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    rickhg12hs
    @rickhg12hs

    @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
    rickhg12hs
    @rickhg12hs
    @timkpaine Hmmm, I beakerx uninstall and then beakerx install ... Now a table appears. I'll work with it and see how it goes.
    Peter Rose
    @pwrose
    Is there a way to specify a local repository with %classpath?
    Joe Pallas
    @jpallas
    @pwrose %classpath config resolver mvnLocal
    rickhg12hs
    @rickhg12hs
    How can beakerx be enabled for only specific jupyter notebooks? Can beakerx be enable/disabled from within the notebook?
    Peter Rose
    @pwrose
    @jpallas Thanks, I tried that, but I get a kernel error (using Java kernel) when I run %classpath config resolver mvnLocal. I have hundreds of dependencies in my ~/.m2/repository directory, could that be an issues?
    Curtis Rueden
    @ctrueden
    @pwrose You could try moving aside your existing ~/.m2/repository and building up a new one, to see if the problem persists.
    Peter Rose
    @pwrose
    @ctrueden @jpallas I created a fresh ~/.m2/repository, now when I run %classpath config resolver mvnLocal it points to /private/var/folders/fs/tlp3yk093qs8clwh1s3gb6540000gn/T/beaker6058009716743700773/outDir instead of ~/.m2/repository.
    Joe Pallas
    @jpallas
    @pwrose It copies files from the repo into its private area.
    Peter Rose
    @pwrose
    @jpallas The private area is empty. So apparently the copying from ~/.m2/repository doesn't seem to work.
    Joe Pallas
    @jpallas
    @pwrose In case it wasn't clear, the copying happens only when you do %classpath add mvn. Configuring the resolver doesn't trigger any copying, it just makes the maven resolution look in your local repository when you do an add mvn.
    Peter Rose
    @pwrose
    @jpallas Thanks for the clarifications. It works!
    Joe Pallas
    @jpallas
    Hurray! :tada:
    Peter Rose
    @pwrose
    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?
    Maarten Breddels
    @maartenbreddels
    I'd use (ana/mini)conda
    I believe then the beakerx kernels are installed automatically
    Peter Rose
    @pwrose
    @maartenbreddels Thanks, I got travis-ci working using miniconda, but my tests fail, but that's a different issue.
    Peter Rose
    @pwrose
    Why doesn't Spark work with the Java Kernel? I get: "ERROR: java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.package$".
    Curtis Rueden
    @ctrueden
    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.)
    Joe Pallas
    @jpallas
    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).
    Curtis Rueden
    @ctrueden
    @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.
    Curtis Rueden
    @ctrueden
    Edgar
    @edgano
    Hi to all,
    Is there any guideline to develop a new kernel for another languaje??
    Scott Draves
    @scottdraves
    not aware of a guide, what language were you thinking?
    Ax Kr
    @axkr
    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
    Curtis Rueden
    @ctrueden
    @axkr For function plot example in Groovy, maybe this one?
    Curtis Rueden
    @ctrueden
    @axkr For generating Markdown dynamically, I whipped up a gist. Is that what you are looking for?
    Ax Kr
    @axkr
    @ctrueden Thanks
    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?
    Ax Kr
    @axkr
    Ok problem solved, got my kernel running locally.
    grafik.png
    Ax Kr
    @axkr
    Which tool is used to create the logo...png ?
    Ax Kr
    @axkr
    How can I improve installing an external kernel? This is my current description: https://github.com/axkr/symja_android_library/wiki/BeakerX-usage
    Peter Rose
    @pwrose
    The San Diego Jupyter Meetup is looking for speakers: https://www.meetup.com/San-Diego-Jupyter-Meetup/, please contact us.
    Shams Ul Azeem
    @ShamsUlAzeem
    Hi guys! Tried to run the following code in beakerX in the scala notebook but the following error keeps coming up:
    %classpath add jar /Users/shamsulazeem/Desktop/SKIL/native/*
    (console):2:61 expected "*/"
    %classpath add jar /Users/shamsulazeem/Desktop/SKIL/native/*
                                                                ^
    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
    Jack Dundon
    @jdundondev
    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?
    paulor3nato
    @paulor3nato
    Hello everyone, I'm a big beakerx table display fan. There is a bug with the last version of the jupyter notebook/lab when the dataframes have boolean type columns. There is also an anoying numpy warning. Any idea how to fix this? Its driving me crazy.
    Shams Ul Azeem
    @ShamsUlAzeem
    @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.
    ranparas
    @ranparas
    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) :
    code
    import numpy as np
    import pandas as pd
    from beakerx.object import beakerx as bx
    df = pd.read_csv('abc.csv')
    df
    code
    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?
    Cy Walker
    @cywalker
    Hi all - just started trying to use BeakerX docker image on Windows 10 and I am trying to connect to a local MS SQL Server instance / database, but I cant find an example for MS SQL Server!
    Does anyone have a good example?
    Thanks.
    Farhan
    @farhan5900
    Hi I want to know that is there a way to provide default classpath, without using %classpath magic, so Spark magic will refer it?
    Kristina Plazonic
    @KristinaPlazonic
    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!
    Nier9S
    @YuzeLiu1029
    I build the beakerx from source somehow the plot can not ben showed, neither is the table. Anyone know how?
    Sandeep Shantharam
    @machbio
    Lastpassucsk27me
    Fiorella Zampetti
    @fzampetti_gitlab
    Hi there, we are conducting a survey about why refactoring-related contributions to software projects get rejected.
    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
    Nick Römer
    @ronnac
    Hi, how do pip install the beakerx-kernel-clojure only, and not the other kernels?