Re: [O] org-ref helm-bibtex notes
On 2015-06-16 Tue 18:28, Titus von der Malsburg wrote: On 2015-06-16 Tue 17:39, Julian Burgos wrote: Dear list, I have been using org-ref for a while, using reftex to insert citations in my org documents. Now I am switching to helm-bibtex, which is pretty awesome. I have a couple of question about the note files. Org-ref uses a single file to keep notes (e.g. notes.org), but helm-bibtex assumes that notes are kept in separate files, one per article. My questions are: a) Do you have a preference in the single file vs multiple files question? Are advantages/disadvantages? I tend to prefer the single file option, it makes search easy and also I can add TODO items that later I can pull out in the agenda view. With multiple files this would not be as easy. Do you agree? Hi, I’m the author of helm-bibtex. There was recently a discussion about this on Github: https://github.com/tmalsburg/helm-bibtex/issues/40 Someone convinced me that storing all notes in one file is better and there is an experimental (and incomplete) implementation in a topic branch: https://github.com/tmalsburg/helm-bibtex/tree/note-files Update: I worked on the note-files branch and as far as I’m concerned it is ready to be merged into master. There are several changes: When one big notes file is used: - The new default template for notes is simpler than what org-ref uses but it should be compatible because it uses the Custom_ID property to store the key. - Note templates can be defined in `helm-bibtex-notes-template`. - The list of publications now shows a mark if notes are available for a publication. - Finding the correct entry is now robust because the code looks for `Custom_ID: key` not just for the key. Multiple note files (one for each publication): - The template for notes is used to populate new note files. (Previously it was only used in the case with one big notes file.) Julian, if you could test this branch, that would be fantastic! Here is the code: https://github.com/tmalsburg/helm-bibtex/tree/note-files Titus (Multiple note files will still be possible for users who prefer that.) b) Helm-bibtex identifies which references have a note file, adding a symbol on the reference list. Can we make helm-bibtex look into a single file (say the notes.org file), look for the :Custom_ID: properties of the entries, and use that to mark the reference list? I am teaching myself emacs-lisp but this is above my capacity right now. Yes, something like that needs to be included. The unresolved question is how BibTeX keys should be stored in the notes file. I find property drawers incredibly clunky and in my experience they can considerably slow down Emacs in large org files (that’s the reason why I don’t use org-contacts as much as a would like). My current favorite format for entries in the notes file is the following: * Author: Title (year) :BibTeXkey: Here are the notes … The only problem I see with this is that BibTeX allows keys to contain colons, and a key with a colon would break org’s tag syntax. Suggestions welcome. Titus Many thanks, Julian signature.asc Description: PGP signature
Re: [O] org-ref helm-bibtex notes
Hi Titus, I think a very simple template for the notes file would suffice. I am using org ref and had originally modified the template by removing the TODO, simplifying the properties drawer (no need to duplicate all the biblatex info here) and adding a link to the pdf file, which is very handy when reading my notes file. * [[/path/to/pdf/files/BibTeXkey.pdf][BibTeXkey]] Title :PROPERTIES: :Custom_ID: BibTeXkey :END: Recently I upgraded org-ref and instead of using my own link to the pdf file, I use a cite statement, which gives me all the goodies from org-ref (opening the pdf file, accesing Google Scholar, etc.etc.). * cite:BibTeXkey Title :PROPERTIES: :Custom_ID: BibTeXkey :END: I have no choice between using drawers or tags. I have not experienced slow downs because of using drawers, although tags would make the notes file look cleaner. The issue with keys containing colons could be solved by replacing the colon with some other acceptable character on the tag, like @ or _. So a reference with BibTeXkey Smith,Jones 2008 would get a tag Smith@Jones2008 or Smith_Jones2008. Julian On 2015-06-16 Tue 17:39, Julian Burgos wrote: Dear list, I have been using org-ref for a while, using reftex to insert citations in my org documents. Now I am switching to helm-bibtex, which is pretty awesome. I have a couple of question about the note files. Org-ref uses a single file to keep notes (e.g. notes.org), but helm-bibtex assumes that notes are kept in separate files, one per article. My questions are: a) Do you have a preference in the single file vs multiple files question? Are advantages/disadvantages? I tend to prefer the single file option, it makes search easy and also I can add TODO items that later I can pull out in the agenda view. With multiple files this would not be as easy. Do you agree? Hi, I’m the author of helm-bibtex. There was recently a discussion about this on Github: https://github.com/tmalsburg/helm-bibtex/issues/40 Someone convinced me that storing all notes in one file is better and there is an experimental (and incomplete) implementation in a topic branch: https://github.com/tmalsburg/helm-bibtex/tree/note-files (Multiple note files will still be possible for users who prefer that.) b) Helm-bibtex identifies which references have a note file, adding a symbol on the reference list. Can we make helm-bibtex look into a single file (say the notes.org file), look for the :Custom_ID: properties of the entries, and use that to mark the reference list? I am teaching myself emacs-lisp but this is above my capacity right now. Yes, something like that needs to be included. The unresolved question is how BibTeX keys should be stored in the notes file. I find property drawers incredibly clunky and in my experience they can considerably slow down Emacs in large org files (that’s the reason why I don’t use org-contacts as much as a would like). My current favorite format for entries in the notes file is the following: * Author: Title (year) :BibTeXkey: Here are the notes … The only problem I see with this is that BibTeX allows keys to contain colons, and a key with a colon would break org’s tag syntax. Suggestions welcome. Titus Many thanks, Julian
Re: [O] org-ref helm-bibtex notes
Thanks John. You are right, although I think having to read too many org files would make the agenda run slower. And creates a lot of buffers (one per file) which makes navigation more complicated. I always wished that the agenda would close those buffers. Anyway, I think that having a single file is the best option. Julian Burgos writes: Dear list, I have been using org-ref for a while, using reftex to insert citations in my org documents. Now I am switching to helm-bibtex, which is pretty awesome. I have a couple of question about the note files. Org-ref uses a single file to keep notes (e.g. notes.org), but helm-bibtex assumes that notes are kept in separate files, one per article. My questions are: a) Do you have a preference in the single file vs multiple files question? Are advantages/disadvantages? I tend to prefer the single file option, it makes search easy and also I can add TODO items that later I can pull out in the agenda view. I prefer the single file, for the reasons you describe. With multiple files this would not be as easy. Do you agree? This is not totally true. You can add your directory of org notes to your org-agenda-files, e.g. (setq org-agenda-files '(~/path/to/org-notes)) and it will add all org files in that directory to your agenda. If you use helm, it is probably easy to search all of the files too. -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu
Re: [O] org-ref helm-bibtex notes
Yeah, helm bibtex is awesome. This has been a major topic of discussion in the module development. See: https://github.com/tmalsburg/helm-bibtex/issues/40 Last I talked with the developer, he was thinking hard about it and had maybe even started development on single-note file options. Julian Burgos jul...@hafro.is writes: Dear list, I have been using org-ref for a while, using reftex to insert citations in my org documents. Now I am switching to helm-bibtex, which is pretty awesome. I have a couple of question about the note files. Org-ref uses a single file to keep notes (e.g. notes.org), but helm-bibtex assumes that notes are kept in separate files, one per article. My questions are: a) Do you have a preference in the single file vs multiple files question? Are advantages/disadvantages? I tend to prefer the single file option, it makes search easy and also I can add TODO items that later I can pull out in the agenda view. With multiple files this would not be as easy. Do you agree? b) Helm-bibtex identifies which references have a note file, adding a symbol on the reference list. Can we make helm-bibtex look into a single file (say the notes.org file), look for the :Custom_ID: properties of the entries, and use that to mark the reference list? I am teaching myself emacs-lisp but this is above my capacity right now. Many thanks, Julian
Re: [O] org-ref helm-bibtex notes
Julian Burgos writes: Dear list, I have been using org-ref for a while, using reftex to insert citations in my org documents. Now I am switching to helm-bibtex, which is pretty awesome. I have a couple of question about the note files. Org-ref uses a single file to keep notes (e.g. notes.org), but helm-bibtex assumes that notes are kept in separate files, one per article. My questions are: a) Do you have a preference in the single file vs multiple files question? Are advantages/disadvantages? I tend to prefer the single file option, it makes search easy and also I can add TODO items that later I can pull out in the agenda view. I prefer the single file, for the reasons you describe. With multiple files this would not be as easy. Do you agree? This is not totally true. You can add your directory of org notes to your org-agenda-files, e.g. (setq org-agenda-files '(~/path/to/org-notes)) and it will add all org files in that directory to your agenda. If you use helm, it is probably easy to search all of the files too. -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu
Re: [O] org-ref helm-bibtex notes
On 2015-06-16 Tue 17:39, Julian Burgos wrote: Dear list, I have been using org-ref for a while, using reftex to insert citations in my org documents. Now I am switching to helm-bibtex, which is pretty awesome. I have a couple of question about the note files. Org-ref uses a single file to keep notes (e.g. notes.org), but helm-bibtex assumes that notes are kept in separate files, one per article. My questions are: a) Do you have a preference in the single file vs multiple files question? Are advantages/disadvantages? I tend to prefer the single file option, it makes search easy and also I can add TODO items that later I can pull out in the agenda view. With multiple files this would not be as easy. Do you agree? Hi, I’m the author of helm-bibtex. There was recently a discussion about this on Github: https://github.com/tmalsburg/helm-bibtex/issues/40 Someone convinced me that storing all notes in one file is better and there is an experimental (and incomplete) implementation in a topic branch: https://github.com/tmalsburg/helm-bibtex/tree/note-files (Multiple note files will still be possible for users who prefer that.) b) Helm-bibtex identifies which references have a note file, adding a symbol on the reference list. Can we make helm-bibtex look into a single file (say the notes.org file), look for the :Custom_ID: properties of the entries, and use that to mark the reference list? I am teaching myself emacs-lisp but this is above my capacity right now. Yes, something like that needs to be included. The unresolved question is how BibTeX keys should be stored in the notes file. I find property drawers incredibly clunky and in my experience they can considerably slow down Emacs in large org files (that’s the reason why I don’t use org-contacts as much as a would like). My current favorite format for entries in the notes file is the following: * Author: Title (year) :BibTeXkey: Here are the notes … The only problem I see with this is that BibTeX allows keys to contain colons, and a key with a colon would break org’s tag syntax. Suggestions welcome. Titus Many thanks, Julian signature.asc Description: PGP signature
[O] org-ref helm-bibtex notes
Dear list, I have been using org-ref for a while, using reftex to insert citations in my org documents. Now I am switching to helm-bibtex, which is pretty awesome. I have a couple of question about the note files. Org-ref uses a single file to keep notes (e.g. notes.org), but helm-bibtex assumes that notes are kept in separate files, one per article. My questions are: a) Do you have a preference in the single file vs multiple files question? Are advantages/disadvantages? I tend to prefer the single file option, it makes search easy and also I can add TODO items that later I can pull out in the agenda view. With multiple files this would not be as easy. Do you agree? b) Helm-bibtex identifies which references have a note file, adding a symbol on the reference list. Can we make helm-bibtex look into a single file (say the notes.org file), look for the :Custom_ID: properties of the entries, and use that to mark the reference list? I am teaching myself emacs-lisp but this is above my capacity right now. Many thanks, Julian
