Responding to [[http://irreal.org/blog/?p=6924][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/ [[http://irreal.org/blog/?p=2895][write about]], it's pretty trivial. In any event,
here it is:
#+BEGIN_SRC emacs-lisp
(defun jcs-insert-url ()
"Insert URL of current browser page into Emacs buffer."
(interactive)
(insert (jcs-retrieve-url)))
#+END_SRC
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:
#+BEGIN_SRC emacs-lisp
(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'")))
#+END_SRC
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, [[http://irreal.org/blog/?p=6924#comment-3732979999][Brad Collins
suggests a solution]] that uses [[https://github.com/xuchunyang/grab-x-link][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 [[http://sachachua.com/blog/2018/01/org-mode-inserting-a-function-definition/][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.
[[http://irreal.org/blog/?p=6926][Link]]
** Calc for Programmers :IRREAL:
:PROPERTIES:
:CREATED: [2018-08-05 Sun 10:04]
:END:
After writing about Florian Adamsky's post on [[http://irreal.org/blog/?p=7040][acronyms in AUCTeX]], I snooped
around on his site and came across a [[https://florian.adamsky.it/2016/03/31/emacs-calc-for-programmers-and-cs.html][nice post]] on [[https://www.gnu.org/software/emacs/manual/html_node/calc/index.html][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.
[[http://irreal.org/blog/?p=7044][Link]]
** Parsing with ~org-element~ :IRREAL:
:PROPERTIES:
:CREATED: [2018-08-10 Fri 17:55]
@ -137,105 +63,6 @@ The relevant code:
'(("" "total:" ":=vsum(@2..@-1);T" "")))
#+end_src
** Emacs Lisp Byte-Code :IRREAL:
:PROPERTIES:
:CREATED: [2018-08-11 Sat 21:40]
:END:
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 [[http://nullprogram.com/blog/2014/01/04/][have shown]], it can sometimes be useful
to have a basic understanding of the bytecodes.
R Bernstein has put together a comprehensive, book-length [[http://rocky.github.io/elisp-bytecode.pdf][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 [[https://github.com/rocky/elisp-bytecode][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.
[[http://irreal.org/blog/?p=7166][Link]]
** Formatting Tables :IRREAL:
:PROPERTIES:
:CREATED: [2018-10-28 Sun 09:13]
:END:
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 [[https://emacsnotes.wordpress.com/2018/09/24/delim-col-a-handy-tool-for-creating-pretty-tables-and-converting-those-to-different-table-formats/][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.
[[http://irreal.org/blog/?p=7540][Link]]
** Org Mode Cookbook :IRREAL:
:PROPERTIES:
:CREATED: [2018-08-04 Sat 12:51]
:END:
Way back in 2014, I [[http://irreal.org/blog/?p=2575][posted]] about Eric Neilsen's excellent [[http://ehneilsen.net/notebook/orgExamples/org-examples.html][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 [[http://ehneilsen.net/notebook/orgExamples/org-examples.html#sec-10][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 [[http://fnal.gov/][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.
[[http://irreal.org/blog/?p=6894][Link]]
** How to paste then copy
:PROPERTIES:
:CREATED: [2018-08-11 Sat 21:47]
:END:
Question: how to set a mark such that all subsequent copy operations move their
*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 [[https://www.reddit.com/r/emacs/comments/9ynsvc/write_a_thesis_using_emacs_and_orgmode/][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, [[https://orgmode.org/manual/In_002dbuffer-settings.html][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:
'(("Open in Emacs" . org-ref-open-pdf-at-point-in-emacs))))
#+end_src
**** 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:
#+begin_src org
#+NAME: figurename
#+CAPTION: This is a figure caption
[[path_to_figure][link_description]]
#+end_src
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 [[https://code.orgmode.org/bzg/org-mode/commit/d81a1d088c74e605c99e90a2835c55df5144f43e][submitted a fix]]
which should land in the next release of Org.
**** Version control documents
[[https://magit.vc/][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, [[https://github.com/jkitchin/scimax/blob/master/ox-word.el][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 [[https://lists.gnu.org/archive/html/emacs-orgmode/2015-06/msg00246.html][hidden deep in the mailing list]], or
in [[https://emacs.stackexchange.com/questions/34923/merging-changes-to-from-docx-files-into-org-files][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 [[https://github.com/jkitchin/org-ref/issues/597][org-ref + pdfgrep]], as shown in my org-ref setup. For
notes linked to documents I've recently started to use [[https://github.com/weirdNox/org-noter][Org-noter.]]
**** Simple syntax for tables and equations
Org tables are a pleasure to work with. The following:
Daniel Borchmann
1 year ago