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; ; The following packages are needed:
; ; 1. elfeed and elfeed-score (available from the rss doom module)
; ; 2. citar
; ; 3. org-ref
; ; 4. org-roam and org-roam-bibtex
(defconst robo/bib-libraries (list " ~/bib-lib/robo-lib.bib" " ~/bib-lib/robo-temp-lib.bib" ; All of my bib databases.
(defconst robo/main-bib-library (nth 0 robo/bib-libraries)) ; The main db is always the first
(defconst robo/main-pdfs-library-paths `(" ~/bib-lib/pdfs/" " /home/robo/bib-lib/temp-pdfs/" ; PDFs directories in a list
(defconst robo/main-pdfs-library-path (nth 0 robo/main-pdfs-library-paths)) ; Main PDFs directory
(defconst robo/bib-notes-dir " ~/bib-lib/roam" ; I use org-roam to manage all my notes, including bib notes.
(setq bibtex-completion-bibliography robo/bib-libraries ; My bibliography PDF location
bibtex-completion-library-path robo/main-pdfs-library-paths ; My PDF lib location
bibtex-completion-notes-path robo/bib-notes-dir
bibtex-completion-pdf-open-function (lambda (fpath )
(call-process " open" nil 0 nil fpath)))
(use-package! elfeed
:config
(add-hook! 'elfeed-search-mode-hook 'elfeed-update )
(defun concatenate-authors (authors-list )
" Given AUTHORS-LIST, list of plists; return string of all authors concatenated."
(if (> (length authors-list) 1 )
(format " %s et al." (plist-get (nth 0 authors-list) :name ))
(plist-get (nth 0 authors-list) :name )))
(defun my-search-print-fn (entry )
" Print ENTRY to the buffer."
(let* ((date (elfeed-search-format-date (elfeed-entry-date entry)))
(title (or (elfeed-meta entry :title )
(elfeed-entry-title entry) " "
(title-faces (elfeed-search--faces (elfeed-entry-tags entry)))
(entry-authors (concatenate-authors
(elfeed-meta entry :authors )))
(title-width (- (window-width ) 10
elfeed-search-trailing-width))
(title-column (elfeed-format-column
title 100
:left ))
(entry-score (elfeed-format-column (number-to-string (elfeed-score-scoring-get-score-from-entry entry)) 10 :left ))
(authors-column (elfeed-format-column entry-authors 40 :left )))
(insert (propertize date 'face 'elfeed-search-date-face ) " "
(insert (propertize title-column
'face title-faces 'kbd-help title) " "
(insert (propertize authors-column
'kbd-help entry-authors) " "
(insert entry-score " "
(defun robo/elfeed-entry-to-arxiv ()
" Fetch an arXiv paper into the local library from the current elfeed entry."
(interactive )
(let* ((link (elfeed-entry-link elfeed-show-entry))
(match-idx (string-match " arxiv.org/abs/\\ ([0-9.]*\\ )" link ))
(matched-arxiv-number (match-string 1 link )))
(when matched-arxiv-number
(message " Going to arXiv: %s " matched-arxiv-number)
(arxiv-get-pdf-add-bibtex-entry matched-arxiv-number robo/main-bib-library robo/main-pdfs-library-path))))
(map! (:after elfeed
(:map elfeed-search-mode-map
:desc " Open entry" " m" #'elfeed-search-show-entry )
(:map elfeed-show-mode-map
:desc " Fetch arXiv paper to the local library" " a" #'robo/elfeed-entry-to-arxiv ))
(setq elfeed-search-print-entry-function #'my-search-print-fn )
(setq elfeed-search-date-format '(" %y-%m-%d" 10 :left ))
(setq elfeed-search-title-max-width 110 )
(setq elfeed-feeds '(" http://export.arxiv.org/api/query?search_query=cat:math.OC&start=0&max_results=100&sortBy=submittedDate&sortOrder=descending" " http://export.arxiv.org/api/query?search_query=cat:stat.ML&start=0&max_results=100&sortBy=submittedDate&sortOrder=descending" " http://export.arxiv.org/api/query?search_query=cat:cs.LG&start=0&max_results=100&sortBy=submittedDate&sortOrder=descending"
(setq elfeed-search-filter " @2-week-ago +unread"
(use-package! elfeed-score
:after elfeed
:config
(elfeed-score-load-score-file " ~/.doom.d/elfeed.score" ; See the elfeed-score documentation for the score file syntax
(setq elfeed-score-serde-score-file " ~/.doom.d/elfeed.serde.score"
(elfeed-score-enable)
(define-key elfeed-search-mode-map " ="
(use-package! org-ref
:after org
:config
(defun robo/reformat-bib-library (&optional filename )
" Formats the bibliography using biber & rebiber and updates the PDF -metadata."
(interactive " P"
(or filename (setq filename robo/main-bib-library))
(let ((cmnd (concat
(format " rebiber -i %s && " filename) ; Get converence versions of arXiv papers
(format " biber --tool --output_align --output_indent=2 --output_fieldcase=lower --configfile=~/bib-lib/biber-myconf.conf --output_file=%s %s && " filename filename) ; Properly format the bibliography
(format " sed -i -e 's/arxiv/arXiv/gI' -e 's/journaltitle/journal /' -e 's/date /year /' %s && " filename) ; Some replacements
(format " git commit -m \" Updating bibliography..\" %s && git push " filename) ; Commit and push the updated bib
)))
(async-shell-command cmnd)))
(defun robo/reformat-bib-lib-hook ()
" Reformat the main bib library whenever it is saved.."
(when (equal (buffer-file-name ) robo/main-bib-library) (robo/reformat-bib-library)))
(add-hook 'after-save-hook 'robo/reformat-bib-lib-hook )
(setq bibtex-dialect 'biblatex ))
(use-package! oc
:config
(require 'oc-biblatex )
(require 'oc-csl )
(require 'citar )
(setq org-cite-global-bibliography robo/bib-libraries
org-cite-insert-processor 'citar
org-cite-follow-processor 'citar
org-cite-activate-processor 'citar
org-cite-export-processors '((latex biblatex)
(t csl))))
(use-package! citar
:hook (doom-after-init-modules . citar-refresh)
:config
; ; This will add watches for the global bib files and in addition add a hook to LaTeX-mode-hook and org-mode-hook to add watches for local bibliographic files.
(citar-filenotify-setup '(LaTeX-mode-hook org-mode-hook))
(require 'citar-org )
(setq citar-bibliography robo/bib-libraries
citar-library-paths robo/main-pdfs-library-paths
citar-file-extensions '(" pdf" " org" " md"
citar-file-open-function #'find-file )
(defun robo/citar-full-names (names )
" Transform names like LastName, FirstName to FirstName LastName."
(when (stringp names)
(mapconcat
(lambda (name )
(if (eq 1 (length name))
(split-string name " "
(let ((split-name (split-string name " , "
(cl-concatenate 'string (nth 1 split-name) " " nth 0 split-name)))))
(split-string names " and " " , "
(setq citar-display-transform-functions
'((t . citar-clean-string)
((" author" " editor" . robo/citar-full-names)))
(setq citar-templates
'((main . " ${author editor:55} ${date year issued:4} ${title:55}"
(suffix . " ${tags keywords keywords:40}"
(preview . " ${author editor} ${title}, ${journal publisher container-title collection-title booktitle} ${volume} (${year issued date}).\n "
(note . " #+title: Notes on ${author editor}, ${title}"
; ; use consult-completing-read for enhanced interface
(advice-add #'completing-read-multiple :override #'consult-completing-read-multiple ))
(map! :leader
:desc " arXiv paper to library" " n x" #'arxiv-get-pdf-add-bibtex-entry
:desc " Elfeed" " n e" #'elfeed )
(after! org-roam
(setq org-roam-v2-ack t
+org-roam-open-buffer-on-find-file nil
org-roam-node-display-template " ${title:80} ${tags:80}"
org-roam-completion-everywhere nil
org-roam-directory robo/bib-notes-dir))
(use-package! org-roam-bibtex
:config
(setq org-roam-capture-templates
'((" d" " default" " %?"
:if-new (file+head " ${slug}.org"
" #+title: ${title}\n #+SETUPFILE: ~/bib-lib/setup_file.org\n * References :ignore:\n #+print_bibliography:"
:unnarrowed t )
; ; capture to inbox
(" i" " inbox" " * TODO %?\n "
:target (node " 45acaadd-02fb-4b93-a741-45d37ff9fd5e"
:unnarrowed t
:empty-lines-before 1
:empty-lines-after 1
:prepend t )
; ; bibliography note template
(" r" " bibliography reference" " %?"
:if-new (file+head " references/notes_${citekey}.org"
" #+title: Notes on ${title}\n #+SETUPFILE: ~/bib-lib/ref_setup_file.org\n * References :ignore:\n #+print_bibliography:"
:unnarrowed t )
; ; for my annotated bibliography needs
(" s" " short bibliography reference (no id)" " * ${title} [cite:@%^{citekey}]\n %?"
:target (node " 01af7246-1b2e-42a5-b8e7-68be9157241d"
:unnarrowed t
:empty-lines-before 1
:prepend t )))
(defun robo/capture-to-inbox ()
" Capture a TODO straight to the inbox."
(interactive )
(org-roam-capture- :goto nil
:keys " i"
:node (org-roam-node-from-id " 45acaadd-02fb-4b93-a741-45d37ff9fd5e"
(require 'org-roam-bibtex )
(setq citar-open-note-function 'orb-citar-edit-note
citar-notes-paths '(" ~/bib-lib/roam/references/"
orb-preformat-keywords '(" citekey" " title" " url" " author-or-editor" " keywords" " file"
orb-process-file-keyword t
orb-file-field-extensions '(" pdf"
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