6 ms·

We would love to hear what you like about Rmarkdown and Sweave. Jupyter tooling is always improving, and we are very interested in engaging with users about the

We would love to hear what you like about Rmarkdown and Sweave. Jupyter tooling is always improving, and we are very interested in engaging with users about their needs, and helping grow the ecosystem to be able to address those.

goerz 8y ago
The number one feature request by far at this point would be collaborative features in the notebook. Not really because I actually want to collaboratively edit a notebook with others, but because I would like to open the same notebook in two separate browser windows (side-by-side), and edit a cell at the top of the notebook in one, and a cell at the bottom in the other, and have things get merged automatically. Or, not having to worry that I left a (remote) notebook open on my work computer when I connect to the same server from home, causing parts of the notebook to be accidentally overwritten.
- targafarian 8y ago
  JupyterLab has the ability to open multiple "views" on the same file. http://jupyterlab.readthedocs.io/en/latest/user/notebook.html?highlight=views http://jupyterlab.readthedocs.io/en/latest/user/notebook.htm...
  - goerz 8y ago
    That's amazing! I'll have to try out JupyterLab sometime very soon. I was holding out because I'm using a whole bunch of plugins for the classic notebook from https://github.com/ipython-contrib/jupyter_contrib_nbextensions https://github.com/ipython-contrib/jupyter_contrib_nbextensi... that I think have't been ported yet
asdlllkasdasd 8y ago
Rmarkdown has the better version control story.
nerdponx 8y ago
My biggest frustrations with Jupyter are (see #4 for comments on Sweave etc): 1. The default front-end is a weak platform for getting work done. It's a JavaScript code editor. It will never be as good as my personal text editor configuration. It will never be as good as an IDE like RStudio, Spyder, or Pycharm. It's good that there are keyboard shortcuts for doing things like adding cells, and extensions for things like folding cells and adding a table of contents. But it still isn't terribly comfortable to use all day. Also I personally hate doing everything in a browser. Apart from some useful notebook extensions, there are no viable alternative front ends yet. 2. Running a remote kernel is a pain in the ass (cat a config file then manually tunnel 4 ports over SSH), and I can't seem to get it to work on Windows at all. This is an issue at my company because we do a lot of work on remote servers that can be accessed only through SSH or JupyterHub. Individual users do not have control over the latter, so we are stuck with the inadequate default experience I just described above. 3. No kernel other than Ipython is mature. IRKernel is getting there. Everything else is at best a beta-quality product. 4. Notebooks are not a plain text file format. Hand editing a notebook is messy. They do not play well with version control systems and diff tools. RMarkdown and Knitr/Sweave are just preprocessors for established plain text formats (Markdown and Latex with some extra syntax). With those formats you can take advantage of a wealth of existing tooling, as well as having the freedom to edit the file in a normal text editor without having to rely on a special front end. Ironically having everything formatted as JSON should make it easier to write those special front ends, but I have not seen any good ones yet.
- goerz 8y ago
  To address “hand editing” problem I wrote a little vim plugin that wraps around notedown (https://github.com/aaren/notedown https://github.com/aaren/notedown) to edit notebooks on the fly in a markdown format. It’s not perfect, but it goes a long way for quickly editing notebooks “as a whole”: https://github.com/goerz/ipynb_notedown.vim https://github.com/goerz/ipynb_notedown.vim Other than that, I try to put any lengthy code in functions that are in a module alongside the notebook, so that the notebook mostly contains one-line commands to do kick off a calculation or to generate a plot. I also have a shortcut that copies the content of the current browser text field (notebook cell) into MacVim, and pastes it back automatically as soon as I close the editor.
gbrown 8y ago
Using a web browser as an IDE just seems like a solution in search of a problem. Also, maybe I just never spent enough time working with Jupyter, but it seemed to me that it encourages a sort of exploratory workflow, really well suited to teaching programming and data science. It was less clear to me how it could be used well in production environments. I use Rmarkdown and Sweave to write homeworks for my students in a very Jupyter way. I also use them to generate data driven static webpages, procedurally generate production quality and easily formatted PDF and HTML reports. I also use them as a templating system for auto-generated model diagnostic emails. Perhaps I need to return to Jupyter to see what I'm missing, but I don't really know what purpose it would serve, or what kind of work it would make easier.
- takluyver 8y ago
  Doing the interface in the web browser has its ups and downs: it makes some things more awkward locally, but it's easy to deliver the same interface remotely - e.g. a university can run a JupyterHub instance for a course, and students visit a URL and login. nteract is an attempt to make a notebook interface as a local application.
  - gbrown 8y ago
    For sure, I totally see how it's useful as a teaching tool. I don't see how it fits into a proper production system.
    - carreau 8y ago
      Different system and requirement need different tools, if you prefer text editor. Depending on your preference look at Emacs IPython Notebook, the Jupyter VS-Code extension, or Atom Hydrogen. That will basically let you select chunk of code and execute in a kernel. You do not have to use the notebook format, or the browser based editor. JupyterLab also allow Rmarkdown-like workflow where code-blocks in a markdown document can be executed to display graph. I believe the important part is to allow interoperability between different ways people want to work. You can't have 1 size fits all, and there are still a lot of work that can be done to cover some use case.
mschuetz 8y ago
I guess it would be nice to make it run within an electron environment, without extra console and browser tabs to run it in. Just jupyter running as an electron app with maybe tabs for each notebook to give it a more native desktop app feel.
- po84 8y ago
  Check out https://nteract.io/ https://nteract.io/. It's based on Jupyter standards (protocol, kernels, notebook format), written in JS, and runs on your desktop.

goerz 8y ago

The number one feature request by far at this point would be collaborative features in the notebook. Not really because I actually want to collaboratively edit a notebook with others, but because I would like to open the same notebook in two separate browser windows (side-by-side), and edit a cell at the top of the notebook in one, and a cell at the bottom in the other, and have things get merged automatically. Or, not having to worry that I left a (remote) notebook open on my work computer when I connect to the same server from home, causing parts of the notebook to be accidentally overwritten.

targafarian 8y ago
JupyterLab has the ability to open multiple "views" on the same file. http://jupyterlab.readthedocs.io/en/latest/user/notebook.html?highlight=views http://jupyterlab.readthedocs.io/en/latest/user/notebook.htm...
- goerz 8y ago
  That's amazing! I'll have to try out JupyterLab sometime very soon. I was holding out because I'm using a whole bunch of plugins for the classic notebook from https://github.com/ipython-contrib/jupyter_contrib_nbextensions https://github.com/ipython-contrib/jupyter_contrib_nbextensi... that I think have't been ported yet

asdlllkasdasd 8y ago

Rmarkdown has the better version control story.

nerdponx 8y ago

My biggest frustrations with Jupyter are (see #4 for comments on Sweave etc): 1. The default front-end is a weak platform for getting work done. It's a JavaScript code editor. It will never be as good as my personal text editor configuration. It will never be as good as an IDE like RStudio, Spyder, or Pycharm. It's good that there are keyboard shortcuts for doing things like adding cells, and extensions for things like folding cells and adding a table of contents. But it still isn't terribly comfortable to use all day. Also I personally hate doing everything in a browser. Apart from some useful notebook extensions, there are no viable alternative front ends yet. 2. Running a remote kernel is a pain in the ass (cat a config file then manually tunnel 4 ports over SSH), and I can't seem to get it to work on Windows at all. This is an issue at my company because we do a lot of work on remote servers that can be accessed only through SSH or JupyterHub. Individual users do not have control over the latter, so we are stuck with the inadequate default experience I just described above. 3. No kernel other than Ipython is mature. IRKernel is getting there. Everything else is at best a beta-quality product. 4. Notebooks are not a plain text file format. Hand editing a notebook is messy. They do not play well with version control systems and diff tools. RMarkdown and Knitr/Sweave are just preprocessors for established plain text formats (Markdown and Latex with some extra syntax). With those formats you can take advantage of a wealth of existing tooling, as well as having the freedom to edit the file in a normal text editor without having to rely on a special front end. Ironically having everything formatted as JSON should make it easier to write those special front ends, but I have not seen any good ones yet.

goerz 8y ago
To address “hand editing” problem I wrote a little vim plugin that wraps around notedown (https://github.com/aaren/notedown https://github.com/aaren/notedown) to edit notebooks on the fly in a markdown format. It’s not perfect, but it goes a long way for quickly editing notebooks “as a whole”: https://github.com/goerz/ipynb_notedown.vim https://github.com/goerz/ipynb_notedown.vim Other than that, I try to put any lengthy code in functions that are in a module alongside the notebook, so that the notebook mostly contains one-line commands to do kick off a calculation or to generate a plot. I also have a shortcut that copies the content of the current browser text field (notebook cell) into MacVim, and pastes it back automatically as soon as I close the editor.

gbrown 8y ago

Using a web browser as an IDE just seems like a solution in search of a problem. Also, maybe I just never spent enough time working with Jupyter, but it seemed to me that it encourages a sort of exploratory workflow, really well suited to teaching programming and data science. It was less clear to me how it could be used well in production environments. I use Rmarkdown and Sweave to write homeworks for my students in a very Jupyter way. I also use them to generate data driven static webpages, procedurally generate production quality and easily formatted PDF and HTML reports. I also use them as a templating system for auto-generated model diagnostic emails. Perhaps I need to return to Jupyter to see what I'm missing, but I don't really know what purpose it would serve, or what kind of work it would make easier.

takluyver 8y ago
Doing the interface in the web browser has its ups and downs: it makes some things more awkward locally, but it's easy to deliver the same interface remotely - e.g. a university can run a JupyterHub instance for a course, and students visit a URL and login. nteract is an attempt to make a notebook interface as a local application.
- gbrown 8y ago
  For sure, I totally see how it's useful as a teaching tool. I don't see how it fits into a proper production system.
  - carreau 8y ago
    Different system and requirement need different tools, if you prefer text editor. Depending on your preference look at Emacs IPython Notebook, the Jupyter VS-Code extension, or Atom Hydrogen. That will basically let you select chunk of code and execute in a kernel. You do not have to use the notebook format, or the browser based editor. JupyterLab also allow Rmarkdown-like workflow where code-blocks in a markdown document can be executed to display graph. I believe the important part is to allow interoperability between different ways people want to work. You can't have 1 size fits all, and there are still a lot of work that can be done to cover some use case.

mschuetz 8y ago

I guess it would be nice to make it run within an electron environment, without extra console and browser tabs to run it in. Just jupyter running as an electron app with maybe tabs for each notebook to give it a more native desktop app feel.

po84 8y ago
Check out https://nteract.io/ https://nteract.io/. It's based on Jupyter standards (protocol, kernels, notebook format), written in JS, and runs on your desktop.