[jupyter] Re: [ANN] nbconvert 5.3.0 — now with tag-based element filtering!

[John Griffiths]

I've tried putting the examples above into notebooks and executing and 
currently get either thrown errors or no filtering. 

Are there some worked notebook example files somewhere you could point to 
for this?


Thanks.





On Saturday, 2 September 2017 00:01:59 UTC-4, M Pacer wrote:
>
> We are pleased to announced the release of nbconvert 5.3.0!
>
> It is available via pypi (pip install nbconvert -U) and conda-forge (conda 
> install nbconvert -c conda-forge).
>
> This release has a number of bug fixes as well as docs, testing, and other 
> miscellaneous improvements. 
>
> In addition, we're excited to share with everyone the news that nbconvert 
> now supports *tag-based element filtering*! 
>
> Cell metadata tags allow filtering cell level elements, which removes: 
>
>- cells with tags that match the tags in TagRemovePreprocessor.
>remove_cell_tags,
>- inputs in cells with tags that match the tags in 
>TagRemovePreprocessor.remove_input_tags, 
>- all outputs in cells with tags that match 
>TagRemovePreprocessor.remove_all_outputs_tags. 
>
> To remove individual output elements (leaving others) you cannot use cell 
> metadata tags — instead, you will need to use output metadata tags (see 
> below for more explanation). Doing so removes:
>
>- Outputs with tags that match the tags in 
>TagRemovePreprocessor.remove_single_output_tags
>
> These different traitlets can be mixed and matched as desired.
>
> A much more comprehensive explanation as to how to use tag-based element 
> filtering is included at the end of this announcement. 
>
> For more details about the full release, see the changelog 
> .
>
> We thank the following 9 authors who contributed 176 commits.
>
> * Benjamin Ragan-Kelley
> * Damián Avila
> * M Pacer
> * Matthias Bussonnier
> * Michael Scott Cuthbert
> * mpacer
> * Patricia Hanus
> * tdalseide
> * Thomas Kluyver
>
> Cheers,
> the nbconvert team
>
> --
>
>
> *Filtering Notebook Content*
>
>
> Users have long asked for a way to remove content from notebooks when 
> converting them with nbconvert. There are lots of use cases for this kind 
> of feature. 
>
> Sometimes content makes sense in interactive contexts, but not when 
> presenting the work to other people. For example, in a data analytic report 
> for non-experts who don't know python, it may not make sense to show them 
> code. It could also makes sense to show *some* code cells, but not 
> others. For example, if you wanted to show data analyst colleagues how you 
> processed the data, but not your import statements or plotting commands. Or 
> if you were showing designer colleagues *how *you plotted your results 
> you might want to hide your analyses but show your plotting code. 
>
> It would be frivolous to have to recreate the same content to generate one 
> report for each of those cases. It should be possible to easily create each 
> of those reports from the same source notebook. This release of nbconvert 
> addresses these (and many other) use cases. 
>
> *Global Content Filtering*
>
> With 5.2 we introduced global content filtering, which allows you to 
> remove every instance of different kinds of elements. This allows you to 
> remove every input, every output, every code or markdown cell, and all the 
> input or output prompts. This release solved the filtering problem for many 
> use-cases.
>
> ***new** Tag-based Element Filtering*
>
> But global content filtering doesn't allow you to remove only some of your 
> code, it will remove every input no matter what you do. In order to remove 
> only some of the content, we have to have a way to specify which content 
> should be removed. 
>
> This release allows you to specify which elements are to be removed 
> through the use of *tags.* 
>
> *What are tags?*
>
> Tags are strings that cannot contain spaces or commas. You can assign tags 
> to cells and they will be accessible in the cell's metadata. See the nbformat 
> cell metadata 
> 
>  docs 
> for more information.
>
> *Tag Toolbar*
>
> In notebook 5.0, we introduced the tag toolbar, which allows you to assign 
> and remove tags to cells in the notebook interface. 
>
> The basic user model for assigning and removing tags to one cell is 
> demonstrated in the gif below:
>
>
>
>
>
> *Using tags for filtering cells*
>
> The simplest case of removing elements is cells, so we'll describe how to 
> do that first. 
>
> If you wanted to remove some cells from your notebook RemoveElements.ipynb, 
> you would apply the same tag to each of those cells. Let's say that this 
> tag is called to_remove.
>
> Let's say that you wanted to just remove those cells and convert it to a 
> static html page, then you would use the following command: 
>
> jupyter nbconvert RemoveElements 
> 

Re: [jupyter] terminal closing error

[Gideon Simpson]

I just checked.  This also happens if I just type exit.

On Tuesday, March 27, 2018 at 6:42:13 AM UTC-4, takowl wrote:
>
> How are you closing it?
>
> On 27 March 2018 at 06:30, Gideon Simpson  > wrote:
>
>> When trying to close a terminal in jupyter, I get the following error.  
>> Any suggestions?
>>
>>
>>
>> [E 00:23:09.324 NotebookApp] Uncaught exception in /terminals/websocket/1
>>
>> Traceback (most recent call last):
>>
>>   File "/anaconda3/lib/python3.6/site-packages/tornado/websocket.py", 
>> line 498, in _run_callback
>>
>> result = callback(*args, **kwargs)
>>
>>   File 
>> "/anaconda3/lib/python3.6/site-packages/notebook/terminal/handlers.py", 
>> line 37, in on_message
>>
>> super(TermSocket, self).on_message(message)
>>
>>   File 
>> "/anaconda3/lib/python3.6/site-packages/terminado/websocket.py", line 81, 
>> in on_message
>>
>> self.terminal.ptyproc.write(command[1])
>>
>>   File 
>> "/anaconda3/lib/python3.6/site-packages/ptyprocess/ptyprocess.py", line 
>> 829, in write
>>
>> return super(PtyProcessUnicode, self).write(b)
>>
>>   File 
>> "/anaconda3/lib/python3.6/site-packages/ptyprocess/ptyprocess.py", line 
>> 555, in write
>>
>> return self._writeb(s, flush=flush)
>>
>>   File 
>> "/anaconda3/lib/python3.6/site-packages/ptyprocess/ptyprocess.py", line 
>> 547, in _writeb
>>
>> self.fileobj.flush()
>>
>> OSError: [Errno 5] Input/output error
>>
>>  
>>
>>
>>
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Re: [jupyter] How would you build a dashboard in a Jupyter notebook?

[Jason Grout]

Christian,

Great questions! Here are a couple of thoughts:

1. The https://github.com/jupyter/dashboards project is, I think,
essentially unmaintained at this point.

2. However, there are lots of people excited about doing dashboards and
working on experiments for doing dashboards using ipywidgets. See
https://github.com/jupyter-widgets/ipywidgets/issues/2018 for some notes on
recent discussion and links to some experimental projects.

3. Another broader discussion about dashboards is happening at
https://github.com/jupyterlab/jupyterlab/issues/1640

We welcome any input, and especially helping push forward in some of these
experiments.

Thanks,

Jason


On Wed, Mar 28, 2018 at 6:25 AM Christian Schafmeister <
drschafmeis...@gmail.com> wrote:

> Thank you very much for the clarification!
> I very much appreciate it.
>
>
> On Mar 28, 2018, at 4:46 AM, Thomas Kluyver  wrote:
>
> For the record, your messages were in the Google Groups spam filter (which
> seems to be problematic lately, because a load of messages got caught in
> it). After a day or so, we get an email telling us that some messages were
> filtered, and we can go and approve them.
>
> On 27 March 2018 at 20:10, Christian Schafmeister 
> wrote:
>
>> I was posting replies under the wrong account (sigh)
>>
>> I discovered Jupyter dashboards while watching videos on this last night
>> - thank you.
>>
>>
>>
>> On Tuesday, March 27, 2018 at 6:33:16 AM UTC-4, takowl wrote:
>>>
>>> Hi Christian,
>>>
>>> Have you had a look at the Jupyter dashboards project? Is this something
>>> like what you want?
>>>
>>> https://github.com/jupyter/dashboards/
>>>
>>> Best wishes,
>>> Thomas
>>>
>>> On 26 March 2018 at 22:37, Christian Schafmeister 
>>>  wrote:
>>>

 Greetings fellow Jovyans!

 I'm setting up an application in a Jupyter notebook that will launch a
 large number of very long (multiple day) jobs/calculations on a cluster of
 GPU machines.

 How would folks recommend setting up a dashboard to monitor the
 progress of those calculations within a Jupyter notebook?

 I was thinking a dashboard made up of jupyter widgets composed of HBox,
 VBox, Buttons, Labels etc that would be updated every couple of seconds
 from a process launched by evaluating a function in a cell.

 The dashboard would contain a button to shut down the process that
 monitors the jobs.

 Has anyone done anything like this?   Are there any examples that folks
 could point me towards?

 Note: I'm not doing this in Python.   We've implemented a new kernel in
 Common Lisp and we have ported Jupyter Widgets 7.1 to this kernel.
 Everything is compiled to native code and we have threading implemented
 using pthreads.

 Best,

 Christian Schafmeister
 Professor,
 Chemistry Department,
 Temple University



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Re: [jupyter] How would you build a dashboard in a Jupyter notebook?

[Christian Schafmeister]

Thank you very much for the clarification!
I very much appreciate it.


> On Mar 28, 2018, at 4:46 AM, Thomas Kluyver  wrote:
> 
> For the record, your messages were in the Google Groups spam filter (which 
> seems to be problematic lately, because a load of messages got caught in it). 
> After a day or so, we get an email telling us that some messages were 
> filtered, and we can go and approve them.
> 
> On 27 March 2018 at 20:10, Christian Schafmeister  > wrote:
> I was posting replies under the wrong account (sigh)
> 
> I discovered Jupyter dashboards while watching videos on this last night - 
> thank you.
> 
> 
> 
> On Tuesday, March 27, 2018 at 6:33:16 AM UTC-4, takowl wrote:
> Hi Christian,
> 
> Have you had a look at the Jupyter dashboards project? Is this something like 
> what you want?
> 
> https://github.com/jupyter/dashboards/ 
> 
> 
> Best wishes,
> Thomas
> 
> On 26 March 2018 at 22:37, Christian Schafmeister > 
> wrote:
> 
> Greetings fellow Jovyans!
> 
> I'm setting up an application in a Jupyter notebook that will launch a large 
> number of very long (multiple day) jobs/calculations on a cluster of GPU 
> machines.
> 
> How would folks recommend setting up a dashboard to monitor the progress of 
> those calculations within a Jupyter notebook?
> 
> I was thinking a dashboard made up of jupyter widgets composed of HBox, VBox, 
> Buttons, Labels etc that would be updated every couple of seconds from a 
> process launched by evaluating a function in a cell.
> 
> The dashboard would contain a button to shut down the process that monitors 
> the jobs.
> 
> Has anyone done anything like this?   Are there any examples that folks could 
> point me towards?
> 
> Note: I'm not doing this in Python.   We've implemented a new kernel in 
> Common Lisp and we have ported Jupyter Widgets 7.1 to this kernel.  
> Everything is compiled to native code and we have threading implemented using 
> pthreads.
> 
> Best,
> 
> Christian Schafmeister
> Professor,
> Chemistry Department,
> Temple University
> 
> 
> 
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>  
> .
> For more options, visit https://groups.google.com/d/optout 
> .
> 
> 
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Re: [jupyter] How would you build a dashboard in a Jupyter notebook?

[Thomas Kluyver]

For the record, your messages were in the Google Groups spam filter (which
seems to be problematic lately, because a load of messages got caught in
it). After a day or so, we get an email telling us that some messages were
filtered, and we can go and approve them.

On 27 March 2018 at 20:10, Christian Schafmeister 
wrote:

> I was posting replies under the wrong account (sigh)
>
> I discovered Jupyter dashboards while watching videos on this last night -
> thank you.
>
>
>
> On Tuesday, March 27, 2018 at 6:33:16 AM UTC-4, takowl wrote:
>>
>> Hi Christian,
>>
>> Have you had a look at the Jupyter dashboards project? Is this something
>> like what you want?
>>
>> https://github.com/jupyter/dashboards/
>>
>> Best wishes,
>> Thomas
>>
>> On 26 March 2018 at 22:37, Christian Schafmeister 
>> wrote:
>>
>>>
>>> Greetings fellow Jovyans!
>>>
>>> I'm setting up an application in a Jupyter notebook that will launch a
>>> large number of very long (multiple day) jobs/calculations on a cluster of
>>> GPU machines.
>>>
>>> How would folks recommend setting up a dashboard to monitor the progress
>>> of those calculations within a Jupyter notebook?
>>>
>>> I was thinking a dashboard made up of jupyter widgets composed of HBox,
>>> VBox, Buttons, Labels etc that would be updated every couple of seconds
>>> from a process launched by evaluating a function in a cell.
>>>
>>> The dashboard would contain a button to shut down the process that
>>> monitors the jobs.
>>>
>>> Has anyone done anything like this?   Are there any examples that folks
>>> could point me towards?
>>>
>>> Note: I'm not doing this in Python.   We've implemented a new kernel in
>>> Common Lisp and we have ported Jupyter Widgets 7.1 to this kernel.
>>> Everything is compiled to native code and we have threading implemented
>>> using pthreads.
>>>
>>> Best,
>>>
>>> Christian Schafmeister
>>> Professor,
>>> Chemistry Department,
>>> Temple University
>>>
>>>
>>> --
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>>> Groups "Project Jupyter" group.
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>>> 
>>> .
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
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Re: [jupyter] How would you build a dashboard in a Jupyter notebook?

[Christian Schafmeister]

I was posting replies under the wrong account (sigh)

I discovered Jupyter dashboards while watching videos on this last night - 
thank you.



On Tuesday, March 27, 2018 at 6:33:16 AM UTC-4, takowl wrote:
>
> Hi Christian,
>
> Have you had a look at the Jupyter dashboards project? Is this something 
> like what you want?
>
> https://github.com/jupyter/dashboards/
>
> Best wishes,
> Thomas
>
> On 26 March 2018 at 22:37, Christian Schafmeister  > wrote:
>
>>
>> Greetings fellow Jovyans!
>>
>> I'm setting up an application in a Jupyter notebook that will launch a 
>> large number of very long (multiple day) jobs/calculations on a cluster of 
>> GPU machines.
>>
>> How would folks recommend setting up a dashboard to monitor the progress 
>> of those calculations within a Jupyter notebook?
>>
>> I was thinking a dashboard made up of jupyter widgets composed of HBox, 
>> VBox, Buttons, Labels etc that would be updated every couple of seconds 
>> from a process launched by evaluating a function in a cell.
>>
>> The dashboard would contain a button to shut down the process that 
>> monitors the jobs.
>>
>> Has anyone done anything like this?   Are there any examples that folks 
>> could point me towards?
>>
>> Note: I'm not doing this in Python.   We've implemented a new kernel in 
>> Common Lisp and we have ported Jupyter Widgets 7.1 to this kernel.  
>> Everything is compiled to native code and we have threading implemented 
>> using pthreads.
>>
>> Best,
>>
>> Christian Schafmeister
>> Professor,
>> Chemistry Department,
>> Temple University
>>
>>
>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "Project Jupyter" group.
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>> .
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>> https://groups.google.com/d/msgid/jupyter/b16cffaf-3d31-49d0-8469-e50f9b1f3ebb%40googlegroups.com
>>  
>> 
>> .
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>

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Re: [jupyter] numeric text description cropped

[Randy Heiland]

It does indeed - thanks! (I need to discard my "ipywidgets Doc Release
7.1.2" pdf) Hmm, maybe the docs you point to will also tell me why tooltip
doesn't seem to work for numeric widgets...


On Sun, Mar 25, 2018 at 12:16 AM, Jason Grout  wrote:

> Does this section in the docs help?
>
> https://ipywidgets.readthedocs.io/en/latest/examples/Widget%20Styling.
> html#Description
>
>
>
> On Sat, Mar 24, 2018 at 3:18 PM Randy Heiland 
> wrote:
>
>> The following crops the description for the FloatText; how can I have it
>> not do that? Basically, I'd like to display the entire description string
>> and shorten the FloatText input box.
>>
>> from ipywidgets import Layout, HBox, FloatText, Label
>> numVal = FloatText (
>> description= 'Enter your value',
>> layout = Layout(flex='0%', constWidth='200px'),  # width = 'auto',
>> )
>> numUnits = Label('Units')
>> HBox([numVal, numUnits], layout=Layout(width='300px'))
>>
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Re: [jupyter] Jupyter notebook for concurrent logins and shared libraries

[rockssk]

JupyterHub is a good idea, but then the authentication and spawners are 
little complex to implement i guess.

On Wednesday, March 21, 2018 at 4:49:53 PM UTC-4, Paul Hobson wrote:
>
> Rockssk,
>
> I think JupyterHub can handle parts 1 and 3:
> https://github.com/jupyterhub/jupyterhub
>
> I'm not sure about your needs for 2, though.
> -paul
>
>
>
> On Wed, Mar 21, 2018 at 1:42 PM, rockssk  
> wrote:
>
>> All,
>>
>>we have multiple python projects going on currently , each have their 
>> own virtual environment and maintain the dependant packages/libraries 
>> within the venv
>>   
>>We are looking for a solution where 
>>   1. Multiple developers can login at the same time into a central 
>> notebook app, and execute code within their venv
>>   2. Maintain dependent libraries/packages at a central location.
>>   3. Be able to execute python and pyspark code from the notebook
>>
>>
>> Any pointers/solution is much appreciated
>>
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Re: [jupyter] How would you build a dashboard in a Jupyter notebook?

[Christian Schafmeister]

My previous response was deleted for some reason...

I just learned about Jupyter dashboards from watching a talk last night - 
thanks.

My question is more how do people go about doing the following.

I have a bunch of processes running on a remote machine, let's say that as 
they complete they write their results to an Amazon web services S3 bucket 
or to a directory that the machine running the jupyter notebook has access 
to.
I will run a process in my jupyter notebook that will check the S3 bucket 
or directory every 30 seconds or so and update the text and color of some 
label widgets to indicate the status of the various jobs that are running.

In the meantime I'd like the jupyter notebook to continue responding to 
evaluation of cells that would gather up the current results and display 
them in another format.

I'm just casting about for other ideas along those lines.


On Tuesday, March 27, 2018 at 6:33:16 AM UTC-4, takowl wrote:
>
> Hi Christian,
>
> Have you had a look at the Jupyter dashboards project? Is this something 
> like what you want?
>
> https://github.com/jupyter/dashboards/
>
> Best wishes,
> Thomas
>
> On 26 March 2018 at 22:37, Christian Schafmeister  > wrote:
>
>>
>> Greetings fellow Jovyans!
>>
>> I'm setting up an application in a Jupyter notebook that will launch a 
>> large number of very long (multiple day) jobs/calculations on a cluster of 
>> GPU machines.
>>
>> How would folks recommend setting up a dashboard to monitor the progress 
>> of those calculations within a Jupyter notebook?
>>
>> I was thinking a dashboard made up of jupyter widgets composed of HBox, 
>> VBox, Buttons, Labels etc that would be updated every couple of seconds 
>> from a process launched by evaluating a function in a cell.
>>
>> The dashboard would contain a button to shut down the process that 
>> monitors the jobs.
>>
>> Has anyone done anything like this?   Are there any examples that folks 
>> could point me towards?
>>
>> Note: I'm not doing this in Python.   We've implemented a new kernel in 
>> Common Lisp and we have ported Jupyter Widgets 7.1 to this kernel.  
>> Everything is compiled to native code and we have threading implemented 
>> using pthreads.
>>
>> Best,
>>
>> Christian Schafmeister
>> Professor,
>> Chemistry Department,
>> Temple University
>>
>>
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>>  
>> 
>> .
>> For more options, visit https://groups.google.com/d/optout.
>>
>
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Re: [jupyter] How would you build a dashboard in a Jupyter notebook?

[Christian Schafmeister]

Why are my responses being deleted?  Twice now.

On Tuesday, March 27, 2018 at 6:33:16 AM UTC-4, takowl wrote:
>
> Hi Christian,
>
> Have you had a look at the Jupyter dashboards project? Is this something 
> like what you want?
>
> https://github.com/jupyter/dashboards/
>
> Best wishes,
> Thomas
>
> On 26 March 2018 at 22:37, Christian Schafmeister  > wrote:
>
>>
>> Greetings fellow Jovyans!
>>
>> I'm setting up an application in a Jupyter notebook that will launch a 
>> large number of very long (multiple day) jobs/calculations on a cluster of 
>> GPU machines.
>>
>> How would folks recommend setting up a dashboard to monitor the progress 
>> of those calculations within a Jupyter notebook?
>>
>> I was thinking a dashboard made up of jupyter widgets composed of HBox, 
>> VBox, Buttons, Labels etc that would be updated every couple of seconds 
>> from a process launched by evaluating a function in a cell.
>>
>> The dashboard would contain a button to shut down the process that 
>> monitors the jobs.
>>
>> Has anyone done anything like this?   Are there any examples that folks 
>> could point me towards?
>>
>> Note: I'm not doing this in Python.   We've implemented a new kernel in 
>> Common Lisp and we have ported Jupyter Widgets 7.1 to this kernel.  
>> Everything is compiled to native code and we have threading implemented 
>> using pthreads.
>>
>> Best,
>>
>> Christian Schafmeister
>> Professor,
>> Chemistry Department,
>> Temple University
>>
>>
>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "Project Jupyter" group.
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>> .
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>> https://groups.google.com/d/msgid/jupyter/b16cffaf-3d31-49d0-8469-e50f9b1f3ebb%40googlegroups.com
>>  
>> 
>> .
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>

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Re: [jupyter] NB2KG 0.2.0 is released!

[Paco Nathan]

Congrats Kevin!  So glad to see these capabilities become available -

On Mon, Mar 26, 2018 at 11:29 AM, Luciano Resende 
wrote:

>
>
> On Mon, Mar 26, 2018 at 11:17 AM, Kevin Bates  wrote:
>
>> *NB2KG* is a Jupyter Notebook server extension that enables the Notebook
>> server to use remote kernels hosted by a Jupyter "Gateway" (i.e., Kernel
>> Gateway  or 
>> Enterprise
>> Gateway ) -
>> essentially enabling a bring-your-own-notebook paradigm.
>>
>> https://github.com/jupyter-incubator/nb2kg/releases/tag/v0.2.0
>>
>> Please feel free to take it (along with a gateway) for a spin,
>> Kevin.
>>
>
> Congrats !!! Hopefully we will see this type of functionality available in
> core Notebook/Labs in the near future.
>
>
>
> --
> Luciano Resende
> http://twitter.com/lresende1975
> http://lresende.blogspot.com/
>
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> 
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>
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Re: [jupyter] Jupyter notebook for concurrent logins and shared libraries

[rockssk]

Thanks Paul for your suggestion,

 here is what we are planning now, to have a seperate notebook server per 
venv/project and let all developers within the project to access the same 
notebook server, will look at the kernel.json .

On Wednesday, March 21, 2018 at 5:29:00 PM UTC-4, Michael Milligan wrote:
>
> For #2 it depends on how complex your dependencies are, but in general 
> making each virtual environment available as a Jupyter kernel should do 
> what you want. Hint: you'll want to edit the "kernel.json" files to give 
> them descriptive names for the UI! 
>
> On Wed, Mar 21, 2018 at 3:49 PM, Paul Hobson  > wrote:
>
>> Rockssk,
>>
>> I think JupyterHub can handle parts 1 and 3:
>> https://github.com/jupyterhub/jupyterhub
>>
>> I'm not sure about your needs for 2, though.
>> -paul
>>
>>
>>
>> On Wed, Mar 21, 2018 at 1:42 PM, rockssk  
>> wrote:
>>
>>> All,
>>>
>>>we have multiple python projects going on currently , each have their 
>>> own virtual environment and maintain the dependant packages/libraries 
>>> within the venv
>>>   
>>>We are looking for a solution where 
>>>   1. Multiple developers can login at the same time into a central 
>>> notebook app, and execute code within their venv
>>>   2. Maintain dependent libraries/packages at a central location.
>>>   3. Be able to execute python and pyspark code from the notebook
>>>
>>>
>>> Any pointers/solution is much appreciated
>>>
>>> -- 
>>> You received this message because you are subscribed to the Google 
>>> Groups "Project Jupyter" group.
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>>> an email to jupyter+u...@googlegroups.com .
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>>> .
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>>> https://groups.google.com/d/msgid/jupyter/85ac7264-fb12-424c-baef-94206e0147e5%40googlegroups.com
>>>  
>>> 
>>> .
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>>>
>>
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>
>
>
>

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