zakandrewking / escher

Build, share, and embed visualizations of metabolic pathways.
https://escher.github.io
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Empty rendering in Jupyter-lab of pathway that renders in classical notebook #270

Closed BjornFJohansson closed 5 years ago

BjornFJohansson commented 6 years ago

I am in the process of reproducing the examples here on my own computer.

I get this output running in the standard jupyter notebook, which seems ok

screenshot from 2018-05-25 15-35-15

However, in jupyterlab (same cell in same notebook running on the same kernel), output is blank.

screenshot from 2018-05-25 15-45-27

The first time I ran there was some sort of warning that I cannot seem to reproduce.

(CONDACOBRAPY) bjorn@bjorn-ThinkPad-T450s:~$ conda info

 active environment : CONDACOBRAPY
active env location : /home/bjorn/anaconda3/envs/CONDACOBRAPY
        shell level : 1
   user config file : /home/bjorn/.condarc

populated config files : /home/bjorn/.condarc conda version : 4.5.4 conda-build version : 3.10.5 python version : 3.6.5.final.0 base environment : /home/bjorn/anaconda3 (writable) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/pro/linux-64 https://repo.anaconda.com/pkgs/pro/noarch https://conda.anaconda.org/BjornFJohansson/linux-64 https://conda.anaconda.org/BjornFJohansson/noarch package cache : /home/bjorn/anaconda3/pkgs /home/bjorn/.conda/pkgs envs directories : /home/bjorn/anaconda3/envs /home/bjorn/.conda/envs platform : linux-64 user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.5 Linux/4.13.0-43-generic linuxmint/18.2 glibc/2.23 UID:GID : 1000:1000 netrc file : None offline mode : False

(CONDACOBRAPY) bjorn@bjorn-ThinkPad-T450s:~$

(CONDACOBRAPY) bjorn@bjorn-ThinkPad-T450s:~$ conda list
# packages in environment at /home/bjorn/anaconda3/envs/CONDACOBRAPY:
#
# Name                    Version                   Build  Channel
asn1crypto                0.24.0                   py36_0    conda-forge
atomicwrites              1.1.5                    py36_0    conda-forge
attrs                     18.1.0                     py_0    conda-forge
backcall                  0.1.0                    py36_0    defaults
blas                      1.0                         mkl    defaults
bleach                    2.1.3                      py_0    conda-forge
blessings                 1.6.1                     <pip>
ca-certificates           2018.4.16                     0    conda-forge
cameo                     0.11.5                    <pip>
certifi                   2018.4.16                py36_0    conda-forge
cffi                      1.11.5                   py36_0    conda-forge
chardet                   3.0.4                    py36_0    conda-forge
chardet                   3.0.4                     <pip>
click                     6.7                       <pip>
cobra                     0.11.3                   py36_0    BjornFJohansson
cryptography              2.2.1                    py36_0    conda-forge
cycler                    0.10.0                   py36_0    conda-forge
cython                    0.28.2                   py36_0    conda-forge
dbus                      1.11.0                        0    conda-forge
decorator                 4.3.0                    py36_0    defaults
entrypoints               0.2.3                    py36_1    conda-forge
escher                    1.6.0                    py36_0    BjornFJohansson
et-xmlfile                1.0.1                     <pip>
expat                     2.2.5                         0    conda-forge
fastcache                 1.0.2            py36h14c3975_2    defaults
fontconfig                2.13.0                        0    conda-forge
freetype                  2.8.1                         0    conda-forge
future                    0.16.0                   py36_1    defaults
gettext                   0.19.8.1                      0    conda-forge
glib                      2.53.6               h5d9569c_2    defaults
glpk                      4.65                          0    conda-forge
gmp                       6.1.2                h6c8ec71_1    defaults
gmpy2                     2.0.8            py36hc8893dd_2    defaults
gnomic                    1.0.1                     <pip>
grako                     3.18.1                    <pip>
gst-plugins-base          1.12.4               h33fb286_0    defaults
gstreamer                 1.12.4               hb53b477_0    defaults
html5lib                  1.0.1                      py_0    conda-forge
icu                       58.2                          0    conda-forge
idna                      2.6                       <pip>
idna                      2.6                      py36_1    conda-forge
inspyred                  1.0.1                     <pip>
intel-openmp              2018.0.0                      8    defaults
IProgress                 0.4                       <pip>
ipykernel                 4.8.2                    py36_0    conda-forge
ipython                   6.4.0                    py36_0    defaults
ipython_genutils          0.2.0            py36hb52b0d5_0    defaults
ipywidgets                7.2.1                    py36_1    conda-forge
jdcal                     1.4                       <pip>
jedi                      0.12.0                   py36_1    defaults
jinja2                    2.10                     py36_0    conda-forge
jpeg                      9b                            2    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_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
kiwisolver                1.0.1                    py36_1    conda-forge
lazy-object-proxy         1.3.1                     <pip>
libedit                   3.1.20170329         h6b74fdf_2    defaults
libffi                    3.2.1                hd88cf55_4    defaults
libgcc                    7.2.0                h69d50b8_2    defaults
libgcc-ng                 7.2.0                hdf63c60_3    defaults
libgfortran-ng            7.2.0                hdf63c60_3    defaults
libiconv                  1.15                          0    conda-forge
libpng                    1.6.34                        0    conda-forge
libsodium                 1.0.16                        0    conda-forge
libstdcxx-ng              7.2.0                hdf63c60_3    defaults
libuuid                   1.0.3                         1    conda-forge
libxcb                    1.13                          0    conda-forge
libxml2                   2.9.8                         0    conda-forge
markupsafe                1.0                      py36_0    conda-forge
matplotlib                2.2.2                    py36_1    conda-forge
mistune                   0.8.3                    py36_1    conda-forge
mkl                       2018.0.2                      1    defaults
mkl_fft                   1.0.1            py36h3010b51_0    defaults
mkl_random                1.0.1            py36h629b387_0    defaults
more-itertools            4.1.0                      py_0    conda-forge
mpc                       1.0.3                hec55b23_5    defaults
mpfr                      3.1.5                h11a74b3_2    defaults
mpmath                    1.0.0            py36hfeacd6b_2    defaults
nbconvert                 5.3.1                      py_1    conda-forge
nbformat                  4.4.0                    py36_0    conda-forge
ncurses                   6.1                  hf484d3e_0    defaults
networkx                  1.9.1                     <pip>
notebook                  5.5.0                    py36_0    conda-forge
numexpr                   2.6.5                     <pip>
numpy                     1.14.3           py36hcd700cb_1    defaults
numpy-base                1.14.3           py36h9be14a7_1    defaults
openpyxl                  2.5.3                     <pip>
openssl                   1.0.2o                        0    conda-forge
optlang                   1.4.2                      py_0    conda-forge
ordered-set               2.0.2                     <pip>
palettable                3.1.1                     <pip>
pandas                    0.23.0           py36h637b7d7_0    defaults
pandoc                    2.2.1                         0    conda-forge
pandocfilters             1.4.2                    py36_0    conda-forge
parso                     0.2.0                    py36_0    defaults
pcre                      8.42                 h439df22_0    defaults
pexpect                   4.5.0                    py36_0    defaults
pickleshare               0.7.4            py36h63277f8_0    defaults
pip                       10.0.1                   py36_0    defaults
plotly                    2.7.0                    py36_0    conda-forge
pluggy                    0.6.0                      py_0    conda-forge
prompt_toolkit            1.0.15           py36h17d85b1_0    defaults
ptyprocess                0.5.2            py36h69acd42_0    defaults
py                        1.5.3                      py_0    conda-forge
pycparser                 2.18                     py36_0    conda-forge
pygments                  2.2.0            py36h0d3125c_0    defaults
pyopenssl                 18.0.0                   py36_0    conda-forge
pyparsing                 2.2.0                    py36_0    conda-forge
pyqt                      5.6.0                    py36_5    conda-forge
pysocks                   1.6.8                    py36_1    conda-forge
pytest                    3.6.0                    py36_1    conda-forge
python                    3.6.5                hc3d631a_2    defaults
python-dateutil           2.7.3                    py36_0    defaults
pytz                      2018.4                   py36_0    defaults
pyzmq                     17.0.0                   py36_4    conda-forge
qt                        5.6.2               h974d657_12    defaults
qtconsole                 4.3.1                    py36_0    conda-forge
readline                  7.0                  ha6073c6_4    defaults
requests                  2.18.4                    <pip>
requests                  2.18.4                   py36_1    conda-forge
ruamel.yaml               0.14.11                  py36_0    conda-forge
scipy                     1.1.0                     <pip>
send2trash                1.5.0                      py_0    conda-forge
setuptools                39.1.0                   py36_0    defaults
simplegeneric             0.8.1                    py36_2    defaults
sip                       4.18                     py36_1    conda-forge
six                       1.11.0           py36h372c433_1    defaults
sqlite                    3.23.1               he433501_0    defaults
swig                      3.0.12               h38cdd7d_3    defaults
swiglpk                   1.4.4                    py36_0    conda-forge
sympy                     1.1.1            py36hc6d1c1c_0    defaults
tabulate                  0.8.2                    py36_0    defaults
terminado                 0.8.1                    py36_0    conda-forge
testpath                  0.3.1                    py36_0    conda-forge
tk                        8.6.7                hc745277_3    defaults
tornado                   5.0.2                    py36_0    conda-forge
traitlets                 4.3.2            py36h674d592_0    defaults
urllib3                   1.22                      <pip>
urllib3                   1.22                     py36_0    conda-forge
wcwidth                   0.1.7            py36hdf4376a_0    defaults
webencodings              0.5                      py36_0    conda-forge
wheel                     0.31.1                   py36_0    defaults
widgetsnbextension        3.2.1                    py36_0    conda-forge
xorg-libxau               1.0.8                         3    conda-forge
xorg-libxdmcp             1.1.2                         3    conda-forge
xz                        5.2.4                h14c3975_4    defaults
zeromq                    4.2.5                         1    conda-forge
zlib                      1.2.11               ha838bed_2    defaults
(CONDACOBRAPY) bjorn@bjorn-ThinkPad-T450s:~$ 
zakandrewking commented 6 years ago

thanks for the report! I'll take a look and see if i can reproduce it

pablormier commented 6 years ago

Same problem with the following libs:

#
# Name                    Version                   Build  Channel
atomicwrites              1.1.5                     <pip>
attrs                     18.1.0                    <pip>
backcall                  0.1.0                     <pip>
bleach                    2.1.3                     <pip>
ca-certificates           2018.03.07                    0  
certifi                   2018.4.16                py36_0  
cobra                     0.13.0                    <pip>
decorator                 4.3.0                     <pip>
depinfo                   1.3.0                     <pip>
entrypoints               0.2.3                     <pip>
Escher                    1.6.0                     <pip>
future                    0.16.0                    <pip>
html5lib                  1.0.1                     <pip>
ipykernel                 4.8.2                     <pip>
ipython                   6.4.0                     <pip>
ipython-genutils          0.2.0                     <pip>
ipywidgets                7.2.1                     <pip>
jedi                      0.12.0                    <pip>
Jinja2                    2.10                      <pip>
jsonschema                2.6.0                     <pip>
jupyter-client            5.2.3                     <pip>
jupyter-core              4.4.0                     <pip>
libedit                   3.1.20170329         h6b74fdf_2  
libffi                    3.2.1                hd88cf55_4  
libgcc-ng                 7.2.0                hdf63c60_3  
libstdcxx-ng              7.2.0                hdf63c60_3  
MarkupSafe                1.0                       <pip>
mistune                   0.8.3                     <pip>
more-itertools            4.2.0                     <pip>
mpmath                    1.0.0                     <pip>
nbconvert                 5.3.1                     <pip>
nbformat                  4.4.0                     <pip>
ncurses                   6.1                  hf484d3e_0  
nglview                   1.1.3                     <pip>
notebook                  5.5.0                     <pip>
numpy                     1.14.4                    <pip>
openssl                   1.0.2o               h20670df_0  
optlang                   1.4.2                     <pip>
pandas                    0.23.0                    <pip>
pandocfilters             1.4.2                     <pip>
parso                     0.2.1                     <pip>
pexpect                   4.6.0                     <pip>
pickleshare               0.7.4                     <pip>
pip                       10.0.1                   py36_0  
pipdeptree                0.12.1                    <pip>
pluggy                    0.6.0                     <pip>
prompt-toolkit            1.0.15                    <pip>
ptyprocess                0.5.2                     <pip>
py                        1.5.3                     <pip>
Pygments                  2.2.0                     <pip>
pytest                    3.6.1                     <pip>
python                    3.6.5                hc3d631a_2  
python-dateutil           2.7.3                     <pip>
pytz                      2018.4                    <pip>
pyzmq                     17.0.0                    <pip>
readline                  7.0                  ha6073c6_4  
ruamel.yaml               0.14.12                   <pip>
Send2Trash                1.5.0                     <pip>
setuptools                39.2.0                   py36_0  
simplegeneric             0.8.1                     <pip>
six                       1.11.0                    <pip>
sqlite                    3.23.1               he433501_0  
swiglpk                   1.4.4                     <pip>
sympy                     1.1.1                     <pip>
tabulate                  0.8.2                     <pip>
terminado                 0.8.1                     <pip>
testpath                  0.3.1                     <pip>
tk                        8.6.7                hc745277_3  
tornado                   5.0.2                     <pip>
traitlets                 4.3.2                     <pip>
wcwidth                   0.1.7                     <pip>
webencodings              0.5.1                     <pip>
wheel                     0.31.1                   py36_0  
widgetsnbextension        3.2.1                     <pip>
xz                        5.2.4                h14c3975_4  
zlib                      1.2.11               ha838bed_2  

I've tried with previous version of the lib without success

zakandrewking commented 6 years ago

FYI, Jupyter Lab has a new extension interface, so Escher versions <= 1.6 will not work there. I am working on a new release that will work in both classic notebooks & jupyter lab using the widget system (#275).