PyXtal: Pyxtal tests fails on build molecular structures

Here is the error:

``` ===Testing generation of molecular 3D crystals. This may take some time. === Spacegroup # |Generated (SPG)|Generated (PMG)| Time Elapsed Traceback (most recent call last): File "/home/haru/miniconda3/envs/group/bin/pyxtal_test.py", line 4, in <module> __import__('pkg_resources').run_script('pyxtal==0.1.7', 'pyxtal_test.py') File "/home/haru/miniconda3/envs/group/lib/python3.8/site-packages/pkg_resources/__init__.py", line 650, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/haru/miniconda3/envs/group/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1446, in run_script exec(code, namespace, namespace) File "/home/haru/miniconda3/envs/group/lib/python3.8/site-packages/pyxtal-0.1.7-py3.8.egg/EGG-INFO/scripts/pyxtal_test.py", line 1321, in <module> eval(modules_lib[module]) File "<string>", line 1, in <module> File "/home/haru/miniconda3/envs/group/lib/python3.8/site-packages/pyxtal-0.1.7-py3.8.egg/EGG-INFO/scripts/pyxtal_test.py", line 373, in test_molecular rand_crystal.from_random(3, sg, ["H2O"], [multiplicity], 2.5) File "/home/haru/miniconda3/envs/group/lib/python3.8/site-packages/pyxtal-0.1.7-py3.8.egg/pyxtal/__init__.py", line 223, in from_random struc = molecular_crystal(group, species, numIons, factor, File "/home/haru/miniconda3/envs/group/lib/python3.8/site-packages/pyxtal-0.1.7-py3.8.egg/pyxtal/molecular_crystal.py", line 73, in __init__ self.init_common( File "/home/haru/miniconda3/envs/group/lib/python3.8/site-packages/pyxtal-0.1.7-py3.8.egg/pyxtal/molecular_crystal.py", line 215, in init_common self.generate_crystal() File "/home/haru/miniconda3/envs/group/lib/python3.8/site-packages/pyxtal-0.1.7-py3.8.egg/pyxtal/molecular_crystal.py", line 457, in generate_crystal output = self._generate_coords() File "/home/haru/miniconda3/envs/group/lib/python3.8/site-packages/pyxtal-0.1.7-py3.8.egg/pyxtal/molecular_crystal.py", line 479, in _generate_coords output = self._generate_mol_wyckoffs( File "/home/haru/miniconda3/envs/group/lib/python3.8/site-packages/pyxtal-0.1.7-py3.8.egg/pyxtal/molecular_crystal.py", line 546, in _generate_mol_wyckoffs ms0 = self._generate_orientation(pyxtal_mol, pt, oris, wp) File "/home/haru/miniconda3/envs/group/lib/python3.8/site-packages/pyxtal-0.1.7-py3.8.egg/pyxtal/molecular_crystal.py", line 588, in _generate_orientation ori = random.choice(oris).copy() File "/home/haru/miniconda3/envs/group/lib/python3.8/site-packages/pyxtal-0.1.7-py3.8.egg/pyxtal/molecule.py", line 311, in copy return deepcopy(self) File "/home/haru/miniconda3/envs/group/lib/python3.8/copy.py", line 172, in deepcopy y = _reconstruct(x, memo, *rv) File "/home/haru/miniconda3/envs/group/lib/python3.8/copy.py", line 270, in _reconstruct state = deepcopy(state, memo) File "/home/haru/miniconda3/envs/group/lib/python3.8/copy.py", line 146, in deepcopy y = copier(x, memo) File "/home/haru/miniconda3/envs/group/lib/python3.8/copy.py", line 230, in _deepcopy_dict y[deepcopy(key, memo)] = deepcopy(value, memo) File "/home/haru/miniconda3/envs/group/lib/python3.8/copy.py", line 172, in deepcopy y = _reconstruct(x, memo, *rv) File "/home/haru/miniconda3/envs/group/lib/python3.8/copy.py", line 264, in _reconstruct y = func(*args) File "/home/haru/miniconda3/envs/group/lib/python3.8/copy.py", line 263, in <genexpr> args = (deepcopy(arg, memo) for arg in args) File "/home/haru/miniconda3/envs/group/lib/python3.8/copy.py", line 146, in deepcopy y = copier(x, memo) File "/home/haru/miniconda3/envs/group/lib/python3.8/copy.py", line 210, in _deepcopy_tuple y = [deepcopy(a, memo) for a in x] File "/home/haru/miniconda3/envs/group/lib/python3.8/copy.py", line 210, in <listcomp> y = [deepcopy(a, memo) for a in x] File "/home/haru/miniconda3/envs/group/lib/python3.8/copy.py", line 161, in deepcopy rv = reductor(4) File "stringsource", line 2, in View.MemoryView._memoryviewslice.__reduce_cython__ TypeError: no default __reduce__ due to non-trivial __cinit__ ```

and here are the dependencies i have in my conda environment.

``` _libgcc_mutex 0.1 main ase 3.20.1 pypi_0 pypi ca-certificates 2020.12.8 h06a4308_0 cairo 1.16.0 h18b612c_1001 conda-forge certifi 2020.12.5 py38h06a4308_0 chardet 4.0.0 pypi_0 pypi cycler 0.10.0 pypi_0 pypi decorator 4.4.2 pypi_0 pypi fontconfig 2.13.1 he4413a7_1000 conda-forge freetype 2.10.4 h5ab3b9f_0 future 0.18.2 pypi_0 pypi glib 2.66.1 h92f7085_0 icu 58.2 he6710b0_3 idna 2.10 pypi_0 pypi kiwisolver 1.3.1 pypi_0 pypi ld_impl_linux-64 2.33.1 h53a641e_7 libedit 3.1.20191231 h14c3975_1 libffi 3.3 he6710b0_2 libgcc-ng 9.1.0 hdf63c60_0 libpng 1.6.37 hbc83047_0 libstdcxx-ng 9.1.0 hdf63c60_0 libuuid 2.32.1 h14c3975_1000 conda-forge libxcb 1.14 h7b6447c_0 libxml2 2.9.10 hb55368b_3 llvmlite 0.35.0 pypi_0 pypi matplotlib 3.3.3 pypi_0 pypi monty 4.0.2 pypi_0 pypi mpmath 1.1.0 pypi_0 pypi ncurses 6.2 he6710b0_1 networkx 2.5 pypi_0 pypi numba 0.52.0 pypi_0 pypi numpy 1.20.0rc2 pypi_0 pypi openbabel 3.1.1 py38hf4b5c11_1 conda-forge openssl 1.1.1i h27cfd23_0 palettable 3.3.0 pypi_0 pypi pandas 1.2.0 pypi_0 pypi pcre 8.44 he6710b0_0 pillow 8.1.0 pypi_0 pypi pip 20.3.3 py38h06a4308_0 pixman 0.38.0 h516909a_1003 conda-forge plotly 4.14.3 pypi_0 pypi py3dmol 0.9.1 pypi_0 pypi pymatgen 2020.12.31 pypi_0 pypi pyparsing 3.0.0b2 pypi_0 pypi python 3.8.5 h7579374_1 python-dateutil 2.8.1 pypi_0 pypi python_abi 3.8 1_cp38 conda-forge pytz 2020.5 pypi_0 pypi pyxtal 0.1.7 pypi_0 pypi readline 8.0 h7b6447c_0 requests 2.25.1 pypi_0 pypi ruamel-yaml 0.16.12 pypi_0 pypi ruamel-yaml-clib 0.2.2 pypi_0 pypi scipy 1.6.0 pypi_0 pypi setuptools 51.1.2 py38h06a4308_4 six 1.15.0 pypi_0 pypi spglib 1.16.0 pypi_0 pypi sqlite 3.33.0 h62c20be_0 swig 3.0.12 h38cdd7d_3 sympy 1.7.1 pypi_0 pypi tabulate 0.8.7 pypi_0 pypi tk 8.6.10 hbc83047_0 tzdata 2020d h14c3975_0 uncertainties 3.1.5 pypi_0 pypi urllib3 1.26.2 pypi_0 pypi wheel 0.36.2 pyhd3eb1b0_0 xorg-kbproto 1.0.7 h14c3975_1002 conda-forge xorg-libice 1.0.10 h516909a_0 conda-forge xorg-libsm 1.2.3 h84519dc_1000 conda-forge xorg-libx11 1.6.12 h516909a_0 conda-forge xorg-libxext 1.3.4 h516909a_0 conda-forge xorg-libxrender 0.9.10 h516909a_1002 conda-forge xorg-renderproto 0.11.1 h14c3975_1002 conda-forge xorg-xextproto 7.3.0 h14c3975_1002 conda-forge xorg-xproto 7.0.31 h27cfd23_1007 xz 5.2.5 h7b6447c_0 zlib 1.2.11 h7b6447c_3 ```

I am not sure where the problem lies, during installation there were few problems related to numpy deprecated syntax, but nothing of serious note (i thought)

About this issue

Original URL
State: closed
Created 3 years ago
Comments: 17 (10 by maintainers)

Commits related to this issue

try to downgrade scipy #126 — committed to qzhu2017/PyXtal by qzhu2017 3 years ago
deepcopy issue was fixed in scipy-v1.6.1 #126 — committed to qzhu2017/PyXtal by qzhu2017 3 years ago

Most upvoted comments

@Tomoki-YAMASHITA Thank you so much!

Following your inspection, I rewrote the SciPy dependence in the setup.py and requirements.txt. Now it passed the GitHub workflow https://github.com/qzhu2017/PyXtal/actions

We haven’t been able to pass the workflow since last December.

qzhu2017 on Feb 6, 2021