Re: [discuss] Installing packages inside an already launched Jupyter notebook from Anaconda GUI

[Pariksheet Nanda]

On Wed, Feb 12, 2020 at 10:23 AM Rémi Rampin  wrote:
> 2020-02-12 07:17 UTC-05, Pariksheet Nanda :
>>
>> Thanks for the link!  It indeed mentions the Jupyter notebook command I
needed:
>> # Install a pip package in the current Jupyter kernel
>> import sys
>> !{sys.executable} -m pip install numpy
>
>
> Note that this blog post is from 2017. A more up-to-date recommendation
would be to use the %pip magic:
>
> %pip install numpy

Thanks, Rémi, that's much simpler!


> Rémi

Pariksheet

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Re: [discuss] Installing packages inside an already launched Jupyter notebook from Anaconda GUI

[Pariksheet Nanda]

Hi Kunal,

On Wed, Feb 12, 2020 at 12:11 PM Kunal Marwaha 
wrote:
>
> I frequently refer to this for personal use:
>
https://jakevdp.github.io/blog/2017/12/05/installing-python-packages-from-jupyter/

Thanks for the link!  It indeed mentions the Jupyter notebook command I
needed:

# Install a pip package in the current Jupyter kernel
import sys
!{sys.executable} -m pip install numpy

Requirement already satisfied: numpy in
/Users/jakevdp/anaconda/lib/python3.6/site-packages


> Kunal

Pariksheet

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[discuss] Installing packages inside an already launched Jupyter notebook from Anaconda GUI

[Pariksheet Nanda]

Hi folks,

I was helping at a Python workshop workshop yesterday and in general I see
learners launch the Anaconda Jupyter notebook from the Anaconda GUI instead
of the terminal.

One such user on Mac OSX had launched the notebook from the Anaconda GUI
but had import errors.  However, if I had him install the packages from
inside the notebook using "! pip install pandas", the installation
succeeded but the import errors continued.

This was a little surprising, because that workaround succeeded in the
past.  I'm assuming that the shell bang pip command inside the cell invokes
pip associated with the running python's PATH, but maybe that's a false
assumption and there is a more sensible to install packages for the running
notebook python version.

It's also possible that the Anaconda GUI had selected a virtual environment
and that pip installed the package globally instead of into the environment.

Has anyone run into something similar and what is the correct way you would
go about installing a package from a running notebook?  Unfortunately I'm
mostly familiar with pip / pipenv instead of conda and don't often use
notebooks in my work.

I know that I could have also had the user not use the Anaconda GUI and run
the jupyter notebook from the terminal, but in the past I've also
encountered situations where users have multiple Anaconda and Miniconda
installations where one has to mangle the ~/.bash_profile and was therefore
hesitant to go down that road and opted to instead work within the context
of using the Anaconda GUI that the user is already familiar with.

Pariksheet

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Re: [discuss] Introducing the Carpentries to colleagues at work (industry)

[Pariksheet Nanda]

Having tried and failed, the best industry introduction to the Carpentries
is having your friends join as helpers; the uncompetitive industry sticker
price derails conversations to plan a workshop and, in any case. it's
difficult to convey the value of the teaching and philosophy without
experiencing it.

Pariksheet

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Re: [discuss] Insight on Data Carpentry and Git?

[Pariksheet Nanda]

Hi Katrin,

Thank you so much for pointing out the new builtin tutorial of GitHub
Desktop!  I don't have MacOS or Windows at home, so I'll have to try the
new tutorial on one of the university computers.  I've noticed at our
workshop last Friday that our users were diligent about their laptop setup
and think any hands on active experience beforehand might go a long way to
reinforcing their understanding at the workshop.  A short tutorial would be
super.

I've recently been teaching git from inside the bare bones RStudio git
interface because we've been skipping the shell lesson when we teach R, and
teaching the command line *and* git at the same time at one workshop, not
surprisingly, made the lesson more confusing.

Last week I observed a user accidentally install GitHub Desktop instead of
the usual official Git installer, and noticed how GitHub desktop can take
care of setting the your name and e-mail address.  We can lose complete
beginners during the initial "introducing yourself to git" setup and
wouldn't mind trying to use the GitHub Desktop interface to save 15 minutes
of the workshop by modifying the setup instructions of the workshop website
for them to "introduce" themselves beforehand.  Not to mention it could
help work around a bug in RStudio for some versions of Windows where
RStudio doesn't set the $HOME directory correctly; at least the git global
settings can be saved at the right place and there's no dependency on
fixing the $HOME directory in the RStudio spawned terminal before
configuring the git global settings.

Pariksheet

On Thu, Oct 17, 2019 at 8:32 AM Leinweber, Katrin 
wrote:

> Hi!
>
>
> > I find that the Git and Github sections of a workshop generate a lot of
> technical questions and errors, notably more than the other sections.
>
> So true!
>
> > […] If git and github could be taught in 5 minutes, I'm guessing it
> would be included in DC material...
>
> https://desktop.github.com/ added a built-in tutorial recently. Has
> anyone used this in a workshop?
>
> I'd be happy to receive some comments on that, because I'm planning to use
> it in a few weeks.
>
>
> Thanks and greetings!
> Katrin
>
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Re: [discuss] Suggestions for Bioinformatics Student Group Development

[Pariksheet Nanda]

Hi Kevin,

That's commendable; weekly meetings are a lot of work!  As far as getting
informal guidance, what been working for us at the University of
Connecticut is having chat groups.  Our bioinformatics core has a Slack
channel that's monitored by the core admins and the Cyber Security club has
Telegram chat groups where they also have undergrads interested in learning
the shell and other things.  The nice thing about chat media is newcomers
who need help with something can get a quick response and it's not as
formal as something like e-mail; if they are working on something and need
help they're not going to wait for an in-person meeting to happen some day
of the week to come get their questions answered.  Either way, sustaining
these types of things still needs interested and responsive people.

Aside from that, most people want structure.  It's hard to get people to
come sit around at a place in the hope of getting help from strangers; it's
easier for them to see a well thought out presentation or attend a hands-on
workshop.

Pariksheet

On Thu, Oct 18, 2018 at 11:50 PM kevin.stachelek via discuss <
discuss@lists.carpentries.org> wrote:

> Hello!
>
> I'm part of a small student group at my university attempting to grow
> coding and data science capacity among students in the life sciences. I am
> interested in getting guidance on how to organize and sustain this kind of
> organization. I have experience and interests in bioinformatics, shell, R,
> and python.
>
> I have limited experience with the carpentries directly, but was guided
> here via a mentoring request. We hold somewhat weekly meetings at which a
> relatively experienced member presents on a given topic. We are alternating
> each semester focusing on python and then on R with some shell skills
> thrown in.
>
> I'm looking for suggestions to make our group more welcoming to newcomers
> and interesting for typical life sciences coding needs.
>
> Thanks!
> *The Carpentries
> *
> / discuss / see discussions
> 
> + participants
> 
> + delivery options
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> 
>

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Re: [discuss] Backup options for R and python for participants experiencing technical problems

[Pariksheet Nanda]

Hi Kartin,

If your attendees don't "own" their machines and have to use institutional
machines, it's possible that the institution itself will help provide
backup machines.  At my most recent workshop at the Jackson labs, most if
not all laptops are configured by the institution and leading up to the
workshop their research IT services install the software required for the
workshop.  One attendee who had trouble ended up swapping out the machine
an hour after we saw the first set of trouble and we got the person caught
up.  So one option would be to talk to the host institution in advance
about machines with anaconda, RStudio, etc and install the required
packages.

Also at the beginning of workshops helpers can proactively go around, to
confirm python or R versions are up to date, upgrade versions, install
packages and use green sticky notes for validated machines.

That's nice that you can run RStudio on Windows off of a USB drive.  So it
looks like you could keep a few of those around just in case.

RStudio Server is what we use for our lab computer, but for the free
version one may want to look into using a reverse proxy with SSL so that
you're not sending unencrypted account logins to the RStudio Server web
page.

Pariksheet


On Sun, Sep 16, 2018 at 2:18 PM Katrin Tirok via discuss <
discuss@lists.carpentries.org> wrote:

> Hi all,
>
> I am thinking about good and easy 'backup' options for R and/or python
> that workshop participants could use when they have technical issues with
> their computer that take longer to sort out. Most of my previous workshops
> ran smoothly, but I remember one workshop with R this year, where we had a
> number of problems with packages that did not install or did not load
> properly, it was a mix of too old R versions and missing rights on machines.
>
> In South Africa we have additional challenges, like old and and very slow
> computers, which can take minutes to generate a plot in R, or very slow
> internet connection, making it difficult to install packages on the fly.
>
> I just discovered RStudioCloud https://rstudio.cloud
> 
>  providing
> full Rstudio setup in the web and the service is offered for free at the
> moment.
> I also started experimenting with Rstudio Server on my workgroup's server,
> however this would only work within my institution.
> And I know that under Windows one can run Rstudio from a usb drive ...
>
> I would like to hear what other people do in such situations ...
>
> Thanks
>
> Katrin
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