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 <jos...@vidal-rosset.net> 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 à 18:35, John Kitchin a écrit : >> Glad to hear it is working again for you! Best wishes, >> >> Joseph Vidal-Rosset <jos...@vidal-rosset.net> 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 à 14:17, Joseph Vidal-Rosset a écrit : >>>> 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 your >>>> 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 that >>>> 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 à 23:16, John Kitchin a écrit : >>>>> >>>>> Joseph Vidal-Rosset <jos...@vidal-rosset.net> 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-buffer))) >>>>>> (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 section >>>>> 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 à 17:33, András Simonyi a écrit : >>>>>>> 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 that >>>>>>> it contains a 'year = 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, >>>>>>> András >>>>>>> >>>>>>> On Wed, 1 Dec 2021 at 16:50, Joseph Vidal-Rosset >>>>>>> <jos...@vidal-rosset.net> wrote: >>>>>>>> >>>>>>>> Dear John, >>>>>>>> >>>>>>>> I must say that to export references in html with org-ref 3, I meet 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-buffer))) >>>>>>>> (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 >>>>>>>> (source)... >>>>>>>> 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 >>>>>>>> (source)... >>>>>>>> Output file: >>>>>>>> Warning (initialization): An error occurred while loading >>>>>>>> ‘/home/joseph/.emacs.d/init.el’: >>>>>>>> >>>>>>>> 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 ‘--debug-init’ 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" . "Spinoza: >>>>>>>> Issues and Directions") ("Year" . "nil") ("Publisher" . "Brill Academic >>>>>>>> Publishers") ("Pages" . "39-52") ("Author" . "Edwin Curley") ("Title" . >>>>>>>> "ON BENNETTS SPINOZA: THE ISSUE OF TELEOLOGY") ("=type=" . "InBook") >>>>>>>> ("=key=" . "curley-nil-on-bennet-spinoz")) nil nil) >>>>>>>> #f(compiled-function (key entry) #<bytecode >>>>>>>> -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" . "Spinoza: >>>>>>>> Issues and Directions") ("Year" . "nil") ("Publisher" . "Brill Academic >>>>>>>> Publishers") ("Pages" . "39-52") ("Author" . "Edwin Curley") ("Title" . >>>>>>>> "ON BENNETTS SPINOZA: THE ISSUE OF TELEOLOGY") ("=type=" . "InBook") >>>>>>>> ("=key=" . "curley-nil-on-bennet-spinoz"))) >>>>>>>> maphash(#f(compiled-function (key entry) #<bytecode >>>>>>>> -0x7fcb46b5c8e80b3>) #<hash-table equal 665/730 0x156f8acb26b7>) >>>>>>>> >>>>>>>> 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(#<buffer *load*-634240> 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/myorgexport...")) >>>>>>>> (progn (message "[Prelude] Loading personal configuration files >>>>>>>> in >>>>>>>> ..." prelude-personal-preload-dir) (mapc 'load (directory-files >>>>>>>> prelude-personal-preload-dir 't "^[^#.].*el$"))) >>>>>>>> (if (file-exists-p prelude-personal-preload-dir) (progn (message >>>>>>>> "[Prelude] Loading personal configuration files in ..." >>>>>>>> prelude-personal-preload-dir) (mapc 'load (directory-files >>>>>>>> prelude-personal-preload-dir 't "^[^#.].*el$")))) >>>>>>>> eval-buffer(#<buffer *load*> nil >>>>>>>> "/home/joseph/.emacs.d/init.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 () #<bytecode >>>>>>>> 0xec639179d6199fa>) #f(compiled-function () #<bytecode >>>>>>>> -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 à 18:31, John Kitchin a écrit : >>>>>>>>> See https://www.youtube.com/watch?v=rRR-5NSpKyE >>>>>>>>> <https://www.youtube.com/watch?v=rRR-5NSpKyE> for an overview of what >>>>>>>>> to >>>>>>>>> do. basically you need a csl file that provides the style you want, >>>>>>>>> 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-csl.org >>>>>>>>> <https://github.com/jkitchin/org-ref/blob/master/examples/basic-csl.org> >>>>>>>>> >>>>>>>>> Here is a minimal way to export your blog file I suppose. >>>>>>>>> >>>>>>>>> (let ((org-export-before-parsing-hook >>>>>>>>> '(org-ref-csl-preprocess-buffer))) >>>>>>>>> (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 <http://kitchingroup.cheme.cmu.edu> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, Nov 30, 2021 at 12:16 PM András Simonyi >>>>>>>>> <andras.simo...@gmail.com <mailto:andras.simo...@gmail.com>> wrote: >>>>>>>>> >>>>>>>>> Dear Joseph, >>>>>>>>> >>>>>>>>> unfortunately, my note on the `citeproc-org` page has become >>>>>>>>> kind of >>>>>>>>> misleading and has to be updated because org-ref didn't >>>>>>>>> switch 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 should >>>>>>>>> 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, >>>>>>>>> András >>>>>>>>> >>>>>>>>> On Tue, 30 Nov 2021 at 18:00, Joseph Vidal-Rosset >>>>>>>>> <jos...@vidal-rosset.net <mailto:jos...@vidal-rosset.net>> >>>>>>>>> wrote: >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > Dear John, and dear Andras, >>>>>>>>> > >>>>>>>>> > Having updated my org-ref to the last version, I see that >>>>>>>>> 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 >>>>>>>>> <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 >> -- 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
