get_pdf_page_number(pdf_path):
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import PyPDF2
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@ -576,17 +597,6 @@ def get_time(colon=True):
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datetime_time = datetime_time.replace(':', '')
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return datetime_time
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# 获取运行的日期和时间并写入文件
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def statistics_with_day_and_time(content='', filename='a', file_format='.txt'):
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import datetime
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datetime_today = str(datetime.date.today())
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datetime_time = datetime.datetime.now().strftime('%H:%M:%S')
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with open(filename+file_format, 'a', encoding="utf-8") as f2:
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if content == '':
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f2.write(datetime_today+' '+datetime_time+'\n')
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else:
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f2.write(datetime_today+' '+datetime_time+' '+content+'\n')
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# 获取本月的所有日期
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def get_date_array_of_the_current_month(str_or_datetime='str'):
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import datetime
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@ -31,4 +31,10 @@ def get_days_of_the_month_before_last(str_or_datetime='str'):
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import guan
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print('Warning: The current function name has been deprecated, which will be deleted in the future version. Please change it into guan.get_date_array_of_the_month_before_last().')
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date_array = guan.get_date_array_of_the_month_before_last(str_or_datetime=str_or_datetime)
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return date_array
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return date_array
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def pdf_to_text(pdf_path):
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import guan
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print('Warning: The current function name has been deprecated, which will be deleted in the future version. Please change it into guan.pdf_to_text_with_pdfminer3k().')
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content = guan.pdf_to_text_with_pdfminer3k(pdf_path)
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return content
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@ -25,6 +25,16 @@ def get_max_min_x_y_from_atom_object_list(atom_object_list):
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min_y = min(y_array)
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return max_x, min_x, max_y, min_y
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# 从原子对象列表中获取满足坐标条件的索引
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def get_index_via_coordinate_from_atom_object_list(atom_object_list, x=0, y=0, z=0, eta=1e-3):
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for atom in atom_object_list:
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x_i = atom.x
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y_i = atom.y
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z_i = atom.z
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index = atom.index
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if abs(x-x_i)<eta and abs(y-y_i)<eta and abs(z-z_i)<eta:
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return index
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# 根据原子对象列表来初始化哈密顿量
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def initialize_hamiltonian_from_atom_object_list(atom_object_list):
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import numpy as np
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