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List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: org-mode-email , =?utf-8?Q?Andr=C3=A1s?= Simonyi Errors-To: emacs-orgmode-bounces+larch=yhetil.org@gnu.org Sender: "Emacs-orgmode" X-Migadu-Flow: FLOW_IN X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1638545197; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding: in-reply-to:in-reply-to:references:references:list-id:list-help: list-unsubscribe:list-subscribe:list-post:dkim-signature; bh=VlcljCUsKHA+L8izky+t8WfGjwoplkhVXk/DUEGDQqE=; b=kKG8bruaZduTKYkD9VJPvd2cQulbXhKWt83ferymZ4Nq40qdM3fkyOdcFbBfRriYXptudd Q0s5CGB6UhuqQ9fAva1BJJMBv4Q2W61l4RQY1zzE7jxgvkioT/ljZAASW4AoUDLKzgKDxS rXenP/qRoFZO73hfvbhhkEouoAjmt82WodG3oT9kfUj61fmh1CRLlbYLXXiK/CeDujGlB2 s0EP9BZPBXCvzapJMIQXvKSBoF6bVqwucs4JunchK0BeUiP4tCFBT+4Wfsp28lRmdLBpD9 IHcf/b/KF/2f3dq+Bg++y1zj8fWn+g8Y0FJxi2aKTMP6YJxfAJmFPUjI1oCkcg== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1638545197; a=rsa-sha256; cv=none; b=EGgfIZLIl6DYJWoHSVBu3BeF0l46w+6vuJZDr6O+AOXV8s1U4NkTeKlvCjb/k/dblO1XH1 IXKas799E0VtnPc1PvX1bbTJs+F8vRAx6lVntn+Y3rG9V0Tt5uLec20Fa2dhm0ylx+wf/W 5YfgblmpZ9YPPBXpMZ0zosgCC0LXGxbequFK6jD0riyVykl0EIjnUs4GLMmn2xtz2UaD9G bQp3+vNj+Y8scOdVfQ3n8IDgqalEvkV9KDDMrT67L4kHJ4GfgvigZOr0Etjt/7Ae8HziSy YlMpckDC6P2hU23WKyRrtwkftE1yfKjoTbB2JFfnMo328o5zGg03LkNnitLMvA== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=MO3Is+uv; dmarc=fail reason="SPF not aligned (relaxed)" header.from=andrew.cmu.edu (policy=none); spf=pass (aspmx1.migadu.com: domain of "emacs-orgmode-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="emacs-orgmode-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: -1.82 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=MO3Is+uv; dmarc=fail reason="SPF not aligned (relaxed)" header.from=andrew.cmu.edu (policy=none); spf=pass (aspmx1.migadu.com: domain of "emacs-orgmode-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="emacs-orgmode-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 8303321CA0 X-Spam-Score: -1.82 X-Migadu-Scanner: scn0.migadu.com X-TUID: t3WdFqRgCcjC I have seen this happen at times, and I think it is style and maybe browser dependent. Could you send me a small example (including the csl file you use) that I could look at? Joseph Vidal-Rosset writes: > Hi John, > > A detail about exporting with org-ref 3 in html when the csl style is > for numeric references. With org-ref 2 + citeproc-org, I got this: > > [1] R. Descartes, Meditations on First Philosophy: with Selections from > the Objections and Replies. Oxford: OUP Oxford, 2008. > > (see the references here : > https://www.vidal-rosset.net/descartess_first_proof_of_gods_existence_in_= first-order_logic.html > ) > > With org-ref 3, with apparently any numeric style, I get this: > > [1] > R. Descartes, Meditations on First Philosophy: with Selections from the > Objections and Replies. Oxford: OUP Oxford, 2008. > > I mean that each bibliographical reference is below its number link, and > it is not very nice. I wonder about the reason of this difference of > output, and a possible solution. > > Best wishes, > > Jo. > > Le 02/12/2021 =C3=A0 18:35, John Kitchin a =C3=A9crit=C2=A0: >> Glad to hear it is working again for you! Best wishes, >> >> Joseph Vidal-Rosset writes: >> >>> Dear all, >>> >>> >>> I just succeeded in solving my problem. >>> >>> l-210-235 of myblogexporter.el, I changed the code for: >>> >>> (defun org-export-head-export-headers (directory-name backend) >>> "Exports each heading to directory-name using backend" >>> (if (equal backend "html") >>> (org-export-head--run-on-each-heading >>> #'(lambda () >>> (org-set-property >>> "EXPORT_FILE_NAME" >>> (concat directory-name (org-export-head--escaped-headline= ))) >>> (deactivate-mark) >>> (let ((org-export-before-parsing-hook >>> '(org-ref-csl-preprocess-buffer))) >>> (cl-letf (((symbol-function 'org-export-get-reference) >>> (symbol-function 'org-export-get-reference-custom))) >>> (if org-export-head-click-toc-h2 >>> (cl-letf (( >>> ;(symbol-function 'org-html-toc) >>> (symbol-function >>> 'org-export-head--custom-toc))) >>> (org-html-export-to-html nil t))))) >>> (set-buffer-modified-p t)) "-noexport-noreexport")) >>> (if (equal backend "pdf") >>> (org-export-head--run-on-each-heading >>> #'(lambda () >>> (org-set-property >>> "EXPORT_FILE_NAME" >>> (concat directory-name (org-export-head--escaped-headline= ))) >>> (deactivate-mark) >>> (org-latex-export-to-pdf nil t) >>> (set-buffer-modified-p t)) "-noexport-noreexport"))) >>> >>> and it works with org-ref 3. >>> >>> Best wishes, I attach myblogexporter.el >>> >>> Jo. >>> >>> Le 02/12/2021 =C3=A0 14:17, Joseph Vidal-Rosset a =C3=A9crit=C2=A0: >>>> Dear John (cc. Ivan), >>>> >>>> First, thanks for your help and for your patience, that's very kind of= you. >>>> >>>> The good news is that indeed, org-ref 3 exports nicely the html >>>> bibliography with my CSL file, it works well with your org file and yo= ur >>>> bibliography. My error was simple: I did not use the specific org-ref >>>> keys but the ordinary h-o keys.. A stupid mistake. >>>> >>>> The bad news is that this new function for exporting with org-ref 3 is >>>> not included in org-export-head, a nice org mode to blog exporter, made >>>> by Ivan Tadeu Ferreira Antunes Filho, which converts each header to a >>>> different file, I find this exporter very convenient. I had no problem >>>> with this org-ref 2 to use this blog-exporter, but it org-ref 3 is >>>> unfortunately not still adapted to its use. Nevertheless, I believe th= at >>>> it should be possible to find the lines to include this function >>>> (let ((org-export-before-parsing-hook '(org-ref-csl-preprocess-buffer= ))) >>>> (org-open-file (org-html-export-to-html))) >>>> in org-export-head. I tried, but without success, because I am simply >>>> not expert enough. I see the best, that is to export both with org-ref= 3 >>>> (i.e. "r h") and org-export-head, but I am unable to code it. >>>> >>>> No doubt that it should be for you and Ivan a piece of cake, but please >>>> do it only if you think that it is interesting and if you find the time >>>> to do it. >>>> >>>> Best wishes, >>>> >>>> Jo. >>>> >>>> PS in attachment, myblogexporter.el in my ~/.emacs.d/personal (usual >>>> path with Prelude Emacs). >>>> >>>> Le 01/12/2021 =C3=A0 23:16, John Kitchin a =C3=A9crit=C2=A0: >>>>> >>>>> Joseph Vidal-Rosset writes: >>>>> >>>>>> Dear Andras, >>>>>> >>>>>> You are very probably right. I will have a look on this entry in my >>>>>> default bibliography file. >>>>>> >>>>>> The code >>>>>> >>>>>> (let ((org-export-before-parsing-hook '(org-ref-csl-preprocess-buff= er))) >>>>>> (org-open-file (org-html-export-to-html))) >>>>>> >>>>>> put in .emacs.d/personal/preload/myorgexport.el >>>>>> >>>>> This code should not go in your init file. It is executed each time, = and >>>>> not what you want. I usually put it a src block at the end in a secti= on >>>>> tagged noexport and run it from there. >>>>> >>>>> Alternatively, if this is the only preprocessing you do, I think you = can >>>>> do C-c C-e rh to export to html (this runs the org-ref html exporter. >>>>> >>>>> Finally, if you really want something in your init file it should be >>>>> like this: >>>>> >>>>> (defun my-html () >>>>> (interactive) >>>>> (let ((org-export-before-parsing-hook '(org-ref-csl-preprocess-= buffer))) >>>>> (org-open-file (org-html-export-to-html)))) >>>>> >>>>> and then later you run it with M-x my-html >>>>> >>>>> >>>>>> provokes the request of opening a html file, when emacs --daemon is >>>>>> started; therefore I conclude that it should not be used as I did... >>>>>> >>>>>> Anyway, every tentative to export in a bibliography in html fails = at >>>>>> the moment, even with a new bibliography file... :( >>>>> >>>>> See of the one at >>>>> https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org >>>>> works. The bib file is in >>>>> https://github.com/jkitchin/org-ref/blob/master/org-ref.bib. >>>>> >>>>> >>>>> >>>>>> >>>>>> Best wishes, >>>>>> >>>>>> Le 01/12/2021 =C3=A0 17:33, Andr=C3=A1s Simonyi a =C3=A9crit=C2=A0: >>>>>>> Dear Joseph, >>>>>>> >>>>>>> based on the error message there seems to be a problem with the >>>>>>> 'curley-nil-on-bennet-spinoz' bibliography entry, is it possible th= at >>>>>>> it contains a 'year =3D nil' row? If yes then I don't think that is >>>>>>> well-formed, at least citeproc-el cannot currently parse it. Anyhow, >>>>>>> apparently I need to improve/add citeproc-el error messages about >>>>>>> bib(la)tex parsing, because several parsing problems have surfaced >>>>>>> lately and the current error messages aren't helpful at all. >>>>>>> >>>>>>> best wishes, >>>>>>> Andr=C3=A1s >>>>>>> >>>>>>> On Wed, 1 Dec 2021 at 16:50, Joseph Vidal-Rosset >>>>>>> wrote: >>>>>>>> >>>>>>>> Dear John, >>>>>>>> >>>>>>>> I must say that to export references in html with org-ref 3, I mee= t a >>>>>>>> lot of problems (with LaTeX, it's fine). >>>>>>>> >>>>>>>> I am using prelude emacs and GNU Emacs 29.0.50 . >>>>>>>> >>>>>>>> Starting emacs --daemon, the code >>>>>>>> >>>>>>>> (let ((org-export-before-parsing-hook '(org-ref-csl-preprocess-bu= ffer))) >>>>>>>> (org-open-file (org-html-export-to-html))) >>>>>>>> >>>>>>>> in my setup provokes this unwanting effect: >>>>>>>> >>>>>>>> [Prelude] Loading personal configuration files in >>>>>>>> /home/joseph/.emacs.d/personal/preload... >>>>>>>> Loading /home/joseph/.emacs.d/personal/preload/myorgexport.el (sou= rce)... >>>>>>>> Output file: >>>>>>>> >>>>>>>> and with Enter : >>>>>>>> >>>>>>>> [Prelude] Loading personal configuration files in >>>>>>>> /home/joseph/.emacs.d/personal/preload... >>>>>>>> Loading /home/joseph/.emacs.d/personal/preload/myorgexport.el (sou= rce)... >>>>>>>> Output file: >>>>>>>> Warning (initialization): An error occurred while loading >>>>>>>> =E2=80=98/home/joseph/.emacs.d/init.el=E2=80=99: >>>>>>>> >>>>>>>> Wrong type argument: stringp, nil >>>>>>>> >>>>>>>> To ensure normal operation, you should investigate and remove the >>>>>>>> cause of the error in your initialization file. Start Emacs with >>>>>>>> the =E2=80=98--debug-init=E2=80=99 option to view a complete error= backtrace. Disable >>>>>>>> showing Disable logging >>>>>>>> Starting Emacs daemon. >>>>>>>> >>>>>>>> With --debug-init, I get: >>>>>>>> >>>>>>>> Debugger entered--Lisp error: (wrong-type-argument stringp nil) >>>>>>>> string-to-number(nil) >>>>>>>> citeproc-bt--to-csl-date("nil" nil) >>>>>>>> citeproc-blt-entry-to-csl((("Url" . >>>>>>>> "http://dx.doi.org/10.1163/9789004246638_005") ("Doi" . >>>>>>>> "10.1163/9789004246638_005") ("Date_added" . "Mon May 16 19:09:37 = 2016") >>>>>>>> ("Booktitle" . "Spinoza: Issues and Directions") ("Series" . "Spin= oza: >>>>>>>> Issues and Directions") ("Year" . "nil") ("Publisher" . "Brill Aca= demic >>>>>>>> Publishers") ("Pages" . "39-52") ("Author" . "Edwin Curley") ("Tit= le" . >>>>>>>> "ON BENNETTS SPINOZA: THE ISSUE OF TELEOLOGY") ("=3Dtype=3D" . "In= Book") >>>>>>>> ("=3Dkey=3D" . "curley-nil-on-bennet-spinoz")) nil nil) >>>>>>>> #f(compiled-function (key entry) #>>>>>>> -0x7fcb46b5c8e80b3>)("curley-nil-on-bennet-spinoz" (("Url" . >>>>>>>> "http://dx.doi.org/10.1163/9789004246638_005") ("Doi" . >>>>>>>> "10.1163/9789004246638_005") ("Date_added" . "Mon May 16 19:09:37 = 2016") >>>>>>>> ("Booktitle" . "Spinoza: Issues and Directions") ("Series" . "Spin= oza: >>>>>>>> Issues and Directions") ("Year" . "nil") ("Publisher" . "Brill Aca= demic >>>>>>>> Publishers") ("Pages" . "39-52") ("Author" . "Edwin Curley") ("Tit= le" . >>>>>>>> "ON BENNETTS SPINOZA: THE ISSUE OF TELEOLOGY") ("=3Dtype=3D" . "In= Book") >>>>>>>> ("=3Dkey=3D" . "curley-nil-on-bennet-spinoz"))) >>>>>>>> maphash(#f(compiled-function (key entry) #>>>>>>> -0x7fcb46b5c8e80b3>) #) >>>>>>>> citeproc-hash-itemgetter-from-any(("~/Dropbox/Orgzly/reforg= .bib")) >>>>>>>> org-ref-process-buffer(html) >>>>>>>> org-ref-csl-preprocess-buffer(html) >>>>>>>> run-hook-with-args(org-ref-csl-preprocess-buffer html) >>>>>>>> org-export-as(html nil nil nil (:output-file "~/test.html")) >>>>>>>> org-export-to-file(html "~/test.html" nil nil nil nil nil) >>>>>>>> org-html-export-to-html() >>>>>>>> (org-open-file (org-html-export-to-html)) >>>>>>>> (let ((org-export-before-parsing-hook >>>>>>>> '(org-ref-csl-preprocess-buffer))) (org-open-file >>>>>>>> (org-html-export-to-html))) >>>>>>>> eval-buffer(# nil >>>>>>>> "/home/joseph/.emacs.d/personal/preload/myorgexport..." nil t) ; >>>>>>>> Reading at buffer position 3196 >>>>>>>> >>>>>>>> load-with-code-conversion("/home/joseph/.emacs.d/personal/preload/= myorgexport..." >>>>>>>> "/home/joseph/.emacs.d/personal/preload/myorgexport..." nil nil) >>>>>>>> load("/home/joseph/.emacs.d/personal/preload/myorgexport...= ") >>>>>>>> mapc(load ("/home/joseph/.emacs.d/personal/preload/myorgexp= ort...")) >>>>>>>> (progn (message "[Prelude] Loading personal configuration f= iles in >>>>>>>> ..." prelude-personal-preload-dir) (mapc 'load (directory-files >>>>>>>> prelude-personal-preload-dir 't "^[^#.].*el$"))) >>>>>>>> (if (file-exists-p prelude-personal-preload-dir) (progn (me= ssage >>>>>>>> "[Prelude] Loading personal configuration files in ..." >>>>>>>> prelude-personal-preload-dir) (mapc 'load (directory-files >>>>>>>> prelude-personal-preload-dir 't "^[^#.].*el$")))) >>>>>>>> eval-buffer(# nil "/home/joseph/.emacs.d/in= it.el" nil >>>>>>>> t) ; Reading at buffer position 4489 >>>>>>>> load-with-code-conversion("/home/joseph/.emacs.d/init.el" >>>>>>>> "/home/joseph/.emacs.d/init.el" t t) >>>>>>>> load("/home/joseph/.emacs.d/init" noerror nomessage) >>>>>>>> startup--load-user-init-file(#f(compiled-function () #>>>>>>> 0xec639179d6199fa>) #f(compiled-function () #>>>>>>> -0x1f3c686ddc0dc635>) t) >>>>>>>> command-line() >>>>>>>> normal-top-level() >>>>>>>> >>>>>>>> It's too complicated for me. >>>>>>>> org-ref version 2 with citeproc-org by Andras worked well, but now= I am >>>>>>>> afraid that to downgrade to org-ref 2 is not necessarily the best >>>>>>>> solution. I am lost. >>>>>>>> >>>>>>>> Best wishes, and thanks for your help. >>>>>>>> >>>>>>>> Jo. >>>>>>>> >>>>>>>> >>>>>>>> Le 30/11/2021 =C3=A0 18:31, John Kitchin a =C3=A9crit : >>>>>>>>> See https://www.youtube.com/watch?v=3DrRR-5NSpKyE >>>>>>>>> for an overview o= f what to >>>>>>>>> do. basically you need a csl file that provides the style you wan= t, and >>>>>>>>> you specify it like this in the org file or in default settings. = You may >>>>>>>>> also need a locale file if you are not blogging in english. >>>>>>>>> >>>>>>>>> #+csl-style: apa-5th-edition.csl >>>>>>>>> >>>>>>>>> #+csl-locale: en-US >>>>>>>>> >>>>>>>>> >>>>>>>>> You can find a basic example org file for html export with CSL at >>>>>>>>> https://github.com/jkitchin/org-ref/blob/master/examples/basic-cs= l.org >>>>>>>>> >>>>>>>>> >>>>>>>>> Here is a minimal way to export your blog file I suppose. >>>>>>>>> >>>>>>>>> (let ((org-export-before-parsing-hook '(org-ref-csl-preprocess-b= uffer))) >>>>>>>>> (org-open-file (org-html-export-to-html))) >>>>>>>>> >>>>>>>>> >>>>>>>>> John >>>>>>>>> >>>>>>>>> ----------------------------------- >>>>>>>>> Professor John Kitchin (he/him/his) >>>>>>>>> Doherty Hall A207F >>>>>>>>> Department of Chemical Engineering >>>>>>>>> Carnegie Mellon University >>>>>>>>> Pittsburgh, PA 15213 >>>>>>>>> 412-268-7803 >>>>>>>>> @johnkitchin >>>>>>>>> http://kitchingroup.cheme.cmu.edu >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, Nov 30, 2021 at 12:16 PM Andr=C3=A1s Simonyi >>>>>>>>> > wrot= e: >>>>>>>>> >>>>>>>>> Dear Joseph, >>>>>>>>> >>>>>>>>> unfortunately, my note on the `citeproc-org` page has bec= ome kind of >>>>>>>>> misleading and has to be updated because org-ref didn't s= witch to the >>>>>>>>> new org-cite citation syntax after all, although this was= the plan for >>>>>>>>> a while. I think if you wish to use org-ref 3 then you sh= ould simply >>>>>>>>> remove citeproc-org entirely -- if I understand correctly= the latest >>>>>>>>> version of org-ref supports the old syntax as well and is= capable of >>>>>>>>> CSL-based export (among others) on its own. >>>>>>>>> >>>>>>>>> best regards, >>>>>>>>> Andr=C3=A1s >>>>>>>>> >>>>>>>>> On Tue, 30 Nov 2021 at 18:00, Joseph Vidal-Rosset >>>>>>>>> = > wrote: >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > Dear John, and dear Andras, >>>>>>>>> > >>>>>>>>> > Having updated my org-ref to the last version, I see t= hat the html >>>>>>>>> > export of bibliography does not work any longer for my= blog. >>>>>>>>> > >>>>>>>>> > Reading Andras's note here >>>>>>>>> > https://github.com/andras-simonyi/citeproc-org >>>>>>>>> >>>>>>>>> > I confess that I am lost. >>>>>>>>> > >>>>>>>>> > What have I to do to not waste too much time with this= problem? >>>>>>>>> > >>>>>>>>> > Best wishes, >>>>>>>>> > >>>>>>>>> > Jo. >>>>>>>>> > >>>>>>>>> >>>>>>>> >>>>> >>>>> >>>>> -- >>>>> Professor John Kitchin >>>>> Doherty Hall A207F >>>>> Department of Chemical Engineering >>>>> Carnegie Mellon University >>>>> Pittsburgh, PA 15213 >>>>> 412-268-7803 >>>>> @johnkitchin >>>>> http://kitchingroup.cheme.cmu.edu >>>>> Pronouns: he/him/his >>>>> >>> >>> [2. text/x-emacs-lisp; myblogexporter.el]... >> >> >> -- >> Professor John Kitchin >> Doherty Hall A207F >> Department of Chemical Engineering >> Carnegie Mellon University >> Pittsburgh, PA 15213 >> 412-268-7803 >> @johnkitchin >> http://kitchingroup.cheme.cmu.edu >> Pronouns: he/him/his >> --=20 Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu Pronouns: he/him/his