pkg update and first config fix

org-brain not working, add org-roam

lisp/org-ref/org-ref-export.el

@@ -47,6 +47,8 @@
 (defvar hfy-user-sheet-assoc)  		; to quiet compiler
 
 (require 'ox-org)
+(if (executable-find "pandoc")
+    (require 'ox-pandoc))
 
 (require 'citeproc)
 
@@ -56,14 +58,15 @@
     (md . plain)
     (org . org)
     (ascii . plain)
-    (odt . org-odt))
+    (odt . org-odt)
+    (docx . org))
   "Mapping of export backend to csl-backends."
   :type '(alist :key-type (symbol) :value-type (symbol))
   :group 'org-ref)
 
 
 (defcustom org-ref-cite-internal-links 'auto
-  "Should be on of
+  "Should be one of
 - 'bib-links :: link cites to bibliography entries
 - 'no-links :: do not link cites to bibliography entries
 - nil or 'auto :: add links based on the style."
@@ -120,6 +123,19 @@ See https://github.com/citation-style-language/documentation/blob/master/specifi
   :group 'org-ref)
 
 
+(defcustom org-ref-export-suppress-affix-types 
+  '("citet"
+    "citet*"
+    "citetitle"
+    "citeyear"
+    "citeauthor"
+    "citenum"
+    "textcite")
+  "List of cite types to suppress affixes (usually parentheses) on."
+  :type '(list (repeat string))
+  :group 'org-ref)
+
+
 (defun org-ref-dealias-label (alias)
   "Return the full, de-aliased label for ALIAS.
 Looked up from `org-ref-csl-label-aliases'.
@@ -164,17 +180,18 @@ REF is a plist data structure returned from `org-ref-parse-cite-path'."
     ;; e.g. {5, 6 and 12}, because he had 3 books.
 
     (if (and (string-match
-	      (rx
-	       ;; optional label
-	       (group-n 1 (optional
-			   (regexp (regexp-opt (cl-loop for (abbrvs . full)
-							in org-ref-csl-label-aliases
-							append (append abbrvs (list full)))))))
-	       (optional (one-or-more space))
-	       ;; number or numeric ranges
-	       (group-n 2 (one-or-more digit) (optional "-" (one-or-more digit)))
-	       ;; everything else
-	       (group-n 3 (* ".")))
+	      (rx-to-string
+	       `(seq
+		 ;; optional label
+		 (group-n 1 (optional
+			     (regexp ,(regexp-opt (cl-loop for (abbrvs . full)
+							   in org-ref-csl-label-aliases
+							   append (append abbrvs (list full)))))))
+		 (optional (one-or-more space))
+		 ;; number or numeric ranges
+		 (group-n 2 (one-or-more digit) (optional "-" (one-or-more digit)))
+		 ;; everything else
+		 (group-n 3 (* "."))))	      
 	      full-suffix)
 	     (match-string 2 full-suffix)
 	     (not (string= "" (match-string 2 full-suffix)))) 
@@ -233,7 +250,7 @@ BACKEND is the org export backend."
 		   ((file-exists-p style)
 		    style)
 		   ;; In a user-dir
-		   ((and (boundp 'org-cite-csl-styles-dir)
+		   ((and (bound-and-true-p org-cite-csl-styles-dir)
 			 (file-exists-p (f-join org-cite-csl-styles-dir style)))
 		    (f-join org-cite-csl-styles-dir style))
 		   ;; provided by org-ref
@@ -249,15 +266,13 @@ BACKEND is the org export backend."
 		    (error "%s not found" style)))
 		  ;; item-getter
 		  ;; (citeproc-itemgetter-from-bibtex (org-ref-find-bibliography))
-		  (citeproc-hash-itemgetter-from-any (org-ref-find-bibliography))
+		  (citeproc-hash-itemgetter-from-any (org-ref-find-bibliography) t)
 		  ;; locale getter
-		  (citeproc-locale-getter-from-dir (cond
-						    ((boundp 'org-cite-csl-locales-dir)
-						     org-cite-csl-locales-dir)
-						    (t
+		  (citeproc-locale-getter-from-dir (if (bound-and-true-p org-cite-csl-locales-dir)
+						       org-cite-csl-locales-dir
 						     (f-join (file-name-directory
 							      (locate-library "org-ref"))
-							     "citeproc/csl-locales"))))
+							     "citeproc/csl-locales")))
 		  ;; the actual locale
 		  locale))
 
@@ -292,12 +307,9 @@ BACKEND is the org export backend."
 			     ;; https://github.com/andras-simonyi/citeproc-el#creating-citation-structures
 			     (citeproc-citation-create
 			      :cites cites
-			      ;; TODO: proof of concept, incomplete if this is
-			      ;; true, the citation is not parenthetical
 			      :suppress-affixes (let ((type (org-element-property :type cl)))
-						  (when (member type '("citet"
-								       "citet*"
-								       "citenum"))
+						  (when (member type
+								org-ref-export-suppress-affix-types)
 						    t))
 
 			      ;; TODO: this is proof of concept, and not complete.
@@ -324,14 +336,17 @@ BACKEND is the org export backend."
 						  (org-element-property :type cl) 0 1))
 			      ;; I don't know where this information would come from.
 			      :note-index nil
-			      :ignore-et-al nil))))
+			      :ignore-et-al nil
+			      :grouped nil))))
 
 	   (rendered-citations (progn (citeproc-append-citations cites proc)
 				      (citeproc-render-citations proc csl-backend org-ref-cite-internal-links)))
 	   ;; I only use the returned bibliography string. citeproc returns a
 	   ;; bunch of other things related to offsets and linespacing, but I
 	   ;; don't know what you do with these, so just ignore them here.
-	   (rendered-bib (car (citeproc-render-bib proc csl-backend)))
+	   (bibdata (citeproc-render-bib proc csl-backend))
+	   (rendered-bib (car bibdata))
+	   (bib-parameters (cdr bibdata))
 	   ;; The idea is we will wrap each citation and the bibliography in
 	   ;; org-code so it exports appropriately.
 	   (cite-formatters '((html . "@@html:%s@@")
@@ -357,6 +372,42 @@ BACKEND is the org export backend."
 						    (org-element-property :post-blank cl) 0)
 						   ? )))))
 
+      ;; Decorate the bibliography for different outputs adapted from
+      ;;  `org-cite-csl-render-bibliography' in oc-csl I don't know what all
+      ;;  these do or how to use them in the CSS for html, or LaTeX. This is to
+      ;;  fix an annoying HTML feature that has an extra line in the numbering.
+      ;;  This seems to do the right thing. I don't support hanging-indent like
+      ;;  oc-csl does, and I don't currently support LaTeX here. It already does
+      ;;  a good job there.
+      ;;
+      ;; (find-library "oc-csl")
+      ;;
+      ;; Here are some examples of what is in the bib-parameters.
+      ;;  (max-offset . 2) (hanging-indent) (second-field-align . flush)
+      ;; (entry-spacing . 0)
+      ;; (line-spacing . 2)
+      ;;
+      ;; Here we add style css for html output.
+      (cond
+       ((eq 'html backend)
+	(let ((s1 "")
+	      (s2 ""))
+	  (when (cdr (assq 'second-field-align bib-parameters))
+	    (setq s1 (format
+		      "<style>.csl-left-margin{float: left; padding-right: 0em;}
+ .csl-right-inline{margin: 0 0 0 %dem;}</style>"
+		      ;; I hard coded this factor of 0.6 from the oc-csl code.  
+		      (* 0.6  (or (cdr (assq 'max-offset bib-parameters)) 0)))))
+
+	  ;; hard-coded the hanging indent. oc-csl uses a variable for this. I
+	  ;; guess we could too, but this seems simpler.
+	  (when (cdr (assq 'hanging-indent bib-parameters))
+	    (setq s2 "<style>.csl-entry{text-indent: -1.5em; margin-left: 1.5em;}</style>"))
+	  
+	  (setq rendered-bib (concat
+			      s1 s2
+			      rendered-bib)))))
+
       ;; replace the bibliography
       (org-element-map (org-element-parse-buffer) 'link
 	(lambda (lnk)
@@ -391,6 +442,7 @@ VISIBLE-ONLY BODY-ONLY and INFO."
 	 (extensions '((html . ".html")
 		       (latex . ".tex")
 		       (ascii . ".txt")
+		       (md . ".md")
 		       (odt . ".odf")))
 	 (cp (point))
 	 (mm) 				;marker to save place
@@ -407,7 +459,6 @@ VISIBLE-ONLY BODY-ONLY and INFO."
      (org-export-expand-include-keyword)
      (goto-char (marker-position mm))
      (org-ref-process-buffer backend subtreep)
-     (message-box (buffer-substring (line-beginning-position) (line-end-position)))
      (set-marker mm nil)
      
      (pcase backend
@@ -415,6 +466,11 @@ VISIBLE-ONLY BODY-ONLY and INFO."
        ('odt (org-open-file (org-odt-export-to-odt async subtreep visible-only
 						   info)
 			    'system))
+       ;; for pandoc, we mean make a docx via pandoc
+       ('docx (org-open-file (plist-get (org-pandoc-export-to-docx async subtreep visible-only
+								   body-only info)
+					'output-file)
+			     'system))
        (_
 	(org-open-file (org-export-to-file backend export-name
 			 async subtreep visible-only
@@ -443,14 +499,25 @@ VISIBLE-ONLY BODY-ONLY and INFO."
 		     body-only info))
 
 
+(defun org-ref-export-to-md (&optional async subtreep visible-only
+				       body-only info)
+  "Export the buffer to md and open.
+See `org-export-as' for the meaning of ASYNC SUBTREEP
+VISIBLE-ONLY BODY-ONLY and INFO."
+  (org-ref-export-to 'md async subtreep visible-only
+		     body-only info))
+
+
 (defun org-ref-export-to-pdf (&optional async subtreep visible-only
 					body-only info)
   "Export the buffer to PDF via LaTeX and open.
 See `org-export-as' for the meaning of ASYNC SUBTREEP
 VISIBLE-ONLY BODY-ONLY and INFO."
-  (let ((org-export-before-parsing-hook '(org-ref-csl-preprocess-buffer)))
+  (let ((org-export-before-parsing-hook (append
+					 org-export-before-parsing-hook
+					 '(org-ref-csl-preprocess-buffer))))
     (org-open-file (org-latex-export-to-pdf async subtreep visible-only
-					body-only info))))
+					    body-only info))))
 
 
 (defun org-ref-export-to-latex (&optional async subtreep visible-only
@@ -473,6 +540,15 @@ VISIBLE-ONLY BODY-ONLY and INFO."
 		     body-only info))
 
 
+(defun org-ref-export-to-docx (&optional async subtreep visible-only
+					 body-only info)
+  "Export the buffer to docx via pandoc and open.
+See `org-export-as' for the meaning of ASYNC SUBTREEP
+VISIBLE-ONLY BODY-ONLY and INFO."
+  (org-ref-export-to 'docx async subtreep visible-only
+		     body-only info))
+
+
 (defun org-ref-export-as-org (&optional _async subtreep visible-only
 					body-only info)
   "Export the buffer to an ORG buffer and open.
@@ -510,12 +586,14 @@ VISIBLE-ONLY BODY-ONLY and INFO."
   :menu-entry
   '(?r "Org-ref export"
        ((?a "to Ascii" org-ref-export-to-ascii)
+	(?m "to markdown" org-ref-export-to-md)
 	(?h "to html" org-ref-export-to-html)
 	(?l "to LaTeX" org-ref-export-to-latex)
 	(?p "to PDF" org-ref-export-to-pdf)
 	(?o "to ODT" org-ref-export-to-odt)
 	(?O "to Org buffer" org-ref-export-as-org)
-	(?e "to email" org-ref-export-to-message))))
+	(?e "to email" org-ref-export-to-message)
+	(?w "to docx" org-ref-export-to-docx))))
 
 ;; An alternative to this exporter is to use an  `org-export-before-parsing-hook'
 ;; (add-hook 'org-export-before-parsing-hook 'org-ref-csl-preprocess-buffer)