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IPython profile configuration - Collection
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Resolve JupyterLab live plotting issue #5

Open mrakitin opened 5 years ago

mrakitin commented 5 years ago

Tried to figure it out with @jklynch on 7/10/2019, were able to enable the live plotting in the classic notebook, but it still failed for the JupyterLab.

Here is the environment on xf17id2-ca:

$ conda list
WARNING conda.core.prefix_data:_load_site_packages(272): Problem reading non-conda package record at lib/python3.7/site-packages/fabio-0.8.0-py3.7-linux-x86_64.egg-info/PKG-INFO. Please verify that you still need this, and if so, that this is still installed correctly. Reinstalling this package may help.
# packages in environment at /opt/conda_envs/collection-2019-3.0-amx:
#
# Name                    Version                   Build  Channel
17-id-amx-collection      2019C3.0                      0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
amostra                   0.2                      py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
anaconda-client           1.7.2                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
analysis                  2019C3.0                      0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
appdirs                   1.4.3            py37h28b3542_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
asciitree                 0.3.3                      py_2    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
asn1crypto                0.24.0                   py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
asteval                   0.9.12                   py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
astropy                   3.1.2            py37h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
atomicwrites              1.3.0                    py37_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
attrs                     19.1.0                   py37_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
backcall                  0.1.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
blas                      1.0                         mkl    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
bleach                    3.1.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
bluesky                   1.5.3                    py37_1    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
bluesky-browser           0.1.0a1                  py37_1    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
bluesky-kafka             0.1                           0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
bokeh                     1.2.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
boltons                   16.3.1                   py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
bottleneck                1.2.1            py37h035aef0_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
bzip2                     1.0.6                h14c3975_5    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ca-certificates           2019.5.15                     0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
cairo                     1.14.12              h8948797_3    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
caproto                   0.4.0                    py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
certifi                   2019.3.9                 py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
cffi                      1.12.3           py37h2e261b9_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
cftime                    1.0.3.4          py37hdd07704_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
chardet                   3.0.4                    py37_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
click                     7.0                      py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
cloudpickle               1.1.1                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
clyent                    1.2.2                    py37_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
collection                2019C3.0                      0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
controls-doctor           0.0.1                    py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
cryptography              2.7              py37h1ba5d50_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
curio                     0.9                      py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
curl                      7.64.1               hbc83047_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
cycler                    0.10.0                   py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
cytoolz                   0.9.0.1          py37h14c3975_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
dask                      1.1.4                    py37_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
dask-core                 1.1.4                    py37_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
databroker                0.13.0                   py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
datamuxer                 0.3.0                    py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
dbus                      1.13.6               h746ee38_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
decorator                 4.4.0                    py37_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
defusedxml                0.6.0                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
dill                      0.2.9                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
distributed               1.26.0                   py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
doct                      1.0.5                    py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
entrypoints               0.3                      py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
epics-base                3.15.6                        0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
et_xmlfile                1.0.1                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
event-model               1.10.0                   py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
expat                     2.2.6                he6710b0_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
fabio                     0.8.0                    py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
fast-histogram            0.7             py37hdd07704_1000    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
fastcache                 1.1.0            py37h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
fasteners                 0.14.1                     py_3    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ffmpeg                    4.0                  hcdf2ecd_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
fftw                      3.3.8                h7b6447c_3    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
flake8                    3.7.7                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
fontconfig                2.13.0               h9420a91_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
freetype                  2.9.1                h8a8886c_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
fribidi                   1.0.5                h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
gevent                    1.4.0            py37h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
glib                      2.56.2               hd408876_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
glue-core                 0.14.2                   py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
glue-vispy-viewers        0.11                       py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
glueviz                   0.13.3                        0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
gmp                       6.1.2                h6c8ec71_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
gmpy2                     2.0.8            py37h10f8cd9_2    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
graphite2                 1.3.13               h23475e2_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
graphviz                  2.40.1               h21bd128_2    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
greenlet                  0.4.15           py37h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
grid-strategy             0.0.1                    py37_1    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
gst-plugins-base          1.14.0               hbbd80ab_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
gstreamer                 1.14.0               hb453b48_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
h5py                      2.9.0            py37h7918eee_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
harfbuzz                  1.8.8                hffaf4a1_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
hdf4                      4.2.13               h3ca952b_2    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
hdf5                      1.10.4               hb1b8bf9_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
heapdict                  1.0.0                    py37_2    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
historydict               1.2.3                      py_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
holoviews                 1.12.1                     py_2    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
humanize                  0.5.1                    py37_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
icu                       58.2                 h9c2bf20_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
idna                      2.8                      py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
imageio                   2.5.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
importlib_metadata        0.17                     py37_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
intake                    0.5.1                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
intake-bluesky            0.1.0a8                       2    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
intake-xarray             0.3.0                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
intel-openmp              2019.4                      243    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ipykernel                 5.1.1            py37h39e3cac_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ipympl                    0.1.1                    py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
ipython                   7.5.0            py37h39e3cac_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ipython_genutils          0.2.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ipywidgets                7.2.1                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jdcal                     1.4.1                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jedi                      0.13.3                   py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jeepney                   0.4                      py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jinja2                    2.10.1                   py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jpeg                      9b                   h024ee3a_2    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jsonschema                3.0.1                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jupyter                   1.0.0                    py37_7    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jupyter_client            5.2.4                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jupyter_console           6.0.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jupyter_core              4.4.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jupyterlab                0.35.5           py37hf63ae98_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jupyterlab_server         0.2.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
kafka-python              1.4.2                      py_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
kazoo                     2.6.1                      py_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
keyring                   18.0.0                   py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
kiwisolver                1.1.0            py37he6710b0_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
krb5                      1.16.1               h173b8e3_7    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libcurl                   7.64.1               h20c2e04_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libedit                   3.1.20181209         hc058e9b_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libffi                    3.2.1                hd88cf55_4    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libgcc-ng                 8.2.0                hdf63c60_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libgcrypt                 1.8.4                h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libgfortran-ng            7.3.0                hdf63c60_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libgpg-error              1.32                 hf484d3e_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libgsasl                  1.8.0                h7b6447c_3    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libnetcdf                 4.6.1                h11d0813_2    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libntlm                   1.5                  h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libopus                   1.3                  h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libpng                    1.6.37               hbc83047_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
librdkafka                1.0.1                         0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
libsodium                 1.0.16               h1bed415_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libssh2                   1.8.2                h1ba5d50_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libstdcxx-ng              8.2.0                hdf63c60_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libtiff                   4.0.10               h2733197_2    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libuuid                   1.0.3                h1bed415_2    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libvpx                    1.7.0                h439df22_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libxcb                    1.13                 h1bed415_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libxml2                   2.9.9                he19cac6_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
lmfit                     0.9.9              pyh5ca1d4c_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
locket                    0.2.0                    py37_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
lz4-c                     1.8.1.2              h14c3975_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
markupsafe                1.1.1            py37h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
matplotlib                3.1.0            py37h5429711_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mccabe                    0.6.1                    py37_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mistune                   0.8.4            py37h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mkl                       2019.4                      243    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mkl_fft                   1.0.12           py37ha843d7b_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mkl_random                1.0.2            py37hd81dba3_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mongoquery                1.1.0                    py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
monotonic                 1.5                        py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
more-itertools            7.0.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mpc                       1.1.0                h10f8cd9_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mpfr                      4.0.1                hdf1c602_3    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mpi                       1.0                     openmpi    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
mpi4py                    3.0.0           py37_openmpi_1004    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
mpl-scatter-density       0.5                        py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mpmath                    1.1.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
msgpack-numpy             0.4.4.2                  py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
msgpack-python            0.6.1            py37hfd86e86_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
nbconvert                 5.5.0                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
nbformat                  4.4.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ncurses                   6.1                  he6710b0_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
netcdf4                   1.4.2            py37h808af73_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
netifaces                 0.10.7                   py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
networkx                  2.3                        py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
nodejs                    10.13.0              he6710b0_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
notebook                  5.7.8                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
nslsii                    0.0.10                   py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
numcodecs                 0.5.4            py37he6710b0_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
numpy                     1.16.4           py37h7e9f1db_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
numpy-base                1.16.4           py37hde5b4d6_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
olefile                   0.46                     py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
openmpi                   3.1.1                      1000    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
openpyxl                  2.6.2                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
openssl                   1.1.1                h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ophyd                     1.3.3                    py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
oscars                    2.1.8                    py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
packaging                 19.0                     py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pandas                    0.24.2           py37he6710b0_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pandoc                    2.2.3.2                       0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pandocfilters             1.4.2                    py37_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pango                     1.42.4               h049681c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
param                     1.9.0                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
parso                     0.4.0                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
partd                     0.3.10                   py37_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pcre                      8.43                 he6710b0_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
peakutils                 1.1.1                      py_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
pexpect                   4.7.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pickleshare               0.7.5                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pillow                    6.0.0            py37h34e0f95_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pims                      0.4.1                      py_1    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
pip                       19.1.1                   py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pixman                    0.38.0               h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
plotly                    3.9.0                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pluggy                    0.12.0                     py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
prettytable               0.7.2                    py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
prometheus_client         0.6.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
prompt_toolkit            2.0.9                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
psutil                    5.6.2            py37h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ptyprocess                0.6.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
py                        1.8.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pycodestyle               2.5.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pycparser                 2.19                     py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyepics                   3.3.0                    py37_1    https://conda.nsls2.bnl.gov/conda/overrides
pyfftw                    0.11.1                   py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
pyflakes                  2.1.1                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pygments                  2.4.2                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pykafka                   2.8.0                 py37_1000    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
pymongo                   3.7.2            py37he6710b0_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyolog                    4.4.2                    py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
pyopengl                  3.1.1a1                  py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyopenssl                 19.0.0                   py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyparsing                 2.4.0                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyqt                      5.9.2            py37h22d08a2_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyrsistent                0.14.11          py37h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyserial                  3.4                      py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pysocks                   1.7.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pytest                    4.6.2                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pytest-arraydiff          0.3              py37h39e3cac_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pytest-astropy            0.5.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pytest-doctestplus        0.3.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pytest-openfiles          0.3.2                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pytest-remotedata         0.3.1                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
python                    3.7.3                h0371630_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
python-confluent-kafka    1.0.0                 py37_1002    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
python-dateutil           2.8.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
python-graphviz           0.10.1                     py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
python-snappy             0.5.4            py37he6710b0_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pytz                      2019.1                     py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyviz_comms               0.7.2                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pywavelets                1.0.3            py37hdd07704_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyyaml                    5.1              py37h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyzmq                     18.0.0           py37he6710b0_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
qt                        5.9.7                h5867ecd_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
qtconsole                 4.5.1                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
qtpy                      1.7.1                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
readline                  7.0                  h7b6447c_5    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
requests                  2.22.0                   py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
retrying                  1.3.3                    py37_2    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ruamel_yaml               0.15.46          py37h14c3975_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
scikit-beam               0.0.14                   py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
scikit-image              0.15.0           py37he6710b0_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
scipy                     1.2.1            py37h7c811a0_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
secretstorage             3.1.1                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
send2trash                1.5.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
setuptools                41.0.1                   py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
sip                       4.19.13          py37he6710b0_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
six                       1.12.0                   py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
slicerator                0.9.8                    py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
snappy                    1.1.7                hbae5bb6_3    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
sortedcontainers          2.1.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
sqlite                    3.28.0               h7b6447c_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
suitcase-jsonl            0.1.1                    py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
suitcase-utils            0.1.1                    py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
super_state_machine       1.0                      py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
sympy                     1.4                      py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
tabulate                  0.8.3                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
tblib                     1.4.0                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
terminado                 0.8.2                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
testpath                  0.4.2                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
tifffile                  0.15.1                   py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
tk                        8.6.8                hbc83047_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
toolz                     0.9.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
tornado                   4.5.3                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
tqdm                      4.31.1                   py37_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
traitlets                 4.3.2                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
tzlocal                   1.5.1                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ujson                     1.35             py37h14c3975_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
urllib3                   1.24.2                   py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
wcwidth                   0.1.7                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
webencodings              0.5.1                    py37_1    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
wheel                     0.33.4                   py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
widgetsnbextension        3.4.2                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
xarray                    0.12.1                     py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
xlrd                      1.2.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
xlwt                      1.3.0                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
xray-vision               0.0.9                    py37_0    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
xraylib                   3.3.0                    py37_1    https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
xz                        5.2.4                h14c3975_4    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
yaml                      0.1.7                had09818_2    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
zarr                      2.2.0                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
zeromq                    4.3.1                he6710b0_3    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
zict                      0.1.4                    py37_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
zipp                      0.5.1                      py_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
zlib                      1.2.11               h7b6447c_3    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
zstd                      1.3.7                h0b5b093_0    https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0

attn @danielballan

mrakitin commented 5 years ago

The labextensions seem to be enabled correctly:

$ jupyter labextension list
JupyterLab v0.35.5
Known labextensions:
   app dir: /opt/conda_envs/collection-2019-3.0-amx/share/jupyter/lab
        @jupyter-widgets/jupyterlab-manager v0.38.1  enabled  OK
        jupyter-matplotlib v0.4.2  enabled  OK
mrakitin commented 5 years ago

We basically tried to follow https://github.com/bluesky/tutorial/blob/master/binder/postBuild, but with the wrong order (@jupyter-widgets/jupyterlab-manager wasn't installed first, but was installed eventually, and then everything was rebuilt.)

mrakitin commented 5 years ago

That's how the server is started from the collection-2019-3.0-amx conda environment (via st.cmd and a systemd service):

jupyter lab --no-browser --notebook-dir=/epics/iocs/notebook/notebooks/ --ip=0.0.0.0 --port=17000 --NotebookApp.token='' --debug > $jupyter_log 2>&1

The relevant kernel config is:

{
    "argv": ["/opt/conda_envs/collection-2019-3.0-amx/bin/python","-m","IPython.kernel","-f","{connection_file}","--profile","collection"],
    "display_name": "Data Collection (2019-3.0)"
}
mrakitin commented 5 years ago

Here are some debug logs from Firefox web console:

image
mrakitin commented 5 years ago

A side note about puppet-managed /opt/conda/.condarc file: https://controlsweb.nsls2.bnl.gov/trac/ticket/3627 (that was observed with @jklynch during the deployment visit).

mrakitin commented 5 years ago

@danielballan, what versions of the libraries would you suggest?

danielballan commented 5 years ago

I suggest upgrade to JupyterLab 1.0.x and trying again.

mrakitin commented 5 years ago

Thanks @danielballan! We will work with @jklynch on that this Thursday afternoon. Will report back after that.

mrakitin commented 5 years ago

This was partially resolved by creating a new environment, installing all the latest jupyterlab and friends and by changing 00-base.py to use the configuration from https://github.com/bluesky/tutorial/blob/master/scripts/beamline_configuration.py (avoiding nslsii.configure_base(...)) via https://github.com/NSLS-II-AMX/profile_collection/commit/ab426a41cc37918e51e0c8d394b5d75e1bc6235e.

However, we found a common issue also observed in our tutorials -- see https://github.com/bluesky/tutorial/issues/37 for details.