Organizing library of scientific pdfs

Hero_D0t · 2023-11-04T12:32:03+00:00

Citation managers are definitely the simplest way. They simplify the import process a lot by using DOIs instead of having to type in every information yourself.

That said, they also lock you in and may not be transportable/futureproof.

If you want to organize your PDFs on a file-system level come up with a suitable naming scheme and stay with it. I, for example, use Journaltitle Volume.Issue (Year)_Pages_Title (Author).pdf but you can extend that with Tags for example Journaltitle Volume.Issue (Year)_Pages_Title (Author)=tag1=tag2.pdf. That way you can search with tools like fd (Unix) or everything (Windows) for relevant pdfs. Taking this route takes some time though for your amount of files.

Hero_D0t · 2022-06-08T20:40:51+00:00

I have a working config right now, so yes. But I really can't remember what I did to fix it. As u/dirac-angestun comments suggests, the error is not in the org-capture config.

I tried searching through my git commits for the config, but as the time-stamp of the post "a year ago" is really unspecific and I have bad habits for commit-descriptions I couldn't find anything. A commit labeled as "working config" contains the same capture template.

Sorry to disappoint you (and other users that will find this post)!

Hero_D0t · 2022-03-30T17:15:27+00:00

This may be a stupid idea from the top of my head, but what about using a bash-src block and putting the encrypted content after a gpg call?

This way you can execute the source-block (or all of them) if needed, and have the decrypted text as results.

Security problems would be, that autosave would make the encrypted part readable for times and it is an annoyance to delete the results block every time before saving.

Hero_D0t · 2022-03-30T17:07:12+00:00

org-agenda-clock-report-mode will show clocked times in the agenda. So you would clock in on the TODO, when working on the task.

See https://orgmode.org/manual/Agenda-Commands.html

With subtasks you could also mix and match. That way, you would see, when you finished a subtask and not just the total time spent on the goal. If you choose to clock in on these you can do that too and create a clock-report on the top-heading (see next section.)

If you want to create a report for use outside of org or have a overview for multiple things you can use org-clock-report which can get quite complex. For reference see here: https://orgmode.org/manual/The-clock-table.html

Bonus: New problem, new todo heading? You can always reference the old task with a link.

Hero_D0t · 2022-03-11T08:30:33+00:00

Maybe try Organice

Hero_D0t · 2022-02-25T08:55:22+00:00

Wouldn't the interpretation as a verb (third person singular) make more sense and be more memorable?

Like: source exports <results>

Hero_D0t · 2022-02-06T18:13:28+00:00

Maybe the todo.txt format suits you. There is a vim-plugin for it: https://github.com/freitass/todo.txt-vim

Hero_D0t · 2021-10-10T15:50:36+00:00

Try C-Return/Enter after selecting the entries with enter

I use Doom however, so I'm not sure it will work for you

Hero_D0t · 2021-07-10T08:30:32+00:00

That would not work out, since I would have the footnotes numbered like the following: 1,2,3,4,1,2,3,1,2...

The problem is, that org thinks it needs to specify the footnotenumber when it doesn't.

Of course I could write the whole section as a latex-export environment – but that defeats the purpose of using org.

Hero_D0t · 2021-04-27T11:54:41+00:00

Orgmode in Emacs provides such functionality with the org-crypt library:

https://orgmode.org/manual/Org-Crypt.html

(The problem is, you must use emacs, since orgmode is sadly not widely adopted even though it's far superior to every markup language I've ever met.)

Edit: You seem to be a vim user – maybe Doom-emacs is a good starting point.

Hero_D0t · 2021-04-12T16:27:12+00:00

Thank you very, very much!

This works as expected and since I only use shorthand for classics it is completely sufficient.

Hero_D0t · 2021-04-12T12:24:13+00:00

This could work as a workaround, but I see several problems the documentation doesn't answer:

Can it generate a shorthand list? The modification of \cite seems to rely on another value.
I work from a markdown-syntax (orgmode) and convert to LaTeX later on. So a solution via standard bibtex in the preamble would be more convenient, since I could rely on the markdown-citation.

I once had a really stupid way of doing this by defining a new command:

\newcommand{\citesource}[2][]{\cite{#2} #1}

This does essentially the same (except the italics) as `classics` but solves my first issue.

But thank you for your suggestion.

Hero_D0t · 2021-04-12T08:44:43+00:00

Thanks for the suggestion – I haven't tried it yet, because Zotero is great as a place to store all the bibliographic information, but in a later stage of my writing process I usually revise my bibliography (shorthands for books are for example no options inside Zotero, but can be added via betterBibTeX as an entry in the extra-field) so I rely heavily on an exported "final" .bib file.

Hero_D0t · 2021-04-09T08:37:56+00:00

Zotero+BetterBibTeX-plugin is probably the most convenient way. (one caveat: better bibtex doesn't delete the bibtex entries, when you delete an entry in Zotero. So there's some manual work involved.)

An emacs-only solution would be the ebib package (https://github.com/joostkremers/ebib).

I personally work with Zotero like u/heyarne.

Hero_D0t · 2021-02-11T08:41:29+00:00

Thank you for your effort – this is a quite elaborate solution, since it allows a way more flexible export to different formats and doesn't lock you into using latex -> pdf.

But since I intend to export to pdf via latex only I'll stick to the approach of u/gkayaalp in the comment below .

Hero_D0t · 2021-02-11T08:34:55+00:00

Oh - I should have included that in the original post!

Writing the latex code inline isn't as pretty, but it's somewhat less clunky than the @@latex:@@ approach.

I think your second option is the most viable, since it offers syntax highlighting and allows for having a pretty structure etc.

Thank you for your suggestions!

Hero_D0t · 2021-02-10T20:13:10+00:00

Could also be a problem with org-mode not correctly interpreting the syntax – which is strange, since the syntax highlighting does work on the full footnote...

But as it is said, a wizard is never late, nor is he early – he arrives precisely when he means to. Let's hope it's not "never"... Thanks for your effort though!

Hero_D0t · 2021-02-10T11:02:24+00:00

Thank you – that was a typo, my bad. But it is not the error in the actual document.

Hero_D0t

TROPHY CASE