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pkg update and first config fix

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org-brain not working, add org-roam
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Daniel Weschke
2022-12-19 23:02:34 +01:00
parent 02b3e07185
commit 82f05baffe
885 changed files with 356098 additions and 36993 deletions
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263
lisp/org-ref/org-ref-citation-links.el
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@@ -96,6 +96,14 @@ This is mostly for multicites and natbib."
:group 'org-ref-faces)
(defcustom org-ref-activate-cite-links t
"If non-nil use font-lock to activate citations.
In large documents with many citations activation can be slow.
Set this to nil to turn that off, which increase performance."
:type 'boolean
:group 'org-ref)
(defcustom org-ref-default-citation-link
"cite"
"The default type of citation link to use."
@@ -106,9 +114,9 @@ This is mostly for multicites and natbib."
(defcustom org-ref-natbib-types
'(("cite" "basic citation")
("nocite" "add key to bibliography, but do not cite it in the text")
("citet" "textual, Jones et al. (1990")
("citet" "textual, Jones et al. (1990)")
("citet*" "textual, full author list Jones, Baker, and Williams (1990)")
("citep" "parenthetical citation (Jones et al. (1990)")
("citep" "parenthetical citation (Jones et al. (1990))")
("citep*" "parenthetical, full author list, (Jones, Baker, and Williams, 1990)")
("citealt" "same as citet, but without parentheses")
("citealt*" "same as citet, with full author list but without parentheses")
@@ -143,7 +151,7 @@ This is mostly for multicites and natbib."
("Parencite" "similar to cite with parentheses and capitalization")
("footcite" "Put the citation in a footnote")
("footcitetext" "Put the citation in a footnote using \footnotetext")
("textcite" "print the authors or editors as a subject of the sentence")
("Textcite" "print the authors or editors as a subject of the sentence with capitalization")
("smartcite" "like parencite in a footnote, and footcite in the body")
@@ -151,29 +159,29 @@ This is mostly for multicites and natbib."
("cite*" "similar to cite, but prints the year or title")
("parencite*" "similar to parencite, but prints the year or title")
("supercite" "superscripted numeric citation (only in numberic styles)")
("autocite" "handles some punctuation nuances")
("Autocite" "handles some punctuation nuances with punctuation")
("autocite*" "same as autocite but * is passed to the backend")
("Autocite*" "same as Autocite but * is passed to the backend")
("citetitle" "the shorttitle or title field")
("citetitle*" "the full title")
("citeyear" "the year field")
("citeyear*" "the year field and extradate information if available")
("citedate" "the full date or year")
("citedate*" "the full date or year, including extradate information if available")
("citeurl" "the url field")
("fullcite" "create a full citation similar to what is in the bibliography")
("footfullcite" "create a full citation as a footnote")
;; "volcite" "Volcite" cannot support the syntax
("notecite" "print prenote and postnote, but no citation")
("Notecite" "print prenote and postnote, but no citation with capitalization")
("pnotecite" "similar to notecite with parentheses")
("Pnotecite" "similar to Notecite with parentheses")
("fnotecite" "similar to notecite in a footnote"))
@@ -256,7 +264,8 @@ This is mostly for multicites and natbib."
(defvar org-ref-citation-key-re
(rx "&" (group-n 1 (one-or-more (any word "-.:?!`'/*@+|(){}<>&_^$#%~"))))
(rx-to-string
'(seq "&" (group-n 1 (one-or-more (any word "-.:?!`'/*@+|(){}<>&_^$#%~")))))
"Numbered regular expression for a version 3 cite key.
Key is in group 1.
Adapted from the expression in org-cite.")
@@ -365,7 +374,7 @@ to a path string."
"Return a list of valid bibtex keys for this buffer.
This is used a lot in `org-ref-cite-activate' so it needs to be
fast, but also up to date."
;; this seems to be needed, but we don't want to do this every time
(unless bibtex-completion-display-formats-internal
(bibtex-completion-init))
@@ -376,7 +385,7 @@ fast, but also up to date."
collect (assoc file bibtex-completion-cache)))
;; We have a cache for each file
;; bibtex-completion-cache contains (filename md5hash entries)
(cl-loop for entry in
(cl-loop for entry in
(cl-loop
for file in files
append (cddr (assoc file bibtex-completion-cache)))
@@ -404,100 +413,105 @@ fast, but also up to date."
(puthash entry t org-ref-valid-keys-cache))))
org-ref-valid-keys-cache)
(defun org-ref-cite-activate (start end path _bracketp)
"Activation function for a cite link.
START and END are the bounds of the link.
PATH has the citations in it."
(let* ((valid-keys (org-ref-valid-keys-cached))
valid-key
substrings)
(goto-char start)
(pcase (org-ref-cite-version path)
(2
;; This makes the brackets visible, but we only need it when there is a
;; description.
(when (looking-at "\\[\\[\\(.*\\)\\]\\[\\(.*\\)\\]\\]")
(remove-text-properties start end '(invisible nil)))
(setq substrings (split-string path ","))
(cl-loop for key in substrings
do
;; get to the substring
(search-forward key end)
(put-text-property (match-beginning 0)
(match-end 0)
'keymap
org-ref-cite-keymap)
(put-text-property (match-beginning 0)
(match-end 0)
'cite-key
key)
(unless (gethash (string-trim key) valid-keys nil)
(put-text-property (match-beginning 0)
(match-end 0)
'face 'org-ref-bad-cite-key-face)
(put-text-property (match-beginning 0)
(match-end 0)
'help-echo "Key not found"))
))
(3
(setq substrings (split-string path ";"))
(cl-loop for i from 0 for s in substrings
do
;; get to the substring
(search-forward s end)
(put-text-property (match-beginning 0)
(match-end 0)
'keymap
org-ref-cite-keymap)
(let* (key-begin
key-end
key)
(when (and org-ref-activate-cite-links
;; Try avoid fontifying org-cite elements. this is based on the
;; path containing @ which makes it likely to be an org-cite. Maybe
;; a text property is better, in case this is an issue in the
;; future.
(not (s-contains-p "@" path)))
(let* ((valid-keys (org-ref-valid-keys))
valid-key
substrings)
(goto-char start)
(pcase (org-ref-cite-version path)
(2
;; This makes the brackets visible, but we only need it when there is a
;; description.
(when (looking-at "\\[\\[\\(.*\\)\\]\\[\\(.*\\)\\]\\]")
(remove-text-properties start end '(invisible nil)))
(setq substrings (split-string path ","))
(cl-loop for key in substrings
do
;; get to the substring
(search-forward key end)
(put-text-property (match-beginning 0)
(match-end 0)
'keymap
org-ref-cite-keymap)
(put-text-property (match-beginning 0)
(match-end 0)
'cite-key
key)
(unless (member (string-trim key) valid-keys)
(put-text-property (match-beginning 0)
(match-end 0)
'face 'org-ref-bad-cite-key-face)
(put-text-property (match-beginning 0)
(match-end 0)
'help-echo "Key not found"))))
(3
(setq substrings (split-string path ";"))
(cl-loop for i from 0 for s in substrings
do
;; get to the substring
(search-forward s end)
(put-text-property (match-beginning 0)
(match-end 0)
'keymap
org-ref-cite-keymap)
(let* (key-begin
key-end
key)
;; Look for a key. common pre/post notes do not have keys in them.
(save-match-data
(when (string-match org-ref-citation-key-re s)
(setq key (match-string-no-properties 1 s)
valid-key (gethash key valid-keys nil)
)))
;; Look for a key. common pre/post notes do not have keys in them.
(save-match-data
(when (string-match org-ref-citation-key-re s)
(setq key (match-string-no-properties 1 s)
valid-key (member key valid-keys))))
;; these are global prefix/suffixes
(when (and (or (= i 0)
(= i (- (length substrings) 1)))
(null key))
(put-text-property (match-beginning 0) (match-end 0)
'face 'org-ref-cite-global-prefix/suffix-face)
(put-text-property (match-beginning 0) (match-end 0)
'help-echo "Global prefix/suffix"))
;; these are global prefix/suffixes
(when (and (or (= i 0)
(= i (- (length substrings) 1)))
(null key))
(put-text-property (match-beginning 0) (match-end 0)
'face 'org-ref-cite-global-prefix/suffix-face)
(put-text-property (match-beginning 0) (match-end 0)
'help-echo "Global prefix/suffix"))
;; we have a key. we have to re-search to get its position
(when key
(save-excursion
(save-match-data
(search-backward (concat "&" key))
(setq key-begin (match-beginning 0)
key-end (match-end 0))))
;; mark the &
(put-text-property key-begin (+ 1 key-begin)
'face 'org-ref-cite-&-face)
;; store key on the whole thing
(put-text-property (match-beginning 0)
(match-end 0)
'cite-key
key)
;; we have a key. we have to re-search to get its position
(when key
(save-excursion
(save-match-data
(search-backward (concat "&" key))
(setq key-begin (match-beginning 0)
key-end (match-end 0))))
;; mark the &
(put-text-property key-begin (+ 1 key-begin)
'face 'org-ref-cite-&-face)
;; store key on the whole thing
(put-text-property (match-beginning 0)
(match-end 0)
'cite-key
key)
;; fontify any prefix /suffix text
(put-text-property (match-beginning 0) key-begin
'face 'org-ref-cite-local-prefix/suffix-face)
;; fontify any prefix /suffix text
(put-text-property (match-beginning 0) key-begin
'face 'org-ref-cite-local-prefix/suffix-face)
(put-text-property key-end (match-end 0)
'face 'org-ref-cite-local-prefix/suffix-face)
(put-text-property key-end (match-end 0)
'face 'org-ref-cite-local-prefix/suffix-face)
;; bad key activation
(unless valid-key
(put-text-property key-begin key-end
'face 'font-lock-warning-face)
(put-text-property key-begin key-end
'help-echo "Key not found")))))))))
;; bad key activation
(unless valid-key
(put-text-property key-begin key-end
'face 'font-lock-warning-face)
(put-text-property key-begin key-end
'help-echo "Key not found"))))))))))
;; * Following citation links
@@ -632,6 +646,15 @@ Use with apply-partially."
("prefix" . ,(if (= 1 (length references))
;; single reference
(cond
;; global and common prefixes exist, combine them
((and (plist-get cite :prefix)
(plist-get (car references) :prefix))
(concat "["
(plist-get cite :prefix)
";" ;; add this back as a separator
(plist-get (car references) :prefix)
"]"))
;; local prefix is not empty, we use it.
((plist-get (car references) :prefix)
(concat "["
@@ -660,7 +683,8 @@ Use with apply-partially."
(concat "["
(string-trim (plist-get (car references) :prefix))
"]"))
;; if you have a suffix, you need an empty prefix
;; if you get here, the prefix is empty.
;; if you have a suffix, you need an empty prefix placeholder
((plist-get cite :suffix)
"[]")
(t
@@ -668,15 +692,25 @@ Use with apply-partially."
("suffix" . ,(if (= 1 (length references))
;; Single reference
(cond
;; local prefix is not empty, so use it
;; local suffix is not empty, so use it
((plist-get (car references) :suffix)
(format "[%s]"
(string-trim (plist-get (car references) :suffix))))
;; global prefix is not empty
;; global suffix is not empty
((plist-get cite :suffix)
(format "[%s]" (string-trim (plist-get cite :suffix))))
(t
""))
;; If there is a prefix, then this should
;; be an empty bracket, and if not it
;; should am empty string. You need an
;; empty bracket, at least for biblatex
;; commands. With just one set of
;; brackets it is interpreted as a
;; suffix.
(if (or (plist-get cite :prefix)
(plist-get (car references) :prefix))
"[]"
"")))
;; Multiple references
(cond
;; this is a common suffix
@@ -786,7 +820,7 @@ Use with apply-partially."
(org-link-set-parameters
"bibentry"
"bibentry"
:complete (apply-partially #'org-ref-cite-link-complete "bibentry")
:follow #'org-ref-cite-follow
:face 'org-ref-cite-face
@@ -874,7 +908,7 @@ arg COMMON, edit the common prefixes instead."
(data (org-ref-parse-cite-path (org-element-property :path cite)))
prefix suffix
(delta 0))
(if (or (null key) common)
(progn
(setq prefix (read-string "prenote: " (plist-get data :prefix))
@@ -883,7 +917,7 @@ arg COMMON, edit the common prefixes instead."
(plist-put data :prefix (if (string= "" prefix)
nil prefix))
(plist-put data :suffix (if (string= "" suffix)
nil suffix)))
@@ -893,7 +927,7 @@ arg COMMON, edit the common prefixes instead."
(lambda (el1 key-at-point)
(string= key-at-point (plist-get el1 :key))))))
;; Pad with spaces after prefix and before suffix
(setq prefix (concat
(setq prefix (concat
(read-string "prenote: "
(string-trim
(plist-get
@@ -914,13 +948,13 @@ arg COMMON, edit the common prefixes instead."
(nth index (plist-get data :references))
:prefix (if (string= "" prefix)
nil prefix))
(plist-put
(nth index (plist-get data :references))
:suffix (if (string= "" suffix)
nil suffix))))
(setf (buffer-substring (org-element-property :begin cite) (org-element-property :end cite))
(format "[[%s:%s]]" type (org-ref-interpret-cite-data data)))
@@ -1182,7 +1216,10 @@ Rules:
(cl-second item))))))
(completion-extra-properties `(:annotation-function ,type-annotation)))
(cond
((derived-mode-p 'latex-mode)
(insert (bibtex-completion-format-citation-cite (list key))))
(t
(cond
;; Not on a link, so we just insert a cite
((null (assoc type org-ref-cite-types))
@@ -1251,12 +1288,16 @@ Rules:
(3 (cl--set-buffer-substring
(org-element-property :begin object)
(org-element-property :end object)
(concat "[[" type ":" (org-ref-interpret-cite-data data) "]]"))))))
(concat "[["
type ":"
(org-ref-interpret-cite-data data)
"]]"
(make-string (org-element-property :post-blank object) ? )))))))
;; Now get to the end of the key you just put in.
(setq object (org-element-context))
(goto-char (org-element-property :end object))
(skip-chars-backward " ")))
(skip-chars-backward " ")))))
(defun org-ref-insert-cite-keys (keys &optional set-type)