Nglview not showing
samuelmurail opened this issue · 9 comments
samuelmurail commented
Hello,
I have issue with nglview widget not showing with show_pdbid or show_file as the demo works well:
Cheers,
Samuel
hainm commented
@samuelmurail Hi, is this is lab or notebook?
samuelmurail commented
@hainm Hi, this is notebook but I just test it with jupyter-lab and I have the same issue.
Here a list of the conda package I use that might be related to the issue:
ipykernel 6.26.0 pyhf8b6a83_0 conda-forge
ipympl 0.9.3 pyhd8ed1ab_0 conda-forge
ipython 8.16.1 pyh0d859eb_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 8.1.1 pyhd8ed1ab_0 conda-forge
jupyter 1.0.0 pyhd8ed1ab_10 conda-forge
jupyter-lsp 2.2.0 pyhd8ed1ab_0 conda-forge
jupyter_client 8.5.0 pyhd8ed1ab_0 conda-forge
jupyter_console 6.6.3 pyhd8ed1ab_0 conda-forge
jupyter_core 5.5.0 py310hff52083_0 conda-forge
jupyter_events 0.8.0 pyhd8ed1ab_0 conda-forge
jupyter_server 2.9.1 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge
jupyterlab 4.0.8 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.25.0 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.9 pyhd8ed1ab_0 conda-forge
nglview 3.0.8 pyh1da8cd4_0 conda-forge
nodejs 20.8.1 h1990674_0 conda-forge
notebook 7.0.6 pyhd8ed1ab_0 conda-forge
notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge
numpy 1.26.0 py310hb13e2d6_0 conda-forge
python 3.10.13 hd12c33a_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.18.1 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge
python_abi 3.10 4_cp310 conda-forge
samuelmurail commented
I create a minimal conda env :
mamba create -n tmp nglview jupyter -c conda-forge
Package Version Build Channel Size
───────────────────────────────────────────────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────────────────────────────────────────────
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+ backports 1.0 pyhd8ed1ab_3 conda-forge/noarch Cached
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+ charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge/noarch Cached
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+ debugpy 1.8.0 py312h30efb56_1 conda-forge/linux-64 3MB
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+ importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge/noarch 30kB
+ ipykernel 6.26.0 pyhf8b6a83_0 conda-forge/noarch Cached
+ ipython 8.17.2 pyh41d4057_0 conda-forge/noarch Cached
+ ipywidgets 8.1.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ isoduration 20.11.0 pyhd8ed1ab_0 conda-forge/noarch Cached
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+ jsonpointer 2.4 py312h7900ff3_3 conda-forge/linux-64 18kB
+ jsonschema 4.19.2 pyhd8ed1ab_0 conda-forge/noarch Cached
+ jsonschema-specifications 2023.7.1 pyhd8ed1ab_0 conda-forge/noarch Cached
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+ jupyter 1.0.0 pyhd8ed1ab_10 conda-forge/noarch Cached
+ jupyter-lsp 2.2.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ jupyter_client 8.6.0 pyhd8ed1ab_0 conda-forge/noarch 106kB
+ jupyter_console 6.6.3 pyhd8ed1ab_0 conda-forge/noarch Cached
+ jupyter_core 5.5.0 py312h7900ff3_0 conda-forge/linux-64 92kB
+ jupyter_events 0.9.0 pyhd8ed1ab_0 conda-forge/noarch 21kB
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+ jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge/noarch Cached
+ jupyterlab 4.0.8 pyhd8ed1ab_0 conda-forge/noarch Cached
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+ jupyterlab_widgets 3.0.9 pyhd8ed1ab_0 conda-forge/noarch Cached
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+ libblas 3.9.0 19_linux64_openblas conda-forge/linux-64 Cached
+ libcblas 3.9.0 19_linux64_openblas conda-forge/linux-64 Cached
+ libexpat 2.5.0 hcb278e6_1 conda-forge/linux-64 Cached
+ libffi 3.4.2 h7f98852_5 conda-forge/linux-64 Cached
+ libgcc-ng 13.2.0 h807b86a_3 conda-forge/linux-64 Cached
+ libgfortran-ng 13.2.0 h69a702a_3 conda-forge/linux-64 Cached
+ libgfortran5 13.2.0 ha4646dd_3 conda-forge/linux-64 Cached
+ libgomp 13.2.0 h807b86a_3 conda-forge/linux-64 Cached
+ liblapack 3.9.0 19_linux64_openblas conda-forge/linux-64 Cached
+ libnsl 2.0.1 hd590300_0 conda-forge/linux-64 Cached
+ libopenblas 0.3.24 pthreads_h413a1c8_0 conda-forge/linux-64 Cached
+ libsodium 1.0.18 h36c2ea0_1 conda-forge/linux-64 Cached
+ libsqlite 3.44.0 h2797004_0 conda-forge/linux-64 Cached
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+ libuuid 2.38.1 h0b41bf4_0 conda-forge/linux-64 Cached
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+ matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge/noarch Cached
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+ nest-asyncio 1.5.8 pyhd8ed1ab_0 conda-forge/noarch Cached
+ nglview 3.0.8 pyh1da8cd4_0 conda-forge/noarch Cached
+ notebook 7.0.6 pyhd8ed1ab_0 conda-forge/noarch Cached
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+ numpy 1.26.0 py312heda63a1_0 conda-forge/linux-64 Cached
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+ pandoc 3.1.3 h32600fe_0 conda-forge/linux-64 Cached
+ pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge/noarch Cached
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+ pickleshare 0.7.5 py_1003 conda-forge/noarch Cached
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+ platformdirs 4.0.0 pyhd8ed1ab_0 conda-forge/noarch 20kB
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+ prompt-toolkit 3.0.40 pyha770c72_0 conda-forge/noarch Cached
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+ psutil 5.9.5 py312h98912ed_1 conda-forge/linux-64 481kB
+ ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge/noarch Cached
+ pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge/noarch Cached
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+ python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge/noarch Cached
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+ typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ tzdata 2023c h71feb2d_0 conda-forge/noarch Cached
+ uri-template 1.3.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ urllib3 2.1.0 pyhd8ed1ab_0 conda-forge/noarch 85kB
+ wcwidth 0.2.9 pyhd8ed1ab_0 conda-forge/noarch Cached
+ webcolors 1.13 pyhd8ed1ab_0 conda-forge/noarch Cached
+ webencodings 0.5.1 pyhd8ed1ab_2 conda-forge/noarch Cached
+ websocket-client 1.6.4 pyhd8ed1ab_0 conda-forge/noarch Cached
+ wheel 0.41.3 pyhd8ed1ab_0 conda-forge/noarch Cached
+ widgetsnbextension 4.0.9 pyhd8ed1ab_0 conda-forge/noarch Cached
+ xz 5.2.6 h166bdaf_0 conda-forge/linux-64 Cached
+ yaml 0.2.5 h7f98852_2 conda-forge/linux-64 Cached
+ zeromq 4.3.5 h59595ed_0 conda-forge/linux-64 Cached
+ zipp 3.17.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ zlib 1.2.13 hd590300_5 conda-forge/linux-64 CachedI still have the same issue with firefox and chromium-browser, I am running ubuntu 22.04. I hope that could help.
Cheers,
Samuel
hainm commented
@samuelmurail I could reproduce the issue. Let me investigate.
hainm commented
if I download the 3pqr.pdb to local disk
nv.show_file('./3pqr.pdb') does NOT work
nv.show_structure_file('./3pqr.pdb') work
um
hainm commented
um, does the CIF format has change that NGL (nglview uses it) doesn't know how to parse it?
samuelmurail commented
Yes I confirm that using show_structure_file() fix the issue.
Cheers,
Samuel
hainm commented
<deleted. wrong thread>
hainm commented
nglview.show_file should work properly in 3.1.0 now. If not, please file a new case. Thanks.