Open feribg opened 5 years ago
tschm
commented
5 years ago I guess you have installed beakerx via pip rather than using the beakerx Docker container. Using Docker this works without problems. Just try docker run -p 8888:8888 beakerx/beakerx and run your code in a notebook. It will work. I had the same issue you have observed while trying to install beakerx in a container from the Jupyter family...
feribg
commented
5 years ago That's surprising, I installed it via conda actually and using it in jupyter lab. Sadly docker is a no go for me. Do you know the root cause for this and what would be the difference between the docker version and the conda version. Could it also be because of using jupyter lab instead of notebook.
tschm
commented
5 years ago Yes, I tried with conda into a Jupyter container, too. Won't work either. I don't know enough about JavaScript to drill into such isssues. I stick to the Docker container. Do yourself a favor :-) You have Jupyter in the beaker container :-) It's much easier using their prebuilt Docker containers...
tschm
commented
5 years ago You may want to check #8003 :-)
feribg
commented
5 years ago You may want to check #8003 :-)
Just out of curiousity whats the jupyter lab and beakerX version you see reported in your docker image? I have a feeling it's a version issue not so much an environment thing, because I had a peak at the Dockerfile and env setup and nothing stands out, it's basically a conda install of beakerx, ipywidget and jupyter, pretty much what i'm doing.
The workaround in the ticket works, using integers, but it's terrible from a usability standpoint, since they carry little meaning to a human observer.
tschm
commented
5 years ago Here's my conda list within the container:
# Name Version Build Channel
alembic 0.9.9 py_0 conda-forge
asn1crypto 0.24.0 py36_0 conda-forge
attrs 18.1.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
beakerx 1.0.0 dev_0 <develop>
bleach 2.1.3 py_0 conda-forge
ca-certificates 2019.3.9 hecc5488_0 conda-forge
certifi 2019.3.9 py36_0 conda-forge
cffi 1.11.5 py36_0 conda-forge
chardet 3.0.4 py36_0 conda-forge
configurable-http-proxy 3.1.0 node8_1 conda-forge
cryptography 2.6.1 py36h9d9f1b6_0 conda-forge
cvxpy 1.0.14 py36hf484d3e_0 conda-forge
cvxpy-base 1.0.14 py36hf484d3e_0 conda-forge
decorator 4.3.0 py_0 conda-forge
dill 0.2.9 py36_0 conda-forge
ecos 2.0.7 py36h3010b51_1000 conda-forge
entrypoints 0.2.3 py36_1 conda-forge
fastcache 1.0.2 py36h14c3975_1001 conda-forge
fontconfig 2.13.1 he4413a7_1000 conda-forge
freetype 2.10.0 he983fc9_0 conda-forge
future 0.17.1 py36_1000 conda-forge
gmp 6.1.2 0 conda-forge
html5lib 1.0.1 py_0 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
idna 2.6 py36_1 conda-forge
intel-openmp 2018.0.0 8
ipykernel 4.8.2 py36_0 conda-forge
ipython 6.4.0 py36_0 conda-forge
ipython_genutils 0.2.0 py36_0 conda-forge
ipywidgets 7.2.1 py36_1 conda-forge
jedi 0.12.0 py36_0 conda-forge
jinja2 2.10 py36_0 conda-forge
jsonschema 2.6.0 py36_1 conda-forge
jupyter 1.0.0 py_1 conda-forge
jupyter_client 5.2.3 py36_0 conda-forge
jupyter_console 5.2.0 py36_1 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
jupyterhub 0.8.1 py36_0 conda-forge
jupyterlab 0.32.1 py36_0 conda-forge
jupyterlab_launcher 0.10.5 py36_0 conda-forge
libblas 3.8.0 4_openblas conda-forge
libcblas 3.8.0 4_openblas conda-forge
libedit 3.1.20170329 h6b74fdf_2
libffi 3.2.1 hd88cf55_4
libgcc-ng 8.2.0 hdf63c60_1
libgfortran-ng 7.2.0 hdf63c60_3
libiconv 1.15 h516909a_1005 conda-forge
liblapack 3.8.0 4_openblas conda-forge
libpng 1.6.36 h84994c4_1000 conda-forge
libsodium 1.0.16 0 conda-forge
libstdcxx-ng 8.2.0 hdf63c60_1
libuuid 2.32.1 h14c3975_1000 conda-forge
libxml2 2.9.8 h143f9aa_1005 conda-forge
mako 1.0.7 pypi_0 pypi
markupsafe 1.0 py36_0 conda-forge
maven 3.5.0 0
mistune 0.8.3 py36_1 conda-forge
mkl 2018.0.2 1
mkl_fft 1.0.1 py36h3010b51_0
mkl_random 1.0.1 py36h629b387_0
more-itertools 4.1.0 py_0 conda-forge
multiprocess 0.70.7 py36h14c3975_0 conda-forge
nbconvert 5.3.1 py_1 conda-forge
nbformat 4.4.0 py36_0 conda-forge
ncurses 6.1 hf484d3e_0
nodejs 8.11.1 hf484d3e_0
notebook 5.5.0 py36_0 conda-forge
numpy 1.16.2 py36h8b7e671_1 conda-forge
openblas 0.3.5 h9ac9557_1001 conda-forge
openjdk 8.0.152 h46b5887_1
openssl 1.1.1b h14c3975_1 conda-forge
osqp 0.4.1 py36h637b7d7_1001 conda-forge
pamela 0.3.0 py36_0 conda-forge
pandas 0.24.1 py36hf484d3e_0 conda-forge
pandoc 2.2.1 0 conda-forge
pandocfilters 1.4.2 py36_0 conda-forge
parso 0.2.0 py_0 conda-forge
pexpect 4.5.0 py36_0 conda-forge
pickleshare 0.7.4 py36_0 conda-forge
pip 19.0.3 pypi_0 pypi
pluggy 0.6.0 py_0 conda-forge
prompt_toolkit 1.0.15 py36_0 conda-forge
ptyprocess 0.5.2 py36_0 conda-forge
py 1.5.3 py_0 conda-forge
py4j 0.10.7 py36_0
pycparser 2.18 py36_0 conda-forge
pygments 2.2.0 py36_0 conda-forge
pyopenssl 18.0.0 py36_0 conda-forge
pyqt 4.11.4 py36_3 conda-forge
pysocks 1.6.8 py36_1 conda-forge
pytest 3.5.1 py36_0 conda-forge
python 3.6.7 h381d211_1004 conda-forge
python-dateutil 2.7.3 py36_0
python-editor 1.0.3 py36_0 conda-forge
python-oauth2 1.0.1 py36_0 conda-forge
pytz 2018.4 py36_0
pyzmq 17.0.0 py36_4 conda-forge
qt 4.8.7 2
qtconsole 4.4.3 py_0 conda-forge
readline 7.0 ha6073c6_4
requests 2.18.4 py36_1 conda-forge
rise 5.4.1 py36_1000 conda-forge
scipy 1.2.1 py36h09a28d5_1 conda-forge
scs 2.0.2 py36hcd175bc_1001 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 39.1.0 py36_0
simplegeneric 0.8.1 py36_0 conda-forge
sip 4.18 py36_1 conda-forge
six 1.11.0 py36h372c433_1
sqlalchemy 1.2.7 py36h65ede16_0 conda-forge
sqlite 3.26.0 h67949de_1001 conda-forge
terminado 0.8.1 py36_0 conda-forge
testpath 0.3.1 py36_0 conda-forge
tk 8.6.9 h84994c4_1000 conda-forge
toolz 0.9.0 py_1 conda-forge
tornado 5.0.2 py36_0 conda-forge
traitlets 4.3.2 py36_0 conda-forge
urllib3 1.22 py36_0 conda-forge
wcwidth 0.1.7 py36_0 conda-forge
webencodings 0.5 py36_0 conda-forge
wheel 0.31.1 py36_0
widgetsnbextension 3.2.1 py36_0 conda-forge
xz 5.2.4 h14c3975_4
zeromq 4.2.5 1 conda-forge
zlib 1.2.11 ha838bed_2 Your version of beakerx is 1.0.0 and mine from conda is 1.3.0, that seems like a meaningful difference.
tschm
commented
5 years ago Yes, that's certainly an issue. Using the beakerx docker container also comes with a lot of extra excitement. For example if you try to install matplotlib or scipy or ... via conda, conda will update tornado and break the entire setup by doing so. beakerx 1.0.0 won't work with tornado 6. At the moment I rely on the beakerx container and stick to pip install for further packages. Dependency hell alive. I guess there must be a way to tell conda to be really defensive when I install packages.
LeeTZ
commented
5 years ago I can reproduce the bug. We will take a look. And also the docker image beakerx:latest will be updated with the tornado fix so latest beakerx would stand with tornado peacefully. Thank you all for report!
The following code and variations of it produce a blank chart
If I switch to using nanoseconds as keys instead of Timestamp then it works as expected. I'm attaching a couple of screenshots of the chart and the log with the error. I'm not even sure how to get to the backend log of beakerX in order to see what's the root exception, any direction would be very helpful.