Friday, March 4, 2016

Bibdesk annotations in TeX preview

If you would like to display the annotations you do in bibdesk in the TeX preview then you can do so as follows.

The annotations you make are kept in a bibtex field called "Annote".

We need a bibtex style file (bst) that supports this annote field.
You can copy paste the plainannotate.bst file at the end of this post.

Next, create the following directory
~/Library/texmf/bibtex/bst
and put the style file there.

Now from Bibdesk set the preferences as follows


That is it





% BibTeX standard bibliography style `plain'
   % Version 0.99b (8-Dec-10 release) for BibTeX versions 0.99a or later.
   % Copyright (C) 1984, 1985, 1988, 2010 Howard Trickey and Oren Patashnik.
   % Unlimited copying and redistribution of this file are permitted as long as
   % it is unmodified.  Modifications (and redistribution of modified versions)
   % are also permitted, but only if the resulting file is renamed to something
   % besides btxbst.doc, plain.bst, unsrt.bst, alpha.bst, and abbrv.bst.
   % This restriction helps ensure that all standard styles are identical.
   % The file btxbst.doc has the documentation for this style.

ENTRY
  { address
    annote
    author
    booktitle
    chapter
    edition
    editor
    howpublished
    institution
    journal
    key
    month
    note
    number
    organization
    pages
    publisher
    school
    series
    title
    type
    volume
    year
  }
  {}
  { label }

INTEGERS { output.state before.all mid.sentence after.sentence after.block }

FUNCTION {init.state.consts}
{ #0 'before.all :=
  #1 'mid.sentence :=
  #2 'after.sentence :=
  #3 'after.block :=
}

STRINGS { s t }

FUNCTION {output.nonnull}
{ 's :=
  output.state mid.sentence =
    { ", " * write$ }
    { output.state after.block =
        { add.period$ write$
          newline$
          "\newblock " write$
        }
        { output.state before.all =
            'write$
            { add.period$ " " * write$ }
          if$
        }
      if$
      mid.sentence 'output.state :=
    }
  if$
  s
}

FUNCTION {output}
{ duplicate$ empty$
    'pop$
    'output.nonnull
  if$
}

FUNCTION {output.check}
{ 't :=
  duplicate$ empty$
    { pop$ "empty " t * " in " * cite$ * warning$ }
    'output.nonnull
  if$
}

FUNCTION {output.bibitem}
{ newline$
  "\bibitem{" write$
  cite$ write$
  "}" write$
  newline$
  ""
  before.all 'output.state :=
}

FUNCTION {fin.entry}
{ add.period$
  write$
  newline$
}

FUNCTION {new.block}
{ output.state before.all =
    'skip$
    { after.block 'output.state := }
  if$
}

FUNCTION {new.sentence}
{ output.state after.block =
    'skip$
    { output.state before.all =
        'skip$
        { after.sentence 'output.state := }
      if$
    }
  if$
}

FUNCTION {not}
{   { #0 }
    { #1 }
  if$
}

FUNCTION {and}
{   'skip$
    { pop$ #0 }
  if$
}

FUNCTION {or}
{   { pop$ #1 }
    'skip$
  if$
}

FUNCTION {new.block.checka}
{ empty$
    'skip$
    'new.block
  if$
}

FUNCTION {new.block.checkb}
{ empty$
  swap$ empty$
  and
    'skip$
    'new.block
  if$
}

FUNCTION {new.sentence.checka}
{ empty$
    'skip$
    'new.sentence
  if$
}

FUNCTION {new.sentence.checkb}
{ empty$
  swap$ empty$
  and
    'skip$
    'new.sentence
  if$
}

FUNCTION {field.or.null}
{ duplicate$ empty$
    { pop$ "" }
    'skip$
  if$
}

FUNCTION {emphasize}
{ duplicate$ empty$
    { pop$ "" }
    { "{\em " swap$ * "}" * }
  if$
}

INTEGERS { nameptr namesleft numnames }

FUNCTION {format.names}
{ 's :=
  #1 'nameptr :=
  s num.names$ 'numnames :=
  numnames 'namesleft :=
    { namesleft #0 > }
    { s nameptr "{ff~}{vv~}{ll}{, jj}" format.name$ 't :=
      nameptr #1 >
        { namesleft #1 >
            { ", " * t * }
            { numnames #2 >
                { "," * }
                'skip$
              if$
              t "others" =
                { " et~al." * }
                { " and " * t * }
              if$
            }
          if$
        }
        't
      if$
      nameptr #1 + 'nameptr :=
      namesleft #1 - 'namesleft :=
    }
  while$
}

FUNCTION {format.authors}
{ author empty$
    { "" }
    { author format.names }
  if$
}

FUNCTION {format.annote}
{ annote empty$
    { "" }
    { " \begin{quotation}\noindent "
      annote
      * " \end{quotation} " *
    }
      if$
}


FUNCTION {format.editors}
{ editor empty$
    { "" }
    { editor format.names
      editor num.names$ #1 >
        { ", editors" * }
        { ", editor" * }
      if$
    }
  if$
}

FUNCTION {format.title}
{ title empty$
    { "" }
    { title "t" change.case$ }
  if$
}

FUNCTION {n.dashify}
{ 't :=
  ""
    { t empty$ not }
    { t #1 #1 substring$ "-" =
        { t #1 #2 substring$ "--" = not
            { "--" *
              t #2 global.max$ substring$ 't :=
            }
            {   { t #1 #1 substring$ "-" = }
                { "-" *
                  t #2 global.max$ substring$ 't :=
                }
              while$
            }
          if$
        }
        { t #1 #1 substring$ *
          t #2 global.max$ substring$ 't :=
        }
      if$
    }
  while$
}

FUNCTION {format.date}
{ year empty$
    { month empty$
        { "" }
        { "there's a month but no year in " cite$ * warning$
          month
        }
      if$
    }
    { month empty$
        'year
        { month " " * year * }
      if$
    }
  if$
}

FUNCTION {format.btitle}
{ title emphasize
}

FUNCTION {tie.or.space.connect}
{ duplicate$ text.length$ #3 <
    { "~" }
    { " " }
  if$
  swap$ * *
}

FUNCTION {either.or.check}
{ empty$
    'pop$
    { "can't use both " swap$ * " fields in " * cite$ * warning$ }
  if$
}

FUNCTION {format.bvolume}
{ volume empty$
    { "" }
    { "volume" volume tie.or.space.connect
      series empty$
        'skip$
        { " of " * series emphasize * }
      if$
      "volume and number" number either.or.check
    }
  if$
}

FUNCTION {format.number.series}
{ volume empty$
    { number empty$
        { series field.or.null }
        { output.state mid.sentence =
            { "number" }
            { "Number" }
          if$
          number tie.or.space.connect
          series empty$
            { "there's a number but no series in " cite$ * warning$ }
            { " in " * series * }
          if$
        }
      if$
    }
    { "" }
  if$
}

FUNCTION {format.edition}
{ edition empty$
    { "" }
    { output.state mid.sentence =
        { edition "l" change.case$ " edition" * }
        { edition "t" change.case$ " edition" * }
      if$
    }
  if$
}

INTEGERS { multiresult }

FUNCTION {multi.page.check}
{ 't :=
  #0 'multiresult :=
    { multiresult not
      t empty$ not
      and
    }
    { t #1 #1 substring$
      duplicate$ "-" =
      swap$ duplicate$ "," =
      swap$ "+" =
      or or
        { #1 'multiresult := }
        { t #2 global.max$ substring$ 't := }
      if$
    }
  while$
  multiresult
}

FUNCTION {format.pages}
{ pages empty$
    { "" }
    { pages multi.page.check
        { "pages" pages n.dashify tie.or.space.connect }
        { "page" pages tie.or.space.connect }
      if$
    }
  if$
}

FUNCTION {format.vol.num.pages}
{ volume field.or.null
  number empty$
    'skip$
    { "(" number * ")" * *
      volume empty$
        { "there's a number but no volume in " cite$ * warning$ }
        'skip$
      if$
    }
  if$
  pages empty$
    'skip$
    { duplicate$ empty$
        { pop$ format.pages }
        { ":" * pages n.dashify * }
      if$
    }
  if$
}

FUNCTION {format.chapter.pages}
{ chapter empty$
    'format.pages
    { type empty$
        { "chapter" }
        { type "l" change.case$ }
      if$
      chapter tie.or.space.connect
      pages empty$
        'skip$
        { ", " * format.pages * }
      if$
    }
  if$
}

FUNCTION {format.in.ed.booktitle}
{ booktitle empty$
    { "" }
    { editor empty$
        { "In " booktitle emphasize * }
        { "In " format.editors * ", " * booktitle emphasize * }
      if$
    }
  if$
}

FUNCTION {empty.misc.check}
{ author empty$ title empty$ howpublished empty$
  month empty$ year empty$ note empty$
  and and and and and
  key empty$ not and
    { "all relevant fields are empty in " cite$ * warning$ }
    'skip$
  if$
}

FUNCTION {format.thesis.type}
{ type empty$
    'skip$
    { pop$
      type "t" change.case$
    }
  if$
}

FUNCTION {format.tr.number}
{ type empty$
    { "Technical Report" }
    'type
  if$
  number empty$
    { "t" change.case$ }
    { number tie.or.space.connect }
  if$
}

FUNCTION {format.article.crossref}
{ key empty$
    { journal empty$
        { "need key or journal for " cite$ * " to crossref " * crossref *
          warning$
          ""
        }
        { "In {\em " journal * "\/}" * }
      if$
    }
    { "In " key * }
  if$
  " \cite{" * crossref * "}" *
}

FUNCTION {format.crossref.editor}
{ editor #1 "{vv~}{ll}" format.name$
  editor num.names$ duplicate$
  #2 >
    { pop$ " et~al." * }
    { #2 <
        'skip$
        { editor #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" =
            { " et~al." * }
            { " and " * editor #2 "{vv~}{ll}" format.name$ * }
          if$
        }
      if$
    }
  if$
}

FUNCTION {format.book.crossref}
{ volume empty$
    { "empty volume in " cite$ * "'s crossref of " * crossref * warning$
      "In "
    }
    { "Volume" volume tie.or.space.connect
      " of " *
    }
  if$
  editor empty$
  editor field.or.null author field.or.null =
  or
    { key empty$
        { series empty$
            { "need editor, key, or series for " cite$ * " to crossref " *
              crossref * warning$
              "" *
            }
            { "{\em " * series * "\/}" * }
          if$
        }
        { key * }
      if$
    }
    { format.crossref.editor * }
  if$
  " \cite{" * crossref * "}" *
}

FUNCTION {format.incoll.inproc.crossref}
{ editor empty$
  editor field.or.null author field.or.null =
  or
    { key empty$
        { booktitle empty$
            { "need editor, key, or booktitle for " cite$ * " to crossref " *
              crossref * warning$
              ""
            }
            { "In {\em " booktitle * "\/}" * }
          if$
        }
        { "In " key * }
      if$
    }
    { "In " format.crossref.editor * }
  if$
  " \cite{" * crossref * "}" *
}

FUNCTION {article}
{ output.bibitem
  format.authors "author" output.check
  new.block
  format.title "title" output.check
  new.block
  crossref missing$
    { journal emphasize "journal" output.check
      format.vol.num.pages output
      format.date "year" output.check
    }
    { format.article.crossref output.nonnull
      format.pages output
    }
  if$
  new.block
  note output
  fin.entry
  format.annote write$
  newline$
}

FUNCTION {book}
{ output.bibitem
  author empty$
    { format.editors "author and editor" output.check }
    { format.authors output.nonnull
      crossref missing$
        { "author and editor" editor either.or.check }
        'skip$
      if$
    }
  if$
  new.block
  format.btitle "title" output.check
  crossref missing$
    { format.bvolume output
      new.block
      format.number.series output
      new.sentence
      publisher "publisher" output.check
      address output
    }
    { new.block
      format.book.crossref output.nonnull
    }
  if$
  format.edition output
  format.date "year" output.check
  new.block
  note output
  fin.entry
}

FUNCTION {booklet}
{ output.bibitem
  format.authors output
  new.block
  format.title "title" output.check
  howpublished address new.block.checkb
  howpublished output
  address output
  format.date output
  new.block
  note output
  fin.entry
}

FUNCTION {inbook}
{ output.bibitem
  author empty$
    { format.editors "author and editor" output.check }
    { format.authors output.nonnull
      crossref missing$
        { "author and editor" editor either.or.check }
        'skip$
      if$
    }
  if$
  new.block
  format.btitle "title" output.check
  crossref missing$
    { format.bvolume output
      format.chapter.pages "chapter and pages" output.check
      new.block
      format.number.series output
      new.sentence
      publisher "publisher" output.check
      address output
    }
    { format.chapter.pages "chapter and pages" output.check
      new.block
      format.book.crossref output.nonnull
    }
  if$
  format.edition output
  format.date "year" output.check
  new.block
  note output
  fin.entry
}

FUNCTION {incollection}
{ output.bibitem
  format.authors "author" output.check
  new.block
  format.title "title" output.check
  new.block
  crossref missing$
    { format.in.ed.booktitle "booktitle" output.check
      format.bvolume output
      format.number.series output
      format.chapter.pages output
      new.sentence
      publisher "publisher" output.check
      address output
      format.edition output
      format.date "year" output.check
    }
    { format.incoll.inproc.crossref output.nonnull
      format.chapter.pages output
    }
  if$
  new.block
  note output
  fin.entry
}

FUNCTION {inproceedings}
{ output.bibitem
  format.authors "author" output.check
  new.block
  format.title "title" output.check
  new.block
  crossref missing$
    { format.in.ed.booktitle "booktitle" output.check
      format.bvolume output
      format.number.series output
      format.pages output
      address empty$
        { organization publisher new.sentence.checkb
          organization output
          publisher output
          format.date "year" output.check
        }
        { address output.nonnull
          format.date "year" output.check
          new.sentence
          organization output
          publisher output
        }
      if$
    }
    { format.incoll.inproc.crossref output.nonnull
      format.pages output
    }
  if$
  new.block
  note output
  fin.entry
  format.annote write$
}

FUNCTION {conference} { inproceedings }

FUNCTION {manual}
{ output.bibitem
  author empty$
    { organization empty$
        'skip$
        { organization output.nonnull
          address output
        }
      if$
    }
    { format.authors output.nonnull }
  if$
  new.block
  format.btitle "title" output.check
  author empty$
    { organization empty$
        { address new.block.checka
          address output
        }
        'skip$
      if$
    }
    { organization address new.block.checkb
      organization output
      address output
    }
  if$
  format.edition output
  format.date output
  new.block
  note output
  fin.entry
}

FUNCTION {mastersthesis}
{ output.bibitem
  format.authors "author" output.check
  new.block
  format.title "title" output.check
  new.block
  "Master's thesis" format.thesis.type output.nonnull
  school "school" output.check
  address output
  format.date "year" output.check
  new.block
  note output
  fin.entry
}

FUNCTION {misc}
{ output.bibitem
  format.authors output
  title howpublished new.block.checkb
  format.title output
  howpublished new.block.checka
  howpublished output
  format.date output
  new.block
  note output
  fin.entry
  empty.misc.check
}

FUNCTION {phdthesis}
{ output.bibitem
  format.authors "author" output.check
  new.block
  format.btitle "title" output.check
  new.block
  "PhD thesis" format.thesis.type output.nonnull
  school "school" output.check
  address output
  format.date "year" output.check
  new.block
  note output
  fin.entry
}

FUNCTION {proceedings}
{ output.bibitem
  editor empty$
    { organization output }
    { format.editors output.nonnull }
  if$
  new.block
  format.btitle "title" output.check
  format.bvolume output
  format.number.series output
  address empty$
    { editor empty$
        { publisher new.sentence.checka }
        { organization publisher new.sentence.checkb
          organization output
        }
      if$
      publisher output
      format.date "year" output.check
    }
    { address output.nonnull
      format.date "year" output.check
      new.sentence
      editor empty$
        'skip$
        { organization output }
      if$
      publisher output
    }
  if$
  new.block
  note output
  fin.entry
}

FUNCTION {techreport}
{ output.bibitem
  format.authors "author" output.check
  new.block
  format.title "title" output.check
  new.block
  format.tr.number output.nonnull
  institution "institution" output.check
  address output
  format.date "year" output.check
  new.block
  note output
  fin.entry
}

FUNCTION {unpublished}
{ output.bibitem
  format.authors "author" output.check
  new.block
  format.title "title" output.check
  new.block
  note "note" output.check
  format.date output
  fin.entry
}

FUNCTION {default.type} { misc }

MACRO {jan} {"January"}

MACRO {feb} {"February"}

MACRO {mar} {"March"}

MACRO {apr} {"April"}

MACRO {may} {"May"}

MACRO {jun} {"June"}

MACRO {jul} {"July"}

MACRO {aug} {"August"}

MACRO {sep} {"September"}

MACRO {oct} {"October"}

MACRO {nov} {"November"}

MACRO {dec} {"December"}

MACRO {acmcs} {"ACM Computing Surveys"}

MACRO {acta} {"Acta Informatica"}

MACRO {cacm} {"Communications of the ACM"}

MACRO {ibmjrd} {"IBM Journal of Research and Development"}

MACRO {ibmsj} {"IBM Systems Journal"}

MACRO {ieeese} {"IEEE Transactions on Software Engineering"}

MACRO {ieeetc} {"IEEE Transactions on Computers"}

MACRO {ieeetcad}
 {"IEEE Transactions on Computer-Aided Design of Integrated Circuits"}

MACRO {ipl} {"Information Processing Letters"}

MACRO {jacm} {"Journal of the ACM"}

MACRO {jcss} {"Journal of Computer and System Sciences"}

MACRO {scp} {"Science of Computer Programming"}

MACRO {sicomp} {"SIAM Journal on Computing"}

MACRO {tocs} {"ACM Transactions on Computer Systems"}

MACRO {tods} {"ACM Transactions on Database Systems"}

MACRO {tog} {"ACM Transactions on Graphics"}

MACRO {toms} {"ACM Transactions on Mathematical Software"}

MACRO {toois} {"ACM Transactions on Office Information Systems"}

MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"}

MACRO {tcs} {"Theoretical Computer Science"}

READ

FUNCTION {sortify}
{ purify$
  "l" change.case$
}

INTEGERS { len }

FUNCTION {chop.word}
{ 's :=
  'len :=
  s #1 len substring$ =
    { s len #1 + global.max$ substring$ }
    's
  if$
}

FUNCTION {sort.format.names}
{ 's :=
  #1 'nameptr :=
  ""
  s num.names$ 'numnames :=
  numnames 'namesleft :=
    { namesleft #0 > }
    { nameptr #1 >
        { "   " * }
        'skip$
      if$
      s nameptr "{vv{ } }{ll{ }}{  ff{ }}{  jj{ }}" format.name$ 't :=
      nameptr numnames = t "others" = and
        { "et al" * }
        { t sortify * }
      if$
      nameptr #1 + 'nameptr :=
      namesleft #1 - 'namesleft :=
    }
  while$
}

FUNCTION {sort.format.title}
{ 't :=
  "A " #2
    "An " #3
      "The " #4 t chop.word
    chop.word
  chop.word
  sortify
  #1 global.max$ substring$
}

FUNCTION {author.sort}
{ author empty$
    { key empty$
        { "to sort, need author or key in " cite$ * warning$
          ""
        }
        { key sortify }
      if$
    }
    { author sort.format.names }
  if$
}

FUNCTION {author.editor.sort}
{ author empty$
    { editor empty$
        { key empty$
            { "to sort, need author, editor, or key in " cite$ * warning$
              ""
            }
            { key sortify }
          if$
        }
        { editor sort.format.names }
      if$
    }
    { author sort.format.names }
  if$
}

FUNCTION {author.organization.sort}
{ author empty$
    { organization empty$
        { key empty$
            { "to sort, need author, organization, or key in " cite$ * warning$
              ""
            }
            { key sortify }
          if$
        }
        { "The " #4 organization chop.word sortify }
      if$
    }
    { author sort.format.names }
  if$
}

FUNCTION {editor.organization.sort}
{ editor empty$
    { organization empty$
        { key empty$
            { "to sort, need editor, organization, or key in " cite$ * warning$
              ""
            }
            { key sortify }
          if$
        }
        { "The " #4 organization chop.word sortify }
      if$
    }
    { editor sort.format.names }
  if$
}

FUNCTION {presort}
{ type$ "book" =
  type$ "inbook" =
  or
    'author.editor.sort
    { type$ "proceedings" =
        'editor.organization.sort
        { type$ "manual" =
            'author.organization.sort
            'author.sort
          if$
        }
      if$
    }
  if$
  "    "
  *
  year field.or.null sortify
  *
  "    "
  *
  title field.or.null
  sort.format.title
  *
  #1 entry.max$ substring$
  'sort.key$ :=
}

ITERATE {presort}

SORT

STRINGS { longest.label }

INTEGERS { number.label longest.label.width }

FUNCTION {initialize.longest.label}
{ "" 'longest.label :=
  #1 'number.label :=
  #0 'longest.label.width :=
}

FUNCTION {longest.label.pass}
{ number.label int.to.str$ 'label :=
  number.label #1 + 'number.label :=
  label width$ longest.label.width >
    { label 'longest.label :=
      label width$ 'longest.label.width :=
    }
    'skip$
  if$
}

EXECUTE {initialize.longest.label}

ITERATE {longest.label.pass}

FUNCTION {begin.bib}
{ preamble$ empty$
    'skip$
    { preamble$ write$ newline$ }
  if$
  "\begin{thebibliography}{"  longest.label  * "}" * write$ newline$
}

EXECUTE {begin.bib}

EXECUTE {init.state.consts}

ITERATE {call.type$}

FUNCTION {end.bib}
{ newline$
  "\end{thebibliography}" write$ newline$
}

EXECUTE {end.bib}

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Continuously monitor GPU usage

 For nvidia GPUs do the follwing: nvidia-smi -l 1