[Feature Request] Auto-sync to a BibTeX File

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DrJJWMac
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Re: [Feature Request] Auto-sync to a BibTeX File

Post by DrJJWMac »

> One thing that would help in this specific case, and perhaps even more in other use cases, is if Bookends could call scripts automatically (i.e. implement AppleScript actions).

I had thought the same and agree. I would for example find use to be able to point to AppleScripts that are to run "Before Opening Database" and "Before Closing Database".
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JJW
joao
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Re: [Feature Request] Auto-sync to a BibTeX File

Post by joao »

DrJJWMac wrote: Fri Oct 01, 2021 9:22 am > I had thought the same and agree. I would for example find use to be able to point to AppleScripts that are to run "Before Opening Database" and "Before Closing Database".
A crude way of doing that would be using your AppleScript as a launcher for bookends, and another attached to a cmd-Q shortcut...
Dellu
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Re: [Feature Request] Auto-sync to a BibTeX File

Post by Dellu »

DrJJWMac wrote: Thu Sep 30, 2021 7:16 pm
I create a BibTeX file solely at the point where I am compiling my final document. Putting in the citations is the last step in the processing. In the meantime, I use citation keys stored in Bookends, trusting that, once I am done, the BibTeX file generated at the end from Bookends will be complete. I do not need BibTeX auto-export each time I add a new citation. I probably never will. In this light, convince me why I should change my approach and also join the call to have auto-export of a BibTeX file built in to Bookends. Explain to me what benefit I am missing in a way that I (as an engineer) can appreciate.
I think you need to understand two things:
1) the citation autocompelete feature in Texstudio (or any other tex software that autocites/compeletes your citation).
2) a bibtex file that is at the root of your tex system. Look at the screenshot I put above. zLib is put in my Library folder.


The zLib.bib is managed by Better Bibtex. Every change I made in Zotero is reflected there. Whether I am writing a shoft paper, or a number of papers papers side by side, or a dissertation, any article or book in my Zotero library is under my fingers via the Texstudio's auto-cite feature.

- assume you are drafting an paper. You find an interesting article in your bookends library, you want to cite it. In your case, you cite it using BE citation (if I understand you correctly), and change citation to bibtex format after you finish the draft, and export your cited papers from Bookends to Bibtex format.

That is a lot of work if you break it down.
Step 1: insert BE citation (you might use the tex format here, in that case, you reduce the friction a bit)
Step 2: mark the papers that you cited
Step 3: export the cited papers
Step 4: change the format of the citation from BE to tex format.

If you avoid step 2, the option is to export the whole library--which could be time taking.


For me (Better Bibtex via Zotero), it is just one step. I simply write \cite{ on my draft. Texstudio pops up all the available references, click the article. That is the end of the story. I don't need to look back to it, it is already synced & cited.

Further, assume you find an interesting article from a publisher; want to cite it. For the Zotero system, the only thing you need to do is download the metadata. Once you put it in Zotero, it is in your tex-editor as well.

- Note that, it is also a good habit to compile your documents occasionally to see everything is going fine. I don't wait to the last point to compile and see

- Personally, I prefer to read my drafts on the pdf output. For that, I constantly compile. It is pleasant to see the references are correctly set on my draft as well. If I want to send my draft to an editor, or a friend, the references need to be there. For that, I don't want to want to the last point to compile, or insert my references.

is it clear?
DrJJWMac
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Re: [Feature Request] Auto-sync to a BibTeX File

Post by DrJJWMac »

> For me (Better Bibtex via Zotero), it is just one step. I simply write \cite{ on my draft. Texstudio pops up all the available references, click the article. That is the end of the story. I don't need to look back to it, it is already synced & cited.

This explains it. Thank you. What is happening is that Texstudio relies on the updated .bib file, and you want Bookends to keep the update dynamic.

My approach is manual. When I prepare to create a paper or report, I initiate a new Bookends library specific to that document. I assemble citations (PDFs) into that library. I keep the Bookends app open as I write the paper (or not ... depending on where I am in my processing). When I type \cite{ in TeXShop, I manually type in the citation key because I see it in Bookends. Or I put some phrase that reminds me what citation I should use when I compile the final document ***later***.

The key here is that I am not in need to be correct in the citation key dynamically while I prepare my document. I have since found this step is more distracting. I want to write my thoughts, play around with them, and then process the nuts and bolts behind them (the citations) later.

> Personally, I prefer to read my drafts on the pdf output. For that, I constantly compile. It is pleasant to see the references are correctly set on my draft as well.

By counter comparison, I not as much concerned if at all ever concerned that my intermediate outputs must have the citations correctly set.

---

Now that I appreciate the need for auto-export, I support the requests that Bookends consider whether it can be implemented in some future version.
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JJW
joao
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Re: [Feature Request] Auto-sync to a BibTeX File

Post by joao »

I'm obviously in the minority here, but I actually prefer to use the Bookends citations pop up to add references quickly, as it gives me a preview of the actual document and lets me check if I'm referencing the right thing. I have Bookends set up to just insert the cite key or a pandoc version, which remains the same in bibtex.

The main benefit in having an auto-synced bibtex is to be able to compile repeatedly during the writing phase, so that latex can fetch the references. I normally have to clean up the bibtex with jabref though since I use biblatex which can be fussy.

But here is another good use-case for actions: add reference to a bookends group if reference is cited through the pop-up or copy citation function. No need to manually add the thing to a group and no need to have a huge database containing all references in bibtex.
Dellu
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Re: [Feature Request] Auto-sync to a BibTeX File

Post by Dellu »

DrJJWMac wrote: Fri Oct 01, 2021 11:39 am Now that I appreciate the need for auto-export, I support the requests that Bookends consider whether it can be implemented in some future version.
Thank you.
Dellu
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Re: [Feature Request] Auto-sync to a BibTeX File

Post by Dellu »

joao wrote: Fri Oct 01, 2021 11:50 am it gives me a preview of the actual document and lets me check if I'm referencing the right thing.
You can actually do that in Texstudio as well. If you click on the popup (known as Tooltip), you can see the full references in there.

But here is another good use-case for actions: add reference to a bookends group if reference is cited through the pop-up or copy citation function. No need to manually add the thing to a group and no need to have a huge database containing all references in bibtex.
I don't understand this. Does BE get a new action feature that I am unaware of?
Jon
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Re: [Feature Request] Auto-sync to a BibTeX File

Post by Jon »

@Dellu Please write to support@sonnysoftware.com about this topic.

Jon
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Nhaps
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Re: [Feature Request] Auto-sync to a BibTeX File

Post by Nhaps »

The following factors might be useful as you consider the issue at hand:

1. About Style Format: I noticed that my references take a long time to output with the legacy default BibTex.fmt. But when I use my custom BiBTex.fmt the output is way faster. I don't know if this is a bug on the legacy format.

2. About Folders: If the option of auto-sync references is not viable at the moment, then focus could be on some sort of auto-output of a static folder. BE allows custom keyboard shortcuts to be used for copying references to static folders, which has been helpful. Something similar could be implemented for auto-output. As soon as a reference hits the auto-output folder, the process could be triggered in the background. Whatever step taken toward this goal is much appreciated. Let me know your ideas.
Jon
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Re: [Feature Request] Auto-sync to a BibTeX File

Post by Jon »

Formats can't really have bugs. Please send me your custom BibTeX format and I'll test to see why it's faster.

Jon
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iandol
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Re: [Feature Request] Auto-sync to a BibTeX File

Post by iandol »

Jon wrote: Fri Oct 01, 2021 7:27 am @iandol -- I as sume that any given paper you write with collaborators doesn't use all 8K references. It would speed things up considerably if you create a group (perhaps a smart group) for a paper and exported that as needed. I suspect your 7-9 minutes would be a log or more faster.

One thing I can look at is the time it takes to create BibTeX-formatted references. I'll see if there any improvements to be had there.
Indeed, I always start with the good intentions of using a group :D , but I find in my non-linear writing style, I jump around and cite things outside of the group and then group management distracts me from the writing flow. Then with an incomplete group I get compile errors, and to smooth these potential bumps in the road end up reverting to my full database. A faster export would be very welcome, thank you for checking if this is possible.
joao wrote: Fri Oct 01, 2021 11:50 am I'm obviously in the minority here, but I actually prefer to use the Bookends citations pop up to add references quickly, as it gives me a preview of the actual document and lets me check if I'm referencing the right thing. I have Bookends set up to just insert the cite key or a pandoc version, which remains the same in bibtex.
I think Jon did a great job with Bookend's floating citations pop-up, it is featureful and flexible enough to adapt to Markdown/LaTeX workflows as well as work in email apps and regular word processors. I normally still stick to my Alfred citation pop-up out of habit and tweakability (I can choose Pandoc / LaTeX / formatted cite output with a modifier, rather than changing the Bookends preferences), but I think if Bookend's pop-up existed when I started writing my Alfred script, I would never have bothered.
joao wrote: Fri Oct 01, 2021 11:50 am But here is another good use-case for actions: add reference to a bookends group if reference is cited through the pop-up or copy citation function. No need to manually add the thing to a group and no need to have a huge database containing all references in bibtex.
Great idea!
DrJJWMac wrote: Fri Oct 01, 2021 11:39 am The key here is that I am not in need to be correct in the citation key dynamically while I prepare my document. I have since found this step is more distracting. I want to write my thoughts, play around with them, and then process the nuts and bolts behind them (the citations) later.
Indeed, you may know or remember well enough when you reference. For those of us with less precise recollection or perhaps a bit more chaotic in how we write :? , using the visual pop-up, to search, confirm and then cite in one step is a useful refinement without bothering about formatting (you don't worry about formatting as you defer that to a later stage, we don't worry abut formatting as the pop-up and compiler does it for us).
iandol
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Re: [Feature Request] Auto-sync to a BibTeX File

Post by iandol »

Jon wrote: Sun Oct 03, 2021 7:04 am Formats can't really have bugs. Please send me your custom BibTeX format and I'll test to see why it's faster.
I made a minimal BibTeX which removes for example the abstract field and this does export faster than the default by trading off the amount of data to be written out. In this case, for making a bibliography, fields like the abstract or keywords etc are not usually needed and it also creates a Bib file that is substantially smaller and so can be processed by other scripts more quickly. This is thanks to the flexibility of Bookends format manager! 8)
Attachments
BibTeX-Minimal.fmt.zip
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Nhaps
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Re: [Feature Request] Auto-sync to a BibTeX File

Post by Nhaps »

There is another function that I have been using for years now in BE, which also improves speed in another way. It allows for faster BibTex output because it deletes empty fields automatically from the BibTex file. If you use this example below for the field author

Code: Select all

{$author = {$a$},$¬^}
you will benefit from a double function. If the field is left blank, namely no author, the format will not output the field. If it is filled out, then the format will output everything. The code at the end prevents any blank field to appear in my BibTex file.
Last edited by Nhaps on Mon Oct 04, 2021 11:13 am, edited 1 time in total.
Jon
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Re: [Feature Request] Auto-sync to a BibTeX File

Post by Jon »

I'm creating a BibTeX format that should not output missing fields, too, it will be included in the next update. It's a bit easier to read/edit than yours.

Jon
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Nhaps
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Re: [Feature Request] Auto-sync to a BibTeX File

Post by Nhaps »

Good idea, Jon. Thank you.
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