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twosigma / beakerx

Beaker Extensions for Jupyter Notebook
http://BeakerX.com
Apache License 2.0
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Nothing displayed pandas dataframe conda install #7819

Open NumesSanguis opened 6 years ago

NumesSanguis commented 6 years ago

After I installed beakerx with conda install -c conda-forge beakerx ipywidgets dataframes don't show any output anymore in Jupyter Notebook

Fresh conda setup:

conda create --name stats python=3.6
conda activate stats
conda install pandas
conda install ipykernel # allows the use of env kernels in jupyter notebook
conda install ipywidgets  # GUI elements in jupyter notebook
python -m ipykernel install --user --name stats --display-name "py36 stats"  # enable env as kernel in jupyter notebook

* test everything works*
jupyter notebook
import pandas as pd
df = pd.DataFrame(data={'col1': [1, 2], 'col2': [3, 4]})
df
* Standard Jupyter Notebook table shows *
* --> everything works; shutdown jupyter notebook *

conda install -c conda-forge beakerx ipywidgets
jupyter notebook
import pandas as pd
df = pd.DataFrame(data={'col1': [1, 2], 'col2': [3, 4]})
df
* No output (even without importing beakerx) *

conda install -c conda-forge beakerx ipywidgets
jupyter notebook
import pandas as pd
df = pd.DataFrame(data={'col1': [1, 2], 'col2': [3, 4]})
df
* No output (even without importing beakerx) *

import pandas as pd
from beakerx import *
df = pd.DataFrame(data={'col1': [1, 2], 'col2': [3, 4]})
df
* Still no output (even without importing beakerx) *

No output is given anymore when running any commands such as df or display(df). Also, I have the same issue as https://github.com/twosigma/beakerx/issues/7766 in which beakerx is used without importing it.

conda uninstall beakerx solves all issues, but I would like fancy tables :')

Jupyter notebook file after install beakerx { "cells": [ { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "20649fd6d3394c92a6db1f97941f72d8", "version_major": 2, "version_minor": 0 } }, "metadata": {}, "output_type": "display_data" } ], "source": [ "import pandas as pd\n", "df = pd.DataFrame(data={'col1': [1, 2], 'col2': [3, 4]})\n", "df" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "py36 stats", "language": "python", "name": "stats" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.6" } }, "nbformat": 4, "nbformat_minor": 2 }
Pandas environment conda list # packages in environment at /home/*user*/anaconda3/envs/stats: # # Name Version Build Channel appdirs 1.4.3 py36h28b3542_0 asn1crypto 0.24.0 py36_0 atomicwrites 1.2.1 py_0 conda-forge attrs 18.2.0 py36h28b3542_0 automat 0.7.0 py36_0 backcall 0.1.0 py36_0 beakerx 1.1.0 py36_0 conda-forge blas 1.0 mkl bleach 2.1.4 py36_0 ca-certificates 2018.8.24 ha4d7672_0 conda-forge certifi 2018.8.24 py36_1001 conda-forge cffi 1.11.5 py36he75722e_1 chardet 3.0.4 py36_1003 conda-forge constantly 15.1.0 py36h28b3542_0 cryptography 2.3.1 py36hc365091_0 decorator 4.3.0 py36_0 entrypoints 0.2.3 py36_2 gmp 6.1.2 h6c8ec71_1 html5lib 1.0.1 py36_0 hyperlink 18.0.0 py36_0 idna 2.7 py36_0 incremental 17.5.0 py36_0 intel-openmp 2019.0 118 ipykernel 5.0.0 py36h39e3cac_0 ipython 7.0.1 py36h39e3cac_0 ipython_genutils 0.2.0 py36_0 ipywidgets 7.4.2 py_0 conda-forge jedi 0.12.1 py36_0 jinja2 2.10 py36_0 jsonschema 2.6.0 py36_0 jupyter_client 5.2.3 py36_0 jupyter_core 4.4.0 py36_0 libedit 3.1.20170329 h6b74fdf_2 libffi 3.2.1 hd88cf55_4 libgcc-ng 8.2.0 hdf63c60_1 libgfortran-ng 7.3.0 hdf63c60_0 libsodium 1.0.16 h1bed415_0 libstdcxx-ng 8.2.0 hdf63c60_1 markupsafe 1.0 py36h14c3975_1 maven 3.5.0 0 conda-forge mistune 0.8.3 py36h14c3975_1 mkl 2019.0 118 mkl_fft 1.0.6 py36h7dd41cf_0 mkl_random 1.0.1 py36h4414c95_1 more-itertools 4.3.0 py36_1000 conda-forge nbconvert 5.3.1 py36_0 nbformat 4.4.0 py36_0 ncurses 6.1 hf484d3e_0 notebook 5.7.0 py36_0 numpy 1.15.2 py36h1d66e8a_1 numpy-base 1.15.2 py36h81de0dd_1 openjdk 8.0.152 h46b5887_1 openssl 1.0.2p h470a237_0 conda-forge pandas 0.23.4 py36h04863e7_0 pandoc 2.2.3.2 0 pandocfilters 1.4.2 py36_1 parso 0.3.1 py36_0 pexpect 4.6.0 py36_0 pickleshare 0.7.5 py36_0 pip 10.0.1 py36_0 pluggy 0.7.1 py_0 conda-forge prometheus_client 0.3.1 py36h28b3542_0 prompt_toolkit 2.0.5 py36_0 ptyprocess 0.6.0 py36_0 py 1.6.0 py_0 conda-forge py4j 0.10.7 py_1 conda-forge pyasn1 0.4.4 py36h28b3542_0 pyasn1-modules 0.2.2 py36_0 pycparser 2.19 py36_0 pygments 2.2.0 py36_0 pyopenssl 18.0.0 py36_0 pysocks 1.6.8 py36_1002 conda-forge pytest 3.8.2 py36_1000 conda-forge python 3.6.6 hc3d631a_0 python-dateutil 2.7.3 py36_0 pytz 2018.5 py36_0 pyzmq 17.1.2 py36h14c3975_0 readline 7.0 h7b6447c_5 requests 2.19.1 py36_1 conda-forge send2trash 1.5.0 py36_0 service_identity 17.0.0 py36h28b3542_0 setuptools 40.4.3 py36_0 simplegeneric 0.8.1 py36_2 six 1.11.0 py36_1 sqlite 3.25.2 h7b6447c_0 terminado 0.8.1 py36_1 testpath 0.4.2 py36_0 tk 8.6.8 hbc83047_0 tornado 5.1.1 py36h7b6447c_0 traitlets 4.3.2 py36_0 twisted 18.7.0 py36h14c3975_1 urllib3 1.23 py36_1 conda-forge wcwidth 0.1.7 py36_0 webencodings 0.5.1 py36_1 wheel 0.32.0 py36_0 widgetsnbextension 3.4.2 py36_0 xz 5.2.4 h14c3975_4 zeromq 4.2.5 hf484d3e_1 zlib 1.2.11 ha838bed_2 zope 1.0 py36_1 zope.interface 4.5.0 py36h14c3975_0
NumesSanguis commented 6 years ago

Even after conda uninstall beakerx it still tries to load some modules when starting Jupter Notebook.

Error output [IPKernelApp] WARNING | Error in loading extension: beakerx.autotranslation Check your config files in /home/*user*/.ipython/profile_default Traceback (most recent call last): File "/home/*user*/anaconda3/envs/dl/lib/python3.6/site-packages/IPython/core/shellapp.py", line 244, in init_extensions self.shell.extension_manager.load_extension(ext) File "/home/*user*/anaconda3/envs/dl/lib/python3.6/site-packages/IPython/core/extensions.py", line 85, in load_extension mod = import_module(module_str) File "/home/*user*/anaconda3/envs/dl/lib/python3.6/importlib/__init__.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 941, in _find_and_load_unlocked File "", line 219, in _call_with_frames_removed File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 953, in _find_and_load_unlocked ModuleNotFoundError: No module named 'beakerx' [IPKernelApp] WARNING | Error in loading extension: beakerx_magics.kernel_magic Check your config files in /home/*user*/.ipython/profile_default Traceback (most recent call last): File "/home/*user*/anaconda3/envs/dl/lib/python3.6/site-packages/IPython/core/shellapp.py", line 244, in init_extensions self.shell.extension_manager.load_extension(ext) File "/home/*user*/anaconda3/envs/dl/lib/python3.6/site-packages/IPython/core/extensions.py", line 85, in load_extension mod = import_module(module_str) File "/home/*user*/anaconda3/envs/dl/lib/python3.6/importlib/__init__.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 941, in _find_and_load_unlocked File "", line 219, in _call_with_frames_removed File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 953, in _find_and_load_unlocked ModuleNotFoundError: No module named 'beakerx_magics' [IPKernelApp] WARNING | Error in loading extension: beakerx_magics.groovy_magic Check your config files in /home/*user*/.ipython/profile_default Traceback (most recent call last): File "/home/*user*/anaconda3/envs/dl/lib/python3.6/site-packages/IPython/core/shellapp.py", line 244, in init_extensions self.shell.extension_manager.load_extension(ext) File "/home/*user*/anaconda3/envs/dl/lib/python3.6/site-packages/IPython/core/extensions.py", line 85, in load_extension mod = import_module(module_str) File "/home/*user*/anaconda3/envs/dl/lib/python3.6/importlib/__init__.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 941, in _find_and_load_unlocked File "", line 219, in _call_with_frames_removed File "", line 994, in _gcd_import File "", line 971, in _find_and_load File "", line 953, in _find_and_load_unlocked ModuleNotFoundError: No module named 'beakerx_magics' ...
LeeTZ commented 6 years ago

Hello, @NumesSanguis I cannot easily reproduce the bug, could you double check the installation guide to see if you could reproduce that with a fresh conda env? Also, if the dataframes are not showing up for you, could you share if there are any error messages either in browser's console or in your console? That would help us identify the issue. Thanks!

NumesSanguis commented 6 years ago

@LeeTZ when I first encountered the new bug I made a new environment exactly following the steps given in my first post and I still got the same error. Have you tried a new environment with exactly my steps? It might be related to conda install ipykernel, ipywidgets or python -m ipykernel install --user --name stats --display-name "py36 stats".

I didn't see any clear error messages given in the browser itself. I don't have time for the moment to play around with this, but if I have time later on, I'll put the error output here.

dhaitz commented 5 years ago

Hi @NumesSanguis ,

I encountered the same errors when starting Jupyter Notebooks and got rid of them by removing miniconda3/etc/ipython/ipython_config.py, which in my case only contained 

c = get_config()
c.InteractiveShellApp.extensions = ['beakerx.autotranslation',
'beakerx_magics.kernel_magic',
'beakerx_magics.groovy_magic',
'beakerx_magics.clojure_magic',
'beakerx_magics.kotlin_magic',
'beakerx_magics.scala_magic',
'beakerx_magics.sql_magic',
'beakerx_magics.java_magic'
]