pyscf parses sys.argv when setting max_memory on a Mole object #470
Description
Dear developers,
while writing & executing some unittests for my own code that uses pyscf I encountered the following issue:
Setting max_memory on a mol object leads to a call of cmd_args() in [...]/pyscf/gto/mole.py. When I execute such code with pytest -m [some mark] then pyscf will parse sys.argv[1:] in cmd_args() and the mark supplied to pytest with -m [some mark] will be interpreted as memory argument py pyscf.
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../../../anaconda3/lib/python3.6/site-packages/pyscf/gto/mole.py:2033: in build
_update_from_cmdargs_(self)
../../../anaconda3/lib/python3.6/site-packages/pyscf/gto/mole.py:3103: in _update_from_cmdargs_
opts = cmd_args.cmd_args()
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def cmd_args():
'''
get input from cmdline
'''
parser = argparse.ArgumentParser()
parser.add_argument('-v', '--verbose',
action='store_false', dest='verbose', default=0,
help='make lots of noise')
parser.add_argument('-q', '--quiet',
action='store_false', dest='quite', default=False,
help='be very quiet')
parser.add_argument('-o', '--output',
dest='output', metavar='FILE', help='write output to FILE')
parser.add_argument('-m', '--max-memory',
action='store', dest='max_memory', metavar='NUM',
help='maximum memory to use (in MB)')
(opts, args_left) = parser.parse_known_args()
if opts.quite:
opts.verbose = pyscf.lib.logger.QUIET
if opts.verbose:
opts.verbose = pyscf.lib.logger.DEBUG
if opts.max_memory:
> opts.max_memory = float(opts.max_memory)
E ValueError: could not convert string to float: 'pyscf'
Here is code that reproduces the issue.
from pyscf import gto
import pytest
# Call with:
# pytest -m pyscf bug.py
@pytest.mark.pyscf
def test_mark():
mol = gto.Mole()
atoms = "H H".split()
coords = [(0., 0., 0.), (0., 0., 1.4)]
mol.atom = [(atom, c) for atom, c
in zip(atoms, coords)]
mol.basis = "321g"
mol.unit = "Bohr"
mol.verbose = 4
mol.max_memory = 2000
mol.build()
return mol
Executing this code with pytest -m pyscf bug.py will lead to the crash. I tested it with pyscf 1.6.5.
That pyscf parses sys.argv[1:] even though it is solely used as a python module is rather suprising.
With best regards & thanks for your work,
Johannes