Use tempfile library to handle temporal folders #586
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When running OrthoFinder in a cluster under an NFS folder, the tests are
so fast that sometimes some internal files are still being deleted whilst
`shutil.rmtree()` is running, raising an error:
```
Traceback (most recent call last):
File "/hps/software/users/ensembl/compara/jalvarez/testbench/OrthoFinder_source/orthofinder.py", line 7, in <module>
main(args)
File "/hps/software/users/ensembl/compara/jalvarez/testbench/OrthoFinder_source/scripts_of/__main__.py", line 1719, in main
CheckDependencies(options, prog_caller, files.FileHandler.GetWorkingDirectory1_Read()[0])
File "/hps/software/users/ensembl/compara/jalvarez/testbench/OrthoFinder_source/scripts_of/__main__.py", line 1310, in CheckDependencies
elif not prog_caller.TestSearchMethod(dirForTempFiles, options.search_program):
File "/hps/software/users/ensembl/compara/jalvarez/testbench/OrthoFinder_source/scripts_of/program_caller.py", line 199, in TestSearchMethod
shutil.rmtree(d)
File "/hps/software/users/ensembl/compara/shared/pyenv/versions/3.9.5/lib/python3.9/shutil.py", line 718, in rmtree
_rmtree_safe_fd(fd, path, onerror)
File "/hps/software/users/ensembl/compara/shared/pyenv/versions/3.9.5/lib/python3.9/shutil.py", line 675, in _rmtree_safe_fd
onerror(os.unlink, fullname, sys.exc_info())
File "/hps/software/users/ensembl/compara/shared/pyenv/versions/3.9.5/lib/python3.9/shutil.py", line 673, in _rmtree_safe_fd
os.unlink(entry.name, dir_fd=topfd)
FileNotFoundError: [Errno 2] No such file or directory: '.nfs491292b75b71b1300002134e'
```
Since this temporary folder is only meant to be alive for the time of
the test(s), I have moved this code inside a context manager using
`tempfile`. This way you let the system handle the cleanup on its own,
and gives the user more control over where the tests are run.
davidemms
approved these changes
Jul 6, 2021
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When running OrthoFinder in a cluster passing the data in an NFS folder, the tests are so fast that sometimes some internal files are still being deleted at the same time
shutil.rmtree()is running, raising an error:Since this temporary folder is only meant to be alive for the time of the test(s), I have moved this code inside a context manager using
tempfile. This way the system handles the cleanup on its own, and gives the user more control over where the tests are run (via$TMPDIR, for instance).