========================================================================================== FAILURES ==========================================================================================
______________________________________________________________________________ test_load_molecular_hamiltonian _______________________________________________________________________________
src = '37316d06-b95c-4ffb-91d3-5beaeb5c9326.hdf5', dst = '/usr/local/lib/python3.9/site-packages/openfermion/testing/data/H1-Li1_sto-3g_singlet.hdf5'
copy_function = <function copy2 at 0x83487a790>
def move(src, dst, copy_function=copy2):
"""Recursively move a file or directory to another location. This is
similar to the Unix "mv" command. Return the file or directory's
destination.
If the destination is a directory or a symlink to a directory, the source
is moved inside the directory. The destination path must not already
exist.
If the destination already exists but is not a directory, it may be
overwritten depending on os.rename() semantics.
If the destination is on our current filesystem, then rename() is used.
Otherwise, src is copied to the destination and then removed. Symlinks are
recreated under the new name if os.rename() fails because of cross
filesystem renames.
The optional `copy_function` argument is a callable that will be used
to copy the source or it will be delegated to `copytree`.
By default, copy2() is used, but any function that supports the same
signature (like copy()) can be used.
A lot more could be done here... A look at a mv.c shows a lot of
the issues this implementation glosses over.
"""
sys.audit("shutil.move", src, dst)
real_dst = dst
if os.path.isdir(dst):
if _samefile(src, dst):
# We might be on a case insensitive filesystem,
# perform the rename anyway.
os.rename(src, dst)
return
# Using _basename instead of os.path.basename is important, as we must
# ignore any trailing slash to avoid the basename returning ''
real_dst = os.path.join(dst, _basename(src))
if os.path.exists(real_dst):
raise Error("Destination path '%s' already exists" % real_dst)
try:
> os.rename(src, real_dst)
E PermissionError: [Errno 13] Permission denied: '37316d06-b95c-4ffb-91d3-5beaeb5c9326.hdf5' -> '/usr/local/lib/python3.9/site-packages/openfermion/testing/data/H1-Li1_sto-3g_singlet.hdf5'
/usr/local/lib/python3.9/shutil.py:825: PermissionError
During handling of the above exception, another exception occurred:
def test_load_molecular_hamiltonian():
geometry = [('Li', (0., 0., 0.)), ('H', (0., 0., 1.4))]
> lih_hamiltonian = openfermionpyscf.generate_molecular_hamiltonian(
geometry, 'sto-3g', 1, 0, 2, 2)
openfermionpyscf/_run_pyscf_test.py:20:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
openfermionpyscf/_run_pyscf.py:237: in generate_molecular_hamiltonian
molecule = run_pyscf(
openfermionpyscf/_run_pyscf.py:205: in run_pyscf
pyscf_molecular_data.save()
/usr/local/lib/python3.9/site-packages/openfermion/chem/molecular_data.py:717: in save
shutil.move("{}.hdf5".format(tmp_name), "{}.hdf5".format(self.filename))
/usr/local/lib/python3.9/shutil.py:845: in move
copy_function(src, real_dst)
/usr/local/lib/python3.9/shutil.py:444: in copy2
copyfile(src, dst, follow_symlinks=follow_symlinks)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
src = '37316d06-b95c-4ffb-91d3-5beaeb5c9326.hdf5', dst = '/usr/local/lib/python3.9/site-packages/openfermion/testing/data/H1-Li1_sto-3g_singlet.hdf5'
def copyfile(src, dst, *, follow_symlinks=True):
"""Copy data from src to dst in the most efficient way possible.
If follow_symlinks is not set and src is a symbolic link, a new
symlink will be created instead of copying the file it points to.
"""
sys.audit("shutil.copyfile", src, dst)
if _samefile(src, dst):
raise SameFileError("{!r} and {!r} are the same file".format(src, dst))
file_size = 0
for i, fn in enumerate([src, dst]):
try:
st = _stat(fn)
except OSError:
# File most likely does not exist
pass
else:
# XXX What about other special files? (sockets, devices...)
if stat.S_ISFIFO(st.st_mode):
fn = fn.path if isinstance(fn, os.DirEntry) else fn
raise SpecialFileError("`%s` is a named pipe" % fn)
if _WINDOWS and i == 0:
file_size = st.st_size
if not follow_symlinks and _islink(src):
os.symlink(os.readlink(src), dst)
else:
with open(src, 'rb') as fsrc:
try:
> with open(dst, 'wb') as fdst:
E PermissionError: [Errno 13] Permission denied: '/usr/local/lib/python3.9/site-packages/openfermion/testing/data/H1-Li1_sto-3g_singlet.hdf5'
/usr/local/lib/python3.9/shutil.py:266: PermissionError
------------------------------------------------------------------------------------ Captured stdout call ------------------------------------------------------------------------------------
overwrite output file: addopts=
_______________________________________________________________________________________ test_run_pyscf _______________________________________________________________________________________
src = 'e420e408-8627-4146-8f01-6d197ff47f0c.hdf5', dst = '/usr/local/lib/python3.9/site-packages/openfermion/testing/data/H2_6-31g_singlet.hdf5'
copy_function = <function copy2 at 0x83487a790>
def move(src, dst, copy_function=copy2):
"""Recursively move a file or directory to another location. This is
similar to the Unix "mv" command. Return the file or directory's
destination.
If the destination is a directory or a symlink to a directory, the source
is moved inside the directory. The destination path must not already
exist.
If the destination already exists but is not a directory, it may be
overwritten depending on os.rename() semantics.
If the destination is on our current filesystem, then rename() is used.
Otherwise, src is copied to the destination and then removed. Symlinks are
recreated under the new name if os.rename() fails because of cross
filesystem renames.
The optional `copy_function` argument is a callable that will be used
to copy the source or it will be delegated to `copytree`.
By default, copy2() is used, but any function that supports the same
signature (like copy()) can be used.
A lot more could be done here... A look at a mv.c shows a lot of
the issues this implementation glosses over.
"""
sys.audit("shutil.move", src, dst)
real_dst = dst
if os.path.isdir(dst):
if _samefile(src, dst):
# We might be on a case insensitive filesystem,
# perform the rename anyway.
os.rename(src, dst)
return
# Using _basename instead of os.path.basename is important, as we must
# ignore any trailing slash to avoid the basename returning ''
real_dst = os.path.join(dst, _basename(src))
if os.path.exists(real_dst):
raise Error("Destination path '%s' already exists" % real_dst)
try:
> os.rename(src, real_dst)
E PermissionError: [Errno 13] Permission denied: 'e420e408-8627-4146-8f01-6d197ff47f0c.hdf5' -> '/usr/local/lib/python3.9/site-packages/openfermion/testing/data/H2_6-31g_singlet.hdf5'
/usr/local/lib/python3.9/shutil.py:825: PermissionError
During handling of the above exception, another exception occurred:
def test_run_pyscf():
> new_mole = run_pyscf(molecule,
run_scf=True,
run_mp2=True,
run_cisd=True,
run_ccsd=True,
run_fci=True,
verbose=1)
openfermionpyscf/tests/_run_pyscf_test.py:32:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
openfermionpyscf/_run_pyscf.py:205: in run_pyscf
pyscf_molecular_data.save()
/usr/local/lib/python3.9/site-packages/openfermion/chem/molecular_data.py:717: in save
shutil.move("{}.hdf5".format(tmp_name), "{}.hdf5".format(self.filename))
/usr/local/lib/python3.9/shutil.py:845: in move
copy_function(src, real_dst)
/usr/local/lib/python3.9/shutil.py:444: in copy2
copyfile(src, dst, follow_symlinks=follow_symlinks)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
src = 'e420e408-8627-4146-8f01-6d197ff47f0c.hdf5', dst = '/usr/local/lib/python3.9/site-packages/openfermion/testing/data/H2_6-31g_singlet.hdf5'
def copyfile(src, dst, *, follow_symlinks=True):
"""Copy data from src to dst in the most efficient way possible.
If follow_symlinks is not set and src is a symbolic link, a new
symlink will be created instead of copying the file it points to.
"""
sys.audit("shutil.copyfile", src, dst)
if _samefile(src, dst):
raise SameFileError("{!r} and {!r} are the same file".format(src, dst))
file_size = 0
for i, fn in enumerate([src, dst]):
try:
st = _stat(fn)
except OSError:
# File most likely does not exist
pass
else:
# XXX What about other special files? (sockets, devices...)
if stat.S_ISFIFO(st.st_mode):
fn = fn.path if isinstance(fn, os.DirEntry) else fn
raise SpecialFileError("`%s` is a named pipe" % fn)
if _WINDOWS and i == 0:
file_size = st.st_size
if not follow_symlinks and _islink(src):
os.symlink(os.readlink(src), dst)
else:
with open(src, 'rb') as fsrc:
try:
> with open(dst, 'wb') as fdst:
E PermissionError: [Errno 13] Permission denied: '/usr/local/lib/python3.9/site-packages/openfermion/testing/data/H2_6-31g_singlet.hdf5'
/usr/local/lib/python3.9/shutil.py:266: PermissionError
------------------------------------------------------------------------------------ Captured stdout call ------------------------------------------------------------------------------------
overwrite output file: addopts=
Hartree-Fock energy for H2_6-31g_singlet (2 electrons) is -1.1267339671165666.
MP2 energy for H2_6-31g_singlet (2 electrons) is -1.1441304105295214.
CISD energy for H2_6-31g_singlet (2 electrons) is -1.1516827321098897.
CCSD energy for H2_6-31g_singlet (2 electrons) is -1.1516828675117317.
FCI energy for H2_6-31g_singlet (2 electrons) is -1.1516827321098888.
====================================================================================== warnings summary ======================================================================================
openfermionpyscf/_pyscf_molecular_data.py:72
/disk-samsung/freebsd-ports/science/py-OpenFermion-PySCF/work-py39/OpenFermion-PySCF-0.5/openfermionpyscf/_pyscf_molecular_data.py:72: DeprecationWarning: invalid escape sequence \i
"""A 4-dimension array for electron repulsion integrals in the MO
../../../../../../usr/local/lib/python3.9/site-packages/pyscf/__init__.py:93
/usr/local/lib/python3.9/site-packages/pyscf/__init__.py:93: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
if LooseVersion(numpy.__version__) <= '1.8.0':
../../../../../../usr/local/lib/python3.9/site-packages/setuptools/_distutils/version.py:346
../../../../../../usr/local/lib/python3.9/site-packages/setuptools/_distutils/version.py:346
../../../../../../usr/local/lib/python3.9/site-packages/setuptools/_distutils/version.py:346
../../../../../../usr/local/lib/python3.9/site-packages/setuptools/_distutils/version.py:346
../../../../../../usr/local/lib/python3.9/site-packages/setuptools/_distutils/version.py:346
../../../../../../usr/local/lib/python3.9/site-packages/setuptools/_distutils/version.py:346
../../../../../../usr/local/lib/python3.9/site-packages/setuptools/_distutils/version.py:346
../../../../../../usr/local/lib/python3.9/site-packages/setuptools/_distutils/version.py:346
/usr/local/lib/python3.9/site-packages/setuptools/_distutils/version.py:346: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
other = LooseVersion(other)
../../../../../../usr/local/lib/python3.9/site-packages/pyscf/__init__.py:99
/usr/local/lib/python3.9/site-packages/pyscf/__init__.py:99: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
elif '1.16.2' <= LooseVersion(numpy.__version__) < '1.18':
../../../../../../usr/local/lib/python3.9/site-packages/numpy/ctypeslib.py:137
/usr/local/lib/python3.9/site-packages/numpy/ctypeslib.py:137: DeprecationWarning:
`numpy.distutils` is deprecated since NumPy 1.23.0, as a result
of the deprecation of `distutils` itself. It will be removed for
Python >= 3.12. For older Python versions it will remain present.
It is recommended to use `setuptools < 60.0` for those Python versions.
For more details, see:
https://numpy.org/devdocs/reference/distutils_status_migration.html
from numpy.distutils.misc_util import get_shared_lib_extension
../../../../../../usr/local/lib/python3.9/site-packages/pyscf/lib/numpy_helper.py:884
../../../../../../usr/local/lib/python3.9/site-packages/pyscf/lib/numpy_helper.py:884
/usr/local/lib/python3.9/site-packages/pyscf/lib/numpy_helper.py:884: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
if LooseVersion(numpy.__version__) <= LooseVersion('1.6.0'):
../../../../../../usr/local/lib/python3.9/site-packages/matplotlib/__init__.py:152
../../../../../../usr/local/lib/python3.9/site-packages/matplotlib/__init__.py:152
../../../../../../usr/local/lib/python3.9/site-packages/matplotlib/__init__.py:152
../../../../../../usr/local/lib/python3.9/site-packages/matplotlib/__init__.py:152
../../../../../../usr/local/lib/python3.9/site-packages/matplotlib/__init__.py:152
/usr/local/lib/python3.9/site-packages/matplotlib/__init__.py:152: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
if LooseVersion(module.__version__) < minver:
../../../../../../usr/local/lib/python3.9/site-packages/openfermion/hamiltonians/hartree_fock.py:11
/usr/local/lib/python3.9/site-packages/openfermion/hamiltonians/hartree_fock.py:11: DeprecationWarning: Please use `OptimizeResult` from the `scipy.optimize` namespace, the `scipy.optimize.optimize` namespace is deprecated.
from scipy.optimize.optimize import OptimizeResult
../../../../../../usr/local/lib/python3.9/site-packages/pyscf/mp/mp2.py:357
../../../../../../usr/local/lib/python3.9/site-packages/pyscf/mp/mp2.py:357
../../../../../../usr/local/lib/python3.9/site-packages/pyscf/mp/mp2.py:357
../../../../../../usr/local/lib/python3.9/site-packages/pyscf/mp/mp2.py:357
openfermionpyscf/tests/_pyscf_molecular_data_test.py::test_accessing_rdm
openfermionpyscf/tests/_run_pyscf_test.py::test_run_pyscf
openfermionpyscf/tests/_run_pyscf_test.py::test_run_pyscf
openfermionpyscf/tests/_run_pyscf_test.py::test_run_pyscf
openfermionpyscf/tests/_run_pyscf_test.py::test_run_pyscf
/usr/local/lib/python3.9/site-packages/pyscf/mp/mp2.py:357: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
moidx = numpy.ones(mp.mo_occ.size, dtype=numpy.bool)
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
==================================================================== 2 failed, 2 passed, 29 warnings in 93.82s (0:01:33) =====================================================================
*** Error code 1
Version: 0.5 Python-3.9 FreeBSD 13.1