emacs-ipython-notebook/Enhancements.org

• Overview
• Design
  • Notebook Format
  • Notebook Buffer
  • Notebooklist Buffer
  • Kernel communication
  • Contents API
  • Connecting to a running Kernel
  • How a Worksheet is Displayed
  • Testing
    • Define testing workflow
    • Migrate from Makefile to setup.py
    • Use conda to create testing environments.
• Enhancements/Fixes
  • Run dynamic javascript
  • Embedding Altair plots
  • Mike DeCandia's Wish and Bug List
    • Wishlist
    • Bugs
  • Switch kernel in running notebook
  • Support company-mode
  • Inline latex
    • For Further Investigation
    • Inline using org-latex-preview
    • Using magic-latex-buffer
  • XWidget Support/Interactive Widgets
    • What Does ipywidgets.interact() return?
      • Websocket data for comm_open
      • Websocket data for comm_msg
  • Working with jupyterhub
  • Imenu/Speedbar Cooperation
  • Live links to other notebooks
  • Use polymode
  • Use dash?
  • Us cl-generic?
  • Access password protected notebooks (issue #57)
  • Connect to non-python kernels
  • Synergies with pymacs?
  • Detect system path of opened notebook
  • Jump to notebook code in traceback (issue #42)
  • The Return of Worksheets
  • Fixing Tests

Overview

Design

Notebook Format

Version 4.0 documented.

Earlier versions might be documented less formally on the wiki. Can also look at the IPython source in the json files.

Notebook Buffer

Notebook information is stored as a struct. Always associated with a buffer, ein:notebook-buffer is used to find buffer associated with a notebook.

Notebook does not hold cells, that is dehttp://glf.swim-team.us/legated to instances of the worksheet class. Instances are stored as a list in the `ein:$notebook-worksheets` slot.

Opened notebooks are kept in the ein:notebook--opened-map hash table. Keys are cons cells of url-or-port and path.

There are a number of helper functions for returning the struct for an opened notebook:

[[file:lisp/ein-notebook.el::(defun%20ein:notebook-get-opened-notebook%20(url-or-port%20path)][ein:notebook-get-opened-notebook]]

[[file:lisp/ein-notebook.el::(defun%20ein:notebook-get-opened-buffer%20(url-or-port%20path)][ein:notebook-get-opened-buffer]]

Notebooklist Buffer

Kernel communication

The messaging protocol.

Contents API

Documented at the IPython Github wiki.

There is also another great online resource for session and kernel REST API.

Connecting to a running Kernel

Entry point is [[file:lisp/ein-notebook.el::ein:notebook-start-kernel][ein:notebook-start-kernel]] which is called from ein:notebook-request-open-callback after successful call to the notebook server requesting the contents of a given notebook.

[[file:lisp/ein-kernel.el::ein:kernel-start][ein:kernel-start]] starts/gets a session with a running kernel using the REST API.

On a successful return ein creates a websocket channel (channels for IPython 2.x) via a call to websocket-open in the emacs-websocket package. The URL request is of the form:

ws://{server_address}:{port}/api/kernels/{kernel id from previous REST query}/channels?session_id={session id}

How a Worksheet is Displayed

EIN relies heavily on EIEIO and EWOC.

EWOC PP eventually calls [[file:lisp/ein-cell.el::ein:cell-append-mime-type][ein:cell-append-mime-type]] for output. Latex is considered text, but should be able to convert to image using dvitopng, imagemagick, other?

Testing

This is too complex. Makefile is used to download dependencies and set up python virtual environment, then Python code actually runs the Emacs tests.

Using Python is good, Makefile less so.

Having project name changed from IPython to Jupyter complicates things (can't rely on ipy-version anymore).

Having python2.7 and python3.x also complicates things.

One option seems to be to do everything in setup.py.

testein.py uses argparse. Maybe there are better options?

You can use conda with travis.

TODO Define testing workflow

1. Update submodules: git submodule update --remote
2. Create/activate python environment.
3. Run testein.py

TODO Migrate from Makefile to setup.py

TODO Use conda to create testing environments.

For both Travis CI and local testing.

• conda install notebooke to install Jupyter notebook.
• conda install ipython=x.x to install pre-jupyter ipython notebook versions.

Enhancements/Fixes

Run dynamic javascript

The development notebook.

Emacs is not a web browser, hence does not know how to execute javascript.

Maybe we can get around this using skewer-mode or js-comint.el.

Skewer-mode uses JS client provided by a web browser, while js-comint depends on nodejs (you understand this difference, right? Right?).

Another thought is to get python to do this for us. The packages naked (an unfortunate name given my corporate firewall) and PyExecJs.

Embedding Altair plots

First get dynamic javascript working…

Relevant issue, pull request and code.

Appears the code has capability of returning javascript and png output. When calling from ein all that gets returned is javascript, which `ein:cell-append-mime-type` chokes on.

Somehow, when running nbconvert, the javascript gets turned into a png. How to trigger that when normally executing cells?

Mike DeCandia's Wish and Bug List

Wishlist

• switch kernel
• getting a true Python mode when editing code in cells, without messing up the other formatting
• If one cuts and pastes read-only text into a cell it can’t be edited
• A full undo history
• Command history / autocomplete like one gets in regular ipython
• Image resizing

Bugs

• emacs ipython notebook fails to follow redirects properly - This is mainly due to the fact that it holds on the original site name internally.
• cookie expiration for long running notebooks - On long running notebooks tornado's default cookie expiration is 30 days. After the cookie expires emacs will continue to attempt autosave, but the notebook will not save. The workaround is to run ein:notebooklist-open to generate a new GET request against /login to get another cookie.

Switch kernel in running notebook

How? Probably by restarting kernel using a new kernelspec.

Support company-mode

Inline latex

See issue #88.

For Further Investigation

• magic-latex-buffer.el
• preview-latex.el
• Another preview-latex package (based on org-latex-preview).

Inline using org-latex-preview

Documentation for this facility in org.

Does it work here?

\begin{equation} x=\sqrt{b} \end{equation}

Some inline Latex math $a^2=b$.

Yes, but nedd MiKTeX installed if on windows.

If org-latex-preview is working then px will also work, though the code for [[file:~/.emacs.d/elpa/px-20141006.548/px.el::(defun%20px--create-preview%20(at)][px--create-preview]] needs to be patched as the signature for `org-format-latex` has changed.

Using magic-latex-buffer

Per the documentation all you need to do to configure is to add a hook:

  (add-hook 'latex-mode-hook 'magic-latex-buffer)

Or manually activate by calling M-x magic-latex-buffer.

Use variable ein:notebook-first-open-hook to enable?

This works, at least for viewing, but the images that get inserted confuse ein when saving a notebook and generate errors in Jupter. Can be worked around by disabling magic-latex-buffer before saving. One hack is to advise ein:notebook-save-notebook-command?

  (defvar ein:magic-latex-enabled-p nil)

  (defun ein:disable-magic-latex-maybe (&rest args)
    (when ein:magic-latex-enabled-p
      (ein:log 'debug "Disabling magic-latex.")
      (magic-latex-buffer -1)))

  (defun ein:enable-magic-latex-maybe (&rest args)
    (when ein:magic-latex-enabled-p
      (ein:log 'debug "Enabling magic-latex.")
      (magic-latex-buffer t)))

  (advice-add #'ein:notebook-save-notebook :before #'ein:disable-magic-latex-maybe)
  (advice-add #'ein:notebook-save-notebook :after #'ein:enable-magic-latex-maybe)

  (advice-add #'ein:cell-execute-internal :before #'ein:disable-magic-latex-maybe)
  (advice-add #'ein:cell-execute-internal :after #'ein:enable-magic-latex-maybe)

XWidget Support/Interactive Widgets

For the most part this is a non-starter since in Jupyter this is built on web and javascript, but maybe with emacs 25's coming integration with xwidgets there is hope?

What Does ipywidgets.interact() return?

A call to `ipywidgets.interact()` creates a custom communications channel with the jupyter server.

1. What are message types (msg_type) comm_msg and comm_open for? These are received when calling interact().

Websocket data for comm_open

[WS] Received: {"msg_id": "56821eaa-cc32-4a34-bac3-8468ea08b7a0", "content": {"execution_state": "busy"}, "channel": "iopub", "metadata": {}, "msg_type": "status", "buffers": [], "header": {"username": "username", "session": "eb518e76-61af-4bff-9fb0-49fb78883056", "msg_id": "56821eaa-cc32-4a34-bac3-8468ea08b7a0", "date": "2016-03-24T07:24:50.879558", "version": "5.0", "msg_type": "status"}, "parent_header": {"username": "username", "session": "5b01e727-3ce9-416f-bb67-f9400b719e33", "msg_id": "6dd8ea4c-325a-4938-8ad9-d68e2e4dbb0b", "date": "2016-03-24T07:24:50.879558", "version": "5.0", "msg_type": "execute_request"}} {"msg_id": "95f88fb5-2e4b-45b5-b78b-79d9274d392a", "content": {"execution_count": 3, "code": "interact(f, x=10)"}, "channel": "iopub", "metadata": {}, "msg_type": "execute_input", "buffers": [], "header": {"username": "username", "session": "eb518e76-61af-4bff-9fb0-49fb78883056", "msg_id": "95f88fb5-2e4b-45b5-b78b-79d9274d392a", "date": "2016-03-24T07:24:50.879558", "version": "5.0", "msg_type": "execute_input"}, "parent_header": {"username": "username", "session": "5b01e727-3ce9-416f-bb67-f9400b719e33", "msg_id": "6dd8ea4c-325a-4938-8ad9-d68e2e4dbb0b", "date": "2016-03-24T07:24:50.879558", "version": "5.0", "msg_type": "execute_request"}} {"msg_id": "ef75371f-9047-46de-8eda-2c8697e2b60b", "content": {"data": {"width": "", "_model_name": "BoxModel", "font_size": "", "children": [], "overflow_x": "", "padding": "", "font_style": "", "_dom_classes": ["widget-interact"], "box_style": "", "height": "", "_view_module": "", "margin": "", "color": null, "msg_throttle": 3, "border_color": null, "font_family": "", "_view_name": "BoxView", "_model_module": null, "version": 0, "overflow_y": "", "background_color": null, "font_weight": "", "_css": [], "border_width": "", "visible": true, "border_style": "", "border_radius": ""}, "target_name": "ipython.widget", "comm_id": "237329515cca473985d6fa52ec0c93a1", "target_module": null}, "channel": "iopub", "metadata": {}, "msg_type": "comm_open", "buffers": [], "header": {"username": "username", "session": "eb518e76-61af-4bff-9fb0-49fb78883056", "msg_id": "ef75371f-9047-46de-8eda-2c8697e2b60b", "date": "2016-03-24T07:24:50.910702", "version": "5.0", "msg_type": "comm_open"}, "parent_header": {"username": "username", "session": "5b01e727-3ce9-416f-bb67-f9400b719e33", "msg_id": "6dd8ea4c-325a-4938-8ad9-d68e2e4dbb0b", "date": "2016-03-24T07:24:50.879558", "version": "5.0", "msg_type": "execute_request"}}

Websocket data for comm_msg

[WS] Received: {"msg_id": "fe357d60-e83a-49ac-821f-7d99cdf20b8a", "content": {"data": {"description": "", "orientation": "horizontal", "continuous_update": true, "_model_name": "WidgetModel", "font_size": "", "step": 1, "background_color": null, "padding": "", "slider_color": null, "height": "", "_view_module": "", "margin": "", "color": null, "width": "", "font_family": "", "border_color": null, "_dom_classes": [], "min": -10, "_range": false, "disabled": false, "_model_module": null, "_view_name": "IntSliderView", "max": 30, "version": 0, "font_style": "", "msg_throttle": 3, "value": 10, "readout": true, "font_weight": "", "_css": [], "border_width": "", "visible": true, "border_style": "", "border_radius": ""}, "target_name": "ipython.widget", "comm_id": "c1059008e6d046209c9d63de036c1aff", "target_module": null}, "channel": "iopub", "metadata": {}, "msg_type": "comm_open", "buffers": [], "header": {"username": "username", "session": "eb518e76-61af-4bff-9fb0-49fb78883056", "msg_id": "fe357d60-e83a-49ac-821f-7d99cdf20b8a", "date": "2016-03-24T07:24:50.948495", "version": "5.0", "msg_type": "comm_open"}, "parent_header": {"username": "username", "session": "5b01e727-3ce9-416f-bb67-f9400b719e33", "msg_id": "6dd8ea4c-325a-4938-8ad9-d68e2e4dbb0b", "date": "2016-03-24T07:24:50.879558", "version": "5.0", "msg_type": "execute_request"}} {"msg_id": "30514644-45e1-45c7-a5db-42c9ee22e9ec", "content": {"data": {"buffers": [], "state": {"description": "x"}, "method": "update"}, "comm_id": "c1059008e6d046209c9d63de036c1aff"}, "channel": "iopub", "metadata": {}, "msg_type": "comm_msg", "buffers": [], "header": {"username": "username", "session": "eb518e76-61af-4bff-9fb0-49fb78883056", "msg_id": "30514644-45e1-45c7-a5db-42c9ee22e9ec", "date": "2016-03-24T07:24:50.964124", "version": "5.0", "msg_type": "comm_msg"}, "parent_header": {"username": "username", "session": "5b01e727-3ce9-416f-bb67-f9400b719e33", "msg_id": "6dd8ea4c-325a-4938-8ad9-d68e2e4dbb0b", "date": "2016-03-24T07:24:50.879558", "version": "5.0", "msg_type": "execute_request"}} {"msg_id": "fc005b54-774c-4920-860f-cec08cb5b5ba", "content": {"data": {"buffers": [], "state": {"children": ["IPY_MODEL_c1059008e6d046209c9d63de036c1aff"]}, "method": "update"}, "comm_id": "237329515cca473985d6fa52ec0c93a1"}, "channel": "iopub", "metadata": {}, "msg_type": "comm_msg", "buffers": [], "header": {"username": "username", "session": "eb518e76-61af-4bff-9fb0-49fb78883056", "msg_id": "fc005b54-774c-4920-860f-cec08cb5b5ba", "date": "2016-03-24T07:24:50.964124", "version": "5.0", "msg_type": "comm_msg"}, "parent_header": {"username": "username", "session": "5b01e727-3ce9-416f-bb67-f9400b719e33", "msg_id": "6dd8ea4c-325a-4938-8ad9-d68e2e4dbb0b", "date": "2016-03-24T07:24:50.879558", "version": "5.0", "msg_type": "execute_request"}} {"msg_id": "65240518-737e-4614-8ad1-7d9fcfc567bd", "content": {"data": {"method": "display"}, "comm_id": "237329515cca473985d6fa52ec0c93a1"}, "channel": "iopub", "metadata": {}, "msg_type": "comm_msg", "buffers": [], "header": {"username": "username", "session": "eb518e76-61af-4bff-9fb0-49fb78883056", "msg_id": "65240518-737e-4614-8ad1-7d9fcfc567bd", "date": "2016-03-24T07:24:50.964124", "version": "5.0", "msg_type": "comm_msg"}, "parent_header": {"username": "username", "session": "5b01e727-3ce9-416f-bb67-f9400b719e33", "msg_id": "6dd8ea4c-325a-4938-8ad9-d68e2e4dbb0b", "date": "2016-03-24T07:24:50.879558", "version": "5.0", "msg_type": "execute_request"}} {"msg_id": "6b0b41e2-5af0-4690-9902-9e73a61cf0e3", "content": {"wait": true}, "channel": "iopub", "metadata": {}, "msg_type": "clear_output", "buffers": [], "header": {"username": "username", "session": "eb518e76-61af-4bff-9fb0-49fb78883056", "msg_id": "6b0b41e2-5af0-4690-9902-9e73a61cf0e3", "date": "2016-03-24T07:24:50.964124", "version": "5.0", "msg_type": "clear_output"}, "parent_header": {"username": "username", "session": "5b01e727-3ce9-416f-bb67-f9400b719e33", "msg_id": "6dd8ea4c-325a-4938-8ad9-d68e2e4dbb0b", "date": "2016-03-24T07:24:50.879558", "version": "5.0", "msg_type": "execute_request"}}

Working with jupyterhub

Jupyterhub requires authentication using username/password, as opposed to just providing a secret when logging into ipython 3.x and earlier.

On logging in a cookie of form "jupyter-hub-token-<username>" is generated and propogated with all calls to server. Emacs request should automatically handle this.

The REST API for this looks like POST http://{host}:{port}/hub/login, username and password parameters in the POST.

Also looks like the content REST API has been modified so that queries are of the form: /user/<username>/<command>.

Imenu/Speedbar Cooperation

Seems to be a couple ways of doing this:

1. Configuring [[http://emacswiki.org/emacs/ImenuMode#toc12][imenu-generic-expression]] regex's.
2. Redefining imenu-create-index ala python.el.

(2) seems to be the more elegant solution.

EIN currently has minimal support for imenu through [[file:lisp/ein-worksheet.el::ein:worksheet-imenu-create-index][ein:worksheet-imenu-create-index]], but all it does is look for headings. Somehow this fails to work with speedbar and also does not handle indexing Python code (i.e. variables, function, classes, etc.).

To get the speedbar working we will need to define a minor mode per the following instructions.

For /name/~-speedbar-menu-items~ can I just use imenu-generic-expression?

Maybe the way to do this is for each [[file:lisp/ein-cell.el::ein:codecell][codecell]] create a temp buffer with the text of that cell and call ein:imenu-create-index.

  (let ((text (ein:cell-get-text cell)))
    (with-temp-buffer
      (insert text)
      (ein:imenu-create-index)))

Still will need way to map temp buffer positions to actual positions in the notebook buffer (ein:cell-input-pos-min and ein:cell-input-pos-max)

Live links to other notebooks

1. Understand how org-mode does it.
2. Steal???
3. Profit!!!

Use polymode

Polymode uses indirect buffers, which may or may not be a good solution for ein notebooks. I think this is what nxhtml is doing…

Use dash?

Get rid of all those cl compile warnings?

Also look at using s and f.

Us cl-generic?

eieio is being deprecated and cl-generic is the recommended replacement..

Access password protected notebooks (issue #57)

This is what I have found out so far:

You can authenticate with the IPython/Jupyter notebook server using ein:notebooklist-login. After calling this a cookie is generated (very easy to see if you are using curl as the backend for emacs-request) and you can then use the REST API to list and get notebook data.

Once authenticated REST calls to get notebook json data and create sessions work fine. After EIN starts a session one can see the kernel is running from the web interface. The problem starts when ein tries to open a websocket connection to the kernel. The notebook server generates a 403 forbidden response. I think because emacs-websocket doesn't know anything about the security cookie generated during the curl request.

Not sure if that makes sense, but for the moment that is my theory on what's happening. Somehow we need to provide the security cookie with the websocket connect request.

<2015-06-09 Tue> SOLVED(?) - issue is that emacs-websocket needs to provide more info with the connection header:

1. Specify the port along with the url.
2. Pass along a security cookie.

Connect to non-python kernels

Synergies with pymacs?

Detect system path of opened notebook

Jump to notebook code in traceback (issue #42)

What needs to be done:

1. Carry notebook reference in the [[file:lisp/ein-traceback.el::ein:traceback][ein:traceback]] structure.
2. Look for <ipython-input-3-05c9758a9c21> in <module>(). The number 3 means input #3 in the notebook.
3. Find cell based on input number. Can iterate through list of cells () and look for matching input-prompt-number.
4. Call ein:cell-goto on that cell. May need to swap buffers first.

The Return of Worksheets

tkf/ein and IPython 2.x allowed for multiple worksheets within an individual notebook. This feature was removed in 3.0 since multiple worksheets do not make much sense in the context of a tabbed web browser interface. EIN's legacy code still supports worksheets, though at the moment that information is lost upon saving a notebook.

Having multiple worksheet support makes some sense for ein; below is thinking on how to reimplement this feature.

IPython nbformat 4 specifies a metadata key which can be used to store general information. Cell metadad has a tag key which is a "A list of string tags on the cell. Commas are not allowed in a tag."

Best place to set the tag key is when generating /hiro/emacs-ipython-notebook/src/commit/d9c9d18fd0eec81064eb7b15c4e8f240073763b9/content for saving a notebook.

Fixing Tests

• Insert output tests are failing - probably due to how we are making the test cell. JSON is per nbformat4, but are we correctly parsing mimetypes (i.e. there is an additional call to do this, are we making it?). Is ein:cell-insert-output getting called?