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474 lines
20 KiB
474 lines
20 KiB
;;; org-ref-helm.el --- Generic helm functions for org-ref -*- lexical-binding: t; -*-
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;; Copyright (C) 2016 John Kitchin
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;; Author: John Kitchin <jkitchin@andrew.cmu.edu>
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;; Keywords:
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;; This program is free software; you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation, either version 3 of the License, or
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;; (at your option) any later version.
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;; This program is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;; You should have received a copy of the GNU General Public License
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;; along with this program. If not, see <http://www.gnu.org/licenses/>.
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;;; Commentary:
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;; These are not specific to helm-bibtex.
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;;; Code:
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(declare-function 'org-ref-get-bibtex-key-and-file "org-ref-core.el")
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(declare-function 'org-ref-bad-file-link-candidates "org-ref-core.el")
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(declare-function 'org-ref-get-labels "org-ref-core.el")
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(declare-function 'org-ref-bad-cite-candidates "org-ref-core.el")
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(declare-function 'org-ref-bad-ref-candidates "org-ref-core.el")
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(declare-function 'org-ref-bad-label-candidates "org-ref-core.el")
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(require 'helm)
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(require 'org-element)
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(require 'org-ref-core)
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;;;###autoload
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(defun org-ref-helm-insert-label-link ()
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"Insert label link at point.
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Helm will display existing labels in the current buffer to avoid
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duplication. If you use a prefix arg insert a radio target
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instead of a label."
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(interactive)
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(let ((labels (org-ref-get-labels)))
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(helm :sources `(,(helm-build-sync-source "Existing labels"
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:candidates labels
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:action (lambda (label)
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(with-helm-current-buffer
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(org-open-link-from-string
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(format "ref:%s" label)))))
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,(helm-build-dummy-source "Create new label"
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:action (lambda (label)
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(with-helm-current-buffer
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(if helm-current-prefix-arg
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(insert (concat "<<" label ">>"))
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(insert (concat "label:" label)))))))
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:buffer "*helm labels*")))
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;;;###autoload
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(defun org-ref-helm-insert-ref-link ()
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"Helm menu to insert ref links to labels in the document.
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If you are on link, replace with newly selected label. Use
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\\[universal-argument] to insert a different kind of ref link.
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Use a double \\[universal-argument] \\[universal-argument] to insert a
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[[#custom-id]] link"
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(interactive)
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(let* ((labels (org-ref-get-labels))
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(contexts (mapcar 'org-ref-get-label-context labels))
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(cb (current-buffer)))
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(helm :input (thing-at-point 'word)
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:sources `(((name . "Available labels to ref")
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(multiline)
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(candidates . ,(cl-loop for label in labels
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for context in contexts
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;; we do some kludgy adding spaces
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;; and bars to make it "easier" to
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;; see in helm.
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collect (cons (concat
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label "\n"
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(mapconcat
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(lambda (x)
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(concat " |" x))
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(split-string context "\n")
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"\n"
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) "\n\n") label)))
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;; default action to replace or insert ref link.
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(action . (lambda (label)
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(switch-to-buffer ,cb)
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(cond
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;; no prefix or on a link
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((equal helm-current-prefix-arg nil)
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(let* ((object (org-element-context))
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(last-char
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(save-excursion
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(goto-char (org-element-property :end object))
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(backward-char)
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(if (looking-at " ")
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" "
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""))))
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(if (-contains? org-ref-ref-types
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(org-element-property :type object))
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;; we are on a link, so replace it.
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(setf
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(buffer-substring
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(org-element-property :begin object)
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(org-element-property :end object))
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(concat
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(replace-regexp-in-string
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(org-element-property :path object)
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label
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(org-element-property :raw-link object))
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last-char))
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;; insert a new link
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(insert
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(concat
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org-ref-default-ref-type ":" label))
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)))
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;; one prefix, alternate ref link
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((equal helm-current-prefix-arg '(4))
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(insert
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(concat
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(helm :sources `((name . "Ref link types")
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(candidates . ,org-ref-ref-types)
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(action . (lambda (x) x))))
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":" label)))
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;; two prefixes, insert section custom-id link
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((equal helm-current-prefix-arg '(16))
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(insert
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(format "[[#%s]]" label)))))))))))
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;;;###autoload
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(defun org-ref ()
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"Opens a helm interface to actions for `org-ref'.
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Shows bad citations, ref links and labels.
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This widens the file so that all links go to the right place."
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(interactive)
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;; (widen)
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;; (org-cycle '(64))
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(let ((cb (current-buffer))
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(bad-citations (org-ref-bad-cite-candidates))
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(bad-refs (org-ref-bad-ref-candidates))
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(bad-labels (org-ref-bad-label-candidates))
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(bad-files (org-ref-bad-file-link-candidates))
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(bib-candidates '())
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(unreferenced-labels '())
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natbib-required
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natbib-used
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cleveref-required
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cleveref-used
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biblatex-required
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biblatex-used
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(org-latex-prefer-user-labels (and (boundp 'org-latex-prefer-user-labels)
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org-latex-prefer-user-labels)))
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;; See if natbib, biblatex or cleveref are required
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(org-element-map (org-element-parse-buffer) 'link
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(lambda (link)
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(when (member (org-element-property :type link) org-ref-natbib-types)
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(setq natbib-required t))
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(when (member (org-element-property :type link) org-ref-biblatex-types)
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(setq biblatex-required t))
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(when (member (org-element-property :type link) '("cref" "Cref"))
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(setq cleveref-required t)))
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nil t)
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;; See if natbib is probably used. This will miss a case where natbib is included somehow.
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(setq natbib-used
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(or
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(member "natbib" (mapcar (lambda (x) (when (listp x) (nth 1 x))) org-latex-default-packages-alist))
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(member "natbib" (mapcar (lambda (x) (when (listp x) (nth 1 x))) org-latex-packages-alist))
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;; see of something like \usepackage{natbib} exists.
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(save-excursion
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(goto-char (point-min))
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(re-search-forward "{natbib}" nil t))))
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(setq biblatex-used
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(or
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(member "biblatex" (mapcar (lambda (x) (when (listp x) (nth 1 x))) org-latex-default-packages-alist))
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(member "biblatex" (mapcar (lambda (x) (when (listp x) (nth 1 x))) org-latex-packages-alist))
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;; see of something like \usepackage{biblatex} exists.
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(save-excursion
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(goto-char (point-min))
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(re-search-forward "{biblatex}" nil t))))
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(setq cleveref-used
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(or
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(member "cleveref" (mapcar (lambda (x) (when (listp x) (nth 1 x))) org-latex-default-packages-alist))
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(member "cleveref" (mapcar (lambda (x) (when (listp x) (nth 1 x))) org-latex-packages-alist))
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;; see of something like \usepackage{cleveref} exists.
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(save-excursion
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(goto-char (point-min))
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(re-search-forward "{cleveref}" nil t))))
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;; setup bib-candidates. This checks a variety of things in the
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;; bibliography, bibtex files. check for which bibliographies are used
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(cl-pushnew
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(cons (format "Using these bibtex files: %s"
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(org-ref-find-bibliography))
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(lambda () nil))
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bib-candidates)
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;; Check bibliography style exists
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(save-excursion
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(goto-char 0)
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(unless (re-search-forward "bibliographystyle:\\|\\\\bibliographystyle{" nil t)
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(cl-pushnew
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(cons "No bibliographystyle found."
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(lambda ()
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(switch-to-buffer "*org-ref*")
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(erase-buffer)
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(insert "No bibliography style found. This may be ok, if your latex class style sets that up, but if not this is an error. Try adding something like:
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bibliographystyle:unsrt
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at the end of you file.
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")
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(org-mode)))
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bib-candidates)))
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;; Check if latex knows of the bibliographystyle. We only check links here.
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;; I also assume this style exists as a bst file that kpsewhich can find.
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(save-excursion
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(goto-char 0)
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(when (re-search-forward "bibliographystyle:" nil t)
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;; on a link. get style
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(let ((path (org-element-property :path (org-element-context))))
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(unless (= 0 (shell-command (format "kpsewhich %s.bst" path)))
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(cl-pushnew
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(cons (format "bibliographystyle \"%s\" may be unknown" path)
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(lambda ()
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(goto-char 0)
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(re-search-forward "bibliographystyle:")))
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bib-candidates)))))
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;; check for multiple bibliography links
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(let* ((bib-links (-filter
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(lambda (el)
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(string= (org-element-property :type el) "bibliography"))
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(org-element-map (org-element-parse-buffer) 'link 'identity)))
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(n-bib-links (length bib-links)))
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(when (> n-bib-links 1)
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(mapc (lambda (link)
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(setq
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bib-candidates
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(append
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bib-candidates
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(list (cons (format "Multiple bibliography link: %s"
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(org-element-property :raw-link link))
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`(lambda ()
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(goto-char ,(org-element-property :begin link))))))))
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bib-links)))
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;; Check for bibliography files existence.
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(mapc (lambda (bibfile)
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(unless (file-exists-p bibfile)
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(cl-pushnew
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(cons
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(format "%s does not exist." bibfile)
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(lambda ()
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(message "Non-existent bibfile.")))
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bib-candidates)))
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(org-ref-find-bibliography))
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;; check for spaces in bibliography
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(let ((bibfiles (mapcar 'expand-file-name
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(org-ref-find-bibliography))))
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(mapc (lambda (bibfile)
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(when (string-match " " bibfile)
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(cl-pushnew
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(cons (format "One or more spaces found in path to %s" bibfile)
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(lambda ()
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(message "No spaces are allowed in bibtex file paths. We recommend replacing them with -. Underscores usually cause other problems if you don't know what you are doing.")))
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bib-candidates)))
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bibfiles))
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;; validate bibtex files
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(let ((bibfiles (mapcar 'expand-file-name
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(org-ref-find-bibliography))))
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(mapc
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(lambda (bibfile)
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(unless (with-current-buffer
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(find-file-noselect bibfile)
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(bibtex-validate))
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(cl-pushnew
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(cons
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(format "Invalid bibtex file found. %S" bibfile)
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`(lambda ()
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(find-file ,bibfile)))
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bib-candidates)))
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bibfiles))
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;; unreferenced labels
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(save-excursion
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(save-restriction
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(widen)
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(goto-char (point-min))
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(let ((matches '()))
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;; these are the org-ref label:stuff kinds
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(while (re-search-forward
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"[^#+]label:\\([a-zA-Z0-9:-]*\\)" nil t)
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(cl-pushnew (cons
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(match-string-no-properties 1)
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(point))
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matches))
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;; now add all the other kinds of labels.
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;; #+label:
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(save-excursion
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(goto-char (point-min))
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(while (re-search-forward "^#\\+label:\\s-+\\(.*\\)\\b" nil t)
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;; do not do this for tables. We get those in `org-ref-get-tblnames'.
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;; who would have thought you have save match data here? Trust me. When
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;; I wrote this, you did.
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(unless (save-match-data (equal (car (org-element-at-point)) 'table))
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(cl-pushnew (cons (match-string-no-properties 1) (point)) matches))))
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;; \label{}
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(save-excursion
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(goto-char (point-min))
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(while (re-search-forward "\\\\label{\\([a-zA-Z0-9:-]*\\)}"
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nil t)
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(cl-pushnew (cons (match-string-no-properties 1) (point)) matches)))
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;; #+tblname: and actually #+label
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(cl-loop for cell in (org-element-map (org-element-parse-buffer 'element) 'table
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(lambda (table)
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(cons (org-element-property :name table)
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(org-element-property :begin table))))
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do
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(cl-pushnew cell matches))
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;; CUSTOM_IDs
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(org-map-entries
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(lambda ()
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(let ((custom_id (org-entry-get (point) "CUSTOM_ID")))
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(when (not (null custom_id))
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(cl-pushnew (cons custom_id (point)) matches)))))
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(goto-char (point-min))
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(while (re-search-forward "^#\\+name:\\s-+\\(.*\\)" nil t)
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(cl-pushnew (cons (match-string 1) (point)) matches))
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;; unreference labels
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(let ((refs (org-element-map (org-element-parse-buffer) 'link
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(lambda (el)
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(when (or (string= "ref" (org-element-property :type el))
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(string= "eqref" (org-element-property :type el))
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(string= "pageref" (org-element-property :type el))
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(string= "nameref" (org-element-property :type el))
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(string= "autoref" (org-element-property :type el))
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(string= "cref" (org-element-property :type el))
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(string= "Cref" (org-element-property :type el)))
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(org-element-property :path el))))))
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(cl-loop for (label . p) in matches
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do
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(when (and label (not (-contains? refs label)))
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(cl-pushnew
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(cons label (set-marker (make-marker) p))
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unreferenced-labels)))))))
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(helm :sources `(((name . "Bad citations")
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(candidates . ,bad-citations)
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(action . (lambda (marker)
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(switch-to-buffer (marker-buffer marker))
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(goto-char marker)
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(org-show-entry))))
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((name . "Multiply defined labels")
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(candidates . ,bad-labels)
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(action . (lambda (marker)
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(switch-to-buffer (marker-buffer marker))
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(goto-char marker)
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(org-show-entry))))
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((name . "Bad ref links")
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(candidates . ,bad-refs)
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(action . (lambda (marker)
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(switch-to-buffer (marker-buffer marker))
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(goto-char marker)
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(org-show-entry))))
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((name . "Bad file links")
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(candidates . ,bad-files)
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(lambda (marker)
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(switch-to-buffer (marker-buffer marker))
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(goto-char marker)
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(org-show-entry)))
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((name . "Labels with no ref links")
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(candidates . ,unreferenced-labels)
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(action . (lambda (marker)
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(switch-to-buffer (marker-buffer marker))
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(goto-char marker)
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(org-show-entry))))
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((name . "Bibliography")
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(candidates . ,bib-candidates)
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(action . (lambda (x)
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(switch-to-buffer ,cb)
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(funcall x))))
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((name . "Miscellaneous")
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(candidates . (,(format "org-latex-prefer-user-labels = %s"
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org-latex-prefer-user-labels)
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,(format "bibtex-dialect = %s" bibtex-dialect)
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,(format "biblatex is%srequired." (if biblatex-required " " " not "))
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,(format "biblatex is%sused." (if biblatex-used " " " not "))
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,(format "org-version = %s" (org-version))
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,(format "completion backend = %s" org-ref-completion-library)
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,(format "org-latex-pdf-process is defined as %s" org-latex-pdf-process)
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,(format "natbib is%srequired." (if natbib-required " " " not "))
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,(format "natbib is%sused." (if natbib-used " " " not "))
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,(format "cleveref is%srequired." (if cleveref-required " " " not "))
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,(format "cleveref is%sused." (if cleveref-used " " " not "))))
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(action . nil))
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((name . "Utilities")
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(candidates . (("Check buffer again" . org-ref)
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("Insert citation" . helm-bibtex)
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("Insert label link" . org-ref-helm-insert-label-link)
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("Insert ref link" . org-ref-helm-insert-ref-link)
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("List of figures" . org-ref-list-of-figures)
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("List of tables" . org-ref-list-of-tables)
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("Table of contents" . helm-org-in-buffer-headings)))
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(action . (lambda (x)
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(switch-to-buffer ,cb)
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(funcall x))))
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((name . "Document utilities")
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(candidates . (("Spell check document" . ispell)))
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(action . (lambda (x)
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(switch-to-buffer ,cb)
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(funcall x))))
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;; Exports
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((name . "Export functions")
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(candidates . (("Extract cited entries" . org-ref-extract-bibtex-entries)
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("Export to html and open" . (lambda ()
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(org-open-file
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(org-html-export-to-html))))
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("Export to pdf and open" . (lambda ()
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(org-open-file
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(org-latex-export-to-pdf))))
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("Export to manuscript pdf and open" . ox-manuscript-export-and-build-and-open)
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("Export submission manuscript pdf and open" . ox-manuscript-build-submission-manuscript-and-open)))
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(action . (lambda (x)
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(switch-to-buffer ,cb)
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(funcall x))))))))
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;;;###autoload
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(defun helm-tag-bibtex-entry ()
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"Helm interface to add keywords to a bibtex entry.
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Run this with the point in a bibtex entry."
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(interactive)
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(let ((keyword-source `((name . "Existing keywords")
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(candidates . ,(org-ref-bibtex-keywords))
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(action . (lambda (candidate)
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(org-ref-set-bibtex-keywords
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(mapconcat
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'identity
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(helm-marked-candidates)
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", "))))))
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(fallback-source `((name . "Add new keywords")
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(dummy)
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(action . (lambda (candidate)
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(org-ref-set-bibtex-keywords helm-pattern))))))
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(helm :sources `(,keyword-source ,fallback-source))))
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(provide 'org-ref-helm)
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;;; org-ref-helm.el ends here
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