gistfile1.txt

Warning (org-element-cache): org-element--cache: (ivy-alt-done) Cached element is incorrect in emacs.org. (Cache tic up to date: "yes") Resetting.
If this warning appears regularly, please report the warning text to Org mode mailing list (M-x org-submit-bug-report).
The element is: "(src-block (:language \"elisp\" :switches nil :parameters nil :begin 36507 :end 40247 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value \"(use-package citar
  :no-require
  :custom
  (org-cite-global-bibliography '(\\\"~/docs/references.bib\\\"))
  (org-cite-insert-processor 'citar)
  (org-cite-follow-processor 'citar)
  (org-cite-activate-processor 'citar)
  (citar-bibliography org-cite-global-bibliography)
  ;; optional: org-cite-insert is also bound to C-c C-x C-@
  :bind
  (:map org-mode-map :package org (\\\"C-c b\\\" . #'org-cite-insert)))


(use-package org-ref
  :config
  (setq
   org-ref-completion-library 'org-ref-ivy-cite
   ;; org-ref-get-pdf-filename-function 'org-ref-get-pdf-filename-helm-bibtex
   org-ref-default-bibliography '(\\\"~/docs/references.bib\\\")
   org-ref-note-title-format \\\"* TODO %y - %t\\\\n :PROPERTIES:\\\\n  :Custom_ID: %k\\\\n  :NOTER_DOCUMENT: %F\\\\n :ROAM_KEY: cite:%k\\\\n  :AUTHOR: %9a\\\\n  :JOURNAL: %j\\\\n  :YEAR: %y\\\\n  :VOLUME: %v\\\\n  :PAGES: %p\\\\n  :DOI: %D\\\\n  :URL: %U\\\\n :END:\\\\n\\\\n\\\"
   org-ref-notes-directory \\\"~/docs/roam/\\\"
   org-ref-notes-function 'orb-edit-notes


   bibtex-align-at-equal-sign t ; prettier formatting
   bibtex-dialect 'biblatex     ; bibtex is apparently very old (1988), so use the new variant

   ;; tell org to output using bibtex
   org-latex-pdf-process (list \\\"latexmk -shell-escape -bibtex -f -pdf %f\\\")

   bibtex-user-optional-fields '((\\\"keywords\\\" \\\"Keywords to describe the entry\\\" \\\"\\\")
                                 (\\\"file\\\" \\\"link to the document file\\\" \\\":\\\")
                                 (\\\"url\\\" \\\"url of the thing\\\" \\\"\\\"))
   bibtex-completion-bibliography '(\\\"~/docs/references.bib\\\")
   bibtex-completion-library-path '(\\\"~/docs/pdfs_for_notes/\\\")
   bibtex-completion-pdf-field \\\"file\\\"

   ;; Not sure about this yet..
   bibtex-completion-notes-template-multiple-files
   (concat
    \\\"#+TITLE: ${title}\\\\n\\\"
    \\\"#+ROAM_KEY: cite:${=key=}\\\\n\\\"
    \\\"* TODO Notes\\\\n\\\"
    \\\":PROPERTIES:\\\\n\\\"
    \\\":Custom_ID: ${=key=}\\\\n\\\"
    \\\":NOTER_DOCUMENT: %(orb-process-file-field \\\\\\\"${=key=}\\\\\\\")\\\\n\\\"
    \\\":AUTHOR: ${author-abbrev}\\\\n\\\"
    \\\":JOURNAL: ${journaltitle}\\\\n\\\"
    \\\":DATE: ${date}\\\\n\\\"
    \\\":YEAR: ${year}\\\\n\\\"
    \\\":DOI: ${doi}\\\\n\\\"
    \\\":URL: ${url}\\\\n\\\"
    \\\":END:\\\\n\\\\n\\\"
    )
   )
  )

(use-package citeproc)

(use-package bibtex
  :config
  (setq bibtex-autokey-year-length 4
        bibtex-autokey-name-year-separator \\\"-\\\"
        bibtex-autokey-year-title-separator \\\"-\\\"
        bibtex-autokey-titleword-separator \\\"-\\\"
        bibtex-autokey-titlewords 2
        bibtex-autokey-titlewords-stretch 1
        bibtex-autokey-titleword-length 5))

(use-package ivy-bibtex
  :config
  (autoload 'ivy-bibtex \\\"ivy-bibtex\\\" \\\"\\\" t)
  ;; ivy-bibtex requires ivy's `ivy--regex-ignore-order` regex builder, which
  ;; ignores the order of regexp tokens when searching for matching candidates.
  ;; Add something like this to your init file:
  (setq ivy-re-builders-alist
        '((ivy-bibtex . ivy--regex-ignore-order)
          (t . ivy--regex-plus))))

;; most of this config taken from http://www.wouterspekkink.org/academia/writing/tool/doom-emacs/2021/02/27/writing-academic-papers-with-org-mode.html
(use-package org-roam-bibtex
  :after org-roam
  :hook org-roam-mode
  :bind (:map org-mode-map (\\\"C-c n b\\\" . orb-note-actions)) ;; yes, really `orb`.
  :config
  (require 'org-ref)
  (org-roam-bibtex-mode)
  (setq orb-preformat-keywords '(\\\"citekey\\\" \\\"title\\\" \\\"url\\\" \\\"author-or-editor\\\" \\\"keywords\\\" \\\"file\\\")
        orb-process-file-keyword t
        orb-file-field-extensions '(pdf))

  (setq orb-templates
        '((\\\"r\\\" \\\"ref\\\" 'org-roam-capture--get-point \\\"\\\"
           :file-name \\\"${citekey}\\\"
           :head \\\"#+TITLE: ${citekey}: ${title}\\\\n#+ROAM_KEY: ${ref}
- tags ::
- keywords :: ${keywords}

* Notes
:PROPERTIES:
:Custom_ID: ${citekey}
:URL: ${url}
:AUTHOR: ${author-or-editor}
:NOTER_DOCUMENT: ${file}
:NOTER_PAGE:
:END:\\\")))
  )

\" :post-blank 1 :post-affiliated 36507 :mode nil :granularity element :cached t :parent (section (:begin 35930 :end 42956 :contents-begin 35930 :contents-end 42955 :robust-begin 35930 :robust-end 42953 :post-blank 1 :post-affiliated 35930 :mode section :granularity element :cached t :parent (headline ...) :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil))"
 The real element is: "(src-block (:language \"elisp\" :switches nil :parameters nil :begin 36477 :end 40217 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value \"(use-package citar
  :no-require
  :custom
  (org-cite-global-bibliography '(\\\"~/docs/references.bib\\\"))
  (org-cite-insert-processor 'citar)
  (org-cite-follow-processor 'citar)
  (org-cite-activate-processor 'citar)
  (citar-bibliography org-cite-global-bibliography)
  ;; optional: org-cite-insert is also bound to C-c C-x C-@
  :bind
  (:map org-mode-map :package org (\\\"C-c b\\\" . #'org-cite-insert)))


(use-package org-ref
  :config
  (setq
   org-ref-completion-library 'org-ref-ivy-cite
   ;; org-ref-get-pdf-filename-function 'org-ref-get-pdf-filename-helm-bibtex
   org-ref-default-bibliography '(\\\"~/docs/references.bib\\\")
   org-ref-note-title-format \\\"* TODO %y - %t\\\\n :PROPERTIES:\\\\n  :Custom_ID: %k\\\\n  :NOTER_DOCUMENT: %F\\\\n :ROAM_KEY: cite:%k\\\\n  :AUTHOR: %9a\\\\n  :JOURNAL: %j\\\\n  :YEAR: %y\\\\n  :VOLUME: %v\\\\n  :PAGES: %p\\\\n  :DOI: %D\\\\n  :URL: %U\\\\n :END:\\\\n\\\\n\\\"
   org-ref-notes-directory \\\"~/docs/roam/\\\"
   org-ref-notes-function 'orb-edit-notes


   bibtex-align-at-equal-sign t ; prettier formatting
   bibtex-dialect 'biblatex     ; bibtex is apparently very old (1988), so use the new variant

   ;; tell org to output using bibtex
   org-latex-pdf-process (list \\\"latexmk -shell-escape -bibtex -f -pdf %f\\\")

   bibtex-user-optional-fields '((\\\"keywords\\\" \\\"Keywords to describe the entry\\\" \\\"\\\")
                                 (\\\"file\\\" \\\"link to the document file\\\" \\\":\\\")
                                 (\\\"url\\\" \\\"url of the thing\\\" \\\"\\\"))
   bibtex-completion-bibliography '(\\\"~/docs/references.bib\\\")
   bibtex-completion-library-path '(\\\"~/docs/pdfs_for_notes/\\\")
   bibtex-completion-pdf-field \\\"file\\\"

   ;; Not sure about this yet..
   bibtex-completion-notes-template-multiple-files
   (concat
    \\\"#+TITLE: ${title}\\\\n\\\"
    \\\"#+ROAM_KEY: cite:${=key=}\\\\n\\\"
    \\\"* TODO Notes\\\\n\\\"
    \\\":PROPERTIES:\\\\n\\\"
    \\\":Custom_ID: ${=key=}\\\\n\\\"
    \\\":NOTER_DOCUMENT: %(orb-process-file-field \\\\\\\"${=key=}\\\\\\\")\\\\n\\\"
    \\\":AUTHOR: ${author-abbrev}\\\\n\\\"
    \\\":JOURNAL: ${journaltitle}\\\\n\\\"
    \\\":DATE: ${date}\\\\n\\\"
    \\\":YEAR: ${year}\\\\n\\\"
    \\\":DOI: ${doi}\\\\n\\\"
    \\\":URL: ${url}\\\\n\\\"
    \\\":END:\\\\n\\\\n\\\"
    )
   )
  )

(use-package citeproc)

(use-package bibtex
  :config
  (setq bibtex-autokey-year-length 4
        bibtex-autokey-name-year-separator \\\"-\\\"
        bibtex-autokey-year-title-separator \\\"-\\\"
        bibtex-autokey-titleword-separator \\\"-\\\"
        bibtex-autokey-titlewords 2
        bibtex-autokey-titlewords-stretch 1
        bibtex-autokey-titleword-length 5))

(use-package ivy-bibtex
  :config
  (autoload 'ivy-bibtex \\\"ivy-bibtex\\\" \\\"\\\" t)
  ;; ivy-bibtex requires ivy's `ivy--regex-ignore-order` regex builder, which
  ;; ignores the order of regexp tokens when searching for matching candidates.
  ;; Add something like this to your init file:
  (setq ivy-re-builders-alist
        '((ivy-bibtex . ivy--regex-ignore-order)
          (t . ivy--regex-plus))))

;; most of this config taken from http://www.wouterspekkink.org/academia/writing/tool/doom-emacs/2021/02/27/writing-academic-papers-with-org-mode.html
(use-package org-roam-bibtex
  :after org-roam
  :hook org-roam-mode
  :bind (:map org-mode-map (\\\"C-c n b\\\" . orb-note-actions)) ;; yes, really `orb`.
  :config
  (require 'org-ref)
  (org-roam-bibtex-mode)
  (setq orb-preformat-keywords '(\\\"citekey\\\" \\\"title\\\" \\\"url\\\" \\\"author-or-editor\\\" \\\"keywords\\\" \\\"file\\\")
        orb-process-file-keyword t
        orb-file-field-extensions '(pdf))

  (setq orb-templates
        '((\\\"r\\\" \\\"ref\\\" 'org-roam-capture--get-point \\\"\\\"
           :file-name \\\"${citekey}\\\"
           :head \\\"#+TITLE: ${citekey}: ${title}\\\\n#+ROAM_KEY: ${ref}
- tags ::
- keywords :: ${keywords}

* Notes
:PROPERTIES:
:Custom_ID: ${citekey}
:URL: ${url}
:AUTHOR: ${author-or-editor}
:NOTER_DOCUMENT: ${file}
:NOTER_PAGE:
:END:\\\")))
  )

\" :post-blank 1 :post-affiliated 36477 :mode nil :granularity element :parent (section (:begin 35900 :end 42926 :contents-begin 35900 :contents-end 42925 :robust-begin 35900 :robust-end 42923 :post-blank 1 :post-affiliated 35900 :mode section :granularity element :parent (headline ...)))))"
 Cache around :begin:
(paragraph (:begin 36316 :end 36507 :contents-begin 36316 :contents-end 36507 :post-blank 0 :post-affiliated 36316 :mode nil :granularity element :cached t :parent (section (:begin 35930 :end 42956 :contents-begin 35930 :contents-end 42955 :robust-begin 35930 :robust-end 42953 :post-blank 1 :post-affiliated 35930 :mode section :granularity element :cached t :parent (headline (:raw-value "Org & PDFs" :begin 35915 :end 42956 :pre-blank 0 :contents-begin 35930 :contents-end 42955 :robust-begin 35932 :robust-end 42953 :level 3 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 35915 :title "Org & PDFs" :mode nil :granularity element :cached t :parent (headline (:raw-value "Org-Mode" :begin 5655 :end 44062 :pre-blank 0 :contents-begin 5667 :contents-end 44060 :robust-begin 5669 :robust-end 44058 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5655 :title "Org-Mode" :mode section :granularity element :cached t :parent (headline (:raw-value "Writing" :begin 5645 :end 48198 :pre-blank 0 :contents-begin 5655 :contents-end 48197 :robust-begin 5657 :robust-end 48195 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5645 :title "Writing" :mode nil :granularity element :cached t :parent (org-data (:begin 1 :contents-begin 1 :contents-end 161525 :end 161525 :robust-begin 3 :robust-end 161523 :post-blank 0 :post-affiliated 1 :path "/Users/jabrahms/src/justin.abrah.ms/blog/_posts/dotfiles/emacs.org" :mode org-data :CATEGORY "emacs" :cached t :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil))
(paragraph (:begin 36316 :end 36507 :contents-begin 36316 :contents-end 36507 :post-blank 0 :post-affiliated 36316 :mode nil :granularity element :cached t :parent (section (:begin 35930 :end 42956 :contents-begin 35930 :contents-end 42955 :robust-begin 35930 :robust-end 42953 :post-blank 1 :post-affiliated 35930 :mode section :granularity element :cached t :parent (headline (:raw-value "Org & PDFs" :begin 35915 :end 42956 :pre-blank 0 :contents-begin 35930 :contents-end 42955 :robust-begin 35932 :robust-end 42953 :level 3 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 35915 :title "Org & PDFs" :mode nil :granularity element :cached t :parent (headline (:raw-value "Org-Mode" :begin 5655 :end 44062 :pre-blank 0 :contents-begin 5667 :contents-end 44060 :robust-begin 5669 :robust-end 44058 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5655 :title "Org-Mode" :mode section :granularity element :cached t :parent (headline (:raw-value "Writing" :begin 5645 :end 48198 :pre-blank 0 :contents-begin 5655 :contents-end 48197 :robust-begin 5657 :robust-end 48195 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5645 :title "Writing" :mode nil :granularity element :cached t :parent (org-data (:begin 1 :contents-begin 1 :contents-end 161525 :end 161525 :robust-begin 3 :robust-end 161523 :post-blank 0 :post-affiliated 1 :path "/Users/jabrahms/src/justin.abrah.ms/blog/_posts/dotfiles/emacs.org" :mode org-data :CATEGORY "emacs" :cached t :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil))
(src-block (:language "elisp" :switches nil :parameters nil :begin 36507 :end 40247 :number-lines nil :preserve-indent nil :retain-labels t :use-labels t :label-fmt nil :value "(use-package citar
  :no-require
  :custom
  (org-cite-global-bibliography '(\"~/docs/references.bib\"))
  (org-cite-insert-processor 'citar)
  (org-cite-follow-processor 'citar)
  (org-cite-activate-processor 'citar)
  (citar-bibliography org-cite-global-bibliography)
  ;; optional: org-cite-insert is also bound to C-c C-x C-@
  :bind
  (:map org-mode-map :package org (\"C-c b\" . #'org-cite-insert)))


(use-package org-ref
  :config
  (setq
   org-ref-completion-library 'org-ref-ivy-cite
   ;; org-ref-get-pdf-filename-function 'org-ref-get-pdf-filename-helm-bibtex
   org-ref-default-bibliography '(\"~/docs/references.bib\")
   org-ref-note-title-format \"* TODO %y - %t\\n :PROPERTIES:\\n  :Custom_ID: %k\\n  :NOTER_DOCUMENT: %F\\n :ROAM_KEY: cite:%k\\n  :AUTHOR: %9a\\n  :JOURNAL: %j\\n  :YEAR: %y\\n  :VOLUME: %v\\n  :PAGES: %p\\n  :DOI: %D\\n  :URL: %U\\n :END:\\n\\n\"
   org-ref-notes-directory \"~/docs/roam/\"
   org-ref-notes-function 'orb-edit-notes


   bibtex-align-at-equal-sign t ; prettier formatting
   bibtex-dialect 'biblatex     ; bibtex is apparently very old (1988), so use the new variant

   ;; tell org to output using bibtex
   org-latex-pdf-process (list \"latexmk -shell-escape -bibtex -f -pdf %f\")

   bibtex-user-optional-fields '((\"keywords\" \"Keywords to describe the entry\" \"\")
                                 (\"file\" \"link to the document file\" \":\")
                                 (\"url\" \"url of the thing\" \"\"))
   bibtex-completion-bibliography '(\"~/docs/references.bib\")
   bibtex-completion-library-path '(\"~/docs/pdfs_for_notes/\")
   bibtex-completion-pdf-field \"file\"

   ;; Not sure about this yet..
   bibtex-completion-notes-template-multiple-files
   (concat
    \"#+TITLE: ${title}\\n\"
    \"#+ROAM_KEY: cite:${=key=}\\n\"
    \"* TODO Notes\\n\"
    \":PROPERTIES:\\n\"
    \":Custom_ID: ${=key=}\\n\"
    \":NOTER_DOCUMENT: %(orb-process-file-field \\\"${=key=}\\\")\\n\"
    \":AUTHOR: ${author-abbrev}\\n\"
    \":JOURNAL: ${journaltitle}\\n\"
    \":DATE: ${date}\\n\"
    \":YEAR: ${year}\\n\"
    \":DOI: ${doi}\\n\"
    \":URL: ${url}\\n\"
    \":END:\\n\\n\"
    )
   )
  )

(use-package citeproc)

(use-package bibtex
  :config
  (setq bibtex-autokey-year-length 4
        bibtex-autokey-name-year-separator \"-\"
        bibtex-autokey-year-title-separator \"-\"
        bibtex-autokey-titleword-separator \"-\"
        bibtex-autokey-titlewords 2
        bibtex-autokey-titlewords-stretch 1
        bibtex-autokey-titleword-length 5))

(use-package ivy-bibtex
  :config
  (autoload 'ivy-bibtex \"ivy-bibtex\" \"\" t)
  ;; ivy-bibtex requires ivy's `ivy--regex-ignore-order` regex builder, which
  ;; ignores the order of regexp tokens when searching for matching candidates.
  ;; Add something like this to your init file:
  (setq ivy-re-builders-alist
        '((ivy-bibtex . ivy--regex-ignore-order)
          (t . ivy--regex-plus))))

;; most of this config taken from http://www.wouterspekkink.org/academia/writing/tool/doom-emacs/2021/02/27/writing-academic-papers-with-org-mode.html
(use-package org-roam-bibtex
  :after org-roam
  :hook org-roam-mode
  :bind (:map org-mode-map (\"C-c n b\" . orb-note-actions)) ;; yes, really `orb`.
  :config
  (require 'org-ref)
  (org-roam-bibtex-mode)
  (setq orb-preformat-keywords '(\"citekey\" \"title\" \"url\" \"author-or-editor\" \"keywords\" \"file\")
        orb-process-file-keyword t
        orb-file-field-extensions '(pdf))

  (setq orb-templates
        '((\"r\" \"ref\" 'org-roam-capture--get-point \"\"
           :file-name \"${citekey}\"
           :head \"#+TITLE: ${citekey}: ${title}\\n#+ROAM_KEY: ${ref}
- tags ::
- keywords :: ${keywords}

* Notes
:PROPERTIES:
:Custom_ID: ${citekey}
:URL: ${url}
:AUTHOR: ${author-or-editor}
:NOTER_DOCUMENT: ${file}
:NOTER_PAGE:
:END:\")))
  )

" :post-blank 1 :post-affiliated 36507 :mode nil :granularity element :cached t :parent (section (:begin 35930 :end 42956 :contents-begin 35930 :contents-end 42955 :robust-begin 35930 :robust-end 42953 :post-blank 1 :post-affiliated 35930 :mode section :granularity element :cached t :parent (headline (:raw-value "Org & PDFs" :begin 35915 :end 42956 :pre-blank 0 :contents-begin 35930 :contents-end 42955 :robust-begin 35932 :robust-end 42953 :level 3 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 35915 :title "Org & PDFs" :mode nil :granularity element :cached t :parent (headline (:raw-value "Org-Mode" :begin 5655 :end 44062 :pre-blank 0 :contents-begin 5667 :contents-end 44060 :robust-begin 5669 :robust-end 44058 :level 2 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 2 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5655 :title "Org-Mode" :mode section :granularity element :cached t :parent (headline (:raw-value "Writing" :begin 5645 :end 48198 :pre-blank 0 :contents-begin 5655 :contents-end 48197 :robust-begin 5657 :robust-end 48195 :level 1 :priority nil :tags nil :todo-keyword nil :todo-type nil :post-blank 1 :footnote-section-p nil :archivedp nil :commentedp nil :post-affiliated 5645 :title "Writing" :mode nil :granularity element :cached t :parent (org-data (:begin 1 :contents-begin 1 :contents-end 161525 :end 161525 :robust-begin 3 :robust-end 161523 :post-blank 0 :post-affiliated 1 :path "/Users/jabrahms/src/justin.abrah.ms/blog/_posts/dotfiles/emacs.org" :mode org-data :CATEGORY "emacs" :cached t :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil)) :org-element--cache-sync-key nil)) Disable showing Disable logging