94 KiB
Notes on Emacs
- Emacs Calc Tutorials
- Irreal
- Random Notes
- How to paste then copy
- Tramp and Telnet over non-standard ports
- Magit Walkthrough
- Fractals in Emacs
- Introduction to Babel
- Presentations with
org-reveal - Writing a PhD thesis with Org Mode
- Why
- What I'll talk about
- My requirements
- Moulding Org Mode for thesis writing
- Prelude: File structure
- Inserting (parts of) external files
- Keep track of references
- Include and reference figures
- Version control documents
- Support for sharing with my supervisor
- Extended search facilities
- Simple syntax for tables and equations
- Support within a proper text editor
- Shortcuts to reach my files and build the thesis
- Gnus and notmuch
- Summary of Search and Replace Commands in Emacs
Emacs Calc Tutorials
By Andrew Hyatt, found here: https://github.com/ahyatt/emacs-calc-tutorials.
LICENSE
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
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README
This repository contains tutorials about emacs calc originally writen on the Emacs community on Google+. The best way to read is probably just to open the org files directly, which Github will display correctly. If anyone would like to correct anything, add any tutorials, or request anything, the normal Github bug / request / or pull request process will work.
Algebra
I think it's time to write about one of the amazing things that calc can do: algebra!
Before we get into how to solve equations, I just want to write about on some cool things you can do with the calc display.
Let's say you have a formula you want to work with a + sqrt(b) = 5. Let's enter
that into calc:
M-x calc
'a + sqrt(b) = 5 (' starts algebraic mode).
Result:
1: a + sqrt(b) = 5
Well, that's not so surprising, that's what we put in. Kind of disappointing, though. Is that it calc? We love your brains, but what about your looks? That's important too!
d B (turn on calc-big-language mode)
Result:
___
1: a + V b = 5
Hey, that's an ASCII square-root symbol. What other cool things can you do here?
a^2
Result:
2
1: a
3:4 (enter the fraction 3/4)
Result:
3
1: -
4
Here's how to get back:
d N (calc-normal-language)
And an alternative, in which all operators are explicitly represented as functions:
1: a + sqrt(b) = 5 (re-enter the formula) d U (calc-unformatted-language) Result: 1: eq(add(a, sqrt(b)), 5)
But, wait, did you think that's all? What if you wanted to enter that equation in Mathematica?
d M (calc-mathematica-language) Result: 1: a + Sqrt[b] == 5
Ooh! Calc! Do c++ next!
d C (calc-c-language) 1: a + sqrt(b) == 5
Latex!
d L (calc-latex-language)
Result:
1: a + \sqrt{b} = 5
I could keep going, but trust me, there's more. And you can even define your own languages by constructing syntax tables, but I won't get into that now.
Bit Manipulation
Quick! What bits are set on the number 925817? What, are you going to convert it to binary and note positions of 1s? Ha! I laugh at such primitive techniques.
M-x calc 925817 b u (unpack the bits into a vector) Result 1: [0, [3 .. 6], 13, [17 .. 19]]
How many bits is that?
v # (count the number of items in a vector) Result: 1: 9
This is convenient! So yes, calc has some nice functions for binary numbers. The interesting thing about calc's binary number functions aren't just that you can do bitwise operations such as AND and OR, but it has the notion of a word size that it works with. Well, it'd have to do things like NOT.
Let's check it out. First, we'll see what the number 925817 looks like in binary.
925817 d 2 Result: 1: 2#11100010000001111001
This is nice, but it'd be better to see the whole word.
d z (Display leading zeroes) Result: 1: 2#00000000000011100010000001111001
Ah, that's more like it. The word size by default is 32 bits, as you can see. Or, wait, can you see? Hard to count. Let's verify it.
d 0 (go back to base-10 mode) 0 (we start with 0) b n (calculate the not) Result: 1: 4294967295
Now we already know how to count the 1's…
b u v # Reuslt: 1: 0000000032
Whoops, looks like we still have leading 0s. But we've confirmed it, so let's just let it go for now.
Now, let's see what the number 925817 is if you reverse all the bits. I can't take credit for this particular bit of cleverness, this technique comes straight from calc's info pages.
d z (get rid of leading 0s) 925817 b u (unpack into a vector) 31 <tab> - (tranform each bit position by subtracting it from 31, the tab just switches the items around on the stack) b p (repack the vector) Result: 1: 2651090944
Woody Allen once praised New York by saying how he loves that you can go to Chinatown and eat a crab in the middle of the night, but in reality what kind of crazy person would need to do that? I feel the same way about all these features. Will I really ever need to reverse the bits of a number? Not sure, but I do love the way that calc has me covered for whatever I really want to do.
By the way, want to go to 64-bit mode? Just change the word size.
b w 64 (change the word size to 64)
Now let's reverse the bits of 925817 again to see what we get. It'll be amusingly huge!
925817 b u (unpack into a vector) 63 <tab> - (tranform each number by subtracting it from 31, the tab just switches the items around on the stack) b p (repack the vector) Result: 1: 11386348903201767424
Ah, that's what it was. I was just about to give that same answer myself.
One more cool thing. If you give a negative word size, calc will interpret binary number as 2's complement numbers. For example:
b w 32 (set the word size to 32) 2 (just to choose a simple number) b n (bitwise not) Result: 1: 4294967293
And now with 2's complement!
b w -32 (set the word size to -32, in other words, a 2's complement version of 32 bit) 2 b n Result: 1: -3
Hope this helps you twiddle those bits in all the ways that make you happy.
Calculus
Quick, integrate 2x + sin(y)! Well, frankly, it's been so long since I've done
calculus by hand I can't remember anymore. Well, knowing calculus is good, but
knowing calc is even more useful!
M-x calc '2x + sin(y) (The single quote enters algebraic mode) a i y (Calculate the integral with respect to y) Result 1: 2 x y - 180 cos(y) / pi
You can also integrate over specific regions by using C-u a i, whereupon it will prompt you for the start and end point of the integration.
As the manual mentions, the results are often not as simplified as they could be. Calc is impressive, but it isn't as sophisticated as Mathematica.
An example of some issues are if we just take the derivative of the integral we just calculated. We should get back to our original formula.
a d y (Calculate the derivative with respect to y) Result: 1: 2 x + 3.14159265358 sin(y) / pi
Clearly this should be 2x + sin(y), but calc may have made an error.
OK, let's make calc do something cool so we can forget this unfortunate incident. Hey, how about making a Taylor series of a function?
'2x + sin(y) (re-enter the formula) a t y 6 (Calculate the Taylor series of a term, over y, for 6 terms) Result: 1: 2 x + y - y^3 / 6 + y^5 / 120 - y^7 / 5040 + y^9 / 362880
This isn't a bad approximation, see Google’s answer for comparison.
So, yes, calc can do college-level math, even if the answers aren't perfectly simplified. It's not Mathematica, but it is free and integrated into emacs, so it's definitely nice to have.
Date
Ever want to know how many seconds old David Hasselhoff is? calc can do many things, but it doesn't know much about Hasselhoff, so first I do a query on Google for [david hasselhoff]. I get a knowledge card on the right saying he was born July 17, 1952. It doesn't give a time, so we'll just assume it was at midnight.
M-x calc t N (put the current time on the stack) '<Jul 17, 1952> (press ' to enter algebraic mode, then you input the date). - (subtract the two to get the number of days David has been alive) 24 (we're going to multiply by 24, the number of hours in a day) 60 (the number of minutes in an hour) 60 (the number of seconds in a minute) * * * Final result: 1: 1910255938.01
There you have it, he's… wait, how many seconds? That's really hard to read.
Back into calc!
d g (toggle digit grouping) The final final result: 1: 1,910,255,938.01
Ah, that's a 1.9 billion seconds. Sweet!
Financial.org
I recently chatted with emacspeak creator T.V. Raman, and told him I was writing a series of short tutorials about calc. He is really a calc fanatic, and told me a story in which he astounded a loan officer by calculating scheduled loan payments with just a few keystrokes in calc. Raman is living proof that calc is a useful tool for so many situations, and it always pays to have emacs running. He also mentioned that he found the explanation in the calc tutorial about the financial functions to be the clearest he's ever read.
So, yes, calc can do finance. Let's say that you were sitting in front of a loan officer, and she told you that for your loan of $500,000, you need to pay in 30 installments with a 5% interest rate. How much do you need to pay each month? Wait a second! Stop right there, loan officer! I have calc!
M-x calc 500000 (the amount of the loan) 30 (the number of payments) '5% (equivalent to typing 0.05) b M (calc-fin-pmt, computing the amount of periodic payments to amortize a loan) Result: 1: 25,000
OK, but that's a bit obvious, since $25,000 is just 5% of $500,000. If the number of payments was much smaller, we'd get a larger value. Let's take another question: if you wanted to only pay $10,000 in each installment? How many installments would it take to pay off the loan?
'5% 10000 (the payment we want to make) 500000 (the loan amount) b # (calc-fin-nper, calculate the number of installments needed) Result 1: nper(0.05, 10,000, 500,000)
What? Oh, I see, I also go the message: "Payment too small to cover interest rate: 10000". Oh, right, 5% of $500,000 is already $25,000, so we'd never pay it off at that rate. What if we payed $50,000 instead?
'5% 50000 (the payment we want to make) 500000 (the loan amount) b # Result: 1: 14.2066908
So, it would take just over 14 payments to pay off the loan.
OK, one more cool one: Let's say you meet an investment banker who gives you the following deal. I've got a investment for you, she says. Just give me $100,000 and I'll give you $10,000 at the end of each year for the next 12 years. Assuming the interest rate will stay at 3% for the next 12 years. Is it a good deal?
Hey, what are you asking me for? I have no idea! Calc knows, though, because it can tell you the break-even point for the cost of an investment that gives periodic payments.
'3% (the interest rate) 12 (the number of payments) 10000 (the payment you get each time) b P (calc-fin-pv, calculate the "present value" of the investment, the break-even point for the investment) Result: 1: 99,540.0399357
In other words, the break-even point for the initial cost is $99,540. If the investment costs more than this, it's no good at that assumed interest rate. Better reject the deal. Trust calc more than any investment banker.
This is just a small sampling of some of the financial calculations that calc can perform. The next time you are making an investment, fire up calc. You'll not only have confidence in the deal, you may just amaze someone with the power of emacs, just like T.V. Raman did.
Fractional Arithmetic
This one is pretty short, but it's about one of my favorite features of calc: the ability to handle fractions as fractions instead of rendering them as real numbers.
Quick, what's 5/8 + 9/21?
Um, ok… better start multiplying things… wait, let's just tell calc to do it.
M-x calc 5:8 (this is how you enter a fraction) 9:21 + Result: 1: 59/56
So easy! If we want to convert it to a float you can do this:
c f (convert to float) Result: 1: 1.05357142857*10.^0
And if you want it back as a fraction, then just do:
c F (convert to fraction) Result: 1: 59/56
That's so awesome!
You could also enter fractions this way:
m f (set fraction mode, integer division will result in fractions) 5 8 / Result: 1: 5/8
Now you can live in the nice world of fractions as much as you like. It's a nice world, full of pleasant to look at integers taking up little horizontal space
HEX
OK, seems like there's interest in some quick calc tips. Here's today's:
How to convert decimal to hexidecimal. Let's say you want to convert number 12345 to hex.
M-x calc d 6 (sets the number radix to 16, meaning all output will be in hex) 10#12345 (inputs the number 12345 in base 10) The output reads: 1: 16#3039
The answer is therefore 0x3039.
And then you can do a d 0 to set the number radix back to normal, base 10.
Here's how to do the other way. Let's convert 0xABCDEF to base 10.
M-x calc 16#ABCDEF The output reads: 1: 11259375
More on Algebra
Jim is 42 years old. He has one brother, and their total age is 100. What is the brother's age? OK, this isn't a very hard problem, but let's just introduce calc algebra by solving it.
M-x calc
'42 + x = 100 (' to enter algebraic input)
a S x (solve for x)
Result:
1: x = 58
Let's make this harder. Jim and Dan's ages sum to 100. Jim is 5 years older than Dan. How old are they?
'[j + d = 100, d + 5 = j] a S j,d Result: 1: [j = 52.5, d = 47.5]
Nice!
And of course it can give you more than just numerical solutions:
'sin(x) + tan(y) = pi / 2 a S y (solve for y) Result: 1: y = arctan(pi / 2 - sin(x))
Sometimes there are more than one solution. For example:
'x^2 = 25 a S x Result: 1: x = 5
Wait, what happened to -5! That's a valid solution, why didn't calc tell us about it? What's happening here is that calc is telling us about the first valid thing it can find, which is basically how it operates. But you can always get everything:
'x^2 = 25 a P x (find the polynomial solutions) Result: 1: [5, -5]
Sometimes there aren't a finite number of results because you aren't dealing with polynomials. You can just get a generalized solution:
'sin(x)^2 = 25 H a S x (solve for x, giving the generalized solution) Result: 1: x = arcsin(5 s1) (-1)^n1 + 180 n1
This uses the calc notation n1, which you just means any integer. You can also
see another notation s1 which means any sign. In this case 5 s1 means that that
number can be 5 or -5.
Looking at how awesome calc is, it's just a shame I never knew about it in high school…
Pi and Precision
This one's about p and P and mostly about pi.
First, let's pi it up:
M-x calc P (this gives you pi) Result: 1: 3.14159265359
Well, I guess that's a reasonable pi. But, c'mon, this is calc. Can't we get a bit more digits? How about 100?
p 100 (sets precisions to 100) P (need to ask calc again for pi, it doesn't recalculate) Result: 1: 3.141592653589793238462643383279502884197169399375105820974944592307816406286208998628034825342117068
Well, but actually evaluating it robs it of its never-ending charm. Let's just use it as a variable. How about calculating the area of a circle with a 5 km radius?
'5000 m 2 ^ 'pi (enter pi as a variable) * We get: 1: 25000000 m^2 pi
Yeah, sure that’s what I said I wanted, but I’ve changed my mind - now I want a number.
= 1: 78539816.3397448309615660845819875721049292349843776455243736148076954101571552249657008706335529267 m^2
Whoops, looked like I forgot to set the precision back to normal. And I can't read this. Let's make it a bit nicer.
Control-_ (normal emacs undo) p 7 d g (turn digit grouping on) = Result: 1: 7.853983e7 m^2
Oh, that's because I didn't have enough precision to render it without resorting to scientific notation. Let's just bump the precision up again.
Control-_ (undo, since we have to redo the pi conversion with more precision) p 10 = Result: 1: 78,539,816.35 m^2
Ah, that's better.
Random
I use calc whenever I need a random number. The interface is easy and the random numbers are (supposedly) high quality.
So, let's start with something simple: A random number between 0 and 100:
M-x calc 100 (the upper bound, all values will be between 0 and this) k r (creates a random number between 0 and the number on the stack) Result: 1: 66 (of course, yours will be different)
I want another one!
k a (creates another number with the same upper bound as the last)
Now that I’ve had a taste of that sweet sweet randomness, I want a vector of 50!
100 (the upper bound, again) 50 (the number to generate) k h (generate a vector of 50 random numbers between 0 and 100) 1: [60, 72, 61, 74, 77, 97, 10, 90, 8, 29, 82, 81, 51, 58, 7, 88, 99, 1, 37, 89, 93, 84, 52, 94, 2, 35, 5, 48, 87, 47, 14, 6, 79, 18, 67, 76, 70, 9, 43, 65, 69, 23, 55, 11, 53, 78, 50, 30, 13, 42]
OK, that's nice. But how about a number between 0 and 1?
1.0 k r Result: 1: 0.636988102539
OK, how about number between -50 and 50? For that we need to use what calc calls an interval form:
[ (Starts interval form) 50 (You can't just type -50 in calc) n (negate, givint -50) .. (the middle part of the interval form) 50] (closing the interval form)
What you see now in calc is:
[-50 .. 50]
And you could have just typed it in with:
'[-50 .. 50]
which would be a lot easier, really.
k r
This produces a random number from the bounds of the interval, in this case both
-50 and 50 are possible, if you wanted them to be exlusive bounds, you'd use the
form (-50 .. 50).
Finally, you can re-arrange a list:
'[1 2 3 4] (our starting vector) -1 (signals to use the vector above, could also be the size of the vector) k h Result: 1: [3, 1, 4, 2]
But k a will not give you more variants, unfortunately.
Strings
Did you know you could work with strings in calc? For an example, let's find out what "Hello world" is in binary:
M-x calc d 2 (change the to binary mode) "Hello world (Enter the string "Hello world" which turns into a vector of numbers) Result: 1: [2#1001000, 2#1100101, 2#1101100, 2#1101100, 2#1101111, 2#100000, 2#1110111, 2#1101111, 2#1110010, 2#1101100, 2#1100100]
And similarly, we can convert back. If someone gave you the binary number:
01001000011011110110110001100001 and asked what the string was, I'd have no
idea… but calc knows:
d " (changes to string mode) C-x b scratch (whaaa, leave calc?) 01001000011011110110110001100001 (enter the number we're parsing) C-a (go to the start of the line) C-x ( (start a macro) 2# (prefix the number with a binary indicator) C-u 8 C-f (Jump forward 8 characters) <space> (insert a space to separate the numbers) C-x ) (end the macro) C-x e (repeat the macro) e e (repeat twice twice more) C-<space> (set mark) C-a (goto beginning of line) C-x <asterisk> g (copy region into calc) Result: 1: "Hola"
And there you have it! Maybe there is an easier way to convert from the giant binary number to a vector of bytes, but I don't know it yet.
Time
Hey, what's the time? It's time to get ill! No, actually I meant the time in seconds since the epoch. Yesterday I went over doing math with time, which is fun but not something I use everyday. Much more useful is converting to and from Unix timestamps.
Let's start by getting the time now in seconds since the epoch:
M-x calc t N (get the time now) t U (convert the time to seconds since the epoch) Result: 1: 1359424746
Oh, and you want to insert that into your last used buffer?
y (that doesn't mean "yes", that means yank into the last buffer)
Done! Just to be complete, let's convert another date we have to input:
'<12:00pm Jul 4, 1776> (single quote to enter algebraic mode, then the date) t U (converts the time to seconds since the epoch)
But wait, what will happen? This is considerably before the epoch.
Result: 1: -6106003200
Oh calc, you never let me down.
Let's do the other way. Remember the Billenium?
1e9 t U (converts the time in seconds since the epoch to text) Result: 1: <9:46:40pm Sat Sep 8, 2001>
Wow, I never realized how close the Billenium was to September 11th. Kind of spooky…
Unit Conversion
You load 16 tons, and what do you get? I mean, in kilograms.
M-x calc
' 16 tons (' to enter algebraic mode, so you can type out the units)
u c kg (u c for "unit convert", and kg being the target unit).
Result:
1: 14514.95584 kg
Calc treats units as special. If you added something, such as:
3 + Result: 1: 14514.95584 kg + 3
But you can remove the units from the above using:
u r (remove units) Result: 1: 14517.95584
OK, that's all well and good. But I've always wondered how much is Grandpa Simpson's gas mileage when he said "My car gets 40 rods to the hogshead and that's the way I likes it."
For that, we need to define the units. Calc knows about a lot of units, but maybe not the rod and hogshead. In fact, in the calc info pages, defining what a "rod" is the example for how to define your own units. Let's get started!
'16 ft (The equivalent to one rod) u d rod Rod (defines a new unit rod, with optional description "Rod")
Now a hogshead is a unit of measurement that varies by what liquid it contains. I don't know what the unit is for gasoline, but let's use sherry as a substitute, in which a hogshead is 245 liters.
'245 liters u d hogshead (don't bother with a description this time) '40 rod '1 hogshead /
Wait, what units should we be using?
u v (show the units table, a handy table of all units) u c mi/gal (the units come from the unit table) Result: 1: 1.87280731429e-3 mi / gal
But wait, we can do better. Why upgrade this measure to something that isn't even standard? Miles per gallon is just a bit better than rods per hogshead (in fact, that was what the original joke was about).
u c si (convert everything to scientific units) Result: 1: 796.212244896 / m^2
Not that I understand this number, but at least in miles per gallon, I can see that that's not such great fuel economy, but what you do expect from Grandpa?
OK, one more cool thing, then I'm out of here. Calc can split up numbers into multiple units. Here's 42 inches in feet and inches:
'42 in u c ft+in (Convert to a mixture of feet and inches) Result: 1: 3 ft + 6. in
Calc, you're sooo coool!
Irreal
A random collection of notes from Irreal's Blog.
Insert URL from Safari IRREAL NOTE
CLOCK: [2018-08-04 Sat 17:44]–[2018-08-04 Sat 17:45] => 0:01
Responding to yesterday's post, Sacha asks if I could post the code for
jcs-insert-url for others to use. I thought I'd already done that but
apparently not. That's probably because except for the part identical to
jcs-get-link, which I did write about, it's pretty trivial. In any event,
here it is:
(defun jcs-insert-url ()
"Insert URL of current browser page into Emacs buffer."
(interactive)
(insert (jcs-retrieve-url)))
The jcs-retrieve-url function does all the work, of course, and is
just the code that I abstracted out of jcs-get-link to actually
retrieve the URL from Safari:
(defun jcs-retrieve-url ()
"Retrieve the URL of the current Safari page as a string."
(org-trim (shell-command-to-string
"osascript -e 'tell application \"Safari\" to return URL of document 1'")))One obvious problem with all this is that it works only for macOS. Not to despair, though, because in the comments to the original post, Brad Collins suggests a solution that uses grab-x-link to do the same thing for FireFox and Chrome on other systems. Be sure to read Brad's comment because there is—or at least was—an issue with the MELPA version.
Finally, Sacha took the part about looking for ways to make your workflow easier
seriously and came up with a bit of Elisp to insert a function definition at the
point, regardless of where it's defined. That's very handy and I immediately
stole her code and used it to insert the two functions above. My old method was
to switch to init.el, find the function, copy it to the kill ring, switch back
to the original buffer, add the source block fences, and insert the code between
them. Sacha's code did all of that for me and I didn't even have to leave my
current buffer. That's splendid. If you find yourself having to add function
definitions to your text, be sure to read Sacha's post. It will save you a lot
of time.
Calc for Programmers IRREAL NOTE
CLOCK: [2018-08-05 Sun 10:04]–[2018-08-05 Sun 10:05] => 0:01
After writing about Florian Adamsky's post on acronyms in AUCTeX, I snooped around on his site and came across a nice post on Emacs Calc from a programmer's and computer scientist's point of view. As regular readers know, I've been working to increase my calc-fu lately so I read the post with interest.
Adamsky demonstrates some of the Calc functions that are useful to programmers and computer scientists. This includes such things as entering and displaying numbers in various radixes and performing the standard logical operations on (the usually binary representation of) numbers. He even shows how to add a new “units” representation to Calc—in this case bits/bytes/bits per second.
Calc is a large subsystem and famously hard to master but worth the effort. It's been described as a “poor man's Mathematica.” It's not nearly as powerful as Mathematica, of course, but it's surprising how many things it can do. If you're a programmer/computer scientist and an Emacs user you should spend a little time investigating Calc. It really can make your life easier. An easy way to get started is to read Adamsky's post. It covers only a small slice of Calc but will give you an idea of its power.
Parsing with Org-Element IRREAL NOTE
The other day, I saw this query on the reddit Emacs subreddit. I already have solutions for this type of problem but I'm always interested in the how people use Org mode to record and report data so I followed the link that primitiveinds provided for his solution to generating time reports.
Even if, like me, you already have your time tracking and reporting needs under control, primitiveinds' solution is worth looking at for its own sake. It works by looking for CLOCK entries in an Org buffer and accumulating the relevant information in the CLOCK line as well data about the associated task. That might seem like it would require routine but tedious text manipulation but primitiveinds leverages the org-element functionality to easily handle the task.
He starts by calling org-element-parse-buffer to generate a tree
representation of the Org buffer. Then he uses org-element-map to examine each
CLOCK element (and only CLOCK elements) to extract the necessary
information. It's a great technique that can easily be adapted for other parsing
of Org data. The code that primitiveinds presents is easy to follow and he
provides a nice explanation of what it's doing.
If you need to programmatically examine Org data for further processing, you should take a look at primitiveinds' post. It's definitely worth a read.
The relevant code:
(nconc
'(("date" "project" "hours" "task"))
'(hline)
(let ((ast (org-element-parse-buffer 'element)))
(org-element-map ast 'clock
(lambda (x)
(let* ((val (org-element-property :value x))
(task (org-element-property :parent (org-element-property :parent x))))
`(,(let ((year (org-element-property :year-start val))
(month (calendar-month-name
(org-element-property :month-start val)))
(day (org-element-property :day-start val)))
;; (insert (org-element-property :raw-value val))
(format "%s %s, %s" month day year))
,(org-element-property :PROJECT task)
,(org-element-property :duration x)
,(org-element-property :title task)
)))))
'(hline)
'(("" "total:" ":=vsum(@2..@-1);T" "")))Emacs Lisp Byte-Code NOTE
Very few Emacs users—no matter how advanced—ever need to worry about the specifics of the Elisp bytecode, or even, for that matter, that it exists. Still, as guys like Chris Wellons have shown, it can sometimes be useful to have a basic understanding of the bytecodes.
R Bernstein has put together a comprehensive, book-length documentation on Elisp bytecodes. After a short introduction, the documentation considers the bytecode environment including the compiler, interpreter, and bytecode optimization. Then there's a long section on the individual bytecode instructions.
Finally, there are sections on the changes in bytecodes between Emacs versions, a table of opcodes, and a reference section. There's also a GitHub repository of the document source.
As I said, you probably will never need this but if you do, you'll be very glad to have Bernstein's documentation. It's another example of the vibrant Emacs community.
Formatting Tables IRREAL NOTE
If you're like me, you automatically think of the Org mode table editor (or
Orgtbl minor mode) when you think of tables in Emacs. It's hard to beat that
functionality and Orgtbl mode makes it available everywhere in Emacs, even if
you're not in an Org buffer. Sometimes, though, you'd like to have special
formatting for some or all of the table. That's where delim-col comes in.
Delim-col is built-in Emacs functionality that allows you to do things like
adjust what string separates the columns, add a beginning or ending string to
each item, add an ending string for each row, and adjust the padding in the
table. It can be really handy for copying and pasting and then reformatting
tables from an external source.
I didn't know about delim-col until I read about it over at Emacs Notes, where
you'll find a good explanation of the facility and what it can do. The Emacs
Notes post also offers at bit of Elisp to make choosing the strings and
delimiters a bit easier. By default you have to set them using a series of
setq statements if you want something different from the built-in choices. The
Emacs Notes codes arranges for you to be prompted for the values.
You probably won't need the delim-col functionality very often but when you do
it's much easier than using something like a keyboard macro. Take a look at the
post and see if you don't agree.
Inserting a function definition CHUA NOTE
CLOCK: [2018-08-04 Sat 17:40]–[2018-08-04 Sat 17:42] => 0:02
While nudging jcs to add a definition of jcs-insert-url to the blog post about
Making Things Easier, I realized it might be handy to have a quick function for
inserting a function definition without thinking about where it's defined. This
tries to use the definition from the source, and it can fall back to using the
stored function definition if necessary. There's probably a better way to do
this, but this was small and fun to write. =)
Naturally, I used it to insert itself:
(defun my/org-insert-defun (function)
"Inserts an Org source block with the definition for FUNCTION."
(interactive (find-function-read))
(let* ((buffer-point (condition-case nil
(find-definition-noselect function nil)
(error nil)))
(new-buf (car buffer-point))
(new-point (cdr buffer-point))
definition)
(if buffer-point
(with-current-buffer new-buf ;; Try to get original definition
(save-excursion
(goto-char new-point)
(setq definition (buffer-substring-no-properties
(point)
(save-excursion (end-of-defun) (point))))))
;; Fallback: Print function definition
(setq definition (concat (prin1-to-string
(symbol-function function))
"\n")))
(insert "#+begin_src emacs-lisp\n" definition "#+end_src\n")))Org Mode Cookbook NOTE
CLOCK: [2018-08-04 Sat 12:51]–[2018-08-04 Sat 12:54] => 0:03
Way back in 2014, I posted about Eric Neilsen's excellent Emacs org-mode examples and cookbook. I recently came across a reference to it and was reminded what a great resource it is. It's easy to browse through and just read one or two entries when you have time. In skimming through it, I learned—or perhaps relearned—how to insert in-line calculations in a document.
As I wrote in the original post, Neilsen is a researcher and his cookbook is oriented at using Org mode to produce documents of various types. Still, that covers a lot of territory and there are many good examples of powerful Org mode use cases in it. The Document has moved or, really, taken up a second residence. It was originally hosted at Fermilab, where Neilsen works, and it's still there but it's also available at his own site. The two documents are identical so it doesn't matter if you use the new link or the original one pointing to FNAL.
If you're an Org user, especially if you use Org to produce documents, you should take a look at Neilsen's cookbook and bookmark it for future use.
Random Notes
How to paste then copy NOTE
CLOCK: [2018-08-11 Sat 21:47]–[2018-08-11 Sat 21:48] => 0:01
Question: how to set a mark such that all subsequent copy operations move their text to that exact mark.
Answer: use cua-selection-mode! See
https://www.reddit.com/r/emacs/comments/8ekz0u/how_to_pastethencopy/.
Update: turns out it doesn’t work so well, disabled it again.
Tramp and Telnet over non-standard ports NOTE
Syntax: /telnet:HOST#PORT:, works also with other protocols.
Magit Walkthrough NOTE
Fractals in Emacs NOTE
CLOCK: [2018-08-04 Sat 13:01]–[2018-08-04 Sat 13:03] => 0:02
From https://nullprogram.com/blog/2012/09/14/
(defun sierpinski (s)
(pop-to-buffer (get-buffer-create "*sierpinski*"))
(fundamental-mode) (erase-buffer)
(labels ((fill-p (x y)
(cond ((or (zerop x) (zerop y)) "0")
((and (= 1 (mod x 3)) (= 1 (mod y 3))) "1")
(t (fill-p (/ x 3) (/ y 3))))))
(insert (format "P1\n%d %d\n" s s))
(dotimes (y s) (dotimes (x s) (insert (fill-p x y) " "))))
(image-mode))
(defun mandelbrot ()
(pop-to-buffer (get-buffer-create "*mandelbrot*"))
(let ((w 400) (h 300) (d 32))
(fundamental-mode) (erase-buffer)
(set-buffer-multibyte nil)
(insert (format "P6\n%d %d\n255\n" w h))
(dotimes (y h)
(dotimes (x w)
(let* ((cx (* 1.5 (/ (- x (/ w 1.45)) w 0.45)))
(cy (* 1.5 (/ (- y (/ h 2.0)) h 0.5)))
(zr 0) (zi 0)
(v (dotimes (i d d)
(if (> (+ (* zr zr) (* zi zi)) 4) (return i)
(psetq zr (+ (* zr zr) (- (* zi zi)) cx)
zi (+ (* (* zr zi) 2) cy))))))
(insert-char (floor (* 256 (/ v 1.0 d))) 3))))
(image-mode)))Introduction to Babel
Tutorial from http://orgmode.org/worg/org-contrib/babel/intro.html
Source Code Execution
(print "Hello, There!")Hello, There!
echo "This file takes up `du -h emacs-org-babel-tutorial.org | sed 's/\([0-9k]*\)[ ]*emacs-org-babel-tutorial.org/\1/'`"This file takes up 4.0K
words <- tolower(scan("emacs-org-babel-tutorial.org", what="", na.strings=c("|",":")))
t(sort(table(words[nchar(words) > 3]), decreasing=TRUE)[1:10])| #+begin_src | #+end_src | #+results: | date | plus | today's | :results | hello, | import | is") |
|---|---|---|---|---|---|---|---|---|---|
| 5 | 5 | 4 | 3 | 3 | 3 | 2 | 2 | 2 | 2 |
Capturing the Results of Code Evaluation
import time
print("Hello, today's date is %s" % time.ctime())
print("Two plus two is")
return 2 + 24
import time
print("Hello, today's date is %s" % time.ctime())
print("Two plus two is")
2 + 2Hello, today's date is Sun Jun 26 16:04:36 2016 Two plus two is
Session-based Evaluation
Have a look into Emacs Speaks Statistics
Arguments to Code Blocks
return x*x36
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
| 2 | 4 | 6 | 8 | 10 | 12 | 14 | 16 | 18 | 20 |
(defun fibonacci (n)
(if (or (= n 0) (= n 1))
n
(+ (fibonacci (- n 1))
(fibonacci (- n 2)))))
(mapcar (lambda (row)
(mapcar #'fibonacci row))
fib-inputs)| 1 | 1 | 2 | 3 | 5 | 8 | 13 | 21 | 34 | 55 |
| 1 | 3 | 8 | 21 | 55 | 144 | 377 | 987 | 2584 | 6765 |
In-line Code Blocks
In-line code can be call without header arguments (like so:
datereturn 10 + 10Code Block Body Expansion
Preview: C-c C-v v, bound to org-babel-expand-src-block
| username | john-doe |
| password | abc123 |
(setq my-special-username (first (first data)))
(setq my-special-password (first (second data)))A Meta-programming Language for Org-mode
cd ~ && du -sc * | grep -v total| 538604 | Desktop |
| 77332656 | Documents |
| 1206668 | |
| 8 | News |
pie(dirs[,1], labels = dirs[,2])
Note: the syntax #+name: directory-pie-chart(dirs=directories) did not work.
Using Code Blocks in Org Tables
Example 1: Data Summaries Using R
runif(n=5, min=0, max=1) colMeans(x)| mean |
|---|
| 0.574235895462334 |
Example 2: Babel Test Suite
No notes
The Library of Babel
Does not do what I expected …
Literate Programming
Tangling with C-c C-v t.
Presentations with org-reveal
Website: https://github.com/yjwen/org-reveal
Sample:
#+title: Foo!
#+author: bar
#+options: author:t toc:t num:nil date:nil timestamp:nil
#+reveal_theme: sky
* Slide 1
* Slide 2
** Subslide 1
** Subslide 2
- Item 1
- Item 2
| a | b | d |
|---+---+---|
| 1 | 2 | 3 |
* Slide 3Writing a PhD thesis with Org Mode
TLDR: I started using Emacs about 3 years ago. I couldn't be more grateful to have seen the light, and to have been rescued from the darkness of Windoze, Goggle and/or friends. After enlightenment, I've taken upon myself the task of customising an environment to write my PhD thesis with Org Mode.*
Why
Post created in response to the current thread in r/emacs on thesis writing with Org Mode.\\ I see most people's reason to avoid Org mode for scientific writing is the fact that supervisors or co-authors use Mic. Word. I'll try to argue that that's not enough reason to accept subpar tools.
What I'll talk about
I'll mention a bit of my motivations, and then I'll discuss how to make use of (mostly) built in Org functionality such as tagging, export, setupfiles and includes, reference management, keyboard shortcuts and advanced searching; all with the purpose of building a useful thesis writing environment. Readers should have a minimum knowledge of Org mode, the Org export system and LaTeX.
My requirements
Here in the Netherlands, most PhD thesis consist of an introduction, 3 to 4 research chapters (as submitted for publication), a summary, bibliography and appendices. What this means for me is that my writing environment has to necessarily satisfy the following minimum requirements:
- Inclusion of (parts of) external files
- Keeping track of references
- Include and reference figures
- Version control documents
- Support for sharing with my supervisor in whatever format he wants
Failure to comply with any of these means the editor is unfit for purpose#fn.1”>1. Unfortunately, this set of requirements are not seamlessly satisfied by likes of Mic. Word or G. Docs. I reckon they can probably be configured to satisfy them, but why bother.
Additionally, a PhD thesis writing environment should also provide the following features:
- Extended searching facilities for both text and references
- Simple syntax for tables and equations
- Support within a proper text editor
- Shortcuts to reach my files and build the thesis
To the best of my knowledge, only Emacs with Org Mode + ox-latex provide all of these out of the box.
Moulding Org Mode for thesis writing
Most of my inspiration comes from reading Kitchin's blogs and code, and reading the Org Mode documentation, mailing list and Emacs Stack Exchange. Here' I'll go one by one through all of the requirements listed above, and how to deal with them.
Prelude: File structure
I have a main thesis.org document, with latex heading declarations and a commented setup file. I also have research.org files, in different directories, with their own latex heading declarations and commented setup files.
The first lines of thesis.org look like the following:
# -*- mode: org; org-latex-title-command: ""; org-latex-toc-command: "" -*-
#+TITLE: Thesis Title
#+LATEX_CLASS: mimosis
# Setupfile with #+LATEX_HEADER, #+OPTIONS and explanations
#+SETUPFILE: thesis.setup
#+LATEX_HEADER: \KOMAoptions{fontsize=12pt,headings=small}
#+LATEX_HEADER: \bibliography{~/Papers/bibtex/Publications}
#+EXCLUDE_TAGS: journal noexport
* Frontmatter :ignore:
#+LATEX: \frontmatter
#+INCLUDE: ./Title.org
#+LATEX: \tableofcontents
* Mainmatter :ignore:
#+LATEX: \mainmatter
* Introduction
* Research 1
#+INCLUDE: "../research1/research.org::*Abstract" :only-contents t
Some stuff.
#+INCLUDE: "../research1/research.org" :lines "5-"
* Research 2
...And the first lines and structure overview of the multiple research.org files:
#+TITLE: Research
#+LATEX_CLASS: elsarticle
#+LATEX_CLASS_OPTIONS: [authoryear,preprint,11pt]
#+SETUPFILE: paper.setup
#+LATEX_HEADER:\bibliography{./ref/Publications-research}
#+EXCLUDE_TAGS: thesis noexport
* Frontmatter :ignore:journal:
#+LATEX: \begin{frontmatter}
** Author List :ignore: Abstract :ignore: Keywords :ignore:
#+LATEX: \end{frontmatter}
* Introduction
...Inserting (parts of) external files
I write my research chapters with LaTeX classes targeting the journal's
format. That means that a research chapter may be written with the elsarticle
class, whereas the thesis as a whole is written with the mimosis class, a
derivative of KOMA scrbook. Here's the class configuration for both:
(add-to-list 'org-latex-classes
'("elsarticle"
"\\documentclass{elsarticle}
[NO-DEFAULT-PACKAGES]
[PACKAGES]
[EXTRA]"
("\\section{%s}"
. "\\section*{%s}") ("\\subsection{%s}"
. "\\subsection*{%s}") ("\\subsubsection{%s}"
. "\\subsubsection*{%s}") ("\\paragraph{%s}"
. "\\paragraph*{%s}") ("\\subparagraph{%s}"
. "\\subparagraph*{%s}")))
(add-to-list 'org-latex-classes
'("mimosis"
"\\documentclass{mimosis}
[NO-DEFAULT-PACKAGES]
[PACKAGES]
[EXTRA]
\\newcommand{\\mboxparagraph}[1]{\\paragraph{#1}\\mbox{}\\\\}
\\newcommand{\\mboxsubparagraph}[1]{\\subparagraph{#1}\\mbox{}\\\\}"
("\\chapter{%s}" . "\\chapter*{%s}")
("\\section{%s}"
. "\\section*{%s}") ("\\subsection{%s}"
. "\\subsection*{%s}") ("\\subsubsection{%s}"
. "\\subsubsection*{%s}") ("\\mboxparagraph{%s}"
. "\\mboxparagraph*{%s}") ("\\mboxsubparagraph{%s}"
. "\\mboxsubparagraph*{%s}")))
Research chapters print the bibliography on their own, and they may contain
acknowledgements that shouldn't be present in the middle of the thesis, so they
should be excluded. In other to insert research chapters into my thesis, I use
Org's #+INCLUDE derivative:
#+INCLUDE: file.orgIn order to not include the some parts of the file, i.e., to exclude the title, setupfile and headers, I narrow down the lines:
# Include line 5 until the end of the file
#+INCLUDE: file.org :lines 5-
In order to exclude parts of the file, I tag research chapter headings that are
only meant for publication with a :journal: tag (such as the bibliography or
acknowledgements). This way they are automatically excluded from the thesis (see
the #+EXCLUDE_TAGS: derivative in the thesis.org file). Also, I could have
thesis specific content in the research.org document tagged with :thesis:,
and it would be excluded in the research.org export, but I currently don't
have any.
Now, the most important piece of advice I can give anyone is to learn how to
use tags, EXCLUDE_TAGS and the org-plus-contributions ignore tag. With the
ignore tag we separate the structuring of the text as a physical document from
the structuring of the text as a semantic unity. This allows an extremely fine
control over pieces of text to include into another document. For example, in a
research chapter written with the elsarticle class, the abstract has to be
included in the Frontmatter. By tagging a headline as follows:
** Abstract :ignore:
I can write the research abstract in it's own heading, pretend that the heading
itself does not exist (so it does not trigger /begin{document}), only its
contents, and then include the contents in the thesis in an arbitrary location:
# in thesis.org
#+INCLUDE: "research.org::*Abstract" :only-contents t
The :ignore: tag is one of the best Org mode features, in my opinion. It's
key to my workflow, and a shame to see it's not a part of Org core, but rather a
contribution to be found in ox-extra.el. To activate it, add the following to
your init:
(require 'ox-extra)
(ox-extras-activate '(ignore-headlines))The realisation that it's possible to have such fine control over where to include or exclude pieces of text opens the door to all sort of interesting experiments: putting figures and captions directly into beamer or org-reveal presentations, creating conference posters, writing blog posts, etc.
Keep track of references
For backwards compatibility I still use Mendeley to track literature. I export
bibtex files for each research project individually, and also a master bibtex
for use in the thesis. These documents are saved to ~/Papers/bibtex/, but for
the research chapters, I keep local copies under
./ref/Publications-research.bib.\\ To insert citations, I use org-ref. It's
documentation says it all. After setting up local bibliography files with the
derivative #+BIBLIOGRAPHY, press C-c ] to see a list of publications and
insert them in place. I also prefer to have parencite citations instead of
cite, because they work nicely with BibLaTeX. My setup for org-ref:
(with-eval-after-load 'org-ref ;; see org-ref for use of these variables
(setq org-ref-default-bibliography '("~/Papers/bibtex/Publications.bib")
org-ref-pdf-directory "~/Papers/MendeleyDesktop/"
org-ref-get-pdf-filename-function 'org-ref-get-mendeley-filename
bibtex-completion-pdf-field "file" org-latex-prefer-user-labels t
org-ref-default-citation-link "parencite"
;; bibtex-dialect 'biblatex
)
(defun org-ref-open-pdf-at-point-in-emacs ()
"Open the pdf for bibtex key under point if it exists."
(interactive)
(let* ((results (org-ref-get-bibtex-key-and-file))
(key (car results))
(pdf-file (funcall org-ref-get-pdf-filename-function key)))
(if (file-exists-p pdf-file)
(find-file-other-window pdf-file)
(message "no pdf found for %s" key))))
;; https://github.com/jkitchin/org-ref/issues/597
(defun org-ref-grep-pdf (&optional _candidate)
"Search pdf files of marked CANDIDATEs."
(interactive)
(let ((keys (helm-marked-candidates))
(get-pdf-function org-ref-get-pdf-filename-function))
(helm-do-pdfgrep-1
(-remove (lambda (pdf) (string= pdf ""))
(mapcar (lambda (key) (funcall get-pdf-function key))
keys)))))
(helm-add-action-to-source "Grep PDF" 'org-ref-grep-pdf helm-source-bibtex 1)
(setq helm-bibtex-map (let ((map (make-sparse-keymap)))
(set-keymap-parent map helm-map)
(define-key map (kbd "C-s") (lambda () (interactive) (helm-run-after-exit 'org-ref-grep-pdf)))
map))
(push `(keymap . ,helm-bibtex-map) helm-source-bibtex)
(setq org-ref-helm-user-candidates
'(("Open in Emacs" . org-ref-open-pdf-at-point-in-emacs))))Include and reference figures
For each research project I keep a ./media directory, where all my figures
live. You can include figures in Org mode by using the following syntax:
#+NAME: figurename
#+CAPTION: This is a figure caption
[[path_to_figure][link_description]]
Currently there is a bug in the ELPA version of Org mode, such that relative
paths to figures in #+INCLUDE 'd files aren't adapted with respect to the
including file, so the latex export cannot find them. I've submitted a fix
which should land in the next release of Org.
Version control documents
Magit. I thought about having the research chapters as git submodules in a thesis git project directory, but I currently don't. This would allow me to always have the thesis code in a saved state, even if I further work on my research chapters to answer to reviewers questions.
Support for sharing with my supervisor
Unfortunately, my supervisor likes to write comments in Mic. Word. I give in that sharing your writing with colleagues is a fundamental part of research.\\ Fortunately, ox-word export via Pandoc & LaTeX is capable of creating nice looking, structured Word files which I send to my supervisor. I then manually work through each comment step by step, though I'm looking for a way to improve this part of my workflow. I think the Emacs community is missing a minor mode to track Word document changes from within Org Mode. There are some ideas laying around on how to implement it hidden deep in the mailing list, or in this Emacs Exchange thread.
I may update this post with more information later.
Extended search facilities
By extended search facilities I mean the ability to quickly search for information in references, and to keep notes linked to the literature. For searching I make use of org-ref + pdfgrep, as shown in my org-ref setup. For notes linked to documents I've recently started to use Org-noter.
Simple syntax for tables and equations
Org tables are a pleasure to work with. The following:
| a | b | c | |---+---+---| | 1 | 2 | 3 |
Turns into:
| a | b | c |
|---|---|---|
| 1 | 2 | 3 |
Equations can be written in LaTeX:
\frac{d \vec{M} (t)}{dt} = \vec{M} (t) \times \gamma \vec{B} (t)
will become omitted
Support within a proper text editor
No need to talk about the synergy of using Emacs to edit text. I personally started using Spacemacs without Evil mode, because I find it aesthetically pleasing and because it offers great support for the languages I use the most, and excellent integration with Helm and Org.\\ The following configurations make the Org editing experience a bit nicer, in my opinion:
;; Writegood https://github.com/bnbeckwith/writegood-mode
(add-hook 'org-mode-hook 'writegood-mode)
;; https://github.com/cadadr/elisp/blob/master/org-variable-pitch.el
(use-package org-variable-pitch
:load-path "~/Elisp")
(add-hook 'org-mode-hook 'org-variable-pitch-minor-mode)
(setq visual-fill-column-width 120 visual-fill-column-center-text t)
(add-hook 'org-mode-hook 'visual-line-mode)
;; https://github.com/joostkremers/visual-fill-column
(add-hook 'org-mode-hook 'visual-fill-column-mode)
(add-hook 'org-mode-hook 'org-display-inline-images)
;; I have a modified version of the following:
;; https://github.com/lepisma/rogue/blob/master/config.el
(load-file "~/Projects/rogue/config.el")
(add-hook 'org-mode-hook '(lambda () (setq-local line-spacing 5)))
;; Aesthetical enhancements.
(setq org-fontify-quote-and-verse-blocks t
org-hide-macro-markers t
org-fontify-whole-heading-line t
org-fontify-done-headline t
org-hide-emphasis-markers t)Shortcuts to reach my files and build the thesis
I have a hydra (defined in Spacemacs as a transient-state) to move between my Thesis files:
;; Spacemacs hydra.
(spacemacs|define-transient-state
thesis-menu
:title "Ph.D. Thesis Menu"
:doc "
^Main Files^ ^Chapters^ ^Actions^
^^^^^^^^-------------------------------------------
_m_: Thesis _1_: Research 1 _o_: Open Thesis.pdf externally
_t_: Title page _2_: Research 2 _c_: Async compile file
_i_: Introduction _3_: Research 3 _a_: things
_s_: thesis.setup _4_: Research 4 ^ ^
"
:bindings
("a" things :exit t)
("m" (find-file "~/thesis/thesis.org") :exit t)
("t" (find-file
"~/thesis/titlepage.org") :exit t)
("s" (find-file
"~/thesis/thesis.setup") :exit t)
("i" (find-file
"~/thesis/intro/intro.org") :exit t)
("1" (find-file
"~/thesis/ch1/research.org") :exit t)
("2" (find-file
"~/thesis/ch2/research.org") :exit t)
("3" (find-file
"~/thesis/ch3/research.org") :exit t)
("4" (find-file
"~/thesis/ch4/research.org") :exit t)
("o" (shell-command "open
~/thesis/thesis.pdf" :exit t))
("c" (org-latex-export-to-pdf :async t)
:exit t))
(global-set-key (kbd "H-t") 'spacemacs/thesis-menu-transient-state/body)Gnus and notmuch
Currently working: notmuch for nnmaildir backend. However, I also have a local nnimap-backend, which uses Maildir format locally. It would be nice to have this working with notmuch as well.
Relevant functions:
-
nnir-compose-result - Goes over the results of notmuch (stored in the
buffer
*nnir*(with an additional leading space) and decides which lines to keep; -
nnir-notmuch-remove-prefix - a server-local variable to decide what to
remove from the lines in
*nnir*.
Summary of Search and Replace Commands in Emacs NOTE
[2016-08-13 Sat 17:50]
http://www.omps.in/blog/2016/01/20/day-10-search-and-replace-using-regex/