Use mkstemp to generate a named temporary file

[tashrifbillah]

Hi @fedemoro,

To eliminate permission issue regarding writing to /tmp/ directory you were facing because of this line:

# copy provided config file to temporary directory
configFile= f'/tmp/harm_config_{getpid()}.ini'
with open(configFile,'w') as f:
    f.write('[DEFAULT]\n')
    f.write(f'N_shm = {self.N_shm}\n')
    f.write(f'N_proc = {self.N_proc}\n')
    f.write(f'N_zero = {self.N_zero}\n')
    ...
    ...

I would like to devise a solution for you that should also contribute to the impeccability of our software.

Can you try the following on ipython and let me know what you get:

from tempfile import mkstemp
f, name= mkstemp()
print(f, name)

[fedemoro]

Can you try the following on ipython and let me know what you get:

from tempfile import mkstemp
f, name= mkstemp()
print(f, name)

44 /var/tmp/pbs.1337292.pbs/tmpsunczqkv

[fedemoro]

Your previously mentioned solution of changing tmp folder works just fine

cd dMRIharmonization/lib
Then, check the occurrences of /tmp/:
grep /tmp *py
sed -i "s+/tmp/+/new_folder/+g" *py

[tashrifbillah]

44 /var/tmp/pbs.1337292.pbs/tmpsunczqkv

I didn't know you can have write access to /var/tmp. Good!

Your previously mentioned solution of changing tmp folder works just fine

I provided you a way around, but not the most desired one. Let's say you want to git pull after you affect those changes. Then, you would have to discard the changes one by one until you can pull recent changes of our software. On the other hand, if I write to the system default directory other than /tmp/, then you won't have to affect those changes in first place. So, to make it more manageable and standard, I shall write to system default temp directory.

Please watch for updates. Thanks!

[tashrifbillah]

Hint:
Replace configFile= f'/tmp/harm_config_{getpid()}.ini' with follows:

from tempfile import gettempdir
configFile= pjoin(gettempdir(), harm_config_{getpid()}.ini')