@timkpaine In a python3 -m venv virtual environment I did python3 -m pip install -UI beakerx and beakerx install.
It looks like there were install problems?
$ jupyter nbextension enable beakerx --py --sys-prefix
Enabling tree extension beakerx/tree...
- Validating: problems found:
- require? X beakerx/tree
Enabling notebook extension beakerx/extension...
- Validating: problems found:
- require? X beakerx/extension
I've setup a notebook using the Java kernel: https://github.com/sbl-sdsc/biojava-notebooks. Next, I've tried to setup travis-ci for this project. Since travis use pip install as the default, I tried to install beakerx with pip, however, travis-ci can find the java kernel. Does anyone have experience with setting up travis-ci with a beakerx project?
I believe then the beakerx kernels are installed automatically
I asked this back in October (see above), but I am looking for a way to import a bill of materials into a BeakerX notebook. Maven has a serious bug surrounding
<dependencyManagement> whereby a project P may itself believe it depends on version X of someLibrary transitively, but if a downstream project Q depends on P, it will pull in version Y of someLibrary instead. (See this SO post for details if interested.) The workaround is to import the project P with import scope so that its dependency management is also used in project Q. Unfortunately, I cannot currently use this workaround in BeakerX notebooks because %classpath does not (directly) support importing BOMs. Would the development team be interested in receiving a PR adding this feature? If so, what syntax would be preferred? %classpath import mvn my.org my.bom 1.2.3 might make sense. (There could theoretically also be %classpath import pom '/path/to/local/pom.xml' although personally I would not need this.)
My personal opinion is that the classpath handling in BeakerX should stay as simple as possible. Beyond a certain point, we just end up creating a new language for specifying a POM, when Maven already has one. Faced with a problem like the above, I’d suggest generating a fat jar (“uber jar”) with the correct versions using Maven (or Ivy or sbt or whatever).
@jpallas Thanks for responding. I definitely appreciate the desire to keep things simple. However, I think the solution of creating an uber-JAR to work around limitations in Maven is untenable. There are serious issues with uber-JARs in many deployment scenarios. I also think it is unreasonable to require creating a new artifact just to use a library in a notebook. The "bill of materials" concept is well established in Maven, and adding a way to import one via
%classpath is natural. Gradle also added support for this since it is a very useful feature.
I guess I should file an issue on the tracker, so there can be a more persistent discussion.
Is there a tutorial:
How can I generate new cell in markdown from a Groovy cell result output?
How can I add a function plot as a result from a Groovy cell result output?
I've an example notebook like this:
https://github.com/axkr/symja_android_library/blob/master/symja_android_library/beakerx/SymjaGroovy.ipynb
How can I generate new cell in markdown from a Groovy cell result output?
How can I add a function plot as a result from a Groovy cell result output?
I've an example notebook like this:
https://github.com/axkr/symja_android_library/blob/master/symja_android_library/beakerx/SymjaGroovy.ipynb
If I have a beakerx distrib. under windows, where must I declare a new kernel language for the startup /tree to see it in the "New" menu?
How can I improve installing an external kernel? This is my current description: https://github.com/axkr/symja_android_library/wiki/BeakerX-usage
The San Diego Jupyter Meetup is looking for speakers: https://www.meetup.com/San-Diego-Jupyter-Meetup/, please contact us.
Any ideas what might be going on?
The same code works perfectly inside the java kernel
Seems like the scala kernel is taking the code as scala code instead of interpreting the %classpath magic
I'm interested in using the BeakerXDataGrid widget in a custom JupyterLab cell renderer (with a custom kernel). I haven't found any examples or documentation on how to do this. I am currently using the phosphorjs DataGrid, but I would like the added functionality of the BeakerXDataGrid. Can anyone point me to some information on how to do this?
@ShamsUlAzeem I found out what the problem was. Seems like jupyter has a bunch of places where it gets the list of kernel. So, for me it wasn't loading the kernel I wanted. I changed the
JUPYTER_PATH env variable to the jupyter install location (under <conda_env>/share/jupyter) and it worked for me.
hi, I've just installed beakerx with conda. I'm editing the notebook via jupyterhub. I am able to get an interactive table displayed with following, although it's partially functional (e.g. heatmap not working) :
import numpy as np
import pandas as pd
from beakerx.object import beakerx as bx
df = pd.read_csv('abc.csv')
df
When i try "beakerx_table = bx.TableDisplay(pd.read_csv('abc.csv'))" ... it's giving error " NameError: name 'TableDisplay' is not defined on the beakerx object". Any idea what i'm doing wrong?
codeimport numpy as np
import pandas as pd
from beakerx.object import beakerx as bx
df = pd.read_csv('abc.csv')
df
codeWhen i try "beakerx_table = bx.TableDisplay(pd.read_csv('abc.csv'))" ... it's giving error " NameError: name 'TableDisplay' is not defined on the beakerx object". Any idea what i'm doing wrong?
Hi, does anyone know how to export Scala notebook with plots? If the notebook is closed, after I open it, I see "Error creating widget: could not find model". I googled and did not see that there is a solution. Many thanks to any pointers (even if it is not a solution). Thanks!
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If you have any related experience, we highly appreciate your input!
Thanks in advance and the survey is available at https://usi.eu.qualtrics.com/jfe/form/SV_cO6Ayah0D6q4eSF
