remove conda imports

[danielschweigert-TRI]

I was able to pip install it using these modifications. Give it a try if it works on your system.

[HakyungKwon-TRI]

[HakyungKwon-TRI]

It doesn't work for me. This is the same error I've gotten in the past. Should we try to compare our envs? I'm on a python 3.6 with the following list of packages:

packages in environment at /Users/ha-kyungkwon/anaconda3/envs/testpip:

#

Name Version Build Channel

anyio 3.5.0 appnope 0.1.2 argon2-cffi 21.3.0 argon2-cffi-bindings 21.2.0 astunparse 1.6.3 async-generator 1.10 attrs 21.4.0 Babel 2.9.1 backcall 0.2.0 bleach 4.1.0 ca-certificates 2021.10.26 hecd8cb5_2 certifi 2021.5.30 py36hecd8cb5_0 cffi 1.15.0 charset-normalizer 2.0.10 contextvars 2.4 coverage 6.2 cycler 0.11.0 dataclasses 0.8 decorator 4.4.2 defusedxml 0.7.1 docopt 0.6.2 entrypoints 0.3 future 0.18.2 googledrivedownloader 0.4 htpmd 0.2.0 idna 3.3 immutables 0.16 importlib-metadata 4.8.3 iniconfig 1.1.1 ipykernel 5.5.6 ipython 7.16.2 ipython-genutils 0.2.0 isodate 0.6.1 jedi 0.17.2 Jinja2 3.0.3 joblib 1.1.0 json5 0.9.6 jsonschema 3.2.0 jupyter-client 7.1.0 jupyter-core 4.9.1 jupyter-server 1.13.1 jupyterlab 3.2.7 jupyterlab-pygments 0.1.2 jupyterlab-server 2.10.3 kiwisolver 1.3.1 libcxx 12.0.0 h2f01273_0 libffi 3.3 hb1e8313_2 MarkupSafe 2.0.1 matplotlib 3.3.4 mdtraj 1.9.7 mistune 0.8.4 monty 2022.1.12.1 mordred 1.2.0 mpmath 1.2.1 nbclassic 0.3.5 nbclient 0.5.9 nbconvert 6.0.7 nbformat 5.1.3 ncurses 6.3 hca72f7f_2 nest-asyncio 1.5.4 networkx 2.5.1 notebook 6.4.7 numpy 1.19.5 openssl 1.1.1m hca72f7f_0 packaging 21.3 palettable 3.3.0 pandas 1.1.5 pandocfilters 1.5.0 parso 0.7.1 pexpect 4.8.0 pickleshare 0.7.5 Pillow 8.4.0 pip 21.2.2 py36hecd8cb5_0 plotly 5.5.0 pluggy 1.0.0 prometheus-client 0.12.0 prompt-toolkit 3.0.24 ptyprocess 0.7.0 py 1.11.0 pycparser 2.21 Pygments 2.11.2 pymatgen 2021.2.8.1 pyparsing 3.0.6 pyrsistent 0.18.0 pytest 6.2.5 pytest-cov 3.0.0 python 3.6.13 h88f2d9e_0 python-dateutil 2.8.2 pytz 2021.3 PyYAML 6.0 pyzmq 22.3.0 rdflib 5.0.0 rdkit-pypi 2021.9.3 readline 8.1.2 hca72f7f_1 requests 2.27.1 ruamel.yaml 0.17.20 ruamel.yaml.clib 0.2.6 scikit-learn 0.23.2 scipy 1.5.4 Send2Trash 1.8.0 setuptools 58.0.4 py36hecd8cb5_0 six 1.16.0 sniffio 1.2.0 spglib 1.16.3 sqlite 3.37.0 h707629a_0 sympy 1.9 tabulate 0.8.9 tenacity 8.0.1 terminado 0.12.1 testpath 0.5.0 threadpoolctl 3.0.0 tk 8.6.11 h7bc2e8c_0 toml 0.10.2 tomli 1.2.3 torch 1.10.1 torch-geometric 2.0.3 torch-scatter 2.0.9 torch-sparse 0.6.12 tornado 6.1 tqdm 4.62.3 traitlets 4.3.3 typing_extensions 4.0.1 uncertainties 3.1.6 urllib3 1.26.8 wcwidth 0.2.5 webencodings 0.5.1 websocket-client 1.2.3 wheel 0.37.1 pyhd3eb1b0_0 xz 5.2.5 h1de35cc_0 yacs 0.1.8 zipp 3.6.0 zlib 1.2.11 h4dc903c_4

[danielschweigert-TRI]

I am on python 3.6.8 MacOS BigSur 11.6

It looks like I have a fewer libraries than you do.

appnope==0.1.2
argon2-cffi==21.3.0
argon2-cffi-bindings==21.2.0
astunparse==1.6.3
async-generator==1.10
attrs==21.4.0
Babel==2.9.1
backcall==0.2.0
bleach==4.1.0
certifi==2021.10.8
cffi==1.15.0
charset-normalizer==2.0.10
contextvars==2.4
coverage==6.2
cycler==0.11.0
dataclasses==0.8
decorator==4.4.2
defusedxml==0.7.1
docopt==0.6.2
entrypoints==0.3
future==0.18.2
googledrivedownloader==0.4
-e git+ssh://git@github.com/TRI-AMDD/htp_md.git@db26a25e2606ec59d7725ee01192094fd0dd3168#egg=htpmd
idna==3.3
immutables==0.16
importlib-metadata==4.8.3
iniconfig==1.1.1
ipykernel==5.5.6
ipython==7.16.2
ipython-genutils==0.2.0
isodate==0.6.1
jedi==0.17.2
Jinja2==3.0.3
joblib==1.1.0
json5==0.9.6
jsonschema==3.2.0
jupyter-client==7.1.0
jupyter-core==4.9.1
jupyter-server==1.13.1
jupyterlab==3.2.7
jupyterlab-pygments==0.1.2
jupyterlab-server==2.10.3
kiwisolver==1.3.1
MarkupSafe==2.0.1
matplotlib==3.3.4
mdtraj==1.9.7
mistune==0.8.4
monty==2022.1.12.1
mordred==1.2.0
mpmath==1.2.1
nbclassic==0.3.5
nbclient==0.5.9
nbconvert==6.0.7
nbformat==5.1.3
nest-asyncio==1.5.4
networkx==2.5.1
notebook==6.4.7
numpy==1.19.5
packaging==21.3
palettable==3.3.0
pandas==1.1.5
pandocfilters==1.5.0
parso==0.7.1
pexpect==4.8.0
pickleshare==0.7.5
Pillow==8.4.0
plotly==5.5.0
pluggy==1.0.0
prometheus-client==0.12.0
prompt-toolkit==3.0.24
ptyprocess==0.7.0
py==1.11.0
pycparser==2.21
Pygments==2.11.2
pymatgen==2021.2.8.1
pyparsing==3.0.6
pyrsistent==0.18.0
pytest==6.2.5
pytest-cov==3.0.0
python-dateutil==2.8.2
pytz==2021.3
PyYAML==6.0
pyzmq==22.3.0
rdflib==5.0.0
rdkit-pypi==2021.9.3
requests==2.27.1
ruamel.yaml==0.17.20
ruamel.yaml.clib==0.2.6
scikit-learn==0.23.2
scipy==1.5.4
Send2Trash==1.8.0
six==1.16.0
sniffio==1.2.0
spglib==1.16.3
sympy==1.9
tabulate==0.8.9
tenacity==8.0.1
terminado==0.12.1
testpath==0.5.0
threadpoolctl==3.0.0
toml==0.10.2
tomli==1.2.3
torch==1.10.1
torch-geometric==2.0.3
torch-scatter==2.0.9
torch-sparse==0.6.12
tornado==6.1
tqdm==4.62.3
traitlets==4.3.3
typing_extensions==4.0.1
uncertainties==3.1.6
urllib3==1.26.8
wcwidth==0.2.5
webencodings==0.5.1
websocket-client==1.2.3
yacs==0.1.8
zipp==3.6.0```

[danielschweigert-TRI]

@HakyungKwon-TRI I found this related to the error you are seeing: https://github.com/pyg-team/pytorch_geometric/issues/3484 In the latest commit, I use the recommended remedy; this might fix it.

[HakyungKwon-TRI]

env.yml (https://github.com/TRI-AMDD/htp_md/blob/master/env.yml) has a cpuonly requirement (instead of CUDA11.3, in the recommended remedy). I'll invoke @txie-93 to shed some light on the cpuonly vs. CUDA requirement.

[txie-93]

Either cpuonly or CUDA will work, but they cannot be installed together. I use cpuonly because our computation is cheap and GPU is probably not needed. But we can use CUDA install as well.

[HakyungKwon-TRI]

Still running into the same issues, even with the newly committed changes.