Re: [O] helm-bibtex questions

[John Kitchin]

In org-ref, I have a function that will copy a bibtex entry to the
clipboard in the helm menu for the cite link actions:

https://github.com/jkitchin/org-ref/blob/master/org-ref.el#L3363

And here a menu item to insert a bibtex entry and attach its pdf to an
email:

https://github.com/jkitchin/org-ref/blob/master/org-ref.el#L3382

exactly for those purposes!

>> 5. i love the insert formatted reference (f5) option and use it often
>> sending people references:
>> a. does it also auto send that to the clipboard?
>
> There is currently no way to copy references directly to the
> clipboard.  My recommendation is to use one of Emacs’ mail clients, then
> you don’t need the clipboard.  Mu4e is absolutely fantastic (especially
> when combined with helm-mu).
>
>> b. it cuts most of the authors name and leaves only the first few. is there
>> a switch to get it to print all authors. is that a latex cite formatting
>> issue?
>
> Not sure what you mean by “cuts most of the authors”.  It doesn’t cut
> anything in my setup.  Could you please provide an example?  (Perhaps
> this is something for the issue tracker on Github.)
>
> Best wishes,
>
>   Titus
>
>
>>
>> best and thanks so much again
>>
>> Z
>>
>> On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg <address@hidden>
>> wrote:
>>
>>>
>>>
>>> Here is my CV in org-mode:
>>>
>>>   https://gist.github.com/tmalsburg/96084ba82281937c26b7
>>>
>>> It’s a pretty straightforward org document except for one thing: the key
>>> to making this work was biblatex which can be used to create several
>>> lists of references filtered according to keywords, author, etc.  This
>>> allowed me to have separate sections for journal articles, conference
>>> presentations, etc.  I store the relevant keywords in the tags field of
>>> the BibTeX entries and since biblatex doesn’t know this field, I copy
>>> the tags on-the-fly to the keywords field (see DeclareSourcemap in the
>>> LaTeX headers).
>>>
>>>   Titus
>>>
>>> On 2015-06-22 Mon 07:28, Xebar Saram wrote:
>>> > Hi John
>>> >
>>> > a bit off topic, but do you also write your academic CV in orgmode or
>>> > lateX? in anycase would you mind sharing your org/latex CV template? it
>>> > would be helpful as a starting point for me if thats possible.
>>> >
>>> > kind regards and thanks so much in advance
>>> >
>>> > Z
>>> >
>>> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <address@hidden>
>>> > wrote:
>>> >
>>> >> sweet! I did not know you could do that! I will be refactoring org-ref
>>> >> soon to do that instead of redefining the commands!
>>> >>
>>> >> John
>>> >>
>>> >> -----------------------------------
>>> >> 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
>>> >>
>>> >>
>>> >> On Sun, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
>>> >> address@hidden> wrote:
>>> >>
>>> >>>
>>> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
>>> >>> > Hi again Titus
>>> >>> >
>>> >>> > 2 quick questions that arose from using helm-bitex today extensively:
>>> >>> >
>>> >>> > how does one exclude in the search items? for example i want to
>>> search
>>> >>> for
>>> >>> > xebar without keyword "progress" (I want to exclude in progress
>>> articles
>>> >>> > not published yet)
>>> >>> >
>>> >>> > is it possible to define default enter command in helm-bibtex ?
>>> >>>
>>> >>> Yes.  Helm uses the first action as the default action.  To move an
>>> >>> action to the top of the list you can use the following code:
>>> >>>
>>> >>>   (helm-delete-action-from-source "Insert BibTeX key"
>>> helm-source-bibtex)
>>> >>>   (helm-add-action-to-source "Insert BibTeX key"
>>> 'helm-bibtex-insert-key
>>> >>> helm-source-bibtex 0)
>>> >>>
>>> >>> The second argument in the second line is the function that executes
>>> the
>>> >>> action.  Here is a list of all actions and their functions:
>>> >>>
>>> >>>   Open PDF file (if present): helm-bibtex-open-pdf
>>> >>>   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
>>> >>>   Insert citation: helm-bibtex-insert-citation
>>> >>>   Insert reference: helm-bibtex-insert-reference
>>> >>>   Insert BibTeX key: helm-bibtex-insert-key
>>> >>>   Insert BibTeX entry: helm-bibtex-insert-bibtex
>>> >>>   Attach PDF to email: helm-bibtex-add-PDF-attachment
>>> >>>   Edit notes: helm-bibtex-edit-notes
>>> >>>   Show entry: helm-bibtex-show-entry
>>> >>>
>>> >>> Best,
>>> >>>
>>> >>>   Titus
>>> >>>
>>> >>> >
>>> >>> > best
>>> >>> >
>>> >>> > Z
>>> >>> >
>>> >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
>>> >>> address@hidden>
>>> >>> > wrote:
>>> >>> >
>>> >>> >>
>>> >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
>>> >>> >> > Hi Titus and thx so much for the answers!
>>> >>> >> >
>>> >>> >> > i will in the future use the github page to make requests.
>>> >>> >> >
>>> >>> >> > "The number of matches will be displayed in the mode line. "
>>> >>> >> >
>>> >>> >> > i see that now thx! :) the problem was(is) that its colored black
>>> on
>>> >>> my
>>> >>> >> > black modline BG which makes it invisible ;-) i assume thats an
>>> helm
>>> >>> >> config
>>> >>> >> > i need to change
>>> >>> >> >
>>> >>> >> >
>>> >>> >> > "If you don’t want to type these search expressions, you could
>>> >>> create a
>>> >>> >> > command that invokes helm-bibtex with a default search expression
>>> and
>>> >>> >> that
>>> >>> >> > command could be bound to a keyboard shortcut."
>>> >>> >> >
>>> >>> >> > that would be prefect for me and a solution to my issue. would you
>>> >>> mind
>>> >>> >> > giving an example of such a code chunk. unfortunately i dont know
>>> >>> elisp
>>> >>> >> though
>>> >>> >> > as john recommended i will do my best this summer when the
>>> semester
>>> >>> ends
>>> >>> >> to
>>> >>> >> > try and pick it up :)
>>> >>> >>
>>> >>> >> Sure, here you go:
>>> >>> >>
>>> >>> >> #+BEGIN_SRC elisp
>>> >>> >> ;; Define helm-search with predefined search expression:
>>> >>> >> (defun helm-bibtex-my-publications ()
>>> >>> >>   "Search BibTeX entries authored by Xebar Saram."
>>> >>> >>   (interactive)
>>> >>> >>   (helm :sources '(helm-source-bibtex)
>>> >>> >>         :full-frame t
>>> >>> >>         :input "xebar saram"
>>> >>> >>         :candidate-number-limit 500))
>>> >>> >>
>>> >>> >> ;; Bind this search function to Ctrl-x p:
>>> >>> >> (global-set-key (kbd "C-x p") 'helm-bibtex-my-publications)
>>> >>> >> #+END_SRC
>>> >>> >>
>>> >>> >> > i will definitely use your tag system as you recommended, sounds
>>> >>> perfect
>>> >>> >> > for me
>>> >>> >>
>>> >>> >> The tag system also comes in handy when generating publication lists
>>> >>> for
>>> >>> >> CVs and web pages because BibTeX does not distinguish between
>>> >>> conference
>>> >>> >> papers, posters, and talks.  If you have tags for that, it’s
>>> relatively
>>> >>> >> easy to create separate sections for these types of publications
>>> using
>>> >>> >> biblatex or bib2bib and bibtex2html in the case of web pages.
>>> >>> >>
>>> >>> >> > thanks again for your kind help and the amazing app ;-)
>>> >>> >>
>>> >>> >> You are welcome.
>>> >>> >>
>>> >>> >>   Titus
>>> >>> >>
>>> >>> >> >
>>> >>> >> > best
>>> >>> >> >
>>> >>> >> > Z
>>> >>> >> >
>>> >>> >> >
>>> >>> >> >
>>> >>> >> > On Wed, Jun 17, 2015 at 11:02 PM, Titus von der Malsburg <
>>> >>> >> address@hidden
>>> >>> >> >> wrote:
>>> >>> >> >
>>> >>> >> >>
>>> >>> >> >> On 2015-06-17 Wed 11:08, Xebar Saram wrote:
>>> >>> >> >> > Hi Titus
>>> >>> >> >> >
>>> >>> >> >> > I have been exploring helm-bibtex a bit today and have some
>>> >>> questions.
>>> >>> >> >> btw
>>> >>> >> >> > is this the preferred way to make requests/ask questions or is
>>> >>> >> >> > github preferred?
>>> >>> >> >>
>>> >>> >> >> Helm-bibtex is not part of org (although it tries to work well
>>> with
>>> >>> >> >> org).  So I’m not sure whether this list is the best place for
>>> >>> >> >> discussing it.  For now the issue tracker on Github might be a
>>> >>> better
>>> >>> >> >> option:
>>> >>> >> >>
>>> >>> >> >>   https://github.com/tmalsburg/helm-bibtex/issues
>>> >>> >> >>
>>> >>> >> >> > in any case i was wondering a few things:
>>> >>> >> >> >
>>> >>> >> >> > 1. is it possible to have custom sorting? i want all views to
>>> >>> sort by
>>> >>> >> >> > Author, year, month
>>> >>> >> >>
>>> >>> >> >> I prefer to see the entries in the (inverse) order in which they
>>> >>> appear
>>> >>> >> >> in the BibTeX file.  This way, recent additions show up at the
>>> >>> >> >> top.  However, I agree that sorting would be useful (see issues
>>> #5
>>> >>> and
>>> >>> >> >> #21); it just doesn’t have high priority for me.  Pull requests
>>> >>> welcome.
>>> >>> >> >>
>>> >>> >> >> > 2. i would really like a way to have stored smart groups (like
>>> the
>>> >>> >> jabref
>>> >>> >> >> > dynamic groups if your aware of that). that is for example
>>> create
>>> >>> a
>>> >>> >> group
>>> >>> >> >> > that auto selects all publications i have (by my first/last
>>> name)
>>> >>> and
>>> >>> >> >> shows
>>> >>> >> >> > the count (in numbers) of these publications.
>>> >>> >> >>
>>> >>> >> >> I’m not familiar with smart groups but it seems that all
>>> >>> helm-bibtex is
>>> >>> >> >> doing is giving you very flexible smart groups defined by your
>>> >>> search
>>> >>> >> >> expressions.  For example, if you want a list of your
>>> publications,
>>> >>> you
>>> >>> >> >> can simple enter your name.  And if you want a list of your
>>> >>> articles,
>>> >>> >> >> you can enter your name + “article”.  If you want all your
>>> articles
>>> >>> from
>>> >>> >> >> 2010, enter your name + “articles 2010”.  And so on.  The number
>>> of
>>> >>> >> >> matches will be displayed in the mode line.  If you don’t want to
>>> >>> type
>>> >>> >> >> these search expressions, you could create a command that invokes
>>> >>> >> >> helm-bibtex with a default search expression and that command
>>> could
>>> >>> be
>>> >>> >> >> bound to a keyboard shortcut.
>>> >>> >> >>
>>> >>> >> >> > Another example is a group to keep track of all the papers im
>>> >>> working
>>> >>> >> on
>>> >>> >> >> or
>>> >>> >> >> > invloved with by matching keyword author and prep/*other key
>>> word
>>> >>> >> >>
>>> >>> >> >> I use two BibTeX fields to tag entries: “keywords” for keywords
>>> >>> >> >> describing the content of the paper (as usual) and “tags” for
>>> meta
>>> >>> >> >> data.  Values that I use in tags are “own”, “manuscript”,
>>> “poster”,
>>> >>> >> >> “talk”, … So if I want a list of all articles in progress, I
>>> search
>>> >>> for
>>> >>> >> >> “own manuscript”.  Since the tags field is non-standard, it has
>>> to
>>> >>> be
>>> >>> >> >> added to `helm-bibtex-additional-search-fields`.
>>> >>> >> >>
>>> >>> >> >> Another solution would be to use the pubstate field and to search
>>> >>> for
>>> >>> >> >> your name and “forthcoming” (add pubstate to
>>> >>> >> >> helm-bibtex-additional-search-fields for this to work).
>>> >>> >> >>
>>> >>> >> >> > 3.is it possible to ass an option to auto generate a bibkey
>>> for a
>>> >>> >> >> selected
>>> >>> >> >> > citation based on user criteria such as
>>> author(date)short-title?
>>> >>> >> >>
>>> >>> >> >> Maintaining the content of the BibTeX file not really in the
>>> scope
>>> >>> of
>>> >>> >> >> helm-bibtex (I prefer to write my BibTeX entries by hand).
>>> Perhaps
>>> >>> >> >> org-ref or ebib can help here?  Once you have a function that
>>> >>> generates
>>> >>> >> >> a new key and inserts it in the BibTeX file, you can easily add
>>> it
>>> >>> to
>>> >>> >> >> the list of actions in helm-bibtex.
>>> >>> >> >>
>>> >>> >> >> Hope that helps.
>>> >>> >> >>
>>> >>> >> >>   Titus
>>> >>> >> >>
>>> >>> >> >> > thx so much in advance, you and john have given me confidence
>>> to
>>> >>> >> finally
>>> >>> >> >> > dive into the whole latex/bibteX world
>>> >>> >> >> >
>>> >>> >> >> > best
>>> >>> >> >> >
>>> >>> >> >> > Z
>>> >>> >> >>
>>> >>> >> >>
>>> >>> >>
>>> >>> >>
>>> >>>
>>> >>>
>>> >>
>>>
>>>

--
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