Just out of curiosity, how do notebooks play in the `reproducible research` space?
Do Carpentries instructors, as a matter of course, tell students how to clear all results and save a notebook with nothing having been exectured? Can such a notebook be executed sequentially, like a .py script can? >From a command line? Can a notebook file replace a .py file? Do instructors show attendees how to export from a notebook to a .py file so that the contents can be used as a script in a multistep workflow or pipeline? A notebook must be sequentially executable from a de novo state to count as reproducible, mustn't it? The context in which most of the people I deal with want to use python is as the driver of one step of many in a sequential processing stream. There isn't a single program that can be 'presented' in a notebook in a meaningful way. Each step may also be separately executed in isolation. Yes, at the very end of the project, there might be something that can be encapsulated in one script that prepares some visualizations and perhaps some statistical or modelling steps, but that is dependent on months of preparatory work. All of the prior processing, QC, validation, etc., is much more fragmented over time, over who does which pieces of the work, in some cases redoes the work, etc. If those folks don't learn how to use python for the most time-consuming, least visual, most fragmented portions of the their work, then its utility drops proportionally. Clearly no one solution is going to satisfy all instructors, nor will one solution be appropriate or all audiences. I think it is good to get the appropriate circumstances discussed, as we are doing here. Possibly the points, uses, counterindicators, etc., for both command line and notebooks could be enumerated somewhere for reference? Perhaps workshop organizers can be pointed to that information source that will help them to gauge what the needs and interests of the intended audience are and to request a workshop curriculum that is best suited to that audience and those needs? Would that result in a better fit of material to audience? to better clarity of advertising what will really be presented in each workshop? to more focused and coordinated approaches among the various lessons of a workshop? An iPad is a wonderful tool for something things, but it is not a replacement for a MacBook Pro. Different purposes, different tools. I certainly think there is a place for both in everyone's work. I also think that if a workshop is going to convincingly going to illustrate the power and utility of the command line, then it should be consistent in its use of the command line throughout. If there is something else you want to teach, that is absolutely fine, but then the whole workshop should support that something else, both in its materials and its tools. On Thu, Aug 30, 2018 at 10:25 AM Rémi Rampin <[email protected]> wrote: > > 2018-08-24 16:47 EDT, Konrad Förstner <[email protected]>: >> >> Beside the fact that this talk is it really funny, it raises a lot of >> issues that I can confirm from my experience: [...] > > > Hi everyone, > > I realize there's been a lot of attempts already to solve this "hidden state" > problem at the software level, but I wonder if a "modal" notebook could help. > > It seems to me that those problems arise because notebooks are trying to > support "exploration/playing around" and "presentation" workflows from the > same interface. There is no reason the full history can't be kept, other that > it makes for a bad presentation; likewise, there is no reason to have every > bit of code in the notebook, other than it is necessary to be able to run it > again. > > So maybe having a separate "exploration" mode where all cells are kept in > order since the last kernel reset, and a "presentation" mode where some of > those cells can be selected for presentation and the rest hidden would do > some good? > > There would be no need for GitHub and similar services that can render > notebooks to show anything but the "presentation" view. But when I download > and open the notebook, I would be able to get to a chronological, > reproducible view if I choose to. > > I do see some problems with this, mainly in that authors might not be aware > of the non-presentation cells they are including (might have private stuff, > or use a lot of space). It seems also a tad more complex (but less so than > using the history magics!). I wonder if something like this has been > attempted or exist in another software. > > Cheers > -- > Rémi > The Carpentries / discuss / see discussions + participants + delivery options > Permalink ------------------------------------------ The Carpentries: discuss Permalink: https://carpentries.topicbox.com/groups/discuss/T1505f74d7f6e32f8-M8b481632cd9315ab82b8c620 Delivery options: https://carpentries.topicbox.com/groups/discuss/subscription
