This workflow provides configuration for managing references
using Emacs
Reference Database
ebib package.
Introduction
GNU/Emacs ebib package is used for organizing .bib files
into a unified reference database. A .bib file entry can
be imported either from clipboard or from online source such as
arXiv directly.
Customization
;;;////////////////////////////////////////////////////////
;; Customization Variables
;;;////////////////////////////////////////////////////////
(defcustom refdb:bib-dir
(expand-file-name "~/Documents/research/bib")
"Storage location for global bibtex .bib files")
(defcustom refdb:pdf-dir
(expand-file-name "~/Documents/research/pdf")
"Storage location for PDF files")
(defcustom refdb:notes-dir (expand-file-name "~/Documents/research/notes")
"Storage location for org note files")Key Bindings
Loading Databases
;;;/////////////////////////////////////////////////////
;;; Key bindings
;;;//////////////////////////////////////////////////////
(kb::def :states 'normal
"r" '(:ignore t :which-key "reference database")
"rr" '(refdb::open-db :which-key "main database")
"rp" '(refdb::project-db-open :which-key "project database"))Database Commands
(kb::defg
:states 'normal
:keymaps '(ebib-index-mode-map ebib-entry-mode-map)
"r" '(:ignore t :which-key "reference")
"rr" '(ebib-view-file :which-key "read paper")
"rd" '(ebib-download-url :which-key "download paper")
"rs" '(refdb::save-db :which-key "save")
"rh" '(refdb::hide-db :which-key "hide")
"rq" '(refdb::quit-db :which-key "close")
"ri" '(:ignore t :which-key "import")
"rib" '(refdb-biblio::start-import :which-key "biblio")
"ric" '(refdb::clipboard-import :which-key "clipboard"))
Importing from Biblio
(kb::def
:states 'normal
:keymaps 'biblio-selection-mode-map
"r" '(:ignore t :which-key "reference")
"ra" '(refdb::biblio-add-import :which-key "add import")
"ri" '(refdb::biblio-finish-import :which-key "finish import"))
Org-mode Citation, inserting citation links, opening cited reference, and
literature review note inside org-mode
(kb::def
:states 'normal
:keymaps 'org-mode-map
"rc" '(:ignore t :which-key "citation")
"rci" '(refdb::citation-insert :which-key "insert")
"rco" '(refdb::citation-open :which-key "open"))Functions
File storage locations
;;;//////////////////////////////////////////////////////////
;;Functions
;;///////////////////////////////////////////////////////////
(defun refdb::bib-dir ( )
"Returns global storage location for .bib files"
(expand-file-name "bib" refdb:bib-dir))
(defun refdb::pdf-dir ( )
"Returns the root downloaded reference database dir"
(expand-file-name refdb:pdf-dir))
(defun refdb::notes-dir ( )
"Returns the root downloaded reference database dir"
(expand-file-name refdb:notes-dir))Utility for listing bib files
(cl-defun refdb::bib-dir-files ( )
"Lists all .bib files found in `refdb:bib-dir'"
(require 'log)
(require 'files)
(require 'cl-lib)
(let ((bib-dir (expand-file-name refdb:bib-dir)))
(when (or (null bib-dir) (not (stringp bib-dir)))
(log::info
"research directory `refdb:root-dir' is not set
to directory path: <%s>" bib-dir)
(cl-return-from refdb::bib-dir-files))
(cl-loop
for bib-file in (directory-files bib-dir t "\\.bib")
collect bib-file)))System wide reference databases,
;; ////////////////////////////////////////
;; system db
;; ///////////////////////////////////////
(defun refdb::open-db ( )
"Runs `ebib' reference database browser"
(interactive)
(require 'ebib)
(ebib))
(defun refdb::quit-db ( )
"Quits ebib reference browser"
(interactive)
(when (featurep 'ebib)
(ebib-quit)))
(defun refdb::save-db ( )
"Save the current database"
(interactive)
(when (featurep 'ebib)
(ebib-save-current-database)))
(defun refdb::hide-db ( )
"Hide ebib browser"
(interactive)
(when (featurep 'ebib)
(ebib-lower)))
(defun refdb::init ( )
"Initializes reference management for the current org-mode buffer"
(interactive)
(require 'org-ref)
(require 'pm)
(when (or
;; inside the main org-mode document of the current project?
(not (null (pm::root-dir)))
(eq major-mode 'org-mode))
(with-current-buffer (current-buffer)
;; ensure project bibliography file ref.bib file is available
(let ((bib-re "^\s*\\\#\\\+bibliography:")
(bib-style-re "^\s*\\\#\\\+print_bibliography:")
(has-bib nil)
(has-bib-print nil)
)
;; initialize has-bib and has-bib-style
;; flags that detect wether the document biblography file(ref.bib)
;; and biblography style have been specified.
(save-excursion
;;(widen)
;;does it have bib print instruction?
(goto-char (point-min))
(setq has-bib-print
(not (null (search-forward-regexp bib-style-re nil t ))))
(goto-char (point-min))
(setq has-bib
(not (null (search-forward-regexp bib-re nil t ))))
;; deos it have bib reference?
(refdb::goto-ref-section)
(unless has-bib
(let ((org-ref-default-bibliography `( ,(refdb::project-db-file-path) ) ))
(org-ref-insert-bibliography-link)
(org-newline-and-indent)
))
;;(unless has-bib-style
;; (org-ref-insert-bibliographystyle-link)
;; (org-newline-and-indent)
;; )
)))))
;; /////////////////////////////////////
;; project ref db
;; /////////////////////////////////////
(defun refdb::project-init ( &optional dont-open-browser )
"Setup and optionally open the reference database for the current project"
(interactive)
(require 'ebib)
(require 'pm)
(require 'fs)
(require 'log)
(let ((project-dir (pm::root-dir))
(project-db-file (refdb::project-db-file-path))
(main-db-file (expand-file-name "main.bib" refdb:bib-dir))
(main-db)
)
(when (not (null project-dir))
(log::sub-info "project: %s" project-dir)
;; init ebib
(unless ebib--initialized
(ebib-init)
(setq ebib--needs-update t))
(setq main-db (ebib--load-bibtex-file-internal main-db-file))
;; is project database available?
(if (file-exists-p project-db-file)
(setq ebib--cur-db (ebib--load-bibtex-file-internal project-db-file))
(let ((project-db))
(log::info "creating project reference ...")
(log::sub-info "database: %s" project-db-file)
(fs::dir-ensure (file-name-directory project-db-file))
(setq project-db (ebib--create-new-database ebib--cur-db))
(ebib-db-set-filename project-db-file project-db)
(setq ebib--cur-db project-db)
(ebib-save-current-database 'force )))
(unless dont-open-browser
(ebib)))))
(defun refdb::project-db-open ( )
"Run reference management with ebib for the current project"
(interactive)
(refdb::project-init))
(defun refdb::project-db-file-path ( )
"Retruns the bib reference database file for the current project"
(require 'f)
(let ((project-dir (pm::root-dir))
(project-db-file nil))
(when (file-directory-p project-dir)
(setq project-db-file "./.config/etc/biblatex/ref.bib" )
(fs::dir-ensure (file-name-directory (f-relative project-db-file project-dir) )))
project-db-file))
;; util
(defun refdb::goto-ref-section ( )
(interactive)
(goto-char (point-min))
(let* ((ast (org-element-parse-buffer))
(ref-hl-end-pos nil))
(org-element-map
ast
'headline
(lambda (hl)
(when (and (= (org-element-property :level hl) 1)
(string= (org-element-property :raw-value hl) "References"))
(goto-char (org-element-property :end hl) )
(org-end-of-line)
(org-newline-and-indent)
(setq ref-hl-end-pos (point))
)))
(unless ref-hl-end-pos
(end-of-buffer)
(insert "** References\n")
(org-beginning-of-line)
(setq ref-hl-end-pos (point)))
ref-hl-end-pos))Clipboard Import
(defun refdb::clipboard-import ( )
"import biblatex reference from the kill-ring"
(interactive)
(require 'ebib)
(with-temp-buffer
(yank)
(ebib-import)
(call-interactively #'ebib)))Biblio Import
(defvar refdb:biblio-import-list nil
"list of biblatex entries waiting import into ebib")
(defun refdb-biblio::start-import ( )
(interactive)
(setq refdb:biblio-import-list nil)
(biblio-lookup))
(defun refdb::biblio-add-import ( )
"Collect selected biblio reference"
(interactive)
(require 'ebib)
(require 'ebib-biblio)
(biblio--selection-forward-bibtex
(lambda ( bibtex _entry )
(cl-pushnew bibtex refdb:biblio-import-list))))
(defun refdb::biblio-finish-import ( )
"Import collected biblatex references into ebib"
(interactive)
(require 'ebib)
(unless (zerop (length refdb:biblio-import-list) )
(with-temp-buffer
(cl-loop
for import in refdb:biblio-import-list
do (insert import "\n"))
(goto-char (point-min))
(call-interactively #'ebib-import)
(quit-window))))Org-Mode Citations
;;; Citation
(defun refdb::citation-insert ( &optional arg )
"Insert org-ref citation"
(interactive "P")
;;(require 'org-ref-cite)
;;(require 'ebib)
(refdb::init)
(org-cite-insert arg))
(defun refdb::citation-open ()
(interactive)
(let ((bib-key nil)
(bib-file nil)
)
(when (and
(eq major-mode 'org-mode)
(or
(setq bib-key (org-ref-get-bibtex-key-under-cursor))
(setq bib-file (org-ref-find-bibliography))))
(ebib bib-file bib-key))))Packages
Package: ebib
(use-package ebib
:guix ( :name emacs-ebib)
:demand t
:custom
;; use internal pdf viewer
(ebib-file-associations '(("pdf" . "~/opt/sioyek/sioyek")))
;; extra fields
(ebib-extra-fields
'((BibTeX "crossref" "annote" "abstract" "keywords" "file" "tags" "timestamp" "url" "doi")
(biblatex "crossref" "annotation" "abstract" "keywords" "file" "tags" "timestamp")))
;; bib dialect can be bibtex or biblatex
;; *biblatex is recommended
(ebib-bibtex-dialect 'biblatex)
;;; setup file paths
;;pdf files
(ebib-file-search-dirs `(,(refdb::pdf-dir)))
;; note files
(ebib-notes-directory (refdb::notes-dir))
;; bib files
(ebib-preload-bib-files (refdb::bib-dir-files))
:general
<<ebib-kb>>
:config
(require 'evil-collection)
(evil-collection-init 'ebib))
Package: biblio
;; online databases
(use-package biblio
:guix ( :profile write :name emacs-biblio)
:after ebib
:custom
(biblio-download-directory (refdb::pdf-dir))
:general
<<biblio-kb>>)
Package: reftex
(use-package reftex
:demand t
:config
(setq reftex-default-bibliography (refdb::bib-dir-files)))
Package: bibtex
Builtin GNU/Emacs bibtex file editing mode.
(use-package bibtex-completion :demand t)
(use-package bibtex
:demand t)
Package: ivy-bibtex
(use-package ivy-bibtex
:guix ( :name emacs-helm-bibtex)
:config
(setq
;;bibtex-completion-additional-search-fields '(keywords)
bibtex-completion-bibliography (refdb::bib-dir)
bibtex-completion-library-path (refdb::pdf-dir)
bibtex-completion-notes-path (refdb::notes-dir)
bibtex-completion-notes-template-multiple-files "#+TITLE: Notes on: ${author-or-editor} (${year}): ${title}\n\nSee [cite/t:@${=key=}]\n"
bibtex-completion-display-formats
'((article . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} ${journal:40}")
(inbook . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} Chapter ${chapter:32}")
(incollection . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} ${booktitle:40}")
(inproceedings . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*} ${booktitle:40}")
(t . "${=has-pdf=:1}${=has-note=:1} ${year:4} ${author:36} ${title:*}"))
bibtex-autokey-year-length 4
bibtex-autokey-titleword-separator "-"
bibtex-autokey-name-year-separator "-"
bibtex-autokey-year-title-separator "-"
bibtex-autokey-titleword-length 8
bibtex-autokey-titlewords 3)
(setq bibtex-completion-pdf-field "File")
;;icons used for indicating availability
;;of notes and pdf files
(setq bibtex-completion-pdf-symbol "⌘")
(setq bibtex-completion-notes-symbol "✎")
;;optional using external pdf viewer
;;(setq bibtex-completion-pdf-open-function
;; (lambda (fpath)
;; (call-process "evince" nil 0 nil fpath)))
(setq bibtex-completion-pdf-extension '(".pdf" ".djvu"))
(setq bibtex-completion-browser-function
(lambda (url)
;;TODO: implement browser launcher
)))
Package: org-ref
Org-ref provides features for managing citations, cross-referencing, linking
and labeling text suitable for LaTex.
;; org ref
(use-package org-ref
:after org-mode
:guix (:name emacs-org-ref)
:general
<<org-ref-kb>>
:config
(setq org-ref-insert-cite-function (lambda () (org-cite-insert nil)))
(setq org-ref-get-pdf-filename-function #'org-ref-get-pdf-filename)
(setq org-ref-default-bibliography (refdb::bib-dir-files))
(setq org-ref-notes-directory (refdb::notes-dir))
(setq org-ref-pdf-directory (refdb::pdf-dir)))
Package: citeproc-el
(use-package citeproc-el
:guix ( :name emacs-citeproc-el )
:after org-ref
:disabled)Resources
styles: IEEE
ieee.csl
<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only">
<info>
<title>IEEE</title>
<id>http://www.zotero.org/styles/ieee</id>
<link href="http://www.zotero.org/styles/ieee" rel="self"/>
<!-- <link href="https://ieeeauthorcenter.ieee.org/wp-content/uploads/IEEE-Reference-Guide.pdf" rel="documentation"/> - 2018 guidelines -->
<link href="http://journals.ieeeauthorcenter.ieee.org/wp-content/uploads/sites/7/IEEE_Reference_Guide.pdf" rel="documentation"/>
<link href="https://journals.ieeeauthorcenter.ieee.org/your-role-in-article-production/ieee-editorial-style-manual/" rel="documentation"/>
<author>
<name>Michael Berkowitz</name>
<email>mberkowi@gmu.edu</email>
</author>
<contributor>
<name>Julian Onions</name>
<email>julian.onions@gmail.com</email>
</contributor>
<contributor>
<name>Rintze Zelle</name>
<uri>http://twitter.com/rintzezelle</uri>
</contributor>
<contributor>
<name>Stephen Frank</name>
<uri>http://www.zotero.org/sfrank</uri>
</contributor>
<contributor>
<name>Sebastian Karcher</name>
</contributor>
<contributor>
<name>Giuseppe Silano</name>
<email>g.silano89@gmail.com</email>
<uri>http://giuseppesilano.net</uri>
</contributor>
<contributor>
<name>Patrick O'Brien</name>
</contributor>
<contributor>
<name>Brenton M. Wiernik</name>
</contributor>
<contributor>
<name>Oliver Couch</name>
<email>oliver.couch@gmail.com</email>
</contributor>
<category citation-format="numeric"/>
<category field="engineering"/>
<category field="generic-base"/>
<summary>IEEE style as per the 2021 guidelines, V 01.29.2021.</summary>
<updated>2021-05-07T00:52:46+10:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
<locale xml:lang="en">
<terms>
<term name="chapter" form="short">ch.</term>
<term name="presented at">presented at the</term>
<term name="available at">available</term>
</terms>
</locale>
<!-- Macros -->
<macro name="status">
<choose>
<if variable="page issue volume" match="none">
<text variable="status" text-case="capitalize-first" suffix="" font-weight="bold"/>
</if>
</choose>
</macro>
<macro name="edition">
<choose>
<if type="bill book chapter graphic legal_case legislation motion_picture paper-conference report song" match="any">
<choose>
<if is-numeric="edition">
<group delimiter=" ">
<number variable="edition" form="ordinal"/>
<text term="edition" form="short"/>
</group>
</if>
<else>
<text variable="edition" text-case="capitalize-first" suffix="."/>
</else>
</choose>
</if>
</choose>
</macro>
<macro name="issued">
<choose>
<if type="article-journal report" match="any">
<date variable="issued">
<date-part name="month" form="short" suffix=" "/>
<date-part name="year" form="long"/>
</date>
</if>
<else-if type="bill book chapter graphic legal_case legislation song thesis" match="any">
<date variable="issued">
<date-part name="year" form="long"/>
</date>
</else-if>
<else-if type="paper-conference" match="any">
<date variable="issued">
<date-part name="month" form="short"/>
<date-part name="year" prefix=" "/>
</date>
</else-if>
<else-if type="motion_picture" match="any">
<date variable="issued" prefix="(" suffix=")">
<date-part name="month" form="short" suffix=" "/>
<date-part name="day" form="numeric-leading-zeros" suffix=", "/>
<date-part name="year"/>
</date>
</else-if>
<else>
<date variable="issued">
<date-part name="month" form="short" suffix=" "/>
<date-part name="day" form="numeric-leading-zeros" suffix=", "/>
<date-part name="year"/>
</date>
</else>
</choose>
</macro>
<macro name="author">
<names variable="author">
<name and="text" et-al-min="7" et-al-use-first="1" initialize-with=". "/>
<label form="short" prefix=", " text-case="capitalize-first"/>
<et-al font-style="italic"/>
<substitute>
<names variable="editor"/>
<names variable="translator"/>
</substitute>
</names>
</macro>
<macro name="editor">
<names variable="editor">
<name initialize-with=". " delimiter=", " and="text"/>
<label form="short" prefix=", " text-case="capitalize-first"/>
</names>
</macro>
<macro name="locators">
<group delimiter=", ">
<text macro="edition"/>
<group delimiter=" ">
<text term="volume" form="short"/>
<number variable="volume" form="numeric"/>
</group>
<group delimiter=" ">
<number variable="number-of-volumes" form="numeric"/>
<text term="volume" form="short" plural="true"/>
</group>
<group delimiter=" ">
<text term="issue" form="short"/>
<number variable="issue" form="numeric"/>
</group>
</group>
</macro>
<macro name="title">
<choose>
<if type="bill book graphic legal_case legislation motion_picture song" match="any">
<text variable="title" font-style="italic"/>
</if>
<else>
<text variable="title" quotes="true"/>
</else>
</choose>
</macro>
<macro name="publisher">
<choose>
<if type="bill book chapter graphic legal_case legislation motion_picture paper-conference song" match="any">
<group delimiter=": ">
<text variable="publisher-place"/>
<text variable="publisher"/>
</group>
</if>
<else>
<group delimiter=", ">
<text variable="publisher"/>
<text variable="publisher-place"/>
</group>
</else>
</choose>
</macro>
<macro name="event">
<choose>
<if type="paper-conference speech" match="any">
<choose>
<!-- Published Conference Paper -->
<if variable="collection-editor editor editorial-director issue page volume" match="any">
<group delimiter=", ">
<group delimiter=" ">
<text term="in"/>
<text variable="container-title" font-style="italic"/>
</group>
<text variable="event-place"/>
</group>
</if>
<!-- Unpublished Conference Paper -->
<else>
<group delimiter=", ">
<group delimiter=" ">
<text term="presented at"/>
<text variable="event"/>
</group>
<text variable="event-place"/>
</group>
</else>
</choose>
</if>
</choose>
</macro>
<macro name="access">
<choose>
<if type="webpage post post-weblog" match="any">
<!-- https://url.com/ (accessed Mon. DD, YYYY). -->
<choose>
<if variable="URL">
<group prefix=" " delimiter=" ">
<text variable="URL"/>
<group delimiter=" " prefix="(" suffix=").">
<text term="accessed"/>
<date variable="accessed">
<date-part name="month" form="short"/>
<date-part name="day" form="numeric-leading-zeros" prefix=" " suffix=", "/>
<date-part name="year" form="long"/>
</date>
</group>
</group>
</if>
</choose>
</if>
<else-if match="any" variable="DOI">
<!-- doi: 10.1000/xyz123. -->
<text variable="DOI" prefix=" doi: " suffix="."/>
</else-if>
<else-if variable="URL">
<!-- Accessed: Mon. DD, YYYY. [Medium]. Available: https://URL.com/ -->
<group delimiter=". " prefix=" " suffix=". ">
<!-- Accessed: Mon. DD, YYYY. -->
<group delimiter=": ">
<text term="accessed" text-case="capitalize-first"/>
<date variable="accessed">
<date-part name="month" form="short" suffix=" "/>
<date-part name="day" form="numeric-leading-zeros" suffix=", "/>
<date-part name="year"/>
</date>
</group>
<!-- [Online Video]. -->
<group prefix="[" suffix="]" delimiter=" ">
<text term="online" text-case="capitalize-first"/>
<choose>
<if type="motion_picture">
<text value="video" text-case="capitalize-first"/>
</if>
</choose>
</group>
</group>
<!-- Available: https://URL.com/ -->
<group delimiter=": ">
<text term="available at" text-case="capitalize-first"/>
<text variable="URL"/>
</group>
</else-if>
</choose>
</macro>
<macro name="page">
<choose>
<if type="article-journal" variable="number" match="all">
<group delimiter=" ">
<text value="Art."/>
<text term="issue" form="short"/>
<text variable="number"/>
</group>
</if>
<else>
<group delimiter=" ">
<label variable="page" form="short"/>
<text variable="page"/>
</group>
</else>
</choose>
</macro>
<macro name="citation-locator">
<group delimiter=" ">
<choose>
<if locator="page">
<label variable="locator" form="short"/>
</if>
<else>
<label variable="locator" form="short" text-case="capitalize-first"/>
</else>
</choose>
<text variable="locator"/>
</group>
</macro>
<macro name="geographic-location">
<group delimiter=", " suffix=".">
<choose>
<if variable="publisher-place">
<text variable="publisher-place" text-case="title"/>
</if>
<else-if variable="event-place">
<text variable="event-place" text-case="title"/>
</else-if>
</choose>
</group>
</macro>
<!-- Citation -->
<citation collapse="citation-number">
<sort>
<key variable="citation-number"/>
</sort>
<layout delimiter=", ">
<group prefix="[" suffix="]" delimiter=", ">
<text variable="citation-number"/>
<text macro="citation-locator"/>
</group>
</layout>
</citation>
<!-- Bibliography -->
<bibliography entry-spacing="0" second-field-align="flush">
<layout>
<!-- Citation Number -->
<text variable="citation-number" prefix="[" suffix="]"/>
<!-- Author(s) -->
<text macro="author" suffix=", "/>
<!-- Rest of Citation -->
<choose>
<!-- Specific Formats -->
<if type="article-journal">
<group delimiter=", " >
<text macro="title"/>
<text variable="container-title" font-style="italic" form="short"/>
<text macro="locators"/>
<text macro="page"/>
<text macro="issued"/>
<text macro="status"/>
</group>
<choose>
<if variable="URL DOI" match="none">
<text value="." />
</if>
<else>
<text value="," />
</else>
</choose>
<text macro="access"/>
</if>
<else-if type="paper-conference speech" match="any">
<group delimiter=", " suffix=".">
<text macro="title"/>
<text macro="event"/>
<text macro="issued"/>
<text macro="locators"/>
<text macro="page"/>
<text macro="status"/>
</group>
<text macro="access"/>
</else-if>
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<translator>
<name>Andrew Dunning</name>
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<translator>
<name>Sebastian Karcher</name>
</translator>
<translator>
<name>Rintze M. Zelle</name>
</translator>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
<updated>2015-10-10T23:31:02+00:00</updated>
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