Re: [jupyter] Re: Internship for people facing discrimination in IT industry (NumFOCUS mini-grants)

[Chris Holdgraf]

In case it's helpful, Sarah G. has been putting together some documentation
and guides while the JupyterHub team went through the latest round of
Outreachy. Maybe you and others would find it helpful:

https://jupyterhub-outreachy.readthedocs.io/en/latest/

In particular the community coordinator role section might be useful:

https://jupyterhub-outreachy.readthedocs.io/en/latest/community-coordinator/role-responsibilities

On Tue, Apr 25, 2023 at 6:52 PM Carol Willing  wrote:

> Hi Mariana,
>
> Thanks so much for thinking about taking on a mini-grant to greater
> diversify the Jupyter contributor base. I've long felt that Jupyter should
> be doing much more to promote diversity in the project. I'm wondering if
> would make sense to limit the scope of the application pool to Africa with
> the hope of increasing adoption and participation there. Then if there was
> a follow up grant to serve the Global South or open to both Africa and the
> Global South.
>
> While I would prefer if we ran the program through Outreachy since it
> would be simpler to implement, but I understand if that is not possible.
>
> The intern salary is very standard for outreach programs, and I see no
> problem with the amount.
>
> How would the selection process for the intern be done?
>
> We can chat more at JupyterCon if you wish.
>
> Thanks!
> Carol
>
> On Wednesday, April 19, 2023 at 4:38:01 AM UTC-6 marian@gmail.com
> wrote:
>
>> Hi all,
>>
>> My name is Mariana, I've been active in the NumFOCUS ecosystem as a
>> developer for a few years and I'm a part of Jupyter's Distinguished
>> Contributors.
>>
>> I was told to circulate this idea in the Jupyter emailing list before
>> moving forward with it. I'd like to apply for a NumFOCUS small development
>> grant to run a one person three months long open source internship where I
>> am the mentor.
>>
>> The structure of the internship would be very similar to the one used in
>> the outreachy  program. Here's a simplified
>> outline:
>>
>> *Objective:* Improve the software quality of Jupyter's expanded universe
>> while at the same time introducing and fostering diversity in the open
>> science ecosystem
>> *Focus group:* People who face systemic bias or discrimination in the
>> technology industry of their country and come from disadvantaged
>> socioeconomic backgrounds [1]
>> *Work scope:* Fix general bugs, add features (tests, greater integration
>> with the rest of NumFOCUS' software stack), system's redesign (propose
>> better API design, etc). The proposed projects are: ipycytoscape
>> , any of the xeus kernels
>> , but I'm also open for tackling other
>> projects here, please see [2]
>> *Internship duration:* 3 months, 30h work/week [3]
>> *Deliverables:* Two blog posts that are somehow related to the work of
>> the intern in the project. A number of issues solved and improved software
>> for Jupyter.
>> *Grant breakdown: *7000 USD - Intern salary [4] 1000 USD - Travel
>> stipend [5]
>>
>> Finally, I’m open to adopt other formats, in case someone would like to
>> pick up on mentoring, for example, or be paid for it, we could increase the
>> amount of money we’re asking in the grant.
>>
>> I’m also very happy to hear about other grants or ideas on how to expand
>> this project. I’m a member of NumFOCUS DISC committee and several people
>> inside the organization support this idea.
>>
>> If you're part of the Executive Council Members the Software Council
>> Members, I'd especially like to hear from you. I'm also interested in the
>> broader spectrum of what Jupyter's community have to say about it. I'm very
>> open to constructive criticism and would love to discuss the idea further
>> with you. I'd like to propose this for the next funding round which give us
>> the deadline of June 2, 2023.
>>
>> [1] I'm not sure how to make this process both dignifying and transparent
>> to the people who apply. I think defining what is "disadvantaged
>> socioeconomic background" is really hard. Right now I'm thinking of a)
>> making it clear in the registration process b) when the candidate is chosen
>> I'll ask them some sort of income proof and do my best to google if their
>> income matches the murky "disadvantaged socioeconomic background"
>> definition. If it does, they will be accepted.
>> [2] The reason why I chose these projects is because I'm a core
>> contributor in them and know them well. I know the scope of these projects
>> is quite small, they have at most a few thousand lines of code and offer a
>> challenge that's not too big nor too small for the intern. However, if the
>> broader community think other projects should be considered I'm happy to
>> re-evaluate.
>> [3] These numbers are copied from outreachy
>> [4] This salary might strike some people as quite high for an internship,
>> especially if we might be focusing in developing countries or
>> "disadvantaged 

Re: [jupyter] SSH into Kubespawner pod?

[Chris Holdgraf]

This new-ish tool might be of use / interest?
https://github.com/yuvipanda/jupyterhub-ssh

On Fri, Dec 18, 2020 at 11:25 PM David Rosenstrauch 
wrote:

> I've recently set up Jupyter with kubespawner for our team, and it's
> working out nicely.  However, one of the next requests from the team is to
> allow them to ssh into their Jupyter pod, and I'm a little stumped on how
> to make that happen.
>
> Setting up the ssh server listening in the pod seems do-able enough.
> However, the challenge is the networking around getting them to connect to
> the ssh server running in their pod (and not anyone else's pod).
>
> My thinking is that I might be able to set up a reverse proxy that
> forwards the SSH traffic to the user's pod.  But that requires matching the
> user's ID to the IP address of their running pod, which I can't see a way
> to do.
>
> I've tried setting up a headless service that selects each of the running
> Jupyter pods - and therefore sets up a dns name for them.  But the dns name
> that gets created is specific to the IP
> (...svc.cluster.local) rather than
> the pod's name (jupyter-), and so again there's no easy way to tie
> that IP back to the user's ID.
>
> Presumably Jupyter is storing that mapping of username to pod IP somewhere
> internally, but I don't see where.
>
> Any suggestions on how it might be possible to accomplish this?
>
> Thanks,
>
> DR
>
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> 
> .
>

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Re: [jupyter] Sprint tasks

[Chris Holdgraf]

No problem! Also just a note that I believe many of the JupyterHub
repositories (at the least, jupyterhub/binderhub, jupyter/repo2docker, and
jupyterhub/the-littlest-jupyterhub) should have "good first issue" tags on
them as well as a few "hacktoberfest" tags. Those should be nice places to
look too. (same is true for jupyter/jupyter-book, if you find somebody
that's interested to work on that!)

On Fri, Oct 18, 2019 at 4:00 AM Thomas Kluyver  wrote:

> Thanks Chris & Jason.
>
> Chris: good idea about asking the Turing Institute team. I've met them
> before at one of the Jupyterhub workshops, so I'll try dropping them a line.
>
> On Wed, 16 Oct 2019 at 22:27, Jason Grout  wrote:
>
>> We try to curate a list of "good first issues" in JupyterLab that might
>> be good for people that want to do stuff in JS/Typescript:
>> https://github.com/jupyterlab/jupyterlab/issues?q=is%3Aopen+is%3Aissue+label%3A%22good+first+issue%22
>>
>> There's also a curated list of good first issues in ipywidgets:
>> https://github.com/jupyter-widgets/ipywidgets/issues?q=is%3Aopen+is%3Aissue+label%3A%22good+first+issue%22
>> - though those might be a bit less curated, and they do include probably
>> more python issues.
>>
>> Thanks,
>>
>> Jason
>>
>>
>> On Wed, Oct 16, 2019 at 2:18 PM Thomas Kluyver  wrote:
>>
>>> Hi all,
>>>
>>> I've said I'll run a Jupyter-related sprint at a Hackathon being
>>> organised in London in a couple of weeks (
>>> https://www.man.com/hackathon2019 ). I'm not as familiar with Jupyter
>>> development as I used to be, so briefly: are there any Jupyter projects, or
>>> Jupyter-related projects, with a good crop of relatively straightforward
>>> issues that people could tackle in a sprint?
>>>
>>> The timetable includes 10 hours (!) of coding time, so ideally it would
>>> be good to have a range of difficulties, including a few more challenging
>>> issues. Maintenance things like adding tests or improving documentation are
>>> in scope.
>>>
>>> I'd like to have maybe 3 specific repositories I can point people to,
>>> because there's a bewildering array of Jupyter projects by now. It's also
>>> easier for people to help each other if they're working on the same pieces.
>>> Of course, if someone wants to work on something from another repo, I'll
>>> still help them.
>>>
>>> I'll look through some repositories myself as well, but if people know
>>> of projects that would be a good fit, I'd be grateful.
>>>
>>> Thanks,
>>> Thomas
>>>
>>> --
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>>> 
>>> .
>>>
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>> .
>>
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Re: [jupyter] Re: jupyter nbconvert - recursive option request?

[Chris Holdgraf]

To that point - on these kind of "quite useful but out-of-scope for a
tightly-scoped project" hacks, I think documentation (or places like
the community
forum ) are a good place for these kinds of
tips

On Mon, Aug 19, 2019 at 2:45 PM Matthew Seal  wrote:

> As one of the nbconvert maintainers, I'd say we're unlikely to add such a
> feature to nbconvert. As Roland mentioned it's easy to script or manage
> above the library and it would make the code harder to maintain over the
> long term.
>
> And +1 for Issues / PRs being the best way to interface for feature
> requests (and for potential features :) )
>
> Best,
> Matt
>
> On Sun, Aug 18, 2019 at 11:09 PM Roland Weber  wrote:
>
>> Personally, I don't think that nbconvert should bother with searching
>> input files in a directory structure. As your post shows, this is easily
>> added through scripting, without causing extra effort for the nbconvert
>> maintainers.
>>
>> Nevertheless, you can always open a feature request:
>> https://github.com/jupyter/nbconvert/issues
>> Submitting a PR will tremendously increase the chances of seeing it
>> implemented.
>>
>> cheers,
>>   Roland
>>
>> --
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>> 
>> .
>>
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> .
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Re: [jupyter] Nbconvert 5.5 Released

[Chris Holdgraf]

wow, congratulations to all!

On Thu, Apr 25, 2019 at 12:59 PM Matthew Seal  wrote:

> NBConvert 5.5
>
> With many significant improvements, we are pleased to announced nbconvert
> 5.5.0!
>
> It is available via pypi (pip install nbconvert -U). For conda it should
> appear in a day or so when the conda-forge feed picks up the new version 
> (conda
> install nbconvert -c conda-forge).
>
> We had some investment in latex and pdf conversions that have been
> longstanding in the Miltestone for 5.5. We got template improvements and
> several bug squashes into the release. However some of the more fundamental
> improvements like spaces in paths/names and http image references are still
> in progresss as we work through better approaches. Look for those
> improvements in the next release.
>
> For full details about the release, see the changelog
> ,
> but we've highlighted the significant changes below, and readthedocs page
> 
> should update shortly.
>
> Contributors
>
> The following 18 authors contributed 144+ commits -- Thank you all!
>
>- Benjamin Ragan-Kelley
>- Clayton A Davis
>- DInne Bosman
>- Doug Blank
>- Henrique Silva
>- Jeff Hale
>- Lukasz Mitusinski
>- M Pacer
>- Maarten Breddels
>- Madhumitha N
>- Matthew Seal
>- Paul Gowder
>- Philipp A
>- Rick Lupton
>- Rüdiger Busche
>- Thomas Kluyver
>- Tyler Makaro
>- WrRan
>
> The full list of changes they made can be seen on GitHub
> 
>
> Significant
> Changes
> 
> Deprecations
>
> Python 3.4 support was dropped. Many of our upstream libraries stopped
> supporting 3.4 and it was found that serious bugs were being caught during
> testing against those libraries updating past 3.4.
>
> See :ghpull:`979`
> 
>  for
> details.
>
> IPyWidget
> Support
>
> Now when a notebook executing contains Jupyter Widgets
> , the state of all the
> widgets can be stored in the notebook's metadata. This allows rendering of
> the live widgets on, for instance nbviewer, or when converting to html.
>
> You can tell nbconvert to not store the state using the store_widget_state
> argument:
>
> jupyter nbconvert --ExecutePreprocessor.store_widget_state=False --to 
> notebook --execute mynotebook.ipynb
>
> This widget rendering is not performed against a browser during execution,
> so only widget default states or states manipulated via user code will be
> calculated during execution. %%javascript cells will execute upon notebook
> rendering, enabling complex interactions to function as expected when
> viewed by a UI.
>
> If you can't view widget results after execution, you may need to select
> Trust Notebook under the File menu of the UI in question.
>
> See :ghpull:`779`
> 
> , :ghpull:`900`
> ,
> and :ghpull:`983`
> 
>  for
> details.
>
> Execute
> Preprocessor Rework
>
> Based on monkey patching required in papermill
>  the
> run_cell code path in the ExecutePreprocessor was reworked to allow for
> accessing individual message parses without reimplementing the entire
> function. Now there is a processs_message function which take a ZeroMQ
> message and applies all of its side-effect updates on the cell/notebook
> objects before returning the output it generated, if it generated any such
> output.
>
> The change required a much more extensive test suite covering cell
> execution as test coverage on the various, sometimes wonky, code paths made
> improvements and reworks impossible to prove undamaging. Now changes to
> kernel message processing has much better coverage, so future additions or
> changes with specs over time will be easier to add.
>
> See :ghpull:`905`
> 
>  and :ghpull:`982`
> 
>  for
> details
>
> 

Re: [jupyter] Restrict Endpoint Access

[Chris Holdgraf]

Hmmm, I've only ever followed the instructions here:
https://github.com/quantstack/voila#installation

if those don't work, try opening an issue in the voila repo? I'm sure
they'd appreciate feedback on what's confusing!

On Wed, Apr 17, 2019 at 9:30 AM Alexander Feiszli 
wrote:

> Thank you Chris, that is exactly what we are looking for as well,
> disabling the ability to run arbitrary code.
>
> Do you happen to have the instructions for installing and enabling the
> extension handy? I'm not getting it quite right.
>
> On Wednesday, April 17, 2019 at 11:17:56 AM UTC-5, Chris Holdgraf wrote:
>>
>> More specifically - one of the goals of Voila is to be more secure. A
>> good default for this is to prevent the user from running arbitrary python
>> code, and keeping their interaction at the javascript layer (which is what
>> widgets are all using).
>>
>> You can find a few cool examples here:
>> https://mybinder.org/v2/gh/QuantStack/voila/stable?urlpath=voila/tree/notebooks
>>
>> The reason you don't see a ton of docs is because Voila is still in early
>> development mode, but I have heard docs are coming :-)
>>
>> On Wed, Apr 17, 2019 at 9:08 AM Tim Paine  wrote:
>>
>>> Widgets are enabled
>>>
>>> Tim Paine
>>> tim.paine.nyc
>>>
>>> On Apr 17, 2019, at 12:07, Alexander Feiszli  wrote:
>>>
>>> Also, it says the notebook is "Read Only" in the docs. I would still
>>> like users to be able to provide input datasets via widgets. Is this
>>> disabled?
>>>
>>> On Wednesday, April 17, 2019 at 10:51:51 AM UTC-5, Alexander Feiszli
>>> wrote:
>>>>
>>>> That's exactly what I'm looking for!
>>>>
>>>> I'm trying to figure out how to use this now; there's very scant
>>>> documentation which makes this a little difficult.
>>>>
>>>> I'm running:
>>>>
>>>> pip install voila
>>>> jupyter nbextension install voila
>>>>
>>>> and get
>>>>
>>>> FileNotFoundError: [Errno 2] No such file or directory: 'voila'
>>>>
>>>> Do you know the apporpriate name/path to point to?
>>>>
>>>> Also, I believe this would be even more valuable running as a
>>>> standalone application, but that I think would be even more challenging to
>>>> set up without documentation. Do you know of any references I can look at?
>>>>
>>>> Thank you!! This extension looks very valuable.
>>>>
>>>> On Wednesday, April 17, 2019 at 10:05:25 AM UTC-5, Chris Holdgraf wrote:
>>>>>
>>>>> Check out Voila! ( https://github.com/QuantStack/voila)  I bet that
>>>>> you'd find it interesting - it's quite similar to app mode :-)
>>>>>
>>>>> On Wed, Apr 17, 2019 at 6:54 AM Alexander Feiszli 
>>>>> wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> At my org we are looking to implement Jupyter notebooks in production
>>>>>> as sort of "mini-apps" for small groups of end users. The idea is that 
>>>>>> the
>>>>>> data scientists can develop in Jupyterhub like an IDE and then push a
>>>>>> notebook into a CICD workflow, and then out pops a production version 
>>>>>> that
>>>>>> is accessible by a particular group of users. The reason for this is that
>>>>>> the data scientists are not app developers, they do not want to write
>>>>>> webapps, just work on their algorithms, and their end users are very 
>>>>>> small
>>>>>> groups, maybe 6-12 internal users, so it is unnecessary to have a
>>>>>> development team devoted to making nice looking apps for every algorithm
>>>>>> they write. We just need a mechanism by which the end user can provide
>>>>>> input data, it gets transformed by the notebook, generates some
>>>>>> charts/graphs, and then they receive transformed output data.
>>>>>>
>>>>>> For the end users, they should not be able to modify or create new
>>>>>> notebooks, simply run a single notebook. For that reason we are looking 
>>>>>> at
>>>>>> the "appmode" plugin (https://github.com/oschuett/appmode). The next
>>>>>> thing we would like to do is have the production URL redirect to the
>>>>>> running "appmode" version

Re: [jupyter] Restrict Endpoint Access

[Chris Holdgraf]

More specifically - one of the goals of Voila is to be more secure. A good
default for this is to prevent the user from running arbitrary python code,
and keeping their interaction at the javascript layer (which is what
widgets are all using).

You can find a few cool examples here:
https://mybinder.org/v2/gh/QuantStack/voila/stable?urlpath=voila/tree/notebooks

The reason you don't see a ton of docs is because Voila is still in early
development mode, but I have heard docs are coming :-)

On Wed, Apr 17, 2019 at 9:08 AM Tim Paine  wrote:

> Widgets are enabled
>
> Tim Paine
> tim.paine.nyc
>
> On Apr 17, 2019, at 12:07, Alexander Feiszli 
> wrote:
>
> Also, it says the notebook is "Read Only" in the docs. I would still like
> users to be able to provide input datasets via widgets. Is this disabled?
>
> On Wednesday, April 17, 2019 at 10:51:51 AM UTC-5, Alexander Feiszli wrote:
>>
>> That's exactly what I'm looking for!
>>
>> I'm trying to figure out how to use this now; there's very scant
>> documentation which makes this a little difficult.
>>
>> I'm running:
>>
>> pip install voila
>> jupyter nbextension install voila
>>
>> and get
>>
>> FileNotFoundError: [Errno 2] No such file or directory: 'voila'
>>
>> Do you know the apporpriate name/path to point to?
>>
>> Also, I believe this would be even more valuable running as a standalone
>> application, but that I think would be even more challenging to set up
>> without documentation. Do you know of any references I can look at?
>>
>> Thank you!! This extension looks very valuable.
>>
>> On Wednesday, April 17, 2019 at 10:05:25 AM UTC-5, Chris Holdgraf wrote:
>>>
>>> Check out Voila! ( https://github.com/QuantStack/voila)  I bet that
>>> you'd find it interesting - it's quite similar to app mode :-)
>>>
>>> On Wed, Apr 17, 2019 at 6:54 AM Alexander Feiszli 
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> At my org we are looking to implement Jupyter notebooks in production
>>>> as sort of "mini-apps" for small groups of end users. The idea is that the
>>>> data scientists can develop in Jupyterhub like an IDE and then push a
>>>> notebook into a CICD workflow, and then out pops a production version that
>>>> is accessible by a particular group of users. The reason for this is that
>>>> the data scientists are not app developers, they do not want to write
>>>> webapps, just work on their algorithms, and their end users are very small
>>>> groups, maybe 6-12 internal users, so it is unnecessary to have a
>>>> development team devoted to making nice looking apps for every algorithm
>>>> they write. We just need a mechanism by which the end user can provide
>>>> input data, it gets transformed by the notebook, generates some
>>>> charts/graphs, and then they receive transformed output data.
>>>>
>>>> For the end users, they should not be able to modify or create new
>>>> notebooks, simply run a single notebook. For that reason we are looking at
>>>> the "appmode" plugin (https://github.com/oschuett/appmode). The next
>>>> thing we would like to do is have the production URL redirect to the
>>>> running "appmode" version of the notebook. In addition, the production
>>>> notebook server should basically just have all the other endpoints shut off
>>>> or restricted, so that only this single "appmode" page is accessible.
>>>>
>>>> Can someone point me in the right direction for how I could modify a
>>>> notebook server to have requests to the base url redirect to this appmode
>>>> page, and how to restrict or turn off the other endpoints? I am a bit lost
>>>> but guessing I will need to modify the handlers here:
>>>> https://github.com/jupyter/notebook/blob/master/notebook/notebook/handlers.py
>>>>
>>>> --
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>>>> Groups "Project Jupyter" group.
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>>>> an email to jup...@googlegroups.com.
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>>>> To view this discussion on the web visit
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>>>> <https://groups.google.com/d/msgid/jupyter/d290d0dd-151e-4af0-a59c-e3cd38f78ccf

Re: [jupyter] Restrict Endpoint Access

[Chris Holdgraf]

Check out Voila! ( https://github.com/QuantStack/voila)  I bet that you'd
find it interesting - it's quite similar to app mode :-)

On Wed, Apr 17, 2019 at 6:54 AM Alexander Feiszli 
wrote:

> Hello,
>
> At my org we are looking to implement Jupyter notebooks in production as
> sort of "mini-apps" for small groups of end users. The idea is that the
> data scientists can develop in Jupyterhub like an IDE and then push a
> notebook into a CICD workflow, and then out pops a production version that
> is accessible by a particular group of users. The reason for this is that
> the data scientists are not app developers, they do not want to write
> webapps, just work on their algorithms, and their end users are very small
> groups, maybe 6-12 internal users, so it is unnecessary to have a
> development team devoted to making nice looking apps for every algorithm
> they write. We just need a mechanism by which the end user can provide
> input data, it gets transformed by the notebook, generates some
> charts/graphs, and then they receive transformed output data.
>
> For the end users, they should not be able to modify or create new
> notebooks, simply run a single notebook. For that reason we are looking at
> the "appmode" plugin (https://github.com/oschuett/appmode). The next
> thing we would like to do is have the production URL redirect to the
> running "appmode" version of the notebook. In addition, the production
> notebook server should basically just have all the other endpoints shut off
> or restricted, so that only this single "appmode" page is accessible.
>
> Can someone point me in the right direction for how I could modify a
> notebook server to have requests to the base url redirect to this appmode
> page, and how to restrict or turn off the other endpoints? I am a bit lost
> but guessing I will need to modify the handlers here:
> https://github.com/jupyter/notebook/blob/master/notebook/notebook/handlers.py
>
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Re: [jupyter] Google season of Docs

[Chris Holdgraf]

Hey Luciano - thanks for noting this! For what it's worth, I am happy to
help participate in any documentation improvements in the jupyter ecosystem!

On Tue, Mar 19, 2019 at 2:21 PM Luciano Resende 
wrote:

> Hey Jovyans,
>
> Google is organizing the "Season of Docs" with the goal of: bring open
> source and technical writer communities together, to the benefit of
> both. Together we raise awareness of open source, of docs, and of
> technical writing. Below there are links to more information: [1]
> season-of-docs website, and [2] the program timeline, but in summary,
> this looks like Google Summer of Code for technical writers to come
> and help with open source projects documentation.
>
> If folks are interested, I could look into this and prepare to enroll
> Jupyter as a participating organization. The only caveat I am not sure
> here is if this becomes "Jupyter" or NumFocus as the 501(c)(3)
> non-profit organization behind Jupyter.
>
> [1] https://developers.google.com/season-of-docs/
> [2] https://developers.google.com/season-of-docs/docs/timeline
>
> --
> Luciano Resende
> http://twitter.com/lresende1975
> http://lresende.blogspot.com/
>
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Re: [jupyter] attribute error: unable to remove columns with low std

[Chris Holdgraf]

Hello!

I'd recommend checking out the Pandas documention (
https://pandas.pydata.org/pandas-docs/stable/) for ideas of how to use it.
Jupyter makes it possible to use interactive tools like Pandas, but it
doesn't create Pandas itself so this isn't the best place to ask for
support (I'd bet Pandas has a mailing list though). Another good option is
the "scipy-lectures" website which has several helpful modules (and I think
covers Pandas) http://scipy-lectures.org/intro/

On Sat, Mar 2, 2019 at 5:42 AM Vaibhav Dixit 
wrote:

> Dear Jupyter users and experts,
> I am new to using Jupyter notebook installed via "anaconda navigator".
> For my ML needs, I need to preprocess data in CSV file i.e. remove columns
> with < 5% std (and remove rows for which > 50% features are zero valued
> etc).
> I tried the std condition with the following code, but it gives the
> following error.
> I couldn't find an easy solution in manuals and with google either.
> Can you please suggest me on a possible fix for this?
> thanks.
>
> Code:
> --
> import pandas as pd
> import numpy as np
> #df = pd.DataFrame()
> with open('test.csv', 'r', encoding="ascii", errors="surrogateescape") as
> f:
> data = f.read()
> #f = pd.read_csv('test.csv')
> df = pd.DataFrame(f)
>
> #pd.std(axis=10)
> rmcols = pd.drop(pd.std()[(pd.std() == 0)].index, axis=1)
> rmcols.to_csv('new.csv')
> -
>
> Error:
> -
>
> AttributeErrorTraceback (most recent call 
> last) in   8   9 #
> pd.std(axis=10)---> 10 rmcols = pd.drop(pd.std()[(pd.std() == 0)].index, 
> axis=1) 11 rmcols.to_csv('new.csv')
> AttributeError: module 'pandas' has no attribute 'drop'
>
> 
>
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Re: [jupyter] IPython 7.4 out.

[Chris Holdgraf]

w way to go!

On Wed, Feb 20, 2019 at 6:00 PM Matthias Bussonnier <
bussonniermatth...@gmail.com> wrote:

> See the full announce on discourse:
>
> https://discourse.jupyter.org/t/release-of-ipython-7-3/409
>
> As usual available on PyPI, and on conda-forge.
> You can update with
> $ pip install ipython --upgrade
> And if you are using conda, once available on conda-forge:
> $ conda upgrade ipython
>
> The biggest update to this release is the addition of %conda and %pip
> magic that should ease the installation of packages in the current
> environment. If you are on the bleeding edge this also adds compatibility
> with Python 3.8.
>
> If you are looking to help for future 7.4 release, subscribe to this
> issue[1], I’ll update it with things you can help with. It is a great way
> to get started contributing.
> --
> M
> 1: https://github.com/ipython/ipython/issues/11614
>
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Re: [jupyter] nbformat: Removing code to read XML notebook files

[Chris Holdgraf]

Maybe deprecate it for a release cycle and see if anybody complains once
they see the warning?

(also I am, in general, always in favor of simplifying things in nbconvert
:-) )

On Fri, Feb 15, 2019 at 5:56 PM Matthew Seal  wrote:

> Do you think we should remove the functionality from nbconvert to simplify
> things there too?
>
> On Thu, Feb 14, 2019 at 1:28 PM Samuel Lelièvre 
> wrote:
>
>> Related: the latest version of nbconvert added defusedxml as a dependency.
>>
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Re: [jupyter] nbformat: Removing code to read XML notebook files

[Chris Holdgraf]

The only major potential stakeholder that (I think) still cares about XML
is large-scale publishers, but I don't think there's been any official
adoption of Jupyter Notebooks there anyway, so it's probably fine. Thanks
for bringing this up Thomas! I'm +1 as well!

On Mon, Feb 11, 2019 at 2:27 PM Brian Granger  wrote:

> +1
>
> On Mon, Feb 11, 2019 at 1:41 PM Matthew Seal  wrote:
>
>> I'm 100% for removing -- I can't think of any recent tools that even
>> support xml. Thanks for making the PR!
>>
>> On Mon, Feb 11, 2019 at 7:01 AM Thomas Kluyver  wrote:
>>
>>> Hi all,
>>>
>>> Way back in 2011, when the first version of the IPython Notebook was
>>> being written, there was an option to store notebooks as XML. JSON was
>>> chosen as the default, and has always been the format all of our
>>> applications use. However, the code to read XML files stayed around, and
>>> recently Danor Cohen pointed out that it is vulnerable to denial of service
>>> attacks.
>>>
>>> I am proposing to *remove this code* rather than maintain it. None of
>>> our applications call it, and I'm not aware of anyone else using it. The
>>> XML format is, as far as I know, an abandoned concept.
>>>
>>> If you are using that code (nbformat.v2.*_xml), and you can't
>>> practically move away from it, now would be a good time to take over
>>> maintenance of it. ;-)
>>>
>>> The removal PR is here: https://github.com/jupyter/nbformat/pull/133
>>>
>>> Thanks,
>>> Thomas
>>>
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>
>
> --
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Re: [jupyter] Help deploying jupyterlab-git extension with jupyterlab under kubernetes

[Chris Holdgraf]

I'm not sure on this one, though you might try posting this to the
JupyterHub discourse page as well! discourse.jupyter.org

It's a pilot aimed at improving community interactions and help!

On Tue, Jan 29, 2019 at 8:32 PM Bryan Sullivan  wrote:

> Does anyone have experience or info about how the jupyterlab-git extension
> can be deployed for jupyterlab running under kubernetes, e.g. deployed
> using https://z2jh.jupyter.org/en/latest/index.html. All I see at
> https://github.com/jupyterlab/jupyterlab-git seems related to deploying
> the extension on your developer workstation. I would like to e.g. configure
> jupyterhub to include the jupyterlab-git extension through the z2jh helm
> chart used to deploy jupyterlab.
>
> For Acumos (a LF Deep Learning community project) we are working to deploy
> jupyterlab as part of the Acumos platform, and are looking at deploying a
> local git server also as a backend service for storage and version control.
> Any input/pointers to how we can integrated such a git server with
> jupyterlab single-user containers via the jupyterlab-git extension, or
> where more info can be found, would be very appreciated.
>
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Re: [jupyter] Re: Working Javascript in HTML rendered notebooks

[Chris Holdgraf]

Though note that projects like thebelab (https://github.com/minrk/thebelab)
are playing around with ways to back a static page with a kernel.

Sent from my phone, apologies for the curtness and type-os

On Tue, Jan 15, 2019, 12:08 AM Roland Weber  Hello Jason,
>
> Is there a way to ensure the javascript components work as per the actual
>> notebooks when the ipynb file has been converted to html?
>>
>
> In general? No. JavaScript that relies on data stored in the notebook
> might work. JavaScript that tries to interact with the running kernel will
> fail, because there is no running kernel when you browse the html of a
> converted ipynb file.
>
>
>> This seems to be possible from this GitHub directory:
>> https://github.com/jupyter-widgets/ipywidgets/tree/master/examples/web3
>>
>
> Instructions there explicitly mention that a notebook server must be
> running. This is not the case when you look at the html of a converted
> notebook. Iirc, ipywidgets/widgetsnbextensions have special logic that
> allows to render captured output even after conversion of the notebook to
> html. But you cannot expect the widgets to interact with the code in the
> kernel, as they do when you are running a notebook.
>
> cheers,
>   Roland
>
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Re: [jupyter] chrome interface problems

[Chris Holdgraf]

Do you have an image of how the interface looked before stuff disappeared?
Or how you 'expect' it to look? Maybe that'll help debug

On Thu, Dec 6, 2018 at 9:46 AM  wrote:

> thank you for the idea!
> But I dont think so, I start it with the alias
> alias jup='cd /0ale;jupyter notebook --allow-root'
>
> and here's the output:
>
> [root@lambda ~]# jup
> [I 09:10:03.860 NotebookApp] JupyterLab extension loaded from 
> /usr/lib/python2.7/site-packages/jupyterlab
>
> [I 09:10:03.860 NotebookApp] JupyterLab application directory is 
> /usr/share/jupyter/lab
>
> [I 09:10:03.867 NotebookApp] Serving notebooks from local directory:/0ale
> [I 09:10:03.868 NotebookApp] 0 active kernels
> [I 09:10:03.868 NotebookApp] The Jupyter Notebook is running at:
> [I 09:10:03.868 NotebookApp] http://localhost:/
> [I 09:10:03.868 NotebookApp] Use Control-C to stop this server and shut
> down all kernels (twice to skip confirmation).
> [I 09:10:04.095 NotebookApp] 302 GET /tree (::1) 2.41ms
> [I 09:10:04.546 NotebookApp] 302 GET /login?next=%2Ftree (::1) 1.63ms
> [I 09:10:04.557 NotebookApp] 302 GET /login?next=%2Ftree (::1) 0.64ms
> [I 09:10:46.017 NotebookApp] Kernel started: 
> df0dcc95-8356-4250-9f56-aaee5c314055
>
> [I 09:10:46.033 NotebookApp] 302 GET 
> /notebooks/High%20Frequency/SW/DMI/vlaminck1.png
> (::1) 1.73ms
>
>
>
>
> On Thursday, December 6, 2018 at 3:32:06 PM UTC+1, Chris Holdgraf wrote:
>>
>> Hello! I you mention a sidebar - perhaps you were running "JupyterLab"
>> before, and switched to the "Jupyter Notebook" interface accidentally? Try
>> replacing everything after the "" with "lab".
>>
>> On Thu, Dec 6, 2018 at 3:28 AM  wrote:
>>
>>> Sorry, I'm a newbie with Jupyter (on chrome, Linux),
>>> but I run into a problem:
>>> due to my inexperience, I often made this mistake: after inserting a new
>>> line (above or below: A or B) I start writing immediately, believing that
>>> I'm already inside the cell, and not still in (I think it's called) command
>>> mode...
>>> Needless to say, doing this I inserted a lot of commands without
>>> intention.
>>> Last time it happened, I noticed that 1) my notebooks are not tabbed
>>> anymore, and 2) my left sidebar (files, running, commands...) disappeared.
>>> I thought I entered without wanting into single document mode, but
>>> ctrl-shift-enter does nothing.
>>>
>>> Can you help me please?
>>>
>>> Alessandro
>>>
>>>
>>>
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Re: [jupyter] chrome interface problems

[Chris Holdgraf]

Hello! I you mention a sidebar - perhaps you were running "JupyterLab"
before, and switched to the "Jupyter Notebook" interface accidentally? Try
replacing everything after the "" with "lab".

On Thu, Dec 6, 2018 at 3:28 AM  wrote:

> Sorry, I'm a newbie with Jupyter (on chrome, Linux),
> but I run into a problem:
> due to my inexperience, I often made this mistake: after inserting a new
> line (above or below: A or B) I start writing immediately, believing that
> I'm already inside the cell, and not still in (I think it's called) command
> mode...
> Needless to say, doing this I inserted a lot of commands without intention.
> Last time it happened, I noticed that 1) my notebooks are not tabbed
> anymore, and 2) my left sidebar (files, running, commands...) disappeared.
> I thought I entered without wanting into single document mode, but
> ctrl-shift-enter does nothing.
>
> Can you help me please?
>
> Alessandro
>
>
>
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Re: [jupyter] Accessibility guidelines?

[Chris Holdgraf]

Perhaps it's be useful if there were a community-driven guide to
accessibility. e.g. it could come with a few pre-made CSS rules and
instructions for where to put them. Even if there are some ways in which it
specifically says jupyterXXX is *not* accessible, I think there'd be value
in making this explicit so it's clear where we need to make improvements.

On Wed, Dec 5, 2018 at 6:06 AM MinRK  wrote:

> Thanks for the question! We are just learning about how to measure
> accessibility and address issues, and help is greatly appreciated.
>
> On Mon, Nov 26, 2018 at 5:07 PM Norman Gray 
> wrote:
>
>>
>> Greetings.
>>
>> I've been asked about accessibility adjustments to JupyterHub.  Is there
>> any current guidance on this that I could be pointed to?
>>
>> I can see a passing mention of the issue in [1], and the beginning of a
>> discussion in [2] which links, inter alia, to [3], all of which look
>> interesting but still preliminary, and all of which show that the
>> Jupyter community is engaged with this as a problem -- which is great.
>> However they don't obviously result in a 'do X, Y and Z' list.
>>
>> Specifically, I have a report from an affected user that JupyterHub is
>> 'considerably harder [...] to see than MATLAB.'  Due to a severe visual
>> impairment it would be necessary to use 'large font, specific fonts, and
>> an inverted colour scheme.'  It's clear that at least part of that could
>> be addressed by a per-user CSS script in the right place, but it's not
>> clear just where that 'right place' is.  So question B: is there a place
>> where I can drop a CSS script and start hacking at it?
>>
>
> A user can put CSS overrides in ~/.jupyter/custom/custom.css for notebook
> classic or create a theme for jupyterlab. Documenting accessibility issues
> an opening an Issue on GitHub about them and what can be done to improve
> them would be hugely helpful (or even better, pull requests!), especially
> on the jupyterlab repo.
>
>
>>
>> (Unfortunately I have few space cycles to support this at present, so
>> while I'd like to learn the details, I'd _really_ love canned answers,
>> if they exist...)
>>
>> I can't find discussion of this on the list archive, but it's possible
>> my google-fu is weak today.
>>
>> Best wishes,
>>
>> Norman
>>
>>
>> [1] https://github.com/jupyterhub/jupyterhub/issues/990
>> [2] https://github.com/jupyter/notebook/issues/1801
>> [3] https://github.com/ipython/ipython/issues/6845
>>
>> --
>> Norman Gray  :  https://nxg.me.uk
>>
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Re: [jupyter] Re: Building Jupyter visualizations using dual canvases youtube video

[Chris Holdgraf]

There's also the jupyterhub discourse channel pilot! discourse.jupyter.org

Sent from my phone, apologies for the curtness and type-os

On Mon, Dec 3, 2018, 3:21 PM 'Aaron Watters' via Project Jupyter <
jupyter@googlegroups.com wrote:

> Manikandan: This thread is not the right place to ask a question about
> jupyterhub
>
> Please either
>
> - ask on the gitter channel for jupyterhub:
> https://gitter.im/jupyterhub/jupyterhub, or
> - maybe create an issue on the jupyterhub repository:
> https://github.com/jupyterhub/jupyterhub
>
> Thanks!  -- Aaron Watters
>
>
> On Monday, December 3, 2018 at 10:39:34 AM UTC-5, Mani kandan wrote:
>>
>> Hi Everyone,
>>
>> Greetings!!
>>
>> I am currently working on a project which requires Jupyter hub
>> installation on Linux Redhat 7.5. Problem is that I don't have internet
>> access from Linux server due to security reasons.
>>
>> I searched in google for almost 2 weeks. I could find a proper document
>> for offline installation. I downloaded all dependent packages in a server
>> with internet access using conda and python PIP both and moved the packages
>> to the server without an internet connection. Somehow I am not able to
>> install all the packages, its throwing multiple errors.
>>
>> Is there any document available for Jupyter Hub offline installation?
>> Could somebody help me with the installation?
>>
>> Thanks in advance.
>>
>> Regards,
>> Manikandan.
>>
>> On Mon, Dec 3, 2018 at 7:52 PM 'Aaron Watters' via Project Jupyter <
>> jup...@googlegroups.com> wrote:
>>
>>> Thanks Tony,
>>>
>>> These are good suggestions.  I added them as an issue to the jp_doodle
>>> repository https://github.com/AaronWatters/jp_doodle/issues/5 .
>>> I think I'll have to add some new API functionality to make a
>>> meta-keystroke workable for dual canvases because right now there
>>> is no way to attach a handler to a single key -- you have to attach a
>>> handler to all possible keystrokes -- so a meta-keystroke would
>>> either override or get overridden by any other keystroke handler for the
>>> specific visualization.
>>>
>>> It's easy to attach a "last snapshot data" slot to the widget
>>> implementation, however.
>>>
>>> Thanks for the feedback!  -- Aaron Watters
>>>
>>>
>>> On Saturday, December 1, 2018 at 6:36:05 PM UTC-5, Tony Hirst wrote:

 Interesting..

 So the idea is that you can build an interactive in the first
 tab/canvas panel, then grab a snapshot of it that appears in the second?

 If there is an interactive where the view is dependent on the mouse
 cursor position, eg in the Simple Python Example notebook, the image color
 sampling demo, is there a keybord short cut to click the Take snapshot
 button? (else how do you get to click the button without moving the mouse
 cursor away from the point you want to sample/snapshot?)

 Is there any way of getting the snapshot into a variable  (eg _ ) with
 a corresponding image data URI value?

 --tony

 On Friday, 30 November 2018 16:20:15 UTC, Aaron Watters wrote:
>
> I just uploaded a video of a presentation I gave at the Flatiron
> Institute about building interactive visualizations:
>
> https://youtu.be/nyuCqlTvf0c
>
> This presentation consists of a collection of Jupyter notebooks which
> introduce dual canvases and how to build interactive visualizations with
> dual canvases.
> Dual canvases are designed to implement special purpose scientific
> visualizations that include complex graphic, mouse and other input
> interactions, animations, transitions, streaming images and other 
> features.
>
> Here is the talk outline as a Jupyter notebook:
> https://github.com/AaronWatters/jp_doodle/blob/master/notebooks/workshop/0%20-%20Outline.ipynb
> I hope you like.  If you don't like for some reason please reply to
> this post privately (use the little gear icon [image: U+21D7.svg]
> )
>
> Thanks!  -- Aaron Watters
>
>
> --
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Re: [jupyter] Setting up JupyterHub with HTCondor batchspawner

[Chris Holdgraf]

You could also give a shot at asking on the JupyterHub discourse pilot!
https://discourse.jupyter.org

On Fri, Nov 9, 2018 at 8:42 AM Michael Milligan  wrote:

> Hi Nikita,
>
> This question will get a better response as an issue at the batchspawner
> GitHub repo: https://github.com/jupyterhub/batchspawner/issues
>
> If you create an issue report there with this information, the appropriate
> developers (including myself) will see it and give you a response as soon
> as they are able.
>
> Thanks,
> Michael
>
>
> On Fri, Nov 9, 2018, 8:54 AM Nikita Balashov  wrote:
>
>> Hi,
>>
>> I'm trying to make batchspawner work with HTCondor but I'm stuck with the
>> following error:
>>
>> [I 2018-11-09 13:35:39.816 JupyterHub batchspawner:242] Spawner
>> submitting job using sudo -i -u testuser condor_submit
>> [I 2018-11-09 13:35:39.816 JupyterHub batchspawner:243] Spawner
>> submitted script:
>>
>> Executable = /bin/sh
>> RequestMemory = 4gb
>> RequestCpus = 1
>> Arguments = "-c 'exec batchspawner-singleuser --ip=""0.0.0.0""'"
>> Remote_Initialdir = /home/testuser
>> Output = /home/testuser/.jupyterhub.condor.out
>> Error = /home/testuser/.jupyterhub.condor.err
>> ShouldTransferFiles = False
>> GetEnv = True
>> Universe = vanilla
>> Queue
>>
>> [I 2018-11-09 13:35:40.119 JupyterHub batchspawner:246] Job submitted.
>> cmd: sudo -i -u testuser condor_submit output: Submitting job(s).
>> 1 job(s) submitted to cluster 19.
>> [D 2018-11-09 13:35:40.120 JupyterHub batchspawner:269] Spawner querying
>> job: sudo -i -u testuser condor_q 19 -format "%s, " JobStatus -format "%s,
>> " RemoteHost -format "
>> " True
>> [E 2018-11-09 13:35:40.356 JupyterHub batchspawner:215] Subprocess
>> returned exitcode 1
>> [E 2018-11-09 13:35:40.357 JupyterHub batchspawner:216] Stdout:
>> [E 2018-11-09 13:35:40.357 JupyterHub batchspawner:217] b''
>> [E 2018-11-09 13:35:40.357 JupyterHub batchspawner:218] Stderr:
>> [E 2018-11-09 13:35:40.357 JupyterHub batchspawner:219] Error: -format
>> requires format and attribute parameters
>> [E 2018-11-09 13:35:40.357 JupyterHub batchspawner:274] Error querying
>> job 19
>> [W 2018-11-09 13:35:40.358 JupyterHub batchspawner:372] Job  neither
>> pending nor running.
>>
>> [E 2018-11-09 13:35:40.359 JupyterHub user:477] Unhandled error starting
>> testuser's server: The Jupyter batch job has disappeared while pending
>> in the queue or died immediately after starting.
>> [D 2018-11-09 13:35:40.373 JupyterHub user:578] Deleting oauth client
>> jupyterhub-user-testuser
>> [E 2018-11-09 13:35:40.410 JupyterHub web:1670] Uncaught exception GET
>> /hub/user/testuser/ (159.93.40.25)
>> HTTPServerRequest(protocol='http', host='jupyterhub.jinr.ru',
>> method='GET', uri='/hub/user/testuser/', version='HTTP/1.1', remote_ip='
>> 159.93.40.25')
>> Traceback (most recent call last):
>>   File
>> "/usr/share/anaconda3/lib/python3.7/site-packages/tornado/web.py", line
>> 1592, in _execute
>> result = yield result
>>   File
>> "/usr/share/anaconda3/lib/python3.7/site-packages/jupyterhub/handlers/base.py",
>> line 1052, in get
>> await self.spawn_single_user(user)
>>   File
>> "/usr/share/anaconda3/lib/python3.7/site-packages/jupyterhub/handlers/base.py",
>> line 705, in spawn_single_user
>> timedelta(seconds=self.slow_spawn_timeout), finish_spawn_future
>>   File
>> "/usr/share/anaconda3/lib/python3.7/site-packages/jupyterhub/handlers/base.py",
>> line 626, in finish_user_spawn
>> await spawn_future
>>   File
>> "/usr/share/anaconda3/lib/python3.7/site-packages/jupyterhub/user.py", line
>> 489, in spawn
>> raise e
>>   File
>> "/usr/share/anaconda3/lib/python3.7/site-packages/jupyterhub/user.py", line
>> 409, in spawn
>> url = await
>> gen.with_timeout(timedelta(seconds=spawner.start_timeout), f)
>>   File
>> "/usr/share/anaconda3/lib/python3.7/site-packages/batchspawner/batchspawner.py",
>> line 373, in start
>> raise RuntimeError('The Jupyter batch job has disappeared'
>> RuntimeError: The Jupyter batch job has disappeared while pending in
>> the queue or died immediately after starting.
>>
>> The condor_q command succeeds if ran manually:
>> # sudo -i -u testuser condor_q 19 -format "%s, " JobStatus -format "%s,
>> " RemoteHost -format "\n" True
>> 1,
>>
>> # echo $?
>> 0
>>
>> I'm using the latest batchspawner (from the master):
>> # pip list |grep batchspawner
>> batchspawner   0.9.0.dev0
>>
>> And the spawner configuration:
>> c.JupyterHub.spawner_class = 'batchspawner.CondorSpawner'
>> c.Spawner.http_timeout = 120
>>
>> c.BatchSpawnerBase.req_nprocs = '1'
>> c.BatchSpawnerBase.req_memory = '1gb'
>> c.BatchSpawnerBase.req_runtime = '12:00:00'
>>
>> c.CondorSpawner.exec_prefix = 'sudo -i -u {username}'
>>
>> What can be the cause of this error?
>>
>> Thanks,
>> Nikita Balashov
>>
>> --
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Re: [jupyter] Sonification techniques for Jupyter notebooks discussed

[Chris Holdgraf]

whoah this sounds fascinating, thanks for sharing!

On Wed, Nov 7, 2018 at 8:30 AM Scot Gresham-Lancaster 
wrote:

> The Center for New Music and Audio Technology is sponsoring an all day
> "convergence" of sonificaiton practitioners. Sonification is a augmentation
> and supplement to visualization techniques that use sound to represent data
> via various audio synthesis techniques.
>
> Of interest to this group is the presentation from the University of Texas
> Art/Sci lab which will be presented between 10:00 and 11:00 AM on Saturday
> Nov, 10th at the CNMAT performance space at 1750 Arch St. very near the UC
> Berkeley Campus. This research group is using the ctcsound csound extension
> to investigate the use of audio in the context of jupyter notebooks.
>
>
> http://cnmat.berkeley.edu/events/crossroads-convergence-sonification-practitioners
>
> Hoping some of you in the area will come by and join the discussion.
>
> Scot Gresham-Lancaster
> Composer- Performer- Research Artist Art/Sci Lab
> ATEC UT Dallas
> Visiting Researcher CNMAT UC Berkeley
> 1st Frank & Marjorie Malina Art/Science Research Fellow
> The HUB - 2018 Winner of the ZKM GigaHertz Lifetime Achievement Award
>
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[jupyter] Re: Building a scheduler for notebook based reports

[Chris Holdgraf]

Super cool! FYI I cross-posted your message in the JupyterHub discourse 
pilot 
here: 
https://discourse.jupyter.org/t/scheduling-jupyter-notebook-reports-with-paperboy/96

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