From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp2 ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id 2IiJFRSKq2FA3gAAgWs5BA (envelope-from ) for ; Sat, 04 Dec 2021 16:32:36 +0100 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp2 with LMTPS id kBA6ERSKq2EhHQAAB5/wlQ (envelope-from ) for ; Sat, 04 Dec 2021 15:32:36 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id DBB9836340 for ; Sat, 4 Dec 2021 16:32:35 +0100 (CET) Received: from localhost ([::1]:48872 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1mtX1e-0005WM-QW for larch@yhetil.org; Sat, 04 Dec 2021 10:32:34 -0500 Received: from eggs.gnu.org ([209.51.188.92]:53462) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mtX0h-0005WA-Ux for emacs-orgmode@gnu.org; Sat, 04 Dec 2021 10:31:35 -0500 Received: from mail-40136.proton.ch ([185.70.40.136]:51245) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mtX0d-0000xg-On for emacs-orgmode@gnu.org; Sat, 04 Dec 2021 10:31:35 -0500 Date: Sat, 04 Dec 2021 15:31:23 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=vidal-rosset.net; s=protonmail3; t=1638631888; bh=9tMLDU2rveE9nCGsFLq36w7quaMMEbSmoedZlg5DF4M=; h=Date:To:From:Cc:Reply-To:Subject:Message-ID:In-Reply-To: References:From:To:Cc; b=byr3bFEPjjz7xa2necFpVIUWm3oB9aoReY31d63PbLttb2Ja7rlxJH4ro+1s1F6gb zbE/MR7t347r3a7gVEU3r8ge8QbgS4tICiLQHVilzGgGIeFd0ZRQ4BrMIw3J7G1br0 PceO6SKOd88uZcBJN4cnyaSPm7igLOYBf2VjNyctGL72QvxwOasLCyqov+PBow6mUy Tk4AG40pUSPD37aX2rq7dbm2vR9eXYMbbP+P3Obk3Kh+2TWJMame+uPED4/1pXg9+r ooiijHlqANMRrxMdwiAvtLoLc3OvPuRd4DxWfRDfOPEkUvGNwQkgii5WVQ5Sjb53ur USg5sse/6LCoQ== To: John Kitchin From: Joseph Vidal-Rosset Subject: Re: citeproc-org and org-ref 3 Message-ID: In-Reply-To: References: <56442351-6f41-3490-01f2-0ca5aa930c6a@vidal-rosset.net> <0d4028ea-8ed6-22f3-023b-20b2df18406c@vidal-rosset.net> <36116c7d-b329-22f7-6ac2-4e747b9abb49@vidal-rosset.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Received-SPF: pass client-ip=185.70.40.136; envelope-from=joseph@vidal-rosset.net; helo=mail-40136.proton.ch X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_MSPIKE_H4=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: emacs-orgmode@gnu.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-To: Joseph Vidal-Rosset 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=1638631956; h=from:from:sender:sender:reply-to: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=9tMLDU2rveE9nCGsFLq36w7quaMMEbSmoedZlg5DF4M=; b=IXD5Wwr0MxCU1tdX7wXjqAo41dHtBMrukJvfon/JYnU01q5KkMqMCdMzpizrzRkgi8k55B yC2zhsIFcujYccpeTXpX3y07DmU3I+ylCDUH2+2v2HWoiwAwC31A4zj1l4hTEkOapev7qb xzJm3eE3gIR/m3Ejzta+kN08fgHshqW5HH0/rniUc8UQRC55BzNEQ8vAC/vsEzafo06Lib RYJDvAUCKsNDHTjReeUhZii2bgzDdeF+412Zl6JkSvdPnEnYTGit4wqaeCqQNnq76n9ItG NQiTw7WMTt/fi0h8J0KbwX9p9XOn3U/jot1l85R7LBtJSh2n+B//LJoidFkN3g== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1638631956; a=rsa-sha256; cv=none; b=ZB4w0NPPOqnnEp+imQgKJCuDmStGpRE43U3ld59lY24/zwFtBHjzixyQJJhoz47rnVEaRe d2AHM+LLUbeIvH+u1yVbKedoFNSy0MbawvroT14Pxft+AqTwBdFXqp9YI67+8Nrc40WiJX ENIwRgERmQWf/yjgbNgr72ANLedv/xnZR2mO7Jhfvpg29lmQzXLdvUY8XZmi5a3Bl812lI sUnkVVO31QMPvvrdyhCSOoW6T0AUewIcWEf81UlSRJO63rSoOYa7SsflzIqFTE5sNBPW4D jvNGcOnWpT3yFeL+ahHAv0LI8XRp2zCztizhMoT66pWlLGVlP3GXc9BivzgLIw== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=pass header.d=vidal-rosset.net header.s=protonmail3 header.b=byr3bFEP; dmarc=pass (policy=none) header.from=vidal-rosset.net; 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: -3.83 Authentication-Results: aspmx1.migadu.com; dkim=pass header.d=vidal-rosset.net header.s=protonmail3 header.b=byr3bFEP; dmarc=pass (policy=none) header.from=vidal-rosset.net; 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: DBB9836340 X-Spam-Score: -3.83 X-Migadu-Scanner: scn0.migadu.com X-TUID: 9knR0bsEjo8I Dear John, It is in fact an org cite issue. With org-ref 2, I used to write: something like [[cite:key][page n]] with C-l + description . With org-ref 3, I see that I must write now: [[cite:key page n]] and it works with ieee csl style also. (I still do not know how to quote directly references of pages in the cite key when I need to quote pages.) Best wishes, and thanks ! Jo. Le 04/12/2021 =C3=A0 16:07, John Kitchin a =C3=A9crit=C2=A0: > AFAICT this is also a style issue. This document: > > #+csl-style: apa-5th-edition.csl > > See [[cite:&scalia-2020-evaluat-scalab pg. 127]]. > > bibliography:~/Dropbox/emacs/bibliography/references.bib > > exports to: > image.png. > > This one: > #+csl-style: apa-numeric-superscript-brackets.csl > > See [[cite:&scalia-2020-evaluat-scalab pg. 127]]. > > bibliography:~/Dropbox/emacs/bibliography/references.bib > exports to > image.png > > and this one (note the extra HTML_HEAD lines which fixes the separate > lines due to the div elements (Thank you for this tip Max!). > > #+csl-style: biochimica-et-biophysica-acta.csl > #+HTML_HEAD: > > See [[cite:&scalia-2020-evaluat-scalab pg. 127]]. > > bibliography:~/Dropbox/emacs/bibliography/references.bib > > > leads to > image.png > > > You can see that the first two styles show the locators, but the last > one you use does not. I don't think that is something org-ref can or > should fix. That would be something to fix in the styles themselves. > > 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 Sat, Dec 4, 2021 at 9:45 AM Joseph Vidal-Rosset > > wrote: > > Dear John, > > Another more important point.=C2=A0 It is now more probably a point w= here > org-ref 3=C2=A0 needs to be improved: it seems to me that the format > [numerical_reference, page] or (name_reference, page) cannot be produ= ced > for the html export. > > (The format [numerical_reference, page]=C2=A0 was produced with org-r= ef2 + > citeproc-org , see for example: > > https://www.vidal-rosset.net/a_logical_remark_on_swinburnes_cartesian= _argument_for_substance_dualism.html > > > Swinburne=E2=80=99s argument is an amended version of Descartes= =E2=80=99s in Discourse > on the Method [1, p. 127]: > ) > > I hope that there is a solution. > > Best wishes, > > Jo. > > Le 03/12/2021 =C3=A0 18:13, John Kitchin a =C3=A9crit=C2=A0: > > I think this is caused by something in the style, or in how citepr= oc > > uses the style. > > > > This document: > > > > #+csl-style: biochimica-et-biophysica-acta.csl > > > > See [[cite:&scalia-2020-evaluat-scalab]]. > > > > bibliography:~/Dropbox/emacs/bibliography/references.bib > > > > Leads to (as you have seen): > > > > image.png > > > > The html for that reference looks like: > >
> >=C2=A0 =C2=A0
> >=C2=A0 =C2=A0 =C2=A0
[1]
> class=3D"csl-right-inline">G. Scalia, C.A. Grambow, B. Pernici, > Y.-P. Li, > > W.H. Green, > > >">Evaluating Scalable > > Uncertainty Estimation Methods for Deep Learning-Based Molecular > > Property Prediction, Journal of Chemical Information and > Modeling, > > 60 (2020) 2697-2717.
> >=C2=A0 =C2=A0
> >
> > > > > > I don't see why there is an extra line there, I guess it is some C= SS > > styling. > > > > if you change the csl style to=C2=A0apa-numeric-superscript-bracke= ts.csl > > > > you get > > image.png > > > > which I think is closer to what you want. The html for this looks > like > > this, and does not have some of the div elements seen above. I gue= ss > > this is something in the style files themselves. > > > >
> >=C2=A0 =C2=A0
1. > Scalia, G., > > Grambow, C. A., Pernici, B., Li, Y.-P., & Green, W. H. (2020). > > Evaluating Scalable Uncertainty Estimation Methods for Deep > > Learning-Based Molecular Property Prediction. Journal of Chemic= al > > Information and Modeling, 60(6), 2697=E2=80=932717. > href=3D"https://doi.org/10.1021/acs.jcim.9b00975 > > > >">https://doi.org/10.1021/= acs.jcim.9b00975 > > > >
> >
> > > > > > > > > > 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 Fri, Dec 3, 2021 at 11:49 AM Joseph Vidal-Rosset > > > >> > wrote: > > > >=C2=A0 =C2=A0 =C2=A0Le 03/12/2021 =C3=A0 16:24, John Kitchin a = =C3=A9crit=C2=A0: > I have seen this > >=C2=A0 =C2=A0 =C2=A0happen at times, and I think it is style and ma= ybe > browser > >=C2=A0 =C2=A0 =C2=A0dependent. > > Could you send me a small exampl= e (including > the csl > >=C2=A0 =C2=A0 =C2=A0file you use) that > I could look at? Dear John= , In > attachment, two > >=C2=A0 =C2=A0 =C2=A0small examples, the same text exported with > >=C2=A0 =C2=A0 =C2=A0biochimica-et-biophysica-acta.csl and with ieee= -with-url.csl Best > >=C2=A0 =C2=A0 =C2=A0wishes, Jo. > > >