Given what happened to the other saguaro, it makes me fear that this one will fall too.

I took this photo of a saguaro a month ago. It had been partially burnt during the fires that happened north of Phoenix earlier this summer. This weekend I realized it had fallen. According to Wikipedia, saguaros grow their first arm around 75–100 years of age. 👋🌵😔

Custom URL Handler for Files With Unique IDs

Yesterday I read a series of posts on custom URL scheme handlers on the Zettelkasten forums. The handler registers itself to open links like zettel://202006061337, where the number is the unique ID of a zettel (here it’s a timestamp). I’m not sure everyone realized the magnitude of what that means.

Combining a custom URL with a unique ID means notes and links can become entirely independent from your apps. Only the handler needs to know about the apps you’re using.

That alone is very nice, but then I thought: URLs can have query parameters… That means I can have URLs like zettel://202006061337&edit that open in my text editor of choice: TextMate, BBEdit, WriteRoom, FoldingText, etc. Or zettel://202006061337&preview to open in Marked. Or I could even pick the app interactively with zettel://202006061337&pick.

Handling the ID alone is pretty easy since the common Zettelkasten-like apps respond to a URL scheme to search and open files. The Archive uses thearchive://match/ID, nvUltra uses x-nvultra://find/ID, and nvAlt uses nvalt://find/ID.

But how to open in a text editor or in Marked given only the ID? With Spotlight. I used mdfind -name ID to find the file. This could be further refined with the -onlyin FOLDER option but I didn’t need it. Then it’s a matter of calling open -a Marked FILEPATH.

There’s also a zettel://create special case that will create a new zettel with the current time stamp (YYYYMMDDHHMM). It’s always done with the default Zettelkasten app because the script doesn’t know where to write the file but the app does.

I wrote the handler in Applecript because it’s the easiest way I know to create something that macOS considers an “app” and that can therefore handle URLs.

The full script is below. To use it:

  1. Open Script Editor and paste the code below in a new file.
  2. [Optional] Modify values in the Configuration section to pick a different URL prefix, default Zettelkasten app URL, editor, and previewer. You can add as many apps as you’d like in the appChoices array.
  3. Save as “Application”. You can save it anywhere. Make sure none of the boxes are checked.
  4. Register the app as a URL handler. You can do it with the SwiftDefaultApps Preference pane, or using the instructions provided by Christian Tietze in the forums:
    • Locate the application file you just created
    • Right-click the app, select “Show Package Contents”
    • Inside, open Contents/Info.plist with a text editor
    • Paste the following in a blank line right below the <dict> line. Replace zettel with the URL prefix you’ve chosen:
<key>CFBundleURLTypes</key>
<array>
    <dict>
        <key>CFBundleURLName</key>
        <string>Zettel Link Opener</string>
        <key>CFBundleURLSchemes</key>
        <array>
            <string>zettel</string>
        </array>
    </dict>
</array>

Here’s the full script:

-- Zettel Link Opener
-- Created by Alexandre Chabot-Leclerc
-- Source: https://alexchabot.net/2020/06/06/custom-url-handler-for-zettels/
-- URL Handler for zettelkasten unique IDs, e.g., zettel://202006061017
-- Handles options after the ID to open different apps:
--    zettel://202006061017&edit to open is a text editor like TextMate
--    zettel://202006061017&preview to open in a preview app like Marked
--    zettel://202006061017&pick to open a menu of apps to pick from

-----------------------------------------------------------
-- CONFIGURATION
-- URL prefix for your custom URL, e.g. zettel://ZETTEL_ID
property urlPrefix : "zettel"

-- Default URL to call to open a note with a given ID. The ID will be appended
property defaultZkAppUrl : "thearchive://match/"
--property defaultZkAppUrl : "nvalt://find/"
--property defaultZkAppUrl : "x-nvultra://find/"

-- URL to use to create a new zettle with the current timestamp YYYYMMDDHHMM
property urlForCreation : "thearchive://matchOrCreate/"
--property urlForCreation : "nvalt://make?txt="
--property urlForCreation : "x-nvultra://make?txt="

-- Apps to use for the different query parameters
property editApp : "FoldingText" -- App to used with "&edit" query parameter
property previewApp : "Marked" -- App to used with "&preview" query parameter 

-- List of app to display in the menu with with &pick query option
-- The apps will appear in the order defined here
property appChoices : {defaultZkAppUrl, editApp, previewApp, "TextMate"}
property defaultApp : {defaultZkAppUrl})
-----------------------------------------------------------

on splitText(theText, theDelimiter)
	set AppleScript's text item delimiters to theDelimiter
	set theTextItems to every text item of theText
	set AppleScript's text item delimiters to ""
	return theTextItems
end splitText

on removeUrlPrefix(original)
	-- Remove URL prefix so we're left with only the ID and the optional query parameter
	return do shell script "echo " & quoted form of original & " | sed 's;" & urlPrefix & "://;;'"
end removeUrlPrefix

on getIdAndOption(resouceAndQuery)
	-- Split the zettel ID and the optional parameter
	-- For example 202006061012&edit or 202006061012&preview
	set theItems to splitText(resouceAndQuery, "&")
	if length of theItems is 1 then
		-- Append an empty string if there's no option so this
		-- function always returns an array of 2 elements
		copy "" to the end of theItems
	end if
	return theItems
end getIdAndOption

on findFilepath(zk_id)
	-- Finds the filepath using Spotlight.
	-- It's easier than finding the proper filename given only the zettel ID
	return do shell script "mdfind -name " & zk_id
end findFilepath

on createZettel()
	set newZkId to do shell script "date +'%Y%m%d%H%M'"
	do shell script "open " & urlForCreation & newZkId
end createZettel

on openInChoosenApp(zkId, zkFilepath)
	--	From Simple List Handler by Patrick Welker <http://rocketink.net>
	-- Promp the use for the app to use
	set selectedApp to item 1 of (choose from list the appChoices with title "Available App" with prompt "Which app do you want to use?" default items defaultApp)
	if selectedApp is false then
		-- Exit prematurly if the user clicked Cancel
		error number -128
	end if
	
	-- Open the URL directly, or open by app name
	if selectedApp contains "://" then
		do shell script "open " & selectedApp & zkId
	else
		do shell script "open -a " & selectedApp & " " & quoted form of zkFilepath
	end if
end openInChoosenApp

on open location thisURL
	set resouceAndQuery to removeUrlPrefix(thisURL)
	set idAndOption to getIdAndOption(resouceAndQuery)
	set zkId to item 1 of idAndOption
	
	if zkId is "create" then
		createZettel()
		return
	end if
	
	set zkFilepath to findFilepath(zkId)
	
	if item 2 of idAndOption is "edit" then
		do shell script "open -a " & editApp & " " & quoted form of zkFilepath
		-- Exit the script immediately so we don't also open in the default app
		return
	else if item 2 of idAndOption is "preview" then
		do shell script "open -a " & previewApp & " " & quoted form of zkFilepath
		-- Exit the script immediately so we don't also open in the default app(
		return
	else if item 2 of idAndOption is "pick" then
		openInChoosenApp(zkId, zkFilepath)
		return
	end if
	
	-- Fall back to the default handler if there was no option
	-- or the option was invalid
	do shell script "open " & defaultZkAppUrl & zkId
end open location

What does %matplotlib do in IPython?

TLDR; Use %matplotlib if you want interactive plotting with matplotlib. If you’re only interested in the GUI’s event loop, %gui <backend> is sufficient.

I never really understood the difference between %gui and %matplotlib in IPython. One of my colleagues at Enthought once told me that at some point in his career, he more or less stopped reading documentation and instead went straight to the code. That’s what I did here. But let’s do a bit of history first.

In the “beginning”, there was pylab. It (still) is a module of matplotlib and was a flag to IPython designed to facilitate the adoption of Python as a numerical computing language by providing a MATLAB-like syntax.1 The reference was so explicit that before being renamed to pylab on Dec 9, 2004, the module was called matplotlib.matlab. IPython adopted the rename on the same day.2 With the ‑‑pylab flag or the %pylab magic function, IPython would set up matplotlib for interactive plotting and executed a number of imports from IPython, NumPy and matplotlib. Even thought it helped a few people transition to Python (including myself), it turned out to be a pretty bad idea from a usability point of view. Matthias Bussonnier wrote up a good list of the many things that are wrong with it in “No Pylab Thanks.”

For the 1.0.0 release of IPython in August 2013, all mentions of %pylab were removed from the examples (in a July 18, 2013 commit) and were replaced by calls to the %matplotlib magic function, which only enables interactive plotting but does not perform any imports. The %matplotlib function had already been introduced in a 2013 refactoring to separate the interatice plotting from the imports. The %gui magic command had already been introduced in 2009 by Brian Granger to “manage the events loops” (hint hint).

Now we know that the (my) confusion with %gui and %matplotlib started in 2013.

This analysis refers to IPython 7.8.0 and ipykernel 5.1.2.

Our entry point will be the %matplotlib magic command. Its source code is in the IPython.core.pylab.py file. The essential call is to shell.enable_matplotlib(gui), which is itself implemented in IPython.core.interactiveshell.InteractiveShell, and does five things:

  1. Select the “backend” given the choice of GUI event loop. This is done by calling IPython.core.pylabtools.find_gui_and_backend(gui). It encapsulates the logic to go from a GUI name, like "qt5" or "tk", to a backend name, like "Qt5Agg" and "TkAgg".
  2. Activate matplotlib for interactive use by calling IPython.core.pylabtools.activate_matplotlib(backend), which:
    1. Activates the interactive mode with matplotlib.interactive(True);
    2. Switches to the new backend with matplotlib.pyplot.switch_backend(backend);
    3. Replaces the matplotlib.pyplot.draw_if_interactive method with the same method, but wrapped by a flag_calls decorator, which adds a called flag to the method. That flag will be used by the new %run runner that’s introduced below at point #5;
  3. Configure inline figure support by calling IPython.core.pylabtools.configure_inline_support(shell, backend). This is where some very interesting stuff happens. It first checks that InlineBackend is actually importable from ipykernel.pylab.backend_inline, otherwise it returns immediately. But if it’s importable and the backend is "inline", it:
    1. Imports the ipykernel.pylab.backend_inline.flush_figures function, and register it as a callback for the "post_execute" event of the shell. As we’ll see later, callbacks for "post_execute" are called after executing every cell;
    2. If the backend was not "inline", it’ll unregister the flush_figures callback;
  4. Enable the GUI by calling shell.enable_gui(gui). This method is not implemented in the IPython.core.interactiveshell.InteractiveShell base class, but rather in IPython.terminal.interactiveshell.TerminalInteractiveShell. If a gui as specified, it gets the name of the active_eventloop and its corresponding inputhook function using IPython.terminal.pt_intputhooks.get_inputhook_name_and_func(gui). The active_eventloop is just a string, such as 'qt', but the inputhook is more interesting. It’s the function to call to start that GUI toolkit’s event loop. Let’s dig further into get_inputhook_name_and_func(gui). That function checks a few things, but it essentially:
    1. Imports the correct inputhook function for the chosen GUI by importing it from IPython.terminal.pt_intputhooks.<gui_mod>. For example, the Qt inputhook is imported from IPython.terminal.pt_intputhooks.qt. Later on, when inputhook is executed for Qt, it will:
      1. Create a QCoreApplication;
      2. Create a QEventLoop for that application;
      3. Execute the event loop and register the right events to make sure the loop is shut down properly. The exact operations to start and stop the loop are slightly different for other GUI toolkits, like tk, wx, or osx, but they all essentially do the same thing. At this point we’re ready to go back up the stack to enable_matplotlib in %matplotlib;
  5. Replace IPython’s default_runner with the one defined in IPython.core.pylabtools.mpl_runner. The default_runner is the function that executes code when using the %run magic. The mpl_runner:
    1. Saves the matplotlib.interactive state, and disables it;
    2. Executes the file;
    3. Restores the interactive state;
    4. Makes the rendering call, if the user asked for it, by checking the plt.draw_if_interactive.called flag that was introduced at point #1.3 above.

As for the other magic, %gui, it only executes a subset of what %matplotlib does. It only calls shell.enable_gui(gui), which is point #4 above. This means that if your application requires interaction with a GUI’s event loop, but doesn’t require matplotlib, then it’s sufficient to use %gui. For example, if you’re writing applications using TraitsUI or PyQt.

The Effect of Calling %gui and %matplotlib

Let’s start with the “simplest” one, %gui. If you execute it in a fresh IPython session, it’ll only start the event loop. On macOS, the obvious effect of this is to start the Rocket icon.

Animation of the Python rocket icon starting because of a call to `%gui`.

At that point, if you import matplotlib and call plt.plot(), no figure will appear unless you either call plt.show() afterwards, or manually enable interactive mode with plt.interactive(True).

On the other hand, if you start your session by calling %matplotlib, it’ll start the Rocket and activate matplotlib’s interactive mode. This way, if you call plt.plot(), your figure will show up immediately and your session will not be blocked.

Using %run

If you call %run my_script.py after calling %matplotlib, my_script.py will be executed with the mpl_runner introduced above at point #5.

Executing a Jupyter Notebok Cell When Using the "inline" Backend

In the terminal the IPython.terminal.interactiveshell.TerminalInteractiveShell.interact() method is where all the fun stuff happens. It prompts you for code, checks if you want to exit, and then executes the cell with InteractiveShell.run_cell(code) and then trigger the "post_execute" event for which we’ve registered the ipykernel.pylab.backend_inline.flush_figures callback. As you might have noticed, the flush_figures function comes from ipykernel, and not from IPython. It tries to return all the figures produced by the cell as PNG of SVG, displays them on screen using IPython’s display function, and then closes all the figures, so matplotlib doesn’t end up littered will all the figures we’ve ever plotted.

Conclusion

To sum it up, use %matplotlib if you want interactive plotting with matplotlib. If you’re only interested in the GUI’s event loop, %gui <backend> is sufficient._ Although as far as I understand, there’s nothing very wrong with using %matplotlib all the time.


  1. Basically, no namespaces, and direct access to functions like plot, figure, subplot, etc. [return]
  2. The earliest commit I found for the IPyhon project was on July 6, 2005 by Fernando Perez, 7 months after the name change. Its Git hash is 6f629fcc23ba63342548f61cc7307eeef4f55799. But the earliest mention is an August 2004 entry in the ChangeLog: “ipythonrc-pylab: Add matplotlib support,” which is before the offical rename in matplotlib. [return]

Manually Merging Day One Journals

My first Day One entry is from January 24, 2012. I used it often to take note about what I was doing during my PhD with the #wwid tag (what was I doing, an idea from Brett Terpstra, I think), and sometimes to clarify some thoughts.

When Day One went The Way of the Subscription, I didn’t bother too much because Dropbox sync still worked. Until it didn’t. I somehow didn’t realized it and kept adding entries to both the iOS and the macOS versions. Not good. It’s been on my to do list for a while to find a way to merge the two journals. I could probably subscribe to the Day One sync service and have it figure out the merging but I didn’t want to subscribe just for that.

I learned somewhere that Day One 2 could export journals as a folder of photos and a JSON file. I figure I could probably write a script to do the merging. So I downloaded Day One 2 on my iPhone and Mac, imported my Day One Classic journals, exported them as JSON to a folder on my Mac, and unzipped them. I also created a merged/ folder where to put the merged journal. The hierarchy looks like this:

$ tree -L 2
.
├── Journal-JSON-ios/
│   ├── Journal.json
│   └── photos/
├── Journal-JSON-ios.zip
├── Journal-JSON-mac/
│   ├── Journal.json
│   └── photos/
├── Journal-JSON-mac.zip
├── merge_journals.py
└── merged/

I first copied the photo folder from Journal-JSON-ios/ to merged/ and the photos from Journal-JSON-mac/photos/. I was pretty confident that I would end up with the union of all the photos because Day One uses UUIDs to identify each photo. The -n option to cp prevents overwriting files.

$ cp -r Journal-JSON-ios/photos merged/
$ cp -n Journal-JSON-mac/photos merged/photos/

I then ran the merge_journals.py script (below) to do a similar merge of the entries, based on the UUIDs. The merging happens by building a dictionary with UUID of each entry as the key and the entry itself as the value. It’s two loops over the iOS and the macOS entries. Entries with the same UUID should have the same contents, unless I’ve edited some metadata on one platform but not the other. I’m not too worried about that.

The output dictionary will be written to the Journal.json file. The entries are sorted chronologically because that’s how it was in the exported journal files, but I doubt it matters.

The output dictionary is written to disk without enforcing the conversion to ASCII since the exported journals are encoded using UTF-8. The indent is there to make the output more readable and diff-able with the exported journals.

import json

with open('./Journal-JSON-ios/Journal.json') as f:
    ios = json.load(f)
with open('./Journal-JSON-mac/Journal.json') as f:
    mac = json.load(f)

# Extract and merge UUIDs
uniques = {entry['uuid']: entry for entry in ios['entries']}
for entry in mac['entries']:
    uniques[entry['uuid']] = entry

# Create the output JSON data structure
output = {}
output['metadata'] = mac['metadata']
output['entries'] = list(uniques.values())
# I'm not sure it matters, but Day One usually exports the entries
# in chronological order
output['entries'].sort(key=lambda e: e['creationDate'])

# ensure_ascii print unicode characters as-is.
with open('merged/Journal.json', 'w', encoding='utf-8') as f:
    json.dump(output, f, indent=True, ensure_ascii=False)

The last step is to zip the journal and photos together, which tripped me up a few times. The Journal.json and the photos/ folder must be at the top level of the archive, so I zip the file from within the merged/ folder and then move it back up one level.

$ cd merged
$ zip -r merged.zip *
$ mv merged.zip ..

I could then import merged.zip in Day One, which created a new Journal, and delete the old one.

I guess I could somewhat automate this to roll my own, DIY, sync between versions of Day One, but I’d rather pay them money once I decide to use Day One frequently again. Still, I really appreciate that the Day One developers picked formats that could be manipulated so easily.

By far the best thing I’ve seen at Disney World so far.

Bread #2.

The Modern, Fort Worth.

The weight of the world.

By Giacometti.

There’s sometimes action out of my window.

Got a new room, with view on the East River. Much upgrade.

Wind tunnel model. Most beautiful item at the Musée des Confluence.

Anna going a bit overboard: crunchy speculoos, crème fraîche, and… maple syrup.

Party prep (Marshmallows + Jello powder)

Place des moulins, Marseille.

“The Cloud” of Lyon’s Musée des Confluences, seen from the roof.

A holiday sight.

Ball and bridge.

At Copenhagen Street Food. (Yes, here, street food is a place.)

Octohook.

Making spruce beer, attempt #2.