Windows paths

[maxim1317]

sf.load_network() Fails to work with windows paths in ini file:

re.sub crashes in load_network_from_gpickle from safe_io.py
I think it's due to path concatenation or escaping error

Try using pathlib

[abarysh]

Hi Maxim, thanks a lot for the bug report. Would you be able to send upload your ini file? Or an example of the path you're using?

[EdoardoGerva]

Hi Anastasia, I am also trying to run SAFE in a Windows OS. I think the problem here is about file paths: several functions in safe_io.py call files as they were in a Linux environment, using "~" to call the User Home Directory for instance, and this is not directly extendable also to a Windows environment. What do you think?

[abarysh]

Hi Edoardo, thanks for the comment! Unfortunately, I don't have a Windows machine to test this out. But my understanding is that expanduser("~") should work on both Unix and Windows (https://www.geeksforgeeks.org/python-os-path-expanduser-method/) and replace "~" with the corresponding home directory. Could you share a more specific description of the error you're getting? Thank you.

[EdoardoGerva]

Actually I am not sure "~" is the only problem. Here I can show you my error message, maybe it can help you:

Loading network from (my path to folder)/ISN/safe-data/networks/Costanzo_Science_2016.gpickle
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
File ~\anaconda3\lib\sre_parse.py:1039, in parse_template(source, state)
   1038 try:
-> 1039     this = chr(ESCAPES[this][1])
   1040 except KeyError:

KeyError: '\\U'

During handling of the above exception, another exception occurred:

error                                     Traceback (most recent call last)
Cell In [3], line 1
----> 1 sf.load_network()

File ~/Desktop/Lavoro/Leuven/ISN/safepy\safe.py:258, in SAFE.load_network(self, **kwargs)
    256     self.graph = load_network_from_mat(self.path_to_network_file, verbose=self.verbose)
    257 elif file_extension == '.gpickle':
--> 258     self.graph = load_network_from_gpickle(self.path_to_network_file, verbose=self.verbose)
    259 elif file_extension == '.txt':
    260     self.graph = load_network_from_txt(self.path_to_network_file,
    261                                        node_key_attribute=self.node_key_attribute,
    262                                        verbose=self.verbose)

File ~/Desktop/Lavoro/Leuven/ISN/safepy\safe_io.py:95, in load_network_from_gpickle(filename, verbose)
     93 def load_network_from_gpickle(filename, verbose=True):
---> 95     filename = re.sub('~', expanduser('~'), filename)
     96     G = nx.read_gpickle(filename)
     98     return G

File ~\anaconda3\lib\re.py:210, in sub(pattern, repl, string, count, flags)
    203 def sub(pattern, repl, string, count=0, flags=0):
    204     """Return the string obtained by replacing the leftmost
    205     non-overlapping occurrences of the pattern in string by the
    206     replacement repl.  repl can be either a string or a callable;
    207     if a string, backslash escapes in it are processed.  If it is
    208     a callable, it's passed the Match object and must return
    209     a replacement string to be used."""
--> 210     return _compile(pattern, flags).sub(repl, string, count)

File ~\anaconda3\lib\re.py:327, in _subx(pattern, template)
    325 def _subx(pattern, template):
    326     # internal: Pattern.sub/subn implementation helper
--> 327     template = _compile_repl(template, pattern)
    328     if not template[0] and len(template[1]) == 1:
    329         # literal replacement
    330         return template[1][0]

File ~\anaconda3\lib\re.py:318, in _compile_repl(repl, pattern)
    315 @functools.lru_cache(_MAXCACHE)
    316 def _compile_repl(repl, pattern):
    317     # internal: compile replacement pattern
--> 318     return sre_parse.parse_template(repl, pattern)

File ~\anaconda3\lib\sre_parse.py:1042, in parse_template(source, state)
   1040         except KeyError:
   1041             if c in ASCIILETTERS:
-> 1042                 raise s.error('bad escape %s' % this, len(this))
   1043         lappend(this)
   1044 else:

error: bad escape \U at position 2

May it also be related to the use of forward slashes / instead of backslashes \?