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My Mathematics PhD compare workflow: LaTeX notes and prompt pdf referencing

My Mathematics PhD compare workflow: LaTeX notes and prompt pdf referencing

These addons are ideal!!

Earlier this 365 days I started a PhD in pure arithmetic at KU Leuven in Belgium and on this weblog post I discuss my compare workflow. I discuss how I take every day notes, every handwritten ones and ones in LaTeX and how I address references, featuring a design to true now add clickable references to my notes.

Doing pure arithmetic compare in all equity unlike moderately about a scientific compare.
I don’t creep experiments, nor attain I acquire records to crunch via. A laptop is surprisingly normally of minute to no lend a hand. It’s correct you and pencil and paper.
Or in my case, me, my laptop laptop and a Wacom capsule.

My compare workflow is hybrid: it consists every of (digital) handwritten notes and typed LaTeX notes. I care for having these two alternatives. Handwritten notes allow me to mediate fully freely, while taking notes in LaTeX forces me more to write down down things neatly, which now and again finally ends Up to to find mistakes within the handwritten notes.

LaTeX Notes

Doing a PhD in arithmetic, it makes most sense to take notes in LaTeX, especially since I acquire a in actuality ambiance tremendous system save of dwelling Up already, as explained in my old weblog posts.
My LaTeX notes stumble on as follows:

This LaTeX doc routinely concatenates the notes of the old 14 days, provides the date of every level to within the margin and provides a hyperlink to my handwritten notes of that day. The global itemizing structure appears to be like to be as follows:

  • phd
    • scripts
    • teaching
    • papers
      • title – authors.pdf
    • notes
      • master.tex
      • preamble.tex
      • references.tex
      • theorems.tex
      • symbols.tex
      • 2022-01-03
        • level to.tex
        • level to.xoj
      • 2022-01-04
      • 2022-01-05

Since I acquire a degree to for on daily foundation I below no circumstances acquire to mediate the save to write down something down. I correct press Alt + N to delivery nowadays’s level to.tex, and I’m save of dwelling.
To delivery the handwritten notes I’m in a position to press Alt + X, which opens Xournal — more on that later.
Yow will stumble on the source code on Github.

Reference administration

Doing compare capacity going via a form of references to papers and books.
I wished to acquire a minimalistic capacity that is friction-free, having three dreams in mind. First, after I am learning a pdf doc, I desire so to add a reference to the sizzling page to my notes with a single keystroke. Secondly, when having a peek the Arxiv, I’d settle to add a paper to my library with a single click and lastly I desire a design to true now delivery papers I acquire in my library, which is in actuality basic all over meetings.

At this time setting Up clickable references

Have a peek back at my notes and win 22 situation the parts that are in dauntless, equivalent to [definition, p. 29] or [Section 5. Infinitesimal deformations, p. 23].
These are hyperlinks to papers, books, … and after I click them, my pdf viewer opens the file at the corresponding page.
This makes it simple to get back within the creep with the circulation learning stale notes: I don’t lose time shopping for particular definitions of ideas, I’m in a position to correct click the hyperlink and get back now heading within the true route true now.

I made it extraordinarily simple to avoid wasting these roughly references. When I acquire any doc delivery in my pdf viewer and I press Alt+F, it copies some LaTeX code relating to the sizzling page of the for the time being opened pdf. I correct press p to stick this in Vim, and the hyperlink is created. This additionally works in Firefox, setting Up a reference to the for the time being opened tab.

An instance of a reference to a web sites:

Referring to a web page

A references to a neighborhood pdf doc:

Referring to a pdf document

In the video above, I generate a reference to page 61 of ‘Generalized Advanced Geometry’, by Marco Gualtieri and I paste the generated code in Vim:

pdfref{gcg}{61}{Gualtieri}

The first argument, gcg, is an identifier I’ve assigned to this doc.
When relating to a doc for the first time,
I web requested once to place it an id, which is then ancient routinely thereafter.
The 2d argument 61 is needless to claim the page quantity, and the third one, Gualtieri, is the title of the pdf file. Here’s what will get printed after I bring together the doc. It is a long way inconspicuous ample to hasty exchange the usage of ci}, or I’m in a position to exchange the default by altering the title of the pdf.

As proven within the video, clicking on the hyperlink opens the doc on the referenced page.
Having made referencing so low effort, I have a tendency to attain it design more normally, which saves me great time in a while.

Even as you’re alive to within the technical aspect of things, click below to bear greater the section, otherwise skip to the following one. Despite every thing you would possibly maybe fetch the code and setup instructions on Github.

Technical facts: Personalized protocol handlers and DBus/gvfs

While reputedly simple, this was once surprisingly complex to pull off.
Setting Up a hyperlink in a pdf that opens a neighborhood file is not inspiring: rather then the usage of the http://route, you’d also use creep:route and this tries to delivery the file located at route. Here’s let’s express how the hyperlinks to the handwritten notes work.

This works similarly for linking to pdf recordsdata, but there would possibly be not a well-liked design to delivery a file at a fresh page. Some pdf viewer increase route#page=1, but not all of them, and mine doesn’t.
The answer? Defining a personalised protocol! I named it phd for lack of greater imagination.
Now I save a hyperlink to phd://delivery-paper?id=gcg&page=61. I configured a personalised protocol handler for going via these form of hyperlinks, which then runs pdf-viewer --page 1 route, opening the file at the appropriate page. Here, route the route of the doc that corresponds to id.

For in actuality getting the route and page quantity of the for the time being opened pdf file, I ancient DBus for my most neatly-liked pdf viewer Zathura, and I managed to web it working via gvfs for Evince, the default pdf viewer on Gnome.
The use of gvfs for that is a minute of a hack, as that is a digital file system for storing metadata on recordsdata, on this case for remembering the page you final checked out. But because Evince updates this at any time once you scroll, that is in actuality equivalent to the sizzling page. Why Evince does not increase retrieving the sizzling page via DBus is beyond me.

At this time adding novel papers

So as to add a brand novel paper to my library, I added a userscript to my browser to add a button to the ArXiv labeled ‘Add to Library’. When I click on this, the pdf file will get downloaded to my papers itemizing and named Title – Authors.pdf. Also the metadata is made Up our minds accordingly and the pdf opens in my pdf reader.




ArXiv add to library button

To delivery a paper in my library, I’m in a position to press Alt+P and fuzzy search via the checklist:

Alt-P opens a fuzzy search

If the paper doesn’t exists, it searches for it on ArXiv.

Handwritten digital notes

While the LaTeX notes are spacious for referencing in a while, I additionally take handwritten notes the usage of Xournal.
Here’s the save I first creep to if I acquire ideas, and handiest later I flip the (most likely) attention-grabbing ones into LaTeX.

I take my handwritten notes the usage of a Wacom drawing capsule (One by Wacom Medium).
I considered shopping for a capsule care for Excellent or an Android capsule, but this setup presents me most flexibility, and it is additionally extraordinarily cheap in comparison with moderately about a approaches (especially once you happen to expend the drawing capsule of your lady friend).

Xournal is a minimalist level to taking app that works properly with Wacom pills. Under you stumble on me the usage of it.

A video showing how I use Xournal

Digital notes acquire hundreds of benefits.
The page dimension is almost infinite, which in actuality helps when going via some injurious expressions. You would also place a button on the pen to delete whole strokes with out prolong, which makes it very simple to hasty redraw a letter or exchange Up some symbols. These settings are not default, you would possibly maybe fetch my configuration on Github. I additionally disable stress sensitivity as I fetch it distracts more than it does wonderful.

Reproduction and paste is additionally something you clearly don’t web with pencil and paper. Having this option makes me attain smaller steps and much less in my head, which decreases the amount of errors I bear. I merely copy the old expression, bear about a minute alterations and repeat. No longer having to rewrite it increases my patience and decreases transcription errors.

One other basic feature is rising or reducing vertical device.
I’m in a position to merely run and save more device to write down something extra or take away device to condense every thing a minute.

Conclusion

I’ve been the usage of this methodology for roughly half a 365 days now and I’m very relaxed with how things are going. Having every thing organized and being ready to serve a watch on references this straightforward makes it a long way more appetizing to attain compare. I especially love how I’m in a position to stumble on back at notes of months ago and get back within the creep with the circulation true now by clicking on the references.

By ask of of many other folks, I published the source code of about a of my lecture notes on Github, to boot to the LaTeX code for my Master’s thesis containing a form of fine photographs.

At this time, I’m engaged on a framework known as Immersion for setting Up mathematical shows.
You would also stumble on about a of the shows I’ve made with it on my talks page.
It aspects LaTeX increase, a visual editor for animating formulae, a straightforward design to animate SVG figures, presenter notes, references, and I’ve been the usage of it for all my shows for the final two years. My neutral is to bear it public within the end to future, but it indubitably collected requires moderately a minute of work to bear it user tremendous.

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About the author: Vanic
“Simplicity, patience, compassion. These three are your greatest treasures. Simple in actions and thoughts, you return to the source of being. Patient with both friends and enemies, you accord with the way things are. Compassionate toward yourself, you reconcile all beings in the world.” ― Lao Tzu, Tao Te Ching

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