sunnyhasija / academic-doom-emacs-config Goto Github PK

Thanks a lot for posting your configuration and the additional comments in Org-roam's discourse (https://org-roam.discourse.group/t/an-opinionated-academics-workflow-for-using-org-roam/601).

In your config, in https://github.com/sunnyhasija/DOOMEmacs#zotxt you say about zotxt : "Allows for syncing of the notes between zotero and emacs." However, as far as I can see, there really is no syncing of notes: zotxt allows (via M-x org-zotxt-noter) to create an org note for the PDF(s) under the zotero entry. But it does not allow to access the notes in Zotero itself, nor are the org notes created via org-zotxt-noter accessible from Zotero. Am I missing something?

Hi,

Doom-doctor tells that org-journal-mode-map is a void-variable with latest master repo (902c49a).

! Attempt to load DOOM failed
  (config.el (void-variable org-journal-mode-map))

Thanks, and stay safe,
/z

@sunnyhasija Thanks for posting your configuration. Appears relevant to researchers. :D

Would you mind posting here or somewhere your workflow of note-taking and academic writing using your configuration? Appreciate that.

Cheers, and stay safe,
/z

Hi!
This might be related to #4, but I am currently using a lot of this in my config.el and the only thing that systematically fails to work/load is org-fancy-priorities and org-super-agenda. doom doctor isn't helping much, but unlike #4 there are no errors.

Is it related to how I implemented it? Thanks in advance

Hi @sunnyhasija

The screencasts in README.org appears to be recorded in a HiDPI (4K) screen and therefore, appears illegible due to extremely tiny fonts rendered!

Would you mind re-recording with a larger font sizes, subject to your convenience? Appreciate that.

Cheers and stay safe,
/z

Hello,

Thanks a lot for this guide, I need to clarify two things though as I struggle to understand all the mechanics of your config:

• I went through your entire config files but I found no clue of where you set up company-org-roam backend as you describe in your reddit post. For what I understand, but I might be wrong, this needs to be explicitly configured to become active when entering org-roam-mode.
• secondly, you set up this file "~/Dropbox/Org/references/articles.org" as org-ref-bibliography-notes and bibtex-completion-notes-path. Does it have any reason to exist as you use a references/notes/ directory to store everything with org-roam?

Hi @sunnyhasija

1. Was it an oversight with the last that nov is disabled in `packages.el (https://github.com/sunnyhasija/DOOMEmacs/blob/902c49a8399cdaae7add0dc996602dd3e2d2b6a2/packages.el#L59), yet enabled in https://github.com/sunnyhasija/DOOMEmacs/blob/902c49a8399cdaae7add0dc996602dd3e2d2b6a2/init.el#L177.

(add-to-list 'auto-mode-alist '("\\.epub\\'" . nov-mode))

2. Likewise, a new file custom.el has been added (https://github.com/sunnyhasija/DOOMEmacs/blob/master/custom.el) which has duplicate entries as in config.el from https://github.com/sunnyhasija/DOOMEmacs/blob/902c49a8399cdaae7add0dc996602dd3e2d2b6a2/config.el#L384 onwards that read:

 '(org-journal-date-format "%A, %d %B %Y" t)
 '(org-journal-date-prefix "#+TITLE: " t)
 '(org-journal-dir "~/Dropbox/Org/Daily/" t)
 '(org-journal-file-format "%Y-%m-%d.org" t)
 '(package-selected-packages (quote (org-fancy-priorities))))

Just wondering? Cheers, and stay safe,
/z

Hi,

Thanks so much for this guide, I was able to adapt your config to get everything working except loading PDFs. I've tried lots of things (including uninstall-reinstall emacs) but have not got it to work yet. Briefly, when I enter a note for a bibliography entry, navigate to the line for the PDF, and call 'M-x org-noter', I'm prompted to install epdfinfo. I accept this and it builds fine, then I call 'M-x pdf-info-check-epdfinfo' and it says it's working. But when I try the 'M-x org-noter' step again (after quitting emacs, doom sync, starting emacs), the pdf file just loads as a bunch of text.

There are lots of workarounds to get pdf-tools working online but I haven't found one that has worked with your setup

What OS do you use?
How did you install emacs (I've installed using homebrew with either emacsport or emacs-plus)?
How did you install doom-emacs?
Have you encountered and solved issues with pdf-tools with your config?

Hi,

When I tried to export an org document to pdf (C-c C-e l p), your config reported that elsarticle was missing which definitely is not a case:

# tlmgr info elsarticle
package:     elsarticle
category:    Package
shortdesc:   Class for articles for submission to Elsevier journals
longdesc:    This class for typesetting journal articles is accepted for submitted articles both in Elsevier's electronic submission system and elsewhere. Please note that this webpage is meant for uploading updates to the elsarticle software itself, not for submitting articles using it .
installed:   Yes
revision:    50786
sizes:       src: 41k, doc: 1525k, run: 133k
relocatable: No
cat-version: 3.2
cat-license: lppl1.2
cat-topics:  journalpub class
collection:  collection-publishers

The same org file without any modifications gets exported without an issue in Prof. John Kitichin's (@jkitichin) scimax config, fyi.

I miss this peculiar export part with multiplicity of export options in doom- and in your configuration. Thanks!

Hi,

doom doctor fails to load org-fancy-priorities,:

$ ~/.emacs.d/bin/doom doctor
The doctor will see you now...

> Checking your Emacs version...
> Checking for Emacs config conflicts...
> Checking for private config conflicts...
> Checking for stale elc files...
> Checking Doom Emacs...

Ignoring ’:ensure t’ in ’org-fancy-priorities’ config
  ✓ Initialized Doom Emacs 2.0.9
  ✓ Detected 41 modules
  ✓ Detected 173 packages
  > Checking Doom core for irregularities...
    Found font material-design-icons.ttf
    Found font weathericons.ttf
    Found font octicons.ttf
    Found font fontawesome.ttf
    Found font file-icons.ttf
    Found font all-the-icons.ttf
  > Checking for stale elc files in your DOOMDIR...
  > Checking your enabled modules...


Everything seems fine, happy Emacs'ing!
✓ Finished! (6.4278s)

Cheers, and stay safe,
/z

Hi @sunnyhasija

The configs are getting more matured.

Meanwhile, there are some variables going to be deprecated/removed in org-ref v3 which needs modifications in your configurations. just a pointer!

Warning (:warning): Warning: You are using deprecated variables in org-ref that will be removed in version 3.

The following variables will not be used in version 3:
- org-ref-bibliography-notes
- org-ref-default-bibliography
- org-ref-pdf-directory 

They are replaced by these variables in `bibtex-completion':
- bibtex-completion-notes-path
- bibtex-completion-bibliography
- bibtex-completion-library-path

There are some other changes that are likely to break existing workflows, for example all non-LaTeX exports will be handled by CSL, and all the old export code has been removed.

For more details see https://github.com/jkitchin/org-ref/tree/org-ref-3#readme.

The release date for org-ref version 3 is planned for [2021-10-18 Mon].

Cheers,
/z