def string_to_tuple(s):
q = s.split(',')
if is_number(q[0]):
q = np.array([float(t) for t in q])
q_type = 'TUPLE_FLOAT'
return q, q_type
if q[0] == 'T' or q[0] == 'F':
q = np.array([bool(t=='T') for t in q])
q_type = 'TUPLE_BOOL'
return q, q_type
if type(q[0]) == type('string'):
q = [t.replace('"','').replace("'", '') for t in q]
q_type = 'TUPLE_STRING'
return q, q_type
print('! ERROR: Could not parse string '+s+' into a tuple!')
print('! DEBUG_BREAKPOINT AKTIVATED - check out the following variables: string s, tuple q, first entry in tuple q[0]')
debug_breakpoint(); return None, None
def string_to_tuple(s):
q = s.split(',')
if is_number(q[0]):
q = np.array([float(t) for t in q])
q_type = 'TUPLE_FLOAT'
return q, q_type
if q[0] == 'T' or q[0] == 'F':
q = np.array([bool(t=='T') for t in q])
q_type = 'TUPLE_BOOL'
return q, q_type
if type(q[0]) == type('string'):
q = [t.replace('"','').replace("'", '') for t in q]
q_type = 'TUPLE_STRING'
return q, q_type
print('! ERROR: Could not parse string '+s+' into a tuple!')
print('! DEBUG_BREAKPOINT AKTIVATED - check out the following variables: string s, tuple q, first entry in tuple q[0]')
debug_breakpoint(); return None, None
def get_value_from_file(filename, quantity, change_quantity_to=None, sim=False, filepath=False, DEBUG=False, silent=False):
""" Use to read in a quantity from
- *.in
- *.local
- submit*, i.e. submit.sh, submit.csh, files, only works if computer is readily specified in pencilnew.io.get_systemid
Please add further functionallity by yourself!
Args:
filename: can be "run.in", "start.in", "cparam.local", path to that file is extraced from filepath or sim object
quantity: variable to read in from file
sim: put simulation object here, file will be found by filename automatically
filepath: normally not needed, specify here where to find the file with filename, can be a list of paths if unshure
DEBUG: make dry run, tell me what you would do but dont change anything!
silent: suppress certain output by setting True
Return:
Returns None if not successful
"""
import os, pencilnew
import numpy as np
from os.path import join, abspath, exists, split, isfile
from pencilnew.math import is_number, is_float, is_int
from pencilnew.io import timestamp, debug_breakpoint, mkdir
def string_to_tuple(s):
q = s.split(',')
if is_number(q[0]):
q = np.array([float(t) for t in q])
q_type = 'TUPLE_FLOAT'
return q, q_type
if q[0] == 'T' or q[0] == 'F':
q = np.array([bool(t=='T') for t in q])
q_type = 'TUPLE_BOOL'
return q, q_type
if type(q[0]) == type('string'):
q = [t.replace('"','').replace("'", '') for t in q]
q_type = 'TUPLE_STRING'
return q, q_type
print('! ERROR: Could not parse string '+s+' into a tuple!')
print('! DEBUG_BREAKPOINT AKTIVATED - check out the following variables: string s, tuple q, first entry in tuple q[0]')
debug_breakpoint(); return None, None
def tuple_to_string(t, q_type):
return ','.join([str(a) for a in t])
######## prepare filename and quantity
filename = filename.strip() # get rid of whitespaces
quantity = quantity.strip()
q_type = False # q_type will store the type of the quantity value once found and identified
split_filename = split(filename)
if sim == False and split_filename[0] != '' and filepath == False:
filepath = split_filename[0]
filename = split_filename[1]
######## find correct file
# prepare search_path list to search filename in
if filepath == False:
if sim == False:
sim = pencilnew.get_sim()
else:
filepath = sim.path
search_paths = [sim.path, join(sim.path, 'src')] # add other search paths here!!
elif type(filepath) == type('string'):
if filepath.endswith(filename): filepath = filepath[:-len(filename)] # clean filepath if filename occures to be in there at the end
search_paths = [abspath(filepath.strip())] # correct path format
elif type(filepath) == type(['list']):
search_paths = filepath
else:
print('! ERROR: Filename '+str(filename)+' could not be interprated or found!'); return None
absolute_filepath = None
for search_path in search_paths:
tmp_path = join(search_path, filename)
if os.path.isfile(tmp_path):
absolute_filepath = tmp_path
break
# Traps the case of not being able to find the file
if absolute_filepath is None:
if DEBUG:
print('~ DEBUG: File {0} not found in {1}!'.format(filename, search_paths))
return None
######## open file
# now having absolute filepath to file, lets check that file and find quantity inside!
if DEBUG: print('~ DEBUG: Found file {0} in {1}'.format(filename,filepath))
with open(absolute_filepath, 'r') as f:
data_raw = f.readlines()
######## find line in file which quantity in
line_matches = []
# scan through file for differently for different files
if filename.endswith('.in') or 'cparam.local' in filename :
FILE_IS = 'IN_LOCAL'
SYM_COMMENT = '!'
SYM_ASSIGN = '='
SYM_SEPARATOR = ','
for ii, line in enumerate(data_raw):
if line.strip().startswith('&'): continue # filter out lines with &something, e.g. &density_run_pars
if quantity in line.split(SYM_COMMENT)[0]: line_matches.append(ii)
elif filename.startswith('submit') and filename.split('.')[-1] in ['csh', 'sh']:
FILE_IS = 'SUBMIT'
SYM_COMMENT = False
SYM_ASSIGN = '='
SYM_SEPARATOR = ','
for ii, line in enumerate(data_raw):
if line.replace(' ', '').startswith('#@') and quantity in line: line_matches.append(ii)
else:
print('! ERROR: Filename unknown! No parsing possible! Please enhance this function to work with '+filename)
if len(line_matches) > 1: print('! ERROR: Found more than one line with keyword "'+quantity+'" inside!'); return None
if len(line_matches) == 0:
if silent == False: print('! ERROR: Found no line with keyword "'+quantity+'" inside '+join(filepath, filename)+'!')
return None
filename = os.path.basename(filename)
######## get line with quantity inside
line = data_raw[line_matches[0]]
######## do separation of quantity from rest of line, i.e. get rid of comments and other quantities defined in this line
comment = ''
if SYM_COMMENT:
tmp = line.partition(SYM_COMMENT) # strip away comment
line = tmp[0]
if tmp[-1] != '': comment = SYM_COMMENT+tmp[-1] # and store for later
line = line.replace(' ','').replace('\n', '') # do cleanup in this line
qs = line.partition(quantity+SYM_ASSIGN)
if SYM_ASSIGN in qs[-1]:
qs = qs[:2]+qs[-1].partition(SYM_ASSIGN)
#qs = qs[:2]+qs[-1].partition(SYM_ASSIGN)
qs = qs[:2]+qs[2].rpartition(',')+qs[3:]
qs = list(qs)
q = qs[2]
while q.endswith('\t'): q = q[:-1]; comment = '\t'+comment # take care of trailing tabulator
while q.endswith(','): q = q[:-1] # remove trailing ,
######## do a cleanup of quantity value q and convert into string, float, int or array, also remember data type of q
if q.startswith("'") and q.endswith("'"): # quantity q is string in form of 'STRING'
q = q[1:-1]
q_type = 'STRING'
elif q.startswith('"') and q.endswith('"'): # quantity q is string in form of "STRING"
q = q[1:-1]
q_type = 'STRING'
elif not is_number(q[0]): # quantity q is string in form of not beeing a number
q = q.strip().replace('"','').replace("'", '')
q_type = 'STRING'
try:
float(q)
q_type = 'FLOAT'
if is_int(q):
q = int(q)
q_type = 'INT'
except:
if type(q) == type('string') and ',' in q:
q, q_type = string_to_tuple(q) # q is a TULPE_something
if type(q) == type('string') and q in ['F', 'f']: # q is BOOL
q = False
q_type = 'BOOL'
if type(q)== type('string') and q in ['T', 't']:
q = True
q_type = 'BOOL'
if type(q) == type('string'):
if is_number(q[0]):
q_type = 'STRING'
if q_type == False: # catch if type of q was not recognized
print('! ERROR: Couldnt identify the data type of the quantity value: '+str(q))
DEBUG = True
debug_breakpoint()
elif DEBUG:
print('~ DEBUG: q_type = '+q_type)
if q_type == 'FLOAT':
q = float(q)
elif q_type == 'INT':
q = int(q)
######## if value of quantity has to be changed do:
if change_quantity_to != None:
####### prepare change_quantity_to for string injection
if q_type == 'STRING':
if not FILE_IS=='SUBMIT':
change_quantity_to = "'"+change_quantity_to+"'"
elif q_type == 'BOOL':
change_quantity_to = bool(change_quantity_to in ['T', 't', True])
if change_quantity_to == True:
change_quantity_to = 'T'
elif change_quantity_to == False:
change_quantity_to = 'F'
else:
print('! ERROR: There is something deeply wrong here! change_quantity_to should be bool...')
debug_breakpoint(); return None
elif q_type == 'FLOAT':
change_quantity_to = '%e' % change_quantity_to
elif q_type.startswith('TUPLE'):
if q_type.endswith('BOOL'):
if type(change_quantity_to) == type(['list', 'of', 'bool', 'or', 'strings']):
for ii, val in enumerate(change_quantity_to):
if val in ['T', 't', True]:
change_quantity_to[ii] = 'T'
elif val in ['F', 'f', False]:
change_quantity_to[ii] = 'F'
else:
print('! ERROR: There is something deeply wrong here! change_quantity_to['+str(ii)+'] should be bool or string representation, but it is '+str(change_quantity_to[ii]))
debug_breakpoint(); return None
change_quantity_to = ','.join([str(t) for t in change_quantity_to])
if DEBUG: print('~ DEBUG: Would change quantity '+quantity+' from '+str(q)+' to '+str(change_quantity_to))
qs[2] = str(change_quantity_to)
######## further formatting
new_line = ''.join(qs).replace(SYM_SEPARATOR, SYM_SEPARATOR+' ')+'\t'+comment # create new line and add comment stripped away before
if not (FILE_IS == 'SUBMIT' or filename == 'cparam.local'): new_line = ' '+new_line
new_line = new_line.rstrip() # clean empty spaces on the right, no one needs that...
if new_line[-1] != '\n': new_line = new_line+'\n'
if FILE_IS=='SUBMIT': new_line = new_line.replace('#@', '#@ ').replace('=', ' = ') # optimizing format of submit script
if DEBUG:
print('~ DEBUG: old line: '+str(data_raw[line_matches[0]])[:-1])
print('~ DEBUG: new line: '+str(new_line)[:-1])
if not DEBUG:
####### do backup of file before changing it
from shutil import copyfile
target = join(sim.path, 'pc/backups/'+timestamp())
mkdir(target); target = join(target, filename)
copyfile(absolute_filepath, target)
# replace line in raw data
data_raw[line_matches[0]] = new_line
# save on drive
f.close()
with open(absolute_filepath, 'w') as f:
for l in data_raw: f.write(l)
######## DONE!
return q
def get_value_from_file(filename, quantity, change_quantity_to=False, sim=False, filepath=False, DEBUG=False, silent=False):
""" Use to read in a quantity from
- *.in
- *.local
- submit*, i.e. submit.sh, submit.csh, files, only works if computer is readily specified in pencilnew.io.get_systemid
Please add further functionallity by yourself!
Args:
filename: can be "run.in", "start.in", "cparam.local", path to that file is extraced from filepath or sim object
quantity: variable to read in from file
sim: put simulation object here, file will be found by filename automatically
filepath: normally not needed, specify here where to find the file with filename, can be a list of paths if unshure
DEBUG: make dry run, tell me what you would do but dont change anything!
silent: suppress certain output by setting True
"""
import os, pencilnew
import numpy as np
from os.path import join, abspath, exists, split, isfile
from pencilnew.math import is_number, is_float, is_int
from pencilnew.io import timestamp, debug_breakpoint, mkdir
def string_to_tuple(s):
q = s.split(',')
if is_number(q[0]):
q = np.array([float(t) for t in q])
q_type = 'TUPLE_FLOAT'
return q, q_type
if q[0] == 'T' or q[0] == 'F':
q = np.array([bool(t=='T') for t in q])
q_type = 'TUPLE_BOOL'
return q, q_type
if type(q[0]) == type('string'):
q = [t.replace('"','').replace("'", '') for t in q]
q_type = 'TUPLE_STRING'
return q, q_type
print('! ERROR: Could not parse string '+s+' into a tuple!')
print('! DEBUG_BREAKPOINT AKTIVATED - check out the following variables: string s, tuple q, first entry in tuple q[0]')
debug_breakpoint(); return None, None
def tuple_to_string(t, q_type):
return ','.join([str(a) for a in t])
######## prepare filename and quantity
filename = filename.strip() # get rid of whitespaces
quantity = quantity.strip()
q_type = False # q_type will store the type of the quantity value once found and identified
split_filename = split(filename)
if sim == False and split_filename[0] != '' and filepath == False:
filepath = split_filename[0]
filename = split_filename[1]
######## find correct file
# prepare search_path list to search filename in
if filepath == False:
if sim == False:
sim = pencilnew.get_sim()
else:
filepath = sim.path
search_paths = [sim.path, join(sim.path, 'src')] # add other search paths here!!
elif type(filepath) == type('string'):
if filepath.endswith(filename): filepath = filepath[:-len(filename)] # clean filepath if filename occures to be in there at the end
search_paths = [abspath(filepath.strip())] # correct path format
elif type(filepath) == type(['list']):
search_paths = filepath
else:
print('! ERROR: Filename '+str(filename)+' could not be interprated or found!'); return False
absolute_filepath = None
for search_path in search_paths:
tmp_path = join(search_path, filename)
if os.path.isfile(tmp_path):
absolute_filepath = tmp_path
break
# Traps the case of not being able to find the file
if absolute_filepath is None:
if DEBUG:
print('~ DEBUG: File {0} not found in {1}!'.format(filename, search_paths))
return None
######## open file
# now having absolute filepath to file, lets check that file and find quantity inside!
if DEBUG: print('~ DEBUG: Found suiting file {0} in {1}'.format(filename,filepath))
with open(absolute_filepath, 'r') as f:
data_raw = f.readlines()
######## find line in file which quantity in
line_matches = []
# scan through file for differently for different files
if filename.endswith('.in') or 'cparam.local' in filename :
FILE_IS = 'IN_LOCAL'
SYM_COMMENT = '!'
SYM_ASSIGN = '='
SYM_SEPARATOR = ','
for ii, line in enumerate(data_raw):
if line.strip().startswith('&'): continue # filter out lines with &something, e.g. &density_run_pars
if quantity in line.split(SYM_COMMENT)[0]: line_matches.append(ii)
elif filename.startswith('submit') and filename.split('.')[-1] in ['csh', 'sh']:
FILE_IS = 'SUBMIT'
SYM_COMMENT = False
SYM_ASSIGN = '='
SYM_SEPARATOR = ','
for ii, line in enumerate(data_raw):
if line.replace(' ', '').startswith('#@') and quantity in line: line_matches.append(ii)
else:
print('! ERROR: Filename unknown! No parsing possible! Please enhance this function to work with '+filename)
if len(line_matches) > 1: print('! ERROR: Found more than one line with keyword "'+quantity+'" inside!'); return None
if len(line_matches) == 0:
if silent == False: print('! ERROR: Found no line with keyword "'+quantity+'" inside '+join(filepath, filename)+'!')
return None
######## get line with quantity inside
line = data_raw[line_matches[0]]
######## do separation of quantity from rest of line, i.e. get rid of comments and other quantities defined in this line
comment = ''
if SYM_COMMENT:
tmp = line.partition(SYM_COMMENT) # strip away comment
line = tmp[0]
if tmp[-1] != '': comment = SYM_COMMENT+tmp[-1] # and store for later
line = line.replace(' ','').replace('\n', '') # do cleanup in this line
qs = line.partition(quantity+SYM_ASSIGN)
if SYM_ASSIGN in qs[-1]:
qs = qs[:2]+qs[-1].partition(SYM_ASSIGN)
#qs = qs[:2]+qs[-1].partition(SYM_ASSIGN)
qs = qs[:2]+qs[2].rpartition(',')+qs[3:]
qs = list(qs)
q = qs[2]
while q.endswith('\t'): q = q[:-1]; comment = '\t'+comment # take care of trailing tabulator
while q.endswith(','): q = q[:-1] # remove trailing ,
######## do a cleanup of quantity value q and convert into string, float, int or array, also remember data type of q
if q.startswith("'") and q.endswith("'"): # quantity q is string in form of 'STRING'
q = q[1:-1]
q_type = 'STRING'
elif q.startswith('"') and q.endswith('"'): # quantity q is string in form of "STRING"
q = q[1:-1]
q_type = 'STRING'
elif not is_number(q[0]): # quantity q is string in form of not beeing a number
q = q.strip().replace('"','').replace("'", '')
q_type = 'STRING'
elif is_float(q):
q = float(q)
q_type = 'FLOAT'
if is_int(q):
q = int(q)
q_type = 'INT'
if type(q) == type('string') and ',' in q:
q, q_type = string_to_tuple(q) # q is a TULPE_something
if type(q) == type('string') and q in ['F', 'f']: # q is BOOL
q = False
q_type = 'BOOL'
if type(q)== type('string') and q in ['T', 't']:
q = True
q_type = 'BOOL'
if type(q) == type('string'):
if is_number(q[0]):
q_type = 'STRING'
if q_type == False: # catch if type of q was not recognized
print('! ERROR: Couldnt identify the data type of the quantity value: '+str(q))
DEBUG = True
debug_breakpoint()
elif DEBUG:
print('~ DEBUG: q_type = '+q_type)
######## if value of quantity has to be changed do:
if change_quantity_to != False:
####### prepare change_quantity_to for string injection
if q_type == 'STRING':
if not FILE_IS=='SUBMIT':
change_quantity_to = "'"+change_quantity_to+"'"
elif q_type == 'BOOL':
change_quantity_to = bool(change_quantity_to in ['T', 't', True])
if change_quantity_to == True:
change_quantity_to = 'T'
elif change_quantity_to == False:
change_quantity_to = 'F'
else:
print('! ERROR: There is something deeply wrong here! change_quantity_to should be bool...')
debug_breakpoint(); return None
elif q_type == 'FLOAT':
change_quantity_to = '%e' % change_quantity_to
elif q_type.startswith('TUPLE'):
if q_type.endswith('BOOL'):
if type(change_quantity_to) == type(['list', 'of', 'bool', 'or', 'strings']):
for ii, val in enumerate(change_quantity_to):
if val in ['T', 't', True]:
change_quantity_to[ii] = 'T'
elif val in ['F', 'f', False]:
change_quantity_to[ii] = 'F'
else:
print('! ERROR: There is something deeply wrong here! change_quantity_to['+str(ii)+'] should be bool or string representation, but it is '+str(change_quantity_to[ii]))
debug_breakpoint(); return None
change_quantity_to = ','.join([str(t) for t in change_quantity_to])
if DEBUG: print('~ DEBUG: Would change quantity '+quantity+' from '+str(q)+' to '+str(change_quantity_to))
qs[2] = str(change_quantity_to)
######## further formatting
new_line = ''.join(qs).replace(SYM_SEPARATOR, SYM_SEPARATOR+' ')+'\t\t'+comment # create new line and add comment stripped away before
if not FILE_IS == 'SUBMIT': new_line = ' '+new_line
if new_line[-1] != '\n': new_line = new_line+'\n'
if FILE_IS=='SUBMIT': new_line = new_line.replace('#@', '#@ ').replace('=', ' = ') # optimizing format of submit script
if DEBUG:
print('~ DEBUG: old line: '+str(data_raw[line_matches[0]])[:-1])
print('~ DEBUG: new line: '+str(new_line)[:-1])
if not DEBUG:
####### do backup of file before changing it
from shutil import copyfile
target = join(sim.path, '.pc/backups/'+timestamp())
mkdir(target); target = join(target, filename)
copyfile(filepath, target)
# replace line in raw data
data_raw[line_matches[0]] = new_line
# save on drive
f.close()
with open(filename, 'w') as f:
for l in data_raw: f.write(l)
######## DONE!
return q
def copy(self,
path_root='.',
name=False,
optionals=True,
quiet=True,
rename_submit_script=False,
OVERWRITE=False):
"""This method does a copy of the simulation object by creating a new directory 'name' in 'path_root' and copy all simulation components and optionals to his directory.
This method neither links/compiles the simulation, nor creates data dir nor does overwrite anything.
Submit Script Rename:
Name in submit scripts will be renamed if possible! Submit scripts will be identified by submit* plus appearenace of old simulation name inside, latter will be renamed!
Args:
path_root: Dir to create new sim.-folder(sim.-name) inside. This folder will be created if not existing! Relative paths are thought to be relative to the python current workdir
name: Name of new simulation, will be used as folder name. Rename will also happen in submit script if found. Simulation folders is not allowed to preexist!!
optionals: Add list of further files to be copied. Wildcasts allowed according to glob module! Set True to use self.optionals.
quiet: Set True to suppress output.
rename_submit_script: Set False if no renames shall be performed in subnmit* files
OVERWRITE: Set True to overwrite no matter what happens!
"""
from os import listdir
from os.path import exists, join, abspath, basename
from shutil import copyfile
from glob import glob
from numpy import size
from pencilnew.sim import is_sim_dir
from pencilnew import get_sim
from pencilnew.io import mkdir, get_systemid, rename_in_submit_script, debug_breakpoint
from pencilnew.sim import is_sim_dir
# set up paths
if path_root == False or type(path_root) != type('string'):
print('! ERROR: No path_root specified to copy the simulation to.')
return False
path_root = abspath(path_root) # simulation root dir
# name and folder of new simulation
# but keep name of old if sim with old name is NOT existing in NEW directory
if name == False:
name = self.name
if exists(join(path_root, name)) and OVERWRITE == False:
name = name + '_copy'
if exists(join(path_root, name)):
name = name + str(
size([f
for f in listdir(path_root) if f.startswith(name)]))
print(
'? Warning: No name specified and simulation with that name already found! New simulation name now '
+ name)
path_newsim = join(path_root, name) # simulation abspath
path_newsim_src = join(path_newsim, 'src')
path_initial_condition = join(self.path, 'initial_condition')
if exists(path_initial_condition):
has_initial_condition_dir = True
path_newsim_initcond = join(path_newsim, 'initial_condition')
else:
has_initial_condition_dir = False
if type(optionals) == type(['list']):
optionals = self.optionals + optionals # optional files to be copied
if optionals == True: optionals = self.optionals
if type(optionals) == type('string'): optionals = [optionals]
if type(optionals) != type(['list']):
print('! ERROR: optionals must be of type list!')
tmp = []
for opt in optionals:
files = glob(join(self.path, opt))
for f in files:
tmp.append(basename(f))
optionals = tmp
## check if the copy was already created
if is_sim_dir(path_newsim) and OVERWRITE == False:
if not quiet:
print(
'? WARNING: Simulation already exists. Returning with existing simulation.'
)
return get_sim(path_newsim, quiet=quiet)
## expand list of optionals wildcasts
# check existance of path_root+name, a reason to stop to not overwrite anything
if OVERWRITE == False and exists(path_newsim):
print(
'! ERROR: Folder to copy simulation to already exists!\n! -> '
+ path_newsim)
return False
# check existance of self.components
for comp in self.components:
if not exists(join(self.path, comp)):
print('! ERROR: Couldnt find component ' + comp +
' from simulation ' + self.name + ' at location ' +
join(self.path, comp))
return False
# check existance of optionals
for opt in optionals:
if not exists(join(self.path, opt)):
print('! ERROR: Couldnt find optinal component ' + opt +
' from simulation ' + self.name + ' at location ' +
join(self.path, opt))
return False
# create folders
if mkdir(path_newsim) == False and OVERWRITE == False:
print('! ERROR: Couldnt create new simulation directory ' +
path_newsim + ' !!')
return False
if mkdir(path_newsim_src) == False and OVERWRITE == False:
print('! ERROR: Couldnt create new simulation src directory ' +
path_newsim_src + ' !!')
return False
# copy files
files_to_be_copied = []
for f in self.components + optionals:
f_path = abspath(join(self.path, f))
copy_to = abspath(join(path_newsim, f))
if f_path == copy_to:
print(
'!! ERROR: file path f_path equal to destination copy_to. Debug this line manually!'
)
debug_breakpoint()
copyfile(f_path, copy_to)
# Organizes any personalized initial conditions
if has_initial_condition_dir:
if mkdir(path_newsim_initcond) == False and OVERWRITE == False:
print(
'! ERROR: Couldnt create new simulation initial_condition directory '
+ path_newsim_initcond + ' !!')
return False
for f in listdir(path_initial_condition):
f_path = abspath(join(path_initial_condition, f))
copy_to = abspath(join(path_newsim_initcond, f))
if f_path == copy_to:
print(
'!! ERROR: file path f_path equal to destination copy_to. Debug this line manually!'
)
debug_breakpoint()
copyfile(f_path, copy_to)
# modify name in submit script files
if rename_submit_script != False:
if type(rename_submit_script) == type('STRING'):
rename_in_submit_script(new_name=rename_submit_script,
sim=get_sim(path_newsim))
else:
print('!! ERROR: Could not understand rename_submit_script=' +
str(rename_submit_script))
# done
return get_sim(path_newsim)
def copy(self, path_root='.', name=False,
optionals=True, quiet=True, rename_submit_script=False, OVERWRITE=False):
"""This method does a copy of the simulation object by creating a new directory 'name' in 'path_root' and copy all simulation components and optionals to his directory.
This method neither links/compiles the simulation, nor creates data dir nor does overwrite anything.
Submit Script Rename:
Name in submit scripts will be renamed if possible! Submit scripts will be identified by submit* plus appearenace of old simulation name inside, latter will be renamed!
Args:
path_root: Dir to create new sim.-folder(sim.-name) inside. This folder will be created if not existing! Relative paths are thought to be relative to the python current workdir
name: Name of new simulation, will be used as folder name. Rename will also happen in submit script if found. Simulation folders is not allowed to preexist!!
optionals: Add list of further files to be copied. Wildcasts allowed according to glob module! Set True to use self.optionals.
quiet: Set True to suppress output.
rename_submit_script: Set False if no renames shall be performed in subnmit* files
OVERWRITE: Set True to overwrite no matter what happens!
"""
from os import listdir
from os.path import exists, join, abspath, basename
from shutil import copyfile
from glob import glob
from numpy import size
from pencilnew.sim import is_sim_dir
from pencilnew import get_sim
from pencilnew.io import mkdir, get_systemid, rename_in_submit_script, debug_breakpoint
from pencilnew.sim import is_sim_dir
# set up paths
if path_root == False or type(path_root) != type('string'):
print('! ERROR: No path_root specified to copy the simulation to.');
return False
path_root = abspath(path_root) # simulation root dir
# name and folder of new simulation
# but keep name of old if sim with old name is NOT existing in NEW directory
if name == False:
name = self.name
if exists(join(path_root, name)) and OVERWRITE == False:
name = name+'_copy'
if exists(join(path_root, name)):
name = name + str(size([f for f in listdir(path_root) if f.startswith(name)]))
print('? Warning: No name specified and simulation with that name already found! New simulation name now '+name)
path_newsim = join(path_root, name) # simulation abspath
path_newsim_src = join(path_newsim, 'src')
path_initial_condition = join(self.path, 'initial_condition')
if exists(path_initial_condition):
has_initial_condition_dir = True
path_newsim_initcond = join(path_newsim, 'initial_condition')
else:
has_initial_condition_dir = False
if type(optionals) == type(['list']): optionals = self.optionals + optionals # optional files to be copied
if optionals == True: optionals = self.optionals
if type(optionals) == type('string'): optionals = [optionals]
if type(optionals) != type(['list']): print('! ERROR: optionals must be of type list!')
tmp = []
for opt in optionals:
files = glob(join(self.path, opt))
for f in files:
tmp.append(basename(f))
optionals = tmp
## check if the copy was already created
if is_sim_dir(path_newsim) and OVERWRITE == False:
if not quiet: print('? WARNING: Simulation already exists. Returning with existing simulation.')
return get_sim(path_newsim, quiet=quiet)
## expand list of optionals wildcasts
# check existance of path_root+name, a reason to stop to not overwrite anything
if OVERWRITE==False and exists(path_newsim):
print('! ERROR: Folder to copy simulation to already exists!\n! -> '+path_newsim)
return False
# check existance of self.components
for comp in self.components:
if not exists(join(self.path, comp)):
print('! ERROR: Couldnt find component '+comp+' from simulation '+self.name+' at location '+join(self.path, comp))
return False
# check existance of optionals
for opt in optionals:
if not exists(join(self.path, opt)):
print('! ERROR: Couldnt find optinal component '+opt+' from simulation '+self.name+' at location '+join(self.path, opt))
return False
# create folders
if mkdir(path_newsim) == False and OVERWRITE==False:
print('! ERROR: Couldnt create new simulation directory '+path_newsim+' !!')
return False
if mkdir(path_newsim_src) == False and OVERWRITE==False:
print('! ERROR: Couldnt create new simulation src directory '+path_newsim_src+' !!')
return False
# copy files
files_to_be_copied = []
for f in self.components+optionals:
f_path = abspath(join(self.path, f))
copy_to = abspath(join(path_newsim, f))
if f_path == copy_to:
print('!! ERROR: file path f_path equal to destination copy_to. Debug this line manually!')
debug_breakpoint()
copyfile(f_path, copy_to)
# Organizes any personalized initial conditions
if has_initial_condition_dir:
if mkdir(path_newsim_initcond) == False and OVERWRITE==False:
print('! ERROR: Couldnt create new simulation initial_condition directory '+path_newsim_initcond+' !!')
return False
for f in listdir(path_initial_condition):
f_path = abspath(join(path_initial_condition, f))
copy_to = abspath(join(path_newsim_initcond, f))
if f_path == copy_to:
print('!! ERROR: file path f_path equal to destination copy_to. Debug this line manually!')
debug_breakpoint()
copyfile(f_path, copy_to)
# modify name in submit script files
if rename_submit_script != False:
if type(rename_submit_script) == type('STRING'):
rename_in_submit_script(new_name = rename_submit_script, sim=get_sim(path_newsim))
else:
print('!! ERROR: Could not understand rename_submit_script='+str(rename_submit_script))
# done
return get_sim(path_newsim)
