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Toolkit fails to read Path objects
See original GitHub issueDescribe the bug
Toolkit fails to read file if a Path object is used instead of a str.
To Reproduce
import traceback
from pathlib import Path
from openff.toolkit.topology import Molecule
SDF_PATH = "ethanol.sdf"
# no error
Molecule.from_file(SDF_PATH)
# Exception: If providing a file-like object for reading molecules, the format must be specified
try:
Molecule.from_file(Path(SDF_PATH))
except Exception as e:
traceback.print_exception(e)
# But this doesn't seem to work either
try:
Molecule.from_file(Path(SDF_PATH), file_format="sdf")
except Exception as e:
traceback.print_exception(e)
Output
Traceback (most recent call last):
File "/home/mmh/Projects/scratch/openff-toolkit-test.py", line 13, in <module>
Molecule.from_file(Path(SDF_PATH))
File "/home/mmh/miniconda3/envs/openff-toolkit-test/lib/python3.10/site-packages/openff/toolkit/topology/molecule.py", line 4625, in from_file
raise Exception(
Exception: If providing a file-like object for reading molecules, the format must be specified
Traceback (most recent call last):
File "/home/mmh/Projects/scratch/openff-toolkit-test.py", line 19, in <module>
Molecule.from_file(Path(SDF_PATH), file_format="sdf")
File "/home/mmh/miniconda3/envs/openff-toolkit-test/lib/python3.10/site-packages/openff/toolkit/topology/molecule.py", line 4718, in from_file
raise Exception("Unable to read molecule from file: {}".format(file_path))
Exception: Unable to read molecule from file: ethanol.sdf
Computing environment (please complete the following information):
- Operating system
$ uname -a
Linux d174 5.17.15-76051715-generic #202206141358~1655919116~22.04~1db9e34 SMP PREEMPT Wed Jun 22 19 x86_64 x86_64 x86_64 GNU/Linux
$ cat /etc/os-release
NAME="Pop!_OS"
VERSION="22.04 LTS"
ID=pop
ID_LIKE="ubuntu debian"
PRETTY_NAME="Pop!_OS 22.04 LTS"
VERSION_ID="22.04"
HOME_URL="https://pop.system76.com"
SUPPORT_URL="https://support.system76.com"
BUG_REPORT_URL="https://github.com/pop-os/pop/issues"
PRIVACY_POLICY_URL="https://system76.com/privacy"
VERSION_CODENAME=jammy
UBUNTU_CODENAME=jammy
LOGO=distributor-logo-pop-os
- Output of running
conda list
# packages in environment at /home/mmh/miniconda3/envs/openff-toolkit-test:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
amberlite 22.0 pypi_0 pypi
ambertools 22.0 py310hfade12a_1 conda-forge
amberutils 21.0 pypi_0 pypi
arpack 3.7.0 hdefa2d7_2 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
black 22.6.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.1 h83bc5f7_3 conda-forge
boost 1.74.0 py310h7c3ba0c_5 conda-forge
boost-cpp 1.74.0 h75c5d50_8 conda-forge
brotli 1.0.9 h166bdaf_7 conda-forge
brotli-bin 1.0.9 h166bdaf_7 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.6.15 ha878542_0 conda-forge
cairo 1.16.0 ha61ee94_1011 conda-forge
certifi 2022.6.15 py310hff52083_0 conda-forge
click 8.1.3 py310hff52083_0 conda-forge
cloudpathlib 0.9.0 py310hff52083_0 conda-forge
cudatoolkit 11.7.0 hd8887f6_10 conda-forge
curl 7.83.1 h7bff187_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.30 py310hd8f1fbe_0 conda-forge
dataclasses 0.8 pyhc8e2a94_3 conda-forge
expat 2.4.8 h27087fc_0 conda-forge
fftw 3.3.10 nompi_h77c792f_102 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.0 h8e229c2_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.34.4 py310h5764c6d_0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
greenlet 1.1.2 py310hd8f1fbe_2 conda-forge
hdf4 4.2.15 h10796ff_3 conda-forge
hdf5 1.12.1 nompi_h2386368_104 conda-forge
icu 70.1 h27087fc_0 conda-forge
importlib-metadata 4.11.4 py310hff52083_0 conda-forge
isort 5.10.1 pyhd8ed1ab_0 conda-forge
jpeg 9e h166bdaf_2 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.3 py310hbf28c38_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 15_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_7 conda-forge
libbrotlidec 1.0.9 h166bdaf_7 conda-forge
libbrotlienc 1.0.9 h166bdaf_7 conda-forge
libcblas 3.9.0 15_linux64_openblas conda-forge
libcurl 7.83.1 h7bff187_0 conda-forge
libdeflate 1.12 h166bdaf_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgfortran-ng 12.1.0 h69a702a_16 conda-forge
libgfortran5 12.1.0 hdcd56e2_16 conda-forge
libglib 2.72.1 h2d90d5f_0 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 15_linux64_openblas conda-forge
libnetcdf 4.8.1 nompi_h329d8a1_102 conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.20 pthreads_h78a6416_0 conda-forge
libpng 1.6.37 h753d276_3 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-ng 12.1.0 ha89aaad_16 conda-forge
libtiff 4.4.0 hc85c160_1 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp 1.2.2 h3452ae3_0 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libzip 1.9.2 hc869a4a_0 conda-forge
libzlib 1.2.12 h166bdaf_1 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
lzo 2.10 h516909a_1000 conda-forge
matplotlib-base 3.5.2 py310h5701ce4_0 conda-forge
mdtraj 1.9.7 py310hd8d60c7_1 conda-forge
mmpbsa-py 16.0 pypi_0 pypi
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mypy_extensions 0.4.3 py310hff52083_5 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
netcdf-fortran 4.5.4 nompi_h2b6e579_100 conda-forge
networkx 2.8.4 pyhd8ed1ab_0 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
numexpr 2.8.0 py310hf05e7a9_102 conda-forge
numpy 1.23.1 py310h53a5b5f_0 conda-forge
ocl-icd 2.3.1 h7f98852_0 conda-forge
ocl-icd-system 1.0.0 1 conda-forge
openff-forcefields 2.0.0 pyh6c4a22f_0 conda-forge
openff-toolkit 0.10.6 pyhd8ed1ab_0 conda-forge
openff-toolkit-base 0.10.6 pyhd8ed1ab_0 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openmm 7.7.0 py310hccf1d78_1 conda-forge
openssl 1.1.1q h166bdaf_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
packmol 20.010 h86c2bf4_0 conda-forge
packmol-memgen 1.2.3rc0 pypi_0 pypi
pandas 1.4.3 py310h769672d_0 conda-forge
parmed 3.4.3 py310hd8f1fbe_2 conda-forge
pathspec 0.9.0 pyhd8ed1ab_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pdb4amber 22.0 pypi_0 pypi
perl 5.32.1 2_h7f98852_perl5 conda-forge
pillow 9.2.0 py310he619898_0 conda-forge
pip 22.1.2 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
platformdirs 2.5.1 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pycairo 1.21.0 py310h96fc21a_1 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pytables 3.7.0 py310hf5df6ce_0 conda-forge
python 3.10.5 h582c2e5_0_cpython conda-forge
python-constraint 1.4.0 py_0 conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.10 2_cp310 conda-forge
pytraj 2.0.6 pypi_0 pypi
pytz 2022.1 pyhd8ed1ab_0 conda-forge
pyupgrade 2.37.1 pyhd8ed1ab_0 conda-forge
rdkit 2022.03.4 py310h1c297d8_0 conda-forge
readline 8.1.2 h0f457ee_0 conda-forge
reportlab 3.5.68 py310h94fcab3_1 conda-forge
sander 22.0 pypi_0 pypi
scipy 1.8.1 py310h7612f91_0 conda-forge
setuptools 63.1.0 py310hff52083_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smirnoff99frosst 1.1.0 pyh44b312d_0 conda-forge
snappy 1.1.9 hbd366e4_1 conda-forge
sqlalchemy 1.4.39 py310h5764c6d_0 conda-forge
sqlite 3.39.0 h4ff8645_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tokenize-rt 4.2.1 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
typed-ast 1.5.4 py310h5764c6d_0 conda-forge
typing-extensions 4.3.0 hd8ed1ab_0 conda-forge
typing_extensions 4.3.0 pyha770c72_0 conda-forge
tzdata 2022a h191b570_0 conda-forge
unicodedata2 14.0.0 py310h5764c6d_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zipp 3.8.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.12 h166bdaf_1 conda-forge
zstd 1.5.2 h8a70e8d_2 conda-forge
Additional context
Issue Analytics
- State:
- Created a year ago
- Reactions:2
- Comments:7 (4 by maintainers)
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My quick impression is that we should use
Pathobjects internally where possible, which I understand to be a popular suggestion[^1]. But we should convert out tostror another object that we trust the wrapped toolkits will digest. This should enableMolecule.from_file(path_object)to work as a user would expect, although maybe a bit trickier to ensureToolkitWrapper.from_fileand similar methods have the same input sanitization.[^1]: I’m apparently forgetful enough to raise the same feature request twice! #943 #740
Great - looks like we have a path forward here. I’ll first to the band-aid fix of making our public API not choke on
Pathobjects and, if that’s as painless as I expect it to be, consider doing more internal refactors. I do want to get this out pretty quickly, though, so I might not refactor everything.