Using Atom for academic writing


#42

Ah, okay. That’s a different limit than the one I thought @santokh was referring to.


#43

I tried switching languages (I was using language-gfm and tried language-markdown), but I still get it. And my languages are up to date. I dont have a problem with very long block quotes. The exact issue I notice is in citations not being highlighted “[@Abc1974]” not when using italics, for example. These get highlighted in the beginning of the line, but if its get long then past 1000 character it no longer highlights (=colors) them.


#44

How many tags do you have in that paragraph?


#45

After about 25 to 27 tags it stops highlighting. Alternatively, after 1000 characters in a line tags are not highlighted. Whichever comes first.


#46

You can try https://atom.io/packages/grammar-token-limit and see if it helps.


#47

Hey @santokh, I just verified the 1000 character limit in language-markdown (I’m the author) and it should work. Can you verify that you have actually selected the “Markdown” grammar in the bottom right-hand corner of the window, and not “Github Flavored Markdown”?


#48

Thanks @burodepeper. You’ve (partly or mostly) solved my issue. If I set the language grammar as “Markdown” or even “GitHub Markdown” then I don’t have this issue. But if I use Pandoc Markdown then I get this problem of no highlights past the 1000 character limit.


#49

@santokh: Pandoc Markdown probably isn’t patched for that yet. If you create an issue over on their repository and refer them to this issue they should be able to sort it out. I think this is the repository you need, although it hasn’t been updated in a long time…


#50

This page has been tremendously helpful - thanks OP!

As I have fought the newbie battles getting to a workflow that doesn’t make my head hurt - big thumbs up to the Marked 2 app.

If you are on a Mac, Marked 2 makes it brain dead simple to export to many formats, especially .docx.


#51

Very helpful selection.
Is anyone has tried https://atom.io/packages/pandoc-convert ?


#52

Hi,

I came to Atom because I thought with appropriate packages it would support CriticMarkup during editing. The now defunct package atom-criticmarkup at least had keyboard shortcuts to apply CriticMarkup. I can’t seem to find any packages that do anything more than CriticMarkup highlighting in the source, which is great if your collaborator places CriticMarkup in the file you get from him or her.

Is there no way to have Atom auto-generate CriticMarkup tags while adding/deleting/replacing text? Isn’t this an important feature for collaborative academic writing?

And what about the ability to trigger something in Atom so it will go through all CriticMarkup tags and ask the user to accept/reject?

What am I missing?


#53

Sure there is. Someone just needs to write up a set of logical rules in code.

  1. Command to toggle markup mode on/off
    a. When in markup mode, if no text is selected and the user starts typing or presses ctrl-v, insert {++ and ++} around the cursor and then perform the operation.
    b. When in markup mode, if text is selected and the user starts typing or presses ctrl-v, insert ~~} at the end of the selection and {~~~> at the beginning. Place the cursor after the second tilde and execute the operation.
    c. When in markup mode, if text is selected and the user presses backspace, delete, or ctrl-x, surround the text with {-- and --}. Optionally, check to see if these tags are adjacent to others like them and merge if possible. If the operation was a cut command, also copy the selected text to the clipboard.
    d. When in markup mode, if no text is selected and the user presses backspace, wrap the character behind the cursor in {-- --}. If the three characters behind the cursor are {--, instead move the character to the left of the tag inside of it.
    e. When in markup mode, if no text is selected and the user presses delete, wrap the character in front of the cursor in {-- --}. If the three characters in front of the cursor are --}, instead move the character to the left of the tag inside of it.
    f. Comment and highlight tags would have to be handled through keybindings.

And what about the ability to trigger something in Atom so it will go through all CriticMarkup tags and ask the user to accept/reject?

Regular expression search. The dialog could be in a modal or a side panel, or the whole thing could be handled through keybindings.


#54

Just today I wanted to use CriticMarkup and I have to agree: Better CriticMarkup support for Atom would be extremely useful. A package that offers keyboard shortcuts, auto-generates CriticMarkup tags while editing, and the accept/reject functionality. At least language-markdown with some syntax themes support CriticMarkup highlighting. I really hope a more talented programmer than me would create something like this :slight_smile:


#55

OK, here is another great addon for writers that deserves more attention: zotero-picker integrates the Zotero visual picker in Atom. This is a great alternative to autocomplete-bibtex for people like me who have a large library. Autocomplete-bibtex loads the entire library on startup which can be painful. zotero-picker doesn’t have this issue.


#56

FYI I recently asked the author of Markdown-Preview-Enhanced if (s)he would add CriticMarkup support and so it was done very quickly. The author is very responsive and the package is excellent, really.


#57

What is the advantage of Marked 2 over markdown preview plus? The latter is free and supports live view whereas in marked 2 u seem to have to save the file. What am I missing why people pay money for that?


#58

I love this thread! I have one question though, downloading all of these packages is making my atom a bit heavy. Is there a way to group my packages so that I can easily disable all of my coding packages when I’m writing, and vice-versa? Thanks!


#59

I don’t know if there is an elegant way to do this. Perhaps you could create shell aliases for apm enable <list of writing-related packages> and apm disable <list of writing-related packages>.

That said, I don’t feel a huge difference in speed. Startup time is a bit worse, but Atom’s startup time is not great anyway so it doesn’t bother me.


#60

There isn’t.

Keep in mind that enabling or disabling a package via configuration has an effect on every open Atom window, so this technique can’t be used to have differently-configured Atom windows at the same time.


#61

Install atom-ctags to enable navigation by sections with cmd-r

The atom manual describes how to navigate by symbols using cmd-r (current file) and cmd-shift-r (project). For this to work, a project needs a ctags file with the locations of markdown sections. There may be better ways, but installing atom-ctags seems to do this fairly painlessly. (It disables the built in symbols-view package and replaces it with a fork which is worrying, but it has nearly 100,000 installs so is probably safe!)