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-M83665a3db57a07f7da5acb8d> > ------------------------------------------ The Carpentries: discuss Permalink: https://carpentries.topicbox.com/groups/discuss/Tb12fc97e5ee621f2-Ma06cd57462eb2853e6366455 Delivery options: https://carpentries.topicbox.com/groups/discuss/subscription
