tridentbio
Cannot show structure in pip version
Hello, I use Arch Linux and I have installed JupyterLab from pip.
I installed trident-chemwidgets tried the Scatter_widget.ipynb from examples but it cannot display structures. Hovering and click "Show Structures" displayed nothing.
I tried conda version with JupyterLab in conda and everything was OK.
This is a list of pip list output:
Package Version
------------------------------ -----------
anyio 3.6.1
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
asttokens 2.0.8
attrs 22.1.0
Babel 2.10.3
backcall 0.2.0
backports.functools-lru-cache 1.6.4
beautifulsoup4 4.11.1
black 22.6.0
bleach 5.0.1
brotlipy 0.7.0
certifi 2022.6.15
cffi 1.15.1
charset-normalizer 2.1.1
click 8.1.3
colorama 0.4.5
conda 4.14.0
conda-package-handling 1.8.1
cryptography 37.0.4
cycler 0.11.0
debugpy 1.6.3
decorator 5.1.1
defusedxml 0.7.1
entrypoints 0.4
executing 1.0.0
fastjsonschema 2.16.1
flit_core 3.7.1
fonttools 4.37.1
greenlet 1.1.3
idna 3.3
importlib-metadata 4.11.4
importlib-resources 5.9.0
ipykernel 6.15.2
ipython 8.4.0
ipython-genutils 0.2.0
ipywidgets 8.0.2
isort 5.10.1
jedi 0.18.1
Jinja2 3.1.2
joblib 1.1.0
json5 0.9.10
jsonschema 4.15.0
jupyter 1.0.0
jupyter_client 7.3.5
jupyter-console 6.4.4
jupyter-core 4.11.1
jupyter-server 1.18.1
jupyterlab 3.4.6
jupyterlab-code-formatter 1.5.3
jupyterlab-language-pack-zh-CN 3.4.post4
jupyterlab-pygments 0.2.2
jupyterlab_server 2.15.1
jupyterlab-widgets 3.0.3
kiwisolver 1.4.4
lxml 4.9.1
MarkupSafe 2.1.1
matplotlib 3.5.3
matplotlib-inline 0.1.6
mistune 2.0.4
munkres 1.1.4
mypy-extensions 0.4.3
nbclassic 0.4.3
nbclient 0.6.7
nbconvert 7.0.0
nbformat 5.4.0
nest-asyncio 1.5.5
notebook 6.4.12
notebook-shim 0.1.0
numpy 1.23.2
packaging 21.3
pandas 1.4.4
pandas-datareader 0.10.0
pandocfilters 1.5.0
parso 0.8.3
pathspec 0.10.1
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.2.0
pip 22.2.2
pkgutil_resolve_name 1.3.10
platformdirs 2.5.2
ply 3.11
Pmw 2.0.1
prometheus-client 0.14.1
prompt-toolkit 3.0.31
psutil 5.9.2
ptyprocess 0.7.0
pure-eval 0.2.2
pycairo 1.21.0
pycosat 0.6.3
pycparser 2.21
Pygments 2.13.0
pymol 2.5.0
pyOpenSSL 22.0.0
pyparsing 3.0.9
PyQt5 5.15.7
PyQt5-sip 12.11.0
pyrsistent 0.18.1
PySocks 1.7.1
python-dateutil 2.8.2
pytz 2022.2.1
pyzmq 23.2.1
qtconsole 5.3.2
QtPy 2.2.0
reportlab 3.5.68
requests 2.28.1
ruamel-yaml-conda 0.15.80
scikit-learn 1.1.2
scipy 1.9.1
Send2Trash 1.8.0
setuptools 65.3.0
sip 6.6.2
six 1.16.0
sniffio 1.3.0
soupsieve 2.3.2.post1
SQLAlchemy 1.4.40
stack-data 0.5.0
terminado 0.15.0
threadpoolctl 3.1.0
tinycss2 1.1.1
toml 0.10.2
tomli 2.0.1
toolz 0.12.0
tornado 6.2
tqdm 4.64.1
traitlets 5.3.0
trident-chemwidgets 0.2.1
typing_extensions 4.3.0
unicodedata2 14.0.0
urllib3 1.26.11
wcwidth 0.2.5
webencodings 0.5.1
websocket-client 1.4.1
wheel 0.37.1
widgetsnbextension 4.0.3
zipp 3.8.1
Could it be a problem of missing package? Thank you.
Thanks for reporting this issue @pikakolendo02! I have a suspicion that this may be related to serving the RDKit JS assets to the front end. We have some custom filesystem manipulations we perform on install and something may be strange with the pip version/Arch Linux combination. We generally test the releases on Mac and Windows, but not Arch Linux. I'll see if I can replicate your issue on Mac first, then in Docker with Arch if I can't replicate it there. I'll let you know if I have a solution for you. If there's no easy fix, we'll make sure to have Linux compatibility in our next release. In the meantime, I'd recommend sticking with the conda version if that's working. Will update here once I've had a chance to test it.
We took a look at this bug again on Windows, MacOS, and Ubuntu and weren't able to replicate the issue: the pip installed version displayed the structures on all systems. Would it be possible for you to load the developer console and report any error messages there? Chrome and Firefox instructions here, respectively. Thanks in advance!
Thank you for reply @TShimko126 .
pip ver:
(匿名) means anonymous.
conda ver:
I hope these could help you.
Thanks for the screenshots, these are very helpful. I believe this is probably a permissions issue with our local assets provider. TCW needs write access to the Jupyter extension directories as well as some other files. I expect that this might not be possible if you're installing with pip globally. My thought is that conda is using a virtualenv directory with looser permissions to which TCW can write on setup.
Are you installing with pip globally or within a different vitualenv provider? Thanks!
@gilberto-md: We should add a warning if TCW doesn't have write permissions to the Jupyter target dirs on install.
These packages are installed locally in ~/.local/lib/python3.10/site-packages
pip list --user
Package Version
------------------------------ -----------
anyio 3.6.1
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
Babel 2.10.3
beautifulsoup4 4.11.1
bleach 5.0.1
debugpy 1.6.3
defusedxml 0.7.1
entrypoints 0.4
fastjsonschema 2.16.1
ipykernel 6.15.2
ipython-genutils 0.2.0
ipywidgets 8.0.2
Jinja2 3.1.2
json5 0.9.10
jsonschema 4.15.0
jupyter_client 7.3.5
jupyter-core 4.11.1
jupyter-server 1.18.1
jupyterlab 3.4.6
jupyterlab-code-formatter 1.5.3
jupyterlab-language-pack-zh-CN 3.4.post4
jupyterlab-pygments 0.2.2
jupyterlab_server 2.15.1
jupyterlab-widgets 3.0.3
MarkupSafe 2.1.1
mistune 2.0.4
nbclassic 0.4.3
nbclient 0.6.7
nbconvert 7.0.0
nbformat 5.4.0
nest-asyncio 1.5.5
notebook 6.4.12
notebook-shim 0.1.0
pandocfilters 1.5.0
prometheus-client 0.14.1
pyrsistent 0.18.1
pyzmq 23.2.1
rdkit 2022.3.5
Send2Trash 1.8.0
sniffio 1.3.0
soupsieve 2.3.2.post1
terminado 0.15.0
tinycss2 1.1.1
tornado 6.2
trident-chemwidgets 0.2.1
webencodings 0.5.1
websocket-client 1.4.1
widgetsnbextension 4.0.3
Hi, I am having the same issue. I did install to global pip on a virtual Linux machine. Everything works except structure drawing from selection or the tooltip in the scatter plot. Do you know if changing permissions somewhere would help here?
I also just installed in a venv on a Mac, same issue. Pip is installing version 0.2.1.
I'm using jupyter notebooks (not lab):
>> jupyter nbextension list
Known nbextensions:
config dir: /Users/.../venv/etc/jupyter/nbconfig
notebook section
jupyterlab-plotly/extension enabled
- Validating: OK
trident_chemwidgets/extension enabled
- Validating: OK
jupyter-js-widgets/extension enabled
- Validating: OK
Thanks for uploading the package. I'm on an M1 mac and I still have the problem that no interactive features of the plots are basically happening. Any advices?
Many thanks
Sorry for the delay here, we've been quite busy with some other projects so maintenance on the chemwidgets package has fallen a bit behind.
@johnberroa - Is it possible for you to try with the conda installation (conda install -c conda-forge trident-chemwidgets)? We seem to have better luck getting the rdkit.js assets to the right location/permissions with conda than with pip.
@GattiMh - I don't think any of the devs have an M1 mac to test the package on. Could you provide some more information regarding your browser (and if possible screenshot the console window in your browser as @johnberroa did in his message above)?
Thanks to both of you for reporting these issues. A fix will probably take a little bit since we are busy working on other tasks at the moment, but for now I'd recommend using the conda version when possible and seeing if that fixes your issues. If not, please let me know and we can bump this higher on the priority list.
Sorry for the delay here, we've been quite busy with some other projects so maintenance on the chemwidgets package has fallen a bit behind.
@johnberroa - Is it possible for you to try with the conda installation (
conda install -c conda-forge trident-chemwidgets)? We seem to have better luck getting the rdkit.js assets to the right location/permissions with conda than with pip.@GattiMh - I don't think any of the devs have an M1 mac to test the package on. Could you provide some more information regarding your browser (and if possible screenshot the console window in your browser as @johnberroa did in his message above)?
Thanks to both of you for reporting these issues. A fix will probably take a little bit since we are busy working on other tasks at the moment, but for now I'd recommend using the conda version when possible and seeing if that fixes your issues. If not, please let me know and we can bump this higher on the priority list.
Thanks! I have sorted the problem by doing conda/mamba install nodejs
I've also done brew install node and brew install npmbut maybe this is not important and the conda will be enough
Hope that helps the others as well.
Best wishes
Same issue on Linux, can't solve it using conda install -c conda-forge trident-chemwidgets. Have you solved it? Any advice? Thanks!
