Install fails with jupyter lab build
Closed this issue · 1 comments
clil16 commented
Describe the bug
Following the instructions for installing the dependencies for cryoDRGN jupyter returns an error when running jupyter lab build.
I realize this is most likely an issue with Jupyter but has anyone resolved the issue? This has been seen on Ubuntu 22.04 and RHEL 8.7 with Miniconda 3.
The relevant error from the jupyter debug log is (as near as I can tell):
...snip....
[LabBuildApp] > node /sw/miniconda/3/envs/cryodrgn/lib/python3.9/site-packages/jupyterlab/staging/yarn.js run build:prod:minimize
[LabBuildApp] yarn run v1.21.1
$ webpack --config webpack.prod.minimize.config.js
[webpack-cli] /sw/miniconda/3/envs/cryodrgn/share/jupyter/lab/staging/node_modules/webpack/lib/cli.js:67
/(\p{Uppercase_Letter}+|\p{Lowercase_Letter}|\d)(\p{Uppercase_Letter}+)/gu,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
SyntaxError: Invalid regular expression: /(\p{Uppercase_Letter}+|\p{Lowercase_Letter}|\d)(\p{Uppercase_Letter}+)/: Invalid property name
...snip...
To Reproduce
(base) $ conda create -y --name cryodrgn python=3.9
(base) $ conda activate cryodrgn
(cryodrgn) $ conda install -y pytorch cudatoolkit -c pytorch
(cryodrgn) $ conda install -y pandas
(cryodrgn) $ conda install -y seaborn scikit-learn
(cryodrgn) $ conda install -y umap-learn jupyterlab ipywidgets cufflinks-py "nodejs>=15.12.0" -c conda-forge
(cryodrgn) $ jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build
(cryodrgn) $ jupyter labextension install jupyterlab-plotly --no-build
(cryodrgn) $ jupyter labextension install plotlywidget --no-build
(cryodrgn) $ jupyter lab build
Expected behavior
The command jupyter lab build should exit successfully.
Additional context
- Conda environment packages and their versions:
(cryodrgn) $ conda list
# packages in environment at /sw/miniconda/3/envs/cryodrgn:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
anyio 3.6.2 pyhd8ed1ab_0 conda-forge
appdirs 1.4.4 pyhd3eb1b0_0
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py39hb9d737c_2 conda-forge
asttokens 2.2.1 pyhd8ed1ab_0 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
babel 2.12.1 pyhd8ed1ab_1 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 pyhd8ed1ab_3 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.2 pyha770c72_0 conda-forge
blas 1.0 mkl
bleach 6.0.0 pyhd8ed1ab_0 conda-forge
bottleneck 1.3.5 py39h7deecbd_0
brotli 1.0.9 h5eee18b_7
brotli-bin 1.0.9 h5eee18b_7
brotlipy 0.7.0 py39h27cfd23_1003
ca-certificates 2023.5.7 hbcca054_0 conda-forge
certifi 2023.5.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py39h5eee18b_3
charset-normalizer 2.0.4 pyhd3eb1b0_0
chart-studio 1.1.0 pyh9f0ad1d_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
colorlover 0.3.0 py_0 conda-forge
contourpy 1.0.5 py39hdb19cb5_0
cryptography 39.0.1 py39h9ce1e76_0
cudatoolkit 11.3.1 h2bc3f7f_2
cufflinks-py 0.17.3 py_0 conda-forge
cycler 0.11.0 pyhd3eb1b0_0
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
executing 1.2.0 pyhd8ed1ab_0 conda-forge
filelock 3.9.0 py39h06a4308_0
flit-core 3.8.0 pyhd8ed1ab_0 conda-forge
fonttools 4.25.0 pyhd3eb1b0_0
freetype 2.12.1 h4a9f257_0
giflib 5.2.1 h5eee18b_3
gmp 6.2.1 h295c915_3
gmpy2 2.1.2 py39heeb90bb_0
icu 58.2 hf484d3e_1000 conda-forge
idna 3.4 py39h06a4308_0
importlib-metadata 6.6.0 pyha770c72_0 conda-forge
importlib_resources 5.2.0 pyhd3eb1b0_1
intel-openmp 2023.1.0 hdb19cb5_46305
ipykernel 5.5.5 py39hef51801_0 conda-forge
ipython 8.13.2 pyh41d4057_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 8.0.6 pyhd8ed1ab_0 conda-forge
jedi 0.18.2 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 py39h06a4308_0
joblib 1.1.1 py39h06a4308_0
jpeg 9e h5eee18b_1
json5 0.9.5 pyh9f0ad1d_0 conda-forge
jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge
jupyter_client 7.0.6 pyhd8ed1ab_0 conda-forge
jupyter_core 4.12.0 py39hf3d152e_0 conda-forge
jupyter_server 1.23.6 pyhd8ed1ab_0 conda-forge
jupyterlab 3.5.3 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.22.1 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.7 pyhd8ed1ab_0 conda-forge
kiwisolver 1.4.4 py39h6a678d5_0
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.38 h1181459_1
lerc 3.0 h295c915_0
libbrotlicommon 1.0.9 h5eee18b_7
libbrotlidec 1.0.9 h5eee18b_7
libbrotlienc 1.0.9 h5eee18b_7
libdeflate 1.17 h5eee18b_0
libffi 3.4.2 h6a678d5_6
libgcc-ng 11.2.0 h1234567_1
libgfortran-ng 11.2.0 h00389a5_1
libgfortran5 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libllvm11 11.1.0 hf817b99_2 conda-forge
libpng 1.6.39 h5eee18b_0
libsodium 1.0.18 h36c2ea0_1 conda-forge
libstdcxx-ng 11.2.0 h1234567_1
libtiff 4.5.0 h6a678d5_2
libuv 1.44.2 h5eee18b_0
libwebp 1.2.4 h11a3e52_1
libwebp-base 1.2.4 h5eee18b_1
llvmlite 0.39.1 py39he621ea3_0
lz4-c 1.9.4 h6a678d5_0
markupsafe 2.1.1 py39h7f8727e_0
matplotlib-base 3.7.1 py39h417a72b_1
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mistune 2.0.5 pyhd8ed1ab_0 conda-forge
mkl 2023.1.0 h6d00ec8_46342
mkl-service 2.4.0 py39h5eee18b_1
mkl_fft 1.3.6 py39h417a72b_1
mkl_random 1.2.2 py39h417a72b_1
mpc 1.1.0 h10f8cd9_1
mpfr 4.0.2 hb69a4c5_1
mpmath 1.2.1 py39h06a4308_0
munkres 1.1.4 py_0
nbclassic 1.0.0 pyh8b2e9e2_0 conda-forge
nbclient 0.7.4 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.3.1 pyhd8ed1ab_0 conda-forge
nbformat 5.8.0 pyhd8ed1ab_0 conda-forge
ncurses 6.4 h6a678d5_0
nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge
networkx 2.8.4 py39h06a4308_1
nodejs 18.15.0 ha637b67_0
notebook 6.5.4 pyha770c72_0 conda-forge
notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge
numba 0.56.4 py39h417a72b_0
numexpr 2.8.4 py39hc78ab66_1
numpy 1.23.5 py39hf6e8229_1
numpy-base 1.23.5 py39h060ed82_1
openssl 1.1.1t h7f8727e_0
packaging 23.0 py39h06a4308_0
pandas 1.5.3 py39h417a72b_0
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pexpect 4.8.0 pyh1a96a4e_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.4.0 py39h6a678d5_0
pip 23.0.1 py39h06a4308_0
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge
plotly 5.14.1 pyhd8ed1ab_0 conda-forge
pooch 1.4.0 pyhd3eb1b0_0
prometheus_client 0.16.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.38 pyha770c72_0 conda-forge
prompt_toolkit 3.0.38 hd8ed1ab_0 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd3eb1b0_0
pygments 2.15.1 pyhd8ed1ab_0 conda-forge
pynndescent 0.5.10 pyh1a96a4e_0 conda-forge
pyopenssl 23.0.0 py39h06a4308_0
pyparsing 3.0.9 py39h06a4308_0
pyrsistent 0.18.0 py39heee7806_0
pysocks 1.7.1 py39h06a4308_0
python 3.9.16 h7a1cb2a_2
python-cufflinks 0.17.3 py_0 conda-forge
python-dateutil 2.8.2 pyhd3eb1b0_0
python-fastjsonschema 2.16.3 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytorch 2.0.1 py3.9_cpu_0 pytorch
pytorch-mutex 1.0 cpu pytorch
pytz 2022.7 py39h06a4308_0
pyzmq 19.0.2 py39hb69f2a1_2 conda-forge
readline 8.2 h5eee18b_0
requests 2.29.0 py39h06a4308_0
retrying 1.3.3 py_2 conda-forge
scikit-learn 1.2.2 py39h6a678d5_0
scipy 1.10.1 py39hf6e8229_1
seaborn 0.12.2 py39h06a4308_0
send2trash 1.8.2 pyh41d4057_0 conda-forge
setuptools 66.0.0 py39h06a4308_0
six 1.16.0 pyhd3eb1b0_1
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge
sqlite 3.41.2 h5eee18b_0
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
sympy 1.11.1 py39h06a4308_0
tbb 2021.8.0 hdb19cb5_0
tenacity 8.2.2 pyhd8ed1ab_0 conda-forge
terminado 0.17.1 pyh41d4057_0 conda-forge
threadpoolctl 2.2.0 pyh0d69192_0
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h1ccaba5_0
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.1 py39hb9d737c_3 conda-forge
tqdm 4.65.0 pyhd8ed1ab_1 conda-forge
traitlets 5.9.0 pyhd8ed1ab_0 conda-forge
typing_extensions 4.5.0 py39h06a4308_0
tzdata 2023c h04d1e81_0
umap-learn 0.5.3 py39hf3d152e_0 conda-forge
urllib3 1.26.15 py39h06a4308_0
wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
websocket-client 1.5.1 pyhd8ed1ab_0 conda-forge
wheel 0.38.4 py39h06a4308_0
widgetsnbextension 4.0.7 pyhd8ed1ab_0 conda-forge
xz 5.4.2 h5eee18b_0
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zipp 3.11.0 py39h06a4308_0
zlib 1.2.13 h5eee18b_0
zstd 1.5.5 hc292b87_0
- Jupyter lab extensions:
(cryodrgn) $ jupyter labextension list
JupyterLab v3.5.3
/sw/miniconda/3/envs/cryodrgn/share/jupyter/labextensions
jupyterlab-plotly v5.14.1 enabled OK
jupyterlab_pygments v0.2.2 enabled OK (python, jupyterlab_pygments)
@jupyter-widgets/jupyterlab-manager v5.0.7 enabled OK (python, jupyterlab_widgets)
Other labextensions (built into JupyterLab)
app dir: /sw/miniconda/3/envs/cryodrgn/share/jupyter/lab
plotlywidget v4.14.3 enabled OK
Build recommended, please run `jupyter lab build`:
plotlywidget needs to be included in build
- The jupyter debug log file is attached to this issue
michal-g commented
As of #331 we recommend avoiding using the plotly widgets if you are having trouble with the jupyterlab installation and using the cryodrgn filter interactive interface instead. The manner in which the jupyterlab extension dependencies are specified is inherently unstable as it is outside of the package indices used by conda, and although this may change at some point, for now we are trying an implementation that only depends on matplotlib.
Example usage:
cryodrgn analyze 01_cryodrgn256 24
cryodrgn filter 01_cryodrgn256