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, 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 / discuss / see discussions + participants + delivery options > Permalink ------------------------------------------ The Carpentries: discuss Permalink: https://carpentries.topicbox.com/groups/discuss/Tb12fc97e5ee621f2-M233340b4d75fc92350f95f37 Delivery options: https://carpentries.topicbox.com/groups/discuss/subscription
