Aleksandra, Can you confirm that issue you encountered with using conda and jupyter is the issue discussed in this blog post?
http://jakevdp.github.io/blog/2017/12/05/installing-python-packages-from-jupyter/index.html Thanks! David On Wed, Jun 12, 2019 at 7:04 PM David Pugh <[email protected]> wrote: > David, > > Thanks for passing this along! I had not seen it before and it looks > highly relevant. > > D > > Sent from my iPhone > > On Jun 12, 2019, at 18:56, David Nicholson <[email protected]> wrote: > > There''s a good Jake Vanderplas blog post on this if you haven't seen it > already: > > http://jakevdp.github.io/blog/2017/12/05/installing-python-packages-from-jupyter/index.html > > Tutorial looks pretty good at first glance, can't wait to teach this > > David Nicholson, Ph.D. > https://nicholdav.info/ > https://github.com/NickleDave > Prinz lab <http://www.biology.emory.edu/research/Prinz/>, Emory > University, Atlanta, GA, USA > > > On Wed, Jun 12, 2019 at 11:39 AM David Pugh <[email protected]> > wrote: > >> Aleksandra, >> >> I have never encountered issues using conda and Jupyter notebooks of the >> kind you describe. But this long thread confirms that you are not alone. >> >> https://github.com/jupyter/notebook/issues/2359 >> >> I will try to add a call out box with a best practice for installing >> jupyter notebook and juypterlab etc. >> >> Thanks for clarifying! >> >> >> >> Sent from my iPhone >> >> On Jun 12, 2019, at 18:20, Giuseppe Profiti <[email protected]> >> wrote: >> >> First, good job David. >> Aleksandra: there are few things to consider when using conda and >> jupyter. Just recently we managed to deploy a jupyterhub on a computing >> cluster, along with several different conda environments. >> Long story short: you should register the environment kernel in the >> jupyter instance. I hope my boss let me write a blog post about it soon. >> >> Best, >> Giuseppe >> >> Il giorno mer 12 giu 2019 alle ore 17:02 Aleksandra Taranov < >> [email protected]> ha scritto: >> >>> David, to answer your question, the reason I stopped using conda and >>> switched to pip installs was that I'd conda install jupyter and conda >>> install packages, but then when I tried to run them, jupyter notebooks >>> couldn't find the package. I'm probably making some very basic error here, >>> but I'm also likely not the only one confused about this. >>> >>> Thanks again for making this great resource. >>> >>> On Wed, Jun 12, 2019, 7:58 AM Michael Sarahan <[email protected]> >>> wrote: >>> >>>> That's a good point, but rather than say "don't use conda at all" - >>>> that's more reason to have custom channels where conda is set up to comply >>>> with those needs. Conda need not be mutually exclusive with these things, >>>> but it does take some setup to get them working together. >>>> >>>> Saying "don't use conda at all" is ignoring the work that has to happen >>>> either way. Either you have to reproduce what conda is providing somehow, >>>> or you have to make conda use the part on the system side. That's >>>> definitely a case-by-case scenario for everyone, and we need to document >>>> both paths. >>>> >>>> For your example of MPI, conda packages are setup to explicitly require >>>> some MPI implementation where necessary. That package can come from an >>>> actual conda MPICH package, or it can come from a known binary compatible >>>> system installation that has a conda package setup to reference it. Conda >>>> is not dogmatic about being hermetic (unlike, say, bazel). Binary >>>> compatibility with external libraries can be pretty tricky, though. >>>> >>>> On Wed, Jun 12, 2019 at 9:48 AM Maxime Boissonneault < >>>> [email protected]> wrote: >>>> >>>>> Hi, >>>>> How about including a part about when *not* to use Conda ? >>>>> >>>>> In particular, if they are going to be computing on a supercomputer, >>>>> they should consult with your cluster specialists first. >>>>> Conda works well on somebody's desktop, but it creates a lot of >>>>> problems on supercomputers, because it does crazy stuff like installing >>>>> MPI >>>>> by itself instead of relying on staff-installed modules and software >>>>> packages. >>>>> >>>>> Cheers, >>>>> >>>>> Maxime >>>>> >>>>> >>>>> On 2019-06-12 9:49 AM, David Pugh wrote: >>>>> >>>>> All, >>>>> >>>>> I have developed a Software Carpentry style lesson for Conda and would >>>>> be keen to get feedback from the community! >>>>> >>>>> Website: >>>>> >>>>> >>>>> https://kaust-vislab.github.io/introduction-to-conda-for-data-scientists/ >>>>> >>>>> Repo: >>>>> >>>>> >>>>> https://github.com/kaust-vislab/introduction-to-conda-for-data-scientists >>>>> >>>>> Thanks and look forward to hearing from you! >>>>> >>>>> David >>>>> >>>>> >>>>> *The Carpentries <https://carpentries.topicbox.com/latest>* / discuss > / see discussions <https://carpentries.topicbox.com/groups/discuss> + > participants <https://carpentries.topicbox.com/groups/discuss/members> + > delivery > options <https://carpentries.topicbox.com/groups/discuss/subscription> > Permalink > <https://carpentries.topicbox.com/groups/discuss/Tb12fc97e5ee621f2-Ma06cd57462eb2853e6366455> > > ------------------------------------------ The Carpentries: discuss Permalink: https://carpentries.topicbox.com/groups/discuss/Tb12fc97e5ee621f2-M92f421e5ca697162859ec6e1 Delivery options: https://carpentries.topicbox.com/groups/discuss/subscription
