Re: re-scanning bibliography for org-cite
On Thu, Jun 9, 2022 at 12:00 PM Fraga, Eric wrote: > > On Thursday, 9 Jun 2022 at 10:34, Bruce D'Arcus wrote: > > It should take another few days of development and testing before I'm > > ready to merge it, but it pretty much works now, and any help with > > code review and/or testing would be much appreciated. > > Okay, let me know. It's easy enough for me to replace 'basic with > 'citar again! Took a bit longer than "days," because we ended up making a ton of other changes, but it's now merged. The result should be a snappy UI that appropriately adapts to local buffer context, and updates the cache as needed.
Re: re-scanning bibliography for org-cite
BTW, just to give some context of why we didn't implement it by default earlier; there are two reasons: 1. it seems vast differences in the size of user bib files, and those with very large ones would be annoyed if it re-generated the completions on every change. 2. citar also covers notes and related files, which get complicated, and subject to further user variety; and the UI needs to keep this in sync with the bib data I think we understand the problem better now, however. On Thu, Jun 9, 2022 at 12:00 PM Fraga, Eric wrote: > > On Thursday, 9 Jun 2022 at 10:34, Bruce D'Arcus wrote: > > It should take another few days of development and testing before I'm > > ready to merge it, but it pretty much works now, and any help with > > code review and/or testing would be much appreciated. > > Okay, let me know. It's easy enough for me to replace 'basic with > 'citar again! > > -- > : Eric S Fraga, with org release_9.5.4-521-g1105da in Emacs 29.0.50
Re: re-scanning bibliography for org-cite
On Thursday, 9 Jun 2022 at 10:34, Bruce D'Arcus wrote: > It should take another few days of development and testing before I'm > ready to merge it, but it pretty much works now, and any help with > code review and/or testing would be much appreciated. Okay, let me know. It's easy enough for me to replace 'basic with 'citar again! -- : Eric S Fraga, with org release_9.5.4-521-g1105da in Emacs 29.0.50
Re: re-scanning bibliography for org-cite
On Thu, Jun 9, 2022 at 10:19 AM Fraga, Eric wrote: > > On Thursday, 26 May 2022 at 18:24, Ihor Radchenko wrote: > > The relevant function is org-cite-basic--parse-bibliography. > > To finally follow up on this, the problem is not with org-cite but > appears to be due to my use of citar. Citar seems to cache the keys > somewhere/somehow and this cache is not updated when the bibliography > file changes. Yes; not currently by default, but can be configured. https://github.com/emacs-citar/citar#refreshing-the-library-display But more importantly I'm currently working on a major change in the caching and completion architecture of citar, where I've actually borrowed ideas and code from oc-basic, so it should work the same WRT to cache updating, without need for any configuration. https://github.com/emacs-citar/citar/pull/628 It should take another few days of development and testing before I'm ready to merge it, but it pretty much works now, and any help with code review and/or testing would be much appreciated. Bruce
Re: re-scanning bibliography for org-cite
On Thursday, 26 May 2022 at 18:24, Ihor Radchenko wrote: > The relevant function is org-cite-basic--parse-bibliography. To finally follow up on this, the problem is not with org-cite but appears to be due to my use of citar. Citar seems to cache the keys somewhere/somehow and this cache is not updated when the bibliography file changes. If I set org-cite-insert-processor to 'basic, everything is fine. Sorry for the noise. -- : Eric S Fraga, with org release_9.5.4-521-g1105da in Emacs 29.0.50
Re: re-scanning bibliography for org-cite
Timothy writes: > Hi Eric, > >> The difficulty will be knowing whether they work or not given the sporadic >> nature of the problem… > > If it’s any help, I consistently have this issue when producing the bib file > by tangling. Then, can you also try the proposed steps? If you can reproduce the problem consistently, you can reveal what helps (or not) far quicker. Best, Ihor
Re: re-scanning bibliography for org-cite
Hi Eric, > The difficulty will be knowing whether they work or not given the sporadic > nature of the problem… If it’s any help, I consistently have this issue when producing the bib file by tangling. All the best, Timothy
Re: re-scanning bibliography for org-cite
Hi Ihor, I will try these out, hopefully tomorrow. The difficulty will be knowing whether they work or not given the sporadic nature of the problem... Thank you, eric -- : Eric S Fraga, with org release_9.5.3-513-g292116 in Emacs 29.0.50
Re: re-scanning bibliography for org-cite
Eric S Fraga writes: > Is there a function I can call to force a rescan? That would satisfy me > as I could put it into a hook for org-bibtex (or advice the function if > no hook available). The relevant function is org-cite-basic--parse-bibliography. You can try 2 things: 1. Set org-cite-basic--file-id-cache to nil in :around advice before calling the function 2. Remove :cite-basic/bibliography from INFO plist in :around advice before calling the function I you find any of these methods helpful, please report back. I have a suspicion that :cite-basic/bibliography might be the cause. Best, Ihor
Re: re-scanning bibliography for org-cite
On Thursday, 26 May 2022 at 13:00, Ihor Radchenko wrote: > In theory, it might be related to one of the changes I made in this > area. I am not 100% sure, but bibliography might not be rescanned if you > edit a bibliography file in Emacs buffer, but do not actually save it. > Is this what is happening? No and, to be fair, I wouldn't expect the scanning to take place if I hadn't saved the file. I have my bibliography in an org file which I export to .bib using org-bibtex. Is there a function I can call to force a rescan? That would satisfy me as I could put it into a hook for org-bibtex (or advice the function if no hook available). Thank you, eric -- : Eric S Fraga, with org release_9.5.3-472-gd2a459 in Emacs 29.0.50
Re: re-scanning bibliography for org-cite
Eric S Fraga writes: > sorry to revisit this but I continue to run into the problem of the > bibliography not being rescanned automatically. What is the easiest way > (other than leaving Emacs and restarting) to force it, assuming there is > one? I.e. maybe I can invalidate or clear the cache? > > I do not know why rescanning doesn't happen. It usually does but then > sometimes it doesn't without any noticeable difference in the actions I > have taken. Frustrating. In theory, it might be related to one of the changes I made in this area. I am not 100% sure, but bibliography might not be rescanned if you edit a bibliography file in Emacs buffer, but do not actually save it. Is this what is happening? Best, Ihor
Re: re-scanning bibliography for org-cite
On Wednesday, 3 Nov 2021 at 17:21, Nicolas Goaziou wrote: > oc-basic relies on a cache. The cache key contains a hash of the > contents of the bib file. So whenever the bib file is modified, the > cache is invalidated, and oc-basic parses again the file. > > IOW, rescanning happens automatically in oc-basic. Hi Nicolas, sorry to revisit this but I continue to run into the problem of the bibliography not being rescanned automatically. What is the easiest way (other than leaving Emacs and restarting) to force it, assuming there is one? I.e. maybe I can invalidate or clear the cache? I do not know why rescanning doesn't happen. It usually does but then sometimes it doesn't without any noticeable difference in the actions I have taken. Frustrating. I hate restarting Emacs... ;-) Thank you, eric -- : Eric S Fraga, with org release_9.5.3-511-g8e69ad in Emacs 29.0.50
Re: re-scanning bibliography for org-cite
On Wed, Nov 3, 2021 at 12:21 PM Nicolas Goaziou wrote: > oc-basic relies on a cache. The cache key contains a hash of the > contents of the bib file. So whenever the bib file is modified, the > cache is invalidated, and oc-basic parses again the file. Of course; clever! Bruce
Re: re-scanning bibliography for org-cite
Hello, "Bruce D'Arcus" writes: > On Thu, Oct 21, 2021 at 10:12 AM Eric S Fraga wrote: >> >> Dear all, >> >> simple question: how can I get org-cite to rescan my bibliography (.bib) >> file when it changes? When I'm writing a paper, as I'm doing now, I add >> entries to my bibliography as I write but org-cite is not aware of any >> new entries. > > Do you mean for org-cite-insert? > > Which insert processor? > > If it's bibtex-actions, you have to configure the filenotify support > mentioned on the README. > > I'm not sure how the oc-basic one handles this. oc-basic relies on a cache. The cache key contains a hash of the contents of the bib file. So whenever the bib file is modified, the cache is invalidated, and oc-basic parses again the file. IOW, rescanning happens automatically in oc-basic. Regards, -- Nicolas Goaziou
Re: re-scanning bibliography for org-cite
On Thu, Oct 21, 2021 at 10:12 AM Eric S Fraga wrote: > > Dear all, > > simple question: how can I get org-cite to rescan my bibliography (.bib) > file when it changes? When I'm writing a paper, as I'm doing now, I add > entries to my bibliography as I write but org-cite is not aware of any > new entries. Do you mean for org-cite-insert? Which insert processor? If it's bibtex-actions, you have to configure the filenotify support mentioned on the README. I'm not sure how the oc-basic one handles this. Bruce
Re: re-scanning bibliography for org-cite
On Thursday, 21 Oct 2021 at 16:51, Uwe Brauer wrote: > Do you use > org-ref-insert-cite-link > org-ref-helm-insert-cite-link Neither. I use org-cite-insert. -- : Eric S Fraga via Emacs 28.0.60, Org release_9.5-149-g781080 : Latest paper written in org: https://arxiv.org/abs/2106.05096
Re: re-scanning bibliography for org-cite
>>> "ESF" == Eric S Fraga writes: > Dear all, > simple question: how can I get org-cite to rescan my bibliography > (.bib) file when it changes? When I'm writing a paper, as I'm doing > now, I add entries to my bibliography as I write but org-cite is not > aware of any new entries. > I have gone through the code but cannot see where the bib entries are > actually read. (my bad) Do you use org-ref-insert-cite-link Or org-ref-helm-insert-cite-link I use the latter in that case, if I finish an entry and update the bib file, then when I call the function again, it is updated, not sure about org-ref-insert-cite-link > Thank you, > eric smime.p7s Description: S/MIME cryptographic signature
re-scanning bibliography for org-cite
Dear all, simple question: how can I get org-cite to rescan my bibliography (.bib) file when it changes? When I'm writing a paper, as I'm doing now, I add entries to my bibliography as I write but org-cite is not aware of any new entries. I have gone through the code but cannot see where the bib entries are actually read. (my bad) Thank you, eric -- : Eric S Fraga via Emacs 28.0.60, Org release_9.5-149-g781080 : Latest paper written in org: https://arxiv.org/abs/2106.05096
