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Tue, 04 Mar 2025 01:47:18 +0100 Date: Tue, 4 Mar 2025 01:47:17 +0100 From: Jakob Kirsch To: guix-patches@gnu.org Subject: [PATCH] gnu: avogadro2: fix open babel input Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="CvqVe5i5AIjPvPUz" Content-Disposition: inline X-Provags-ID: V03:K1:1dhnA4g3PyGbsfS2aZki9Pjn04r48f4MzAMZEVC9QhfyDCPIGaZ Zv83RSerD0Wk/MVxeR+tn8V64tR5jGGbiwXXrxlpo/L6XWKEGpqAdZeYN3O/w00RvIogaah Ga00q6kFbo6GL0MDKFfih5iRZyfdOe1Acl5csrEHa4C1sxiph1avHzjLr294h6Hym86z6V3 WwqEsTmhZbJTGB/+zWEgA== X-Spam-Flag: NO UI-OutboundReport: notjunk:1;M01:P0:EAnTLS+/5AA=;TnPNNo84fVUQPhnpZeXypcrhRio Hz3k2B0+RbC/9x/NADrdQLcHetKTgHe3WP4+tiDXobjdLD45Ec95+L1grQ55wp/OZUX6Ftgfe gMGxuAszWAmtcRuAzsc0ZpGs2//jBrDwkmKYG46Bryj3EJBRTMXEFFjdiPYmryqNlDQPauy/t i5OeAxbBW4E3gCA4X9SwDyt17pQL6NqqftPIdEkUZIjN8kDDgIVjA3XJBnWNYqJ858jRvOf9z bCW9cqGdryr/jZ6ELslcrAu/15F/KlKRtZPSgmL7pVOddJlRZQDvd143WAo75tICCa2LJeIJ1 BmEFkZ+7ECp8MEowupTExCwRCyQqIH3tS0Ic9hYRD+OIkNkqg9STBwpCosVHz81T+uq+uIfpg oHWm3xXR/CBjAlSwMxL0eenTwFpeH/EXYH3g96oEwGmhzT9Al+U1OLh2SKa3Dg/JCn4DSqxHe Q5/xSyt1VaQMsOhSu229TDV7/S2kXdZ7r6CLk09ckh3l6AulBhD0KaJpXvxR7Yax9iu8o+9jc tg5zOYhYeIKobeIAWDBxIdSDH6w0nbkSyadHPGfd6WOvPw4PjsamgyMJLM2g7b7m01rHC5ntu 7TdzlRq58LXl6hOx5bIUwyG2uO3YZ3EZeQ1GD2hyCXoNcNFSFqVpxeYEqgyXUZYl7ISWX+wXR 6eyMNOZ2DEb8ejiHAjN+nzWotU6wvLpxlGTInPdUBme74OZVwNwE9oqSBgvLniIZBCGjKyBWC Np+qwKFAJHubkwk97Sf7IsgA3u6yFRUpDt5sEQ7ogULf1lTMZbLMKVy7lZTSXzgKAurjE6x68 tyJYaWJa5zSNt2MqoIkbnobmE+nqMVsoTMCHNg8MKx1ao0Vn0Fc0YVmZD72UKjsWBYIplTBlL 02UTsYmaRwQ4TEKSobZ31JObjf4dgG6okF58BDD/wiVS5lFO2TI08BXSAGarshOiqwsT5ttKk 968Ts3EW+sE2nuc91hNwB+SemX1sZLXPr7onTQJPS1bHRSsPLrDSJRuQAPTOin8Bp3wwhLAXB +18KSDIDfeY/Dw5rhl1HdNjBRzE1skCwJMckxX4FbQuS0MOtfSALpdEsFooJ3tYRHtbol5kTQ Sr4xoSidycfZlqhTNUDHWdhlmWVjnuAoxoFQa3HPfL+H1mp1i9SLoCdhiA2A44Ti1wtmDIKpe FfZYaAA8Ze6byo3G/qFZfQZ3ofaLNiua70ib4HpykbDEdRdF5V/nv4l4eNaqmnqu9V/YYWiDq xMMAhLEuH9fjo243TpiV6UcFxSlRS88uQuoycyFLEI0na1zXpS8gJHcXQ4vNLGgldhOj+/Dwa A3Ybu6Ij9ngrwfLe/dl/YpQxSWWCjz5L9d+G5L9TBpeILPE6zIAKWkeMVoy/Hbt3ziECQL24y Ji6nlr8+L0QjnnqmcfweO9rv8/ff1z/98aITg2LutYZ8LiBCvN32yXeyTq Received-SPF: pass client-ip=212.227.15.14; envelope-from=jakob.kirsch@web.de; helo=mout.web.de X-Spam_score_int: -37 X-Spam_score: -3.8 X-Spam_bar: --- X-Spam_report: (-3.8 / 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, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_LOW=-0.7, RCVD_IN_MSPIKE_H5=-1, RCVD_IN_MSPIKE_WL=-0.01, RCVD_IN_VALIDITY_CERTIFIED_BLOCKED=0.001, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, SPF_PASS=-0.001, T_SPF_HELO_TEMPERROR=0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --CvqVe5i5AIjPvPUz Content-Type: text/plain; charset=us-ascii Content-Disposition: inline avogadro2 needs open babel at runtime so we should add this to the propagated inputs. --CvqVe5i5AIjPvPUz Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename="v1-0001-gnu-avogadro2-Update-to-1.93.0.patch" Content-Transfer-Encoding: quoted-printable =46rom b353ae32e3b160b47ae1b34fe65e79b141caf05f Mon Sep 17 00:00:00 2001 Message-ID: From: Jakob Kirsch Date: Tue, 4 Mar 2025 01:44:43 +0100 Subject: [PATCH v1] gnu: avogadro2: Update to 1.93.0. * gnu/packages/chemistry.scm (avogadro2): Update to 1.93.0. [propagated-inputs]: Add openbabel. Change-Id: Ia7f02e66d9caced61a6a206076513806bb7b29a9 =2D-- gnu/packages/chemistry.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index bd27bfad7a..46728bb407 100644 =2D-- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -130,6 +130,8 @@ (define-public avogadro2 (list eigen pkg-config)) (inputs (list avogadrolibs hdf5 molequeue qtbase-5)) + (propagated-inputs + (list openbabel)) ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag. (arguments '(#:tests? #f)) base-commit: 72923a75af53a819f2be9dc4ae3c096aa3147d3f =2D- 2.48.1 --CvqVe5i5AIjPvPUz-- From debbugs-submit-bounces@debbugs.gnu.org Mon Mar 03 22:18:55 2025 Received: (at 76728) by debbugs.gnu.org; 4 Mar 2025 03:18:55 +0000 Received: from localhost ([127.0.0.1]:53839 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tpIo2-000579-SF for submit@debbugs.gnu.org; Mon, 03 Mar 2025 22:18:55 -0500 Received: from mail.z572.online ([88.99.160.180]:40994) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tpInz-00056x-Vc for 76728@debbugs.gnu.org; Mon, 03 Mar 2025 22:18:53 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=z572.online; s=me; t=1741058668; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: in-reply-to:in-reply-to:references:references; bh=pkwJz4t/dJ9dJHJMTs9YvQ4K43icGZ1oQCKZQUKWzkU=; b=p2+GdjZrgwh8McOACH9pBsu2cgKf16bbAAQCS+yFzOODwDBlICx5PcIe4Qwi15BqzoDL+c aCiyyuODXUKtmgHEfiaAxFUeO6FCfQGY065xTI96F3XBy0VU+1hwipnGnWJRmvPSzOdLHu hGD+RqvrLyjfSlH2Cubt0S2+zxlkeB4= Received: from m (mail1.85362086.com [107.174.64.25]) by mail.z572.online (OpenSMTPD) with ESMTPSA id 65867ca5 (TLSv1.3:TLS_AES_256_GCM_SHA384:256:NO); Tue, 4 Mar 2025 03:24:27 +0000 (UTC) From: Z572 To: Jakob Kirsch via Guix-patches via Subject: Re: [bug#76728] [PATCH] gnu: avogadro2: fix open babel input In-Reply-To: (Jakob Kirsch via Guix-patches via's message of "Tue, 4 Mar 2025 01:47:17 +0100") References: User-Agent: mu4e 1.12.7; emacs 30.0.92 Date: Tue, 04 Mar 2025 11:18:34 +0800 Message-ID: <87wmd5jxf9.fsf@z572.online> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" X-Spam-Score: 2.0 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: Jakob Kirsch via Guix-patches via writes: > avogadro2 needs open babel at runtime so we should add this to the propagated inputs. > > [2. text/plain; v1-0001-gnu-avogadro2-Update-to-1.93.0.patch]... Content analysis details: (2.0 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 0.0 RCVD_IN_VALIDITY_SAFE_BLOCKED RBL: ADMINISTRATOR NOTICE: The query to Validity was blocked. See https://knowledge.validity.com/hc/en-us/articles/20961730681243 for more information. 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The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: Jakob Kirsch via Guix-patches via writes: > avogadro2 needs open babel at runtime so we should add this to the propagated inputs. > > [2. text/plain; v1-0001-gnu-avogadro2-Update-to-1.93.0.patch]... Content analysis details: (2.0 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 0.0 RCVD_IN_VALIDITY_RPBL_BLOCKED RBL: ADMINISTRATOR NOTICE: The query to Validity was blocked. See https://knowledge.validity.com/hc/en-us/articles/20961730681243 for more information. [88.99.160.180 listed in bl.score.senderscore.com] 0.0 RCVD_IN_VALIDITY_SAFE_BLOCKED RBL: ADMINISTRATOR NOTICE: The query to Validity was blocked. See https://knowledge.validity.com/hc/en-us/articles/20961730681243 for more information. [88.99.160.180 listed in sa-accredit.habeas.com] -0.0 SPF_PASS SPF: sender matches SPF record 2.0 PDS_OTHER_BAD_TLD Untrustworthy TLDs [URI: z572.online (online)] 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record 0.0 FROM_SUSPICIOUS_NTLD From abused NTLD 1.0 BULK_RE_SUSP_NTLD Precedence bulk and RE: from a suspicious TLD -1.0 MAILING_LIST_MULTI Multiple indicators imply a widely-seen list manager --=-=-= Content-Type: text/plain Jakob Kirsch via Guix-patches via writes: > avogadro2 needs open babel at runtime so we should add this to the propagated inputs. > > [2. text/plain; v1-0001-gnu-avogadro2-Update-to-1.93.0.patch]... I think wrapper might be better, if it's just an application. --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEfr6klGDOXiwIdX/bO1qpk+Gi3/AFAmfGcQoACgkQO1qpk+Gi 3/DgWQ/9F9LG/GzBAUAem54hKcG67foMG3d/Npmejh7Lf5Bv/5FC/98mrOeatxjC FfbShhMx5zZ4SVwX0lCKc6ff1kjEFffsd+jfFZmHgsgB/BVarf9gv0W5zQaFjvwg VMmot4jtDf68fGFVT/kOXh+JfEWL0SCKREeUChAskik01y1rrNGQ2rI5gvyzMfBq rSXF9a/YKMuG0SiDmhriADQC1NMKyX8kzKDUpWIjMq88dRSOr16k6ObMqZqAt7rP nns+3GZ+ewtNzJjLA0613cftl+X77DCyq0QpPoDmqcuP/krRetgkncL1j5kizP5A yDiBWWdRW1Ah1YN5GhOYda27m29RI56LBFFOvmfR06HVa6qVbLE2+RtpXniLOTPK 0A/M626MQyB8Dr6IUVhCNIGAKrWrPeXA4XUVQCBG2yR7vcPTdAuy3Ef5GnGcWiW9 3DMjcreQpmZUo+kWg2AVSjoK14awRTv1viUh8Alf2cPCSoOjcK2Ur6Da9bJqulc9 wHXqohqbN88VEIunVU+vR/nmQIFiccevXn8J6Ov8Q95ofFH/f37Egr/59kVB4CzH cjX8/rk8o4XYgTD5iHmmPIXXe+OM98uSe4yJZN5qVvFNvU25ea+l0eZaZVdq/zVh zogqImwIWrWbIEp9MoZf+FrSXYz+3q/JvpkU/T/1YekSive4yvM= =Keha -----END PGP SIGNATURE----- --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 04 14:16:38 2025 Received: (at 76728) by debbugs.gnu.org; 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Tue, 04 Mar 2025 20:16:25 +0100 Date: Tue, 4 Mar 2025 20:16:26 +0100 From: Jakob Kirsch To: 76728@debbugs.gnu.org Subject: [PATCH] v2 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="Iyl16qkj3h7qFc1d" Content-Disposition: inline X-Provags-ID: V03:K1:20/Jg5GFaBgENqDkyBhCCV7ToThWvaNCJweAjOK+98xSvzHiYeh 9ew00FO5lYXfBXbplLvXh/6NKIcW8jfICVaWUALS5VNYaWISlfM7o7IbyUpsnjlRYTpJ8RC AicA8tY61DOzzW0tpscMbBfK+J6Fwka6v4IBJrlA8MbTMSPwmyQmJTjjUBNbVouO49geZXP 7l6l3ditQaBXNU+4+u9Gw== X-Spam-Flag: NO UI-OutboundReport: notjunk:1;M01:P0:Rq3bEpKA4Fo=;EP5IMyFJA7/CODJ3GTuwM1fkXME uNnuI0GpgjwmTlI05hZBWa1pU6lqspFaHf2w6bVL7Ntn8dxslqEsHNgphBjWDTDkgMGRxSHqS A71W4C5eJ+X6Ic7bxOdGtHLIcWkGfL5C5/smEmo384C9yIVH5TnjZvErQ0F42D3hk0D6Pn7Tk /Ur4WQi7mnPxYrW52qXCF9+Mb0uC/hWOs1M1WpQoI3hi3K6lcc7gFiO57XMunQ4i3hAfljTRY +p027tr1WhRTdWoAx1l3RpYRfZCWeEPW9QXXc6Upe0vhBaLb1F6lHKH1AeNmglG+3BrDfl3qf pMOG4w5dxKbBs5IuO1VtUu1lN1n+DrAEw5qg/7LBggV2OEpMWdZRwje/CMk/G1RgruU3VX/J1 5/fIU+WInz/cM1rzpf6+BT8tn30j/lPLCJjpbZ0d6ljGLFjZ6B+5OUzhKZoWqYZs1+f3HRP0b yDotV8rbp640Ss8mMBHwpw/gtlF6zsk2h6M3Pd4HeFXVRucgLWd1F8nVFPo+lb/2sfX4Da2fT j4onrALG7nM1nrHFXW6UlMp/nR7vKsj22DMrr0zjugkBmDXdnO+LPpKIH6+wUmyg6z120deis GLzHg/p5HiWprG0UVvoKS0swiGi1FoBqswekhP/R0L0BnvEHchYQkYXdAKEYef8cYbpybRKwi lrLNAW/ijYKdcF23tACiqF+xHyCuSESaTDxCBUoTqNDKnr1qA255v1gcjK8DwL6onmP/tlL5m ilW4QlCgj36AOYRNkTHLtDpu7m+xJyI+G1zsAs2qmxth1GRG8oZkYX2E+oiAOyck9sXuDqXdI nwXWeB8c5xxwuzaVFAg4dSBa9Z7Hnpv1fIf8EjQaTg1VTGrOTS3P85Y3xR8+MZY/3AD5u4QUo 79q5vnNuR4d0AqqWg1kuulMr0AIIAjaZEanZqbRS+SfXIJFW2pi9dZPDqum0oZcoOWzXj0rYy ISGiMPq6ejv9KGcS3IE6PgF4FRFN4wfD8CxwwU53CHpxVAYksbRC898atrY5gQdc2mbhbKQMJ 934GoRZ6SXpmrCe6TA9RXsdY+BErutpdSIX1swvXJSHd8U4kNpy5FzSYPOhAAX1Kq+HiBSPcE Qx0L29OYYLO/I83p7u1wYYEtTyoBR0Rvw1qGk+7Mrzu2XGtTiyhYksb0ucIlJ63qNO68y/iMZ IC0AS4QyiNMkxsPW09reViV6TKuitxr1Ll0Y1lXFyKMBrX05UezDjIZX1BbMtKoKa7nY6+jov KOtDhiev1bzK/YX/cQi8tfRBRvOWLmN6AHEqM7XMXyVwtUJaKzRvBfcn35YX5gHZZoaJBmahd sOaQ6W8cxat2lxTXmK3ezaSlyHuK10AccT5I1PeMW+rOsEcEOrH0C38lVpI7lQzOIsAs8mFkO Ks0Mz9ruErbNow+nbgZEjH/RvB+kFD30A64+gNVyD+82ZZknrcypMD/RmnH8KXa6MNnOBqnkp OPvvYLr+R2a9EWxyQnwpB/wkuyBo= X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 76728 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) --Iyl16qkj3h7qFc1d Content-Type: text/plain; charset=us-ascii Content-Disposition: inline This is the v2 with wrap-program instead of propagated-inputs. --Iyl16qkj3h7qFc1d Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename="v2-0001-gnu-avogadro2-Update-to-1.93.0.patch" Content-Transfer-Encoding: quoted-printable =46rom 5608c37f14b7b5d46f6ac0a31b4f0c073bd186aa Mon Sep 17 00:00:00 2001 Message-ID: <5608c37f14b7b5d46f6ac0a31b4f0c073bd186aa.1741115763.git.jakob= .kirsch@web.de> From: Jakob Kirsch Date: Tue, 4 Mar 2025 20:15:05 +0100 Subject: [PATCH v2] gnu: avogadro2: Update to 1.93.0. * gnu/packages/chemistry.scm (avogadro2): Update to 1.93.0. Change-Id: Ic133ed59aac11d9f48443c1d297d69060514d01f =2D-- gnu/packages/chemistry.scm | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index bd27bfad7a..78fedfd34f 100644 =2D-- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -122,17 +122,23 @@ (define-public avogadro2 (url "https://github.com/OpenChemistry/avogadroapp") (commit version))) (sha256 - (base32 - "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7")) + (base32 "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7")) (file-name (git-file-name name version)))) (build-system cmake-build-system) - (native-inputs - (list eigen pkg-config)) - (inputs - (list avogadrolibs hdf5 molequeue qtbase-5)) + (native-inputs (list eigen pkg-config)) + (inputs (list avogadrolibs hdf5 molequeue qtbase-5)) ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag. (arguments - '(#:tests? #f)) + (list + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-after 'install 'wrap-program + (lambda _ + (wrap-program (string-append #$output "/bin/avogadro2") + (list "PATH" + 'suffix + (list (string-append #$openbabel "/bin"))))))))) (home-page "https://www.openchemistry.org/projects/avogadro2/") (synopsis "Advanced molecule editor") (description base-commit: c1ec9e8d53da209ba1d6f8466d03180d195d7334 =2D- 2.48.1 --Iyl16qkj3h7qFc1d-- From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 06 09:53:40 2025 Received: (at 76728) by debbugs.gnu.org; 6 Mar 2025 14:53:40 +0000 Received: from localhost ([127.0.0.1]:42144 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tqCbT-0007EE-Cp for submit@debbugs.gnu.org; Thu, 06 Mar 2025 09:53:40 -0500 Received: from mout.web.de ([212.227.17.12]:53835) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tqCbP-0007Dv-1B for 76728@debbugs.gnu.org; Thu, 06 Mar 2025 09:53:37 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=web.de; s=s29768273; t=1741272808; x=1741877608; i=jakob.kirsch@web.de; bh=BnIjyWFUeJBOSsPtv85OiIAAw8ChzNJAolGRMUbX7hk=; h=X-UI-Sender-Class:Date:From:To:Subject:Message-ID:MIME-Version: Content-Type:cc:content-transfer-encoding:content-type:date:from: message-id:mime-version:reply-to:subject:to; b=D5srXLWU2z1mCgM3pSmgyrMErc5vhTSuebUvlk35z2NiR/oQH/l2mjkr2DOWS1bO +DUuTjlTOd6trsJchLavirUWLjAen/z7iE+ToAvXAbcL1k7YpRbb+osBq49hQ0Lnh r5uYHVQ7WF+1DE7/fi5Q9aLEojJdM8UBk07LMA8T06zM1NxuqIri7RIsFPGBUmFIp I+4Tkv2udGb/NPqMNZU7fSB8GGnCJvFBUxHRnFYz1VGxS5NNY/ZgubxqsJKIxYYP3 flGsbcRPkpwMErKP/pWAS1EOHb4OeT44EkkKxzvHJYCzST8FiEzow/U6pdpKEwZ6D Wo3t438G9w3q7HE+gQ== X-UI-Sender-Class: 814a7b36-bfc1-4dae-8640-3722d8ec6cd6 Received: from kernelpanicroom ([134.19.29.228]) by smtp.web.de (mrweb106 [213.165.67.124]) with ESMTPSA (Nemesis) id 1N4NDQ-1t9kDe1cxC-00urFX for <76728@debbugs.gnu.org>; Thu, 06 Mar 2025 15:53:28 +0100 Date: Thu, 6 Mar 2025 15:53:25 +0100 From: Jakob Kirsch To: 76728@debbugs.gnu.org Subject: New patch Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="Jjo27NijAr/RneYV" Content-Disposition: inline X-Provags-ID: V03:K1:SAvT12QFRRYTE+h3H+fvxSZ/y1xxe1zCyfor+QiwMkLCn29N2Eq b1FFRF0+h2L6bSVSHfWHanGxSCRd8/iR03QqHWMK8HyfPKDBdlcH8xV1am7NsMuGyYgHbW6 cUw3cBtb3uiFOMKFNzrzjJ3R407vSFVI7JbXswUIA6pX75sy2w7O8XUbf/axtoRsGiOmDls EXzUbhI2oRkybyaMkIHrA== X-Spam-Flag: NO UI-OutboundReport: notjunk:1;M01:P0:jpLop3ZuXJY=;cwdOf9kt7BaHahqfwcBrr5BTnBq 7IhP2sZIMhL4zDb4Ek8Gjxu7wAREe9otLNZG/GIoU/+W7t68tovY3XyUHplHh8MpRa0urY6O2 VJLuBr6DaC0A59st0KVFKgHg48fo9AuDgBmyHxtqSub50rl7mZ/FWWsVDFZ98RSZUuHG33Vwq ZXU48QqccvRnBXMYBMAEm27L05V2kmv9y58+u7jYE6xtlkFFRJCmAXOgRGCjbFWiscg+bUTrA qIB/3n9oDSDUmlhsSfmZZmJ8PPIt6ykrauJSFWibC8ntnQ64tJSG2PSU5zIDkWQvV4VB7+8N+ FfjP4B/+AGTWqdEHvbbaLHPs/3AGMykMvudpfIh/wT3MJxsK6VAFu8TkVZ4AhjMhDx80tEkWe sj3N7oAr8f7sgHhmf28OJviHL71vzBe7hnC/JdRVm2H4xQ/MVa8eRi6gV2avdRe82KAazmywf WgqM1uewSAfQYfwyzUHymM2zsf7ItLeQQ8kYOrbhZUbbjzyKH+XYcwgxSJZAOKL6jBrF1PGIq jlCqj0ouxra2m9HgfvubePRJ0jIcrb6raL+Q9/IVd/yKfhJK1BWu3BKkFyhkHuRMkS6tPpf25 UNDdG1MxlC+lf6OWq8jPIRHMEB0CNWbepSnd0RYPZDLT91QhssjmyOj+/p4pbM8NNuWBTLorw n2JiTYR+LBkV7/A65MYBLDfrOdtUhkTV/hJw9KdOQwWUfp6E0qishJnha4Rf4KBYeXSZWlOhA rL0wa2Ta9/o7dzMB95csbAMWsDoXTE1Dd1YWvIA71cLP2jeOlE4wG/c3XM2WDjZVuxevv5ymz YzCQKu4EHj7qwVfaTAOPuxkhJO836u9UGPmHaetJ2ZvhlVj8vwzFhApBvg0qzCeHw6eTWSDV9 2wc0n5Y893dmws8h75mZ4wPMIDw0dv6aGHMjM+7qBF76Wn0tzZh/XeniT7PEVSyPoA5PM/Akg 0bUudjGxxlwNa4YUPzNYXyvtZ3lcAIZeUfa+epthvFK5GGYIGTGfq9JTpFZ5hBmFDR7Dmfrwe fGfxNBKsV5hXGj2LvSboZQsOgz39ybdmpAjsmbINlX2qVnA7E0p0eGUiOvpAy15MRsWXdqL0x OXys34SNbKdWZevHQohXnyDb9lVX6XtUx5b6FlBU1hn+/zzK153Co83ZKdT4dYFE3JSadwOg8 ixopSgnZuKU28vzo014jsRXExPaAKOVVMvZ16wmkfk5ACYI3CDS4jXjWMATimmuo01RJEdlNy tP1Sl2sBakqxlK550TUfuUB90LLaKa8vNAqcqLA+5ceHtInla9dHB3i2G0ZNC4nDjZuHaE3pH 1CKZ6ht6XBXjEawB6T9yf//fl4o1hRKzWbnFmL50PJvSXUjO9vifx692FCZ8MAManebUioYXA qq/yEusonXdqFMrwY3KZlSuGQ4LJu7wDyImx5QwTuvh2RcaYLpgi1fGR7f3cTcOcYLvwmyX1d /tp/72YAQ1SgW7PuWjryAVrnQWzc= X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 76728 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --Jjo27NijAr/RneYV Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Since we're rebuilding avogadro2, we might as well update it to the new version. Btw etc/committer.scm is broken with this patch so the merger would have to properly format the commits or fix the committer. --Jjo27NijAr/RneYV Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: attachment; filename="v1-0001-Update-avogadro2-to-1.100.patch" Content-Transfer-Encoding: quoted-printable =46rom 8a4aec3970b8eb31410933b77cd92937dca81309 Mon Sep 17 00:00:00 2001 Message-ID: <8a4aec3970b8eb31410933b77cd92937dca81309.1741272703.git.jakob= .kirsch@web.de> From: Jakob Kirsch Date: Thu, 6 Mar 2025 15:51:33 +0100 Subject: [PATCH v1] Update avogadro2 to 1.100 Change-Id: Ia97823f9950a587b52b274b17338102cf4340e71 =2D-- gnu/packages/chemistry.scm | 217 +++++++++++++++++++++++++++++-------- 1 file changed, 170 insertions(+), 47 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index bd27bfad7a..af51fc4d55 100644 =2D-- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -7,6 +7,7 @@ ;;; Copyright =A9 2020 Vincent Legoll ;;; Copyright =A9 2021 Ricardo Wurmus ;;; Copyright =A9 2022, 2023, 2024 David Elsing +;;; Copyright =A9 2025 Jakob Kirsch ;;; ;;; This file is part of GNU Guix. ;;; @@ -67,13 +68,75 @@ (define-module (gnu packages chemistry) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (guix build-system cmake) + #:use-module (guix build-system copy) #:use-module (guix build-system gnu) #:use-module (guix build-system python)) +(define-public avogadro-molecules + (package + (name "avogadro-molecules") + (version "1.100") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openchemistry/molecules") + (commit "8a37883"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "00mfx0bwmqazbiklrvaijjd5n4wa5lp3z73291ihm78q0v9dzhl4")))= ) + (build-system copy-build-system) + (home-page "https://two.avogadro.cc/") + (synopsis "Common molecule fragments for visualization in Avogadro") + (description + "Common molecule fragments including a variety of organic functional= groups.") + (license license:bsd-3))) + +(define-public avogadro-crystals + (package + (name "avogadro-crystals") + (version "1.100") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openchemistry/crystals") + (commit "28404bd"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0kcz99q5nfl2v2qmm9cqnbb2c2qqzw79vsnv557i7x64bxsxrw1m")))= ) + (build-system copy-build-system) + (home-page "https://two.avogadro.cc/") + (synopsis + "Crystallographic files of common materials, elements, oxides, for v= isualization in Avogadro") + (description + "Crystal structures of over 500 common materials, elements, oxides."= ) + (license license:bsd-3))) + +(define-public avogadro-fragments + (package + (name "avogadro-fragments") + (version "1.100") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openchemistry/fragments") + (commit "c4943b5"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "17l6qmkc25wb0nvic708l25fxiy89b3vfs0x5d40qcnn27bid32n")))= ) + (build-system copy-build-system) + (home-page "https://two.avogadro.cc/") + (synopsis "Molecular fragments for Avogadro") + (description + "Molecular fragments and inorganic ligands for rapidly building stru= ctures") + (license license:bsd-3))) + (define-public avogadrolibs (package (name "avogadrolibs") - (version "1.93.0") + (version "1.100.0") (source (origin (method git-fetch) @@ -81,28 +144,39 @@ (define-public avogadrolibs (url "https://github.com/OpenChemistry/avogadrolibs") (commit version))) (sha256 - (base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39")) + (base32 "1l9bp3ba8yx9mk2in5v375jzi1w4y7l1xl37xqv869810drgjffc")) (file-name (git-file-name name version)))) (build-system cmake-build-system) - (native-inputs - (list eigen - mmtf-cpp - googletest - pkg-config - pybind11)) - (inputs - (list glew - libarchive - libmsym - molequeue - python - spglib - qtbase-5)) + (native-inputs (list eigen + mmtf-cpp + googletest + pkg-config + pybind11 + avogadro-molecules + avogadro-crystals + avogadro-fragments)) + (inputs (list glew + libarchive + libmsym + molequeue + python + spglib + qtbase-5 + qtsvg-5)) (arguments - '(#:configure-flags (list "-DENABLE_TESTING=3DON" - (string-append "-DSPGLIB_INCLUDE_DIR=3D" - (assoc-ref %build-inputs "s= pglib") - "/include")))) + (list + #:configure-flags + #~(list "-DENABLE_TESTING=3DON" + (string-append "-DSPGLIB_INCLUDE_DIR=3D" + (assoc-ref %build-inputs "spglib") "/include= ")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'symlink + (lambda _ + (begin + (symlink #$avogadro-molecules "../molecules") + (symlink #$avogadro-crystals "../crystals") + (symlink #$avogadro-fragments "../fragments"))))))) (home-page "https://www.openchemistry.org/projects/avogadro2/") (synopsis "Libraries for chemistry, bioinformatics, and related areas= ") (description @@ -111,10 +185,30 @@ (define-public avogadrolibs bioinformatics, materials science, and related areas.") (license license:bsd-3))) +(define-public avogadro-i18n + (package + (name "avogadro-i18n") + (version "1.100") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openchemistry/avogadro-i18n") + (commit "07bee85"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1vhjh0gilmm90269isrkvyzwwh1cj3bwcxls394psadw1a89mk14")))= ) + (build-system copy-build-system) + (home-page "https://two.avogadro.cc/") + (synopsis "Translations for Avogadro app and libraries") + (description + "Translations for the Avogadro app and libraries. Contributions and = edits are always welcome through Weblate.") + (license license:bsd-3))) + (define-public avogadro2 (package (name "avogadro2") - (version "1.93.0") + (version "1.100.0") (source (origin (method git-fetch) @@ -122,17 +216,28 @@ (define-public avogadro2 (url "https://github.com/OpenChemistry/avogadroapp") (commit version))) (sha256 - (base32 - "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7")) + (base32 "19cd5aqvcw6xj0x1kmzmxl0vrnbhk5ymnl9p2p4d9504ma5k6aim")) (file-name (git-file-name name version)))) (build-system cmake-build-system) - (native-inputs - (list eigen pkg-config)) - (inputs - (list avogadrolibs hdf5 molequeue qtbase-5)) + (native-inputs (list eigen pkg-config avogadro-i18n)) + (inputs (list avogadrolibs hdf5 molequeue qtbase-5)) ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag. (arguments - '(#:tests? #f)) + (list + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'symlink + (lambda _ + (begin + (symlink #$avogadro-i18n "../avogadro-i18n")))) + + (add-after 'install 'wrap-program + (lambda _ + (wrap-program (string-append #$output "/bin/avogadro2") + (list "PATH" + 'suffix + (list (string-append #$openbabel "/bin"))))))))) (home-page "https://www.openchemistry.org/projects/avogadro2/") (synopsis "Advanced molecule editor") (description @@ -481,7 +586,7 @@ (define-public openbabel (define-public spglib (package (name "spglib") - (version "1.16.0") + (version "2.5.0") (source (origin (method git-fetch) @@ -489,26 +594,44 @@ (define-public spglib (url "https://github.com/spglib/spglib") (commit (string-append "v" version)))) (sha256 - (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws")) - (file-name (git-file-name name version)))) + (base32 "0x5igrqwx7r2shysmi9sqcjg4hpb7hba3ddlwg05z6c57a3ifbqc")) + (file-name (git-file-name name version)) + (modules '((guix build utils))) + (snippet #~(begin + (substitute* "CMakeLists.txt" + (("include\\(cmake/DynamicVersion.cmake\\)") + "") + (("dynamic_version.*") + "") + (("PROJECT_PREFIX.*") + "") + (("FALLBACK_VERSION.*") + "set (PROJECT_VERSION 2.5.0") + (("\\$\\{PROJECT_VERSION_FULL\\}") + "2.5.0") + (("\\$\\{GIT_COMMIT\\}") + "\"\"")) + (substitute* "src/CMakeLists.txt" + ((".*Spglib_GitHash.*") + "")))))) (build-system cmake-build-system) (arguments - '(#:test-target "check" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-header-install-dir - (lambda _ - ;; As of the writing of this package, CMake and GNU build sy= stems - ;; install the header to two different location. This patch= makes - ;; the CMake build system's choice of header directory compa= tible - ;; with the GNU build system's choice and with what avogadro= libs - ;; expects. - ;; See https://github.com/spglib/spglib/issues/75 and the re= levant - ;; part of https://github.com/OpenChemistry/avogadroapp/issu= es/97. - (substitute* "CMakeLists.txt" - (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir) - (string-append include-dir "/spglib"))) - #t))))) + '(#:tests? #f + #:configure-flags '("-DSPGLIB_WITH_TESTS=3DOFF") + #:phases (modify-phases %standard-phases + (add-after 'unpack 'patch-header-install-dir + (lambda _ + ;; As of the writing of this package, CMake and GNU= build systems + ;; install the header to two different location. T= his patch makes + ;; the CMake build system's choice of header direct= ory compatible + ;; with the GNU build system's choice and with what= avogadrolibs + ;; expects. + ;; See https://github.com/spglib/spglib/issues/75 a= nd the relevant + ;; part of https://github.com/OpenChemistry/avogadr= oapp/issues/97. + (substitute* "CMakeLists.txt" + (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir= ) + (string-append include-dir "/spglib"))) + #t))))) (home-page "https://spglib.github.io/spglib/index.html") (synopsis "Library for crystal symmetry search") (description "Spglib is a library for finding and handling crystal base-commit: f2229c2afdb32ddba46bce6f37aba812af39eec5 =2D- 2.48.1 --Jjo27NijAr/RneYV-- From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 06 09:58:04 2025 Received: (at 76728) by debbugs.gnu.org; 6 Mar 2025 14:58:05 +0000 Received: from localhost ([127.0.0.1]:44684 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tqCfk-00085F-H2 for submit@debbugs.gnu.org; Thu, 06 Mar 2025 09:58:04 -0500 Received: from mout.web.de ([212.227.17.11]:54143) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tqCfh-00084c-Ip for 76728@debbugs.gnu.org; Thu, 06 Mar 2025 09:58:02 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=web.de; s=s29768273; t=1741273075; x=1741877875; i=jakob.kirsch@web.de; bh=OhroqgPvQgVoW5os0hacUNGju1+9Q5ruLJUcfCY0Qtc=; h=X-UI-Sender-Class:Date:From:To:Message-ID:MIME-Version: Content-Type:cc:content-transfer-encoding:content-type:date:from: message-id:mime-version:reply-to:subject:to; b=qFPrP6NLprYD5QibHtF/VRKwP+Rc5bUmJruqtd+lcj979FEIPwSA9ajfjuuKrJqH zOBvmTDVVZfJxX2q7wRyd23VjOiRaCFbGsyMdoHHG0+AGeODktuxv0y7loBvbQQnQ IzVvNH5FM6aN35fVi5OU8hsOyQBQ4hxFq2idgB0kYYdNoODofNPGRCZ5ei7bukblA pQ4ZDzmSIRG53Jk7hqgGFOxRpjzoms7AOm4SlabB+1AzLmw6Ar+XpfbSG8oOimSCS nXlpqvFIoYq5O9FP62ePu/zCfR1SVlvq+K743SUuQgGjL56ax67343RJUoLEMdiSD e/LIVYj44xbnryHxZQ== X-UI-Sender-Class: 814a7b36-bfc1-4dae-8640-3722d8ec6cd6 Received: from kernelpanicroom ([134.19.29.228]) by smtp.web.de (mrweb105 [213.165.67.124]) with ESMTPSA (Nemesis) id 1MOUtg-1tcVXJ0lJ8-00OxBz for <76728@debbugs.gnu.org>; Thu, 06 Mar 2025 15:57:55 +0100 Date: Thu, 6 Mar 2025 15:57:54 +0100 From: Jakob Kirsch To: 76728@debbugs.gnu.org Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline X-Provags-ID: V03:K1:cHIqI8rIZfB18aCVp8P2KmI7Qy4l8lQKneD+KaoliTfKwqitHBF q4aryP6cB1NRvHdHJteL5NIvL6+irpdV42IODrtxoHTxYGPW2QO9cMZiugVkYGFF0wAJ7rK Yjm3RIuL632Zkv3Pl5z2nYTM3rR/LDxsQYqFwVDPXi7iyhgT+ve+sSQnmgPnMQ9oEtiqENZ on7P9aApFqCmVMJjoZV9w== X-Spam-Flag: NO UI-OutboundReport: notjunk:1;M01:P0:bNZuHQCXd54=;kbz7BgnPuUGYPkT+6IOKKfokOTX 1Yu8lhb6+wuKhT1yjSiC1Fiow1f0NKxPkSmNeu96ZNQpGr/ZC93mwGQvYWuogHPCw+v7ikVQW HLuqBIiNvT5BqdvWVGReGBqg2RI8u3Ya2KsAHektry26sDxvXDNCespw7/Goy0LHczVri4jx9 Orv8EGL0WmV9OzJ1k/2XUpdvI7MvY+PxP2h2GOr5PakFhS3a/V0NXDBhSNOHge6EhGaSNor7k I61YN3AmQ74fcuNDH5rkF+rBXafxQJtyj+ycQOIvMHZYjgD+O2Xsu/2HEorSYdT54h8rXItdT ydJKMtS+JTS4ueqxz2tUQgnX9hCqfZXq0xl8BrsgvKrOUwO0BjxUQNMAvI6VDSDlA55zb0g+j RA5R+VeiyTAobvGzhmZWRSOOH6EmT71WVhlFnagcSfVqtC9Spm8AH3bVBDCoCRqlzdE/c+BtC 1pKWA9yueUaGirKqVlXxzG3AlHCVQuulP7KNH0LlcSj/9Vie/Xw+CQehi8gs/ErDhCB//aQ36 0SGr0yRJiOmX2A1imWwY8PNCv7gNuQVQ5uxPxO6UE8vvIL+9vDAQH71rSflJjdAdK/isqS+bT Lu5gAmaDhd4TiBlHk5TV4JQQFbR4qna/5WSEC4oQ8JgAAx5kISaCXohZ3PGIGhQEyIM5zYRaX AKPUxvuQb7BVRrfUzHkdBtBTi/g1kNUMJCo7iDqzRUNUxCpMRHjVGAC5NdDTlVPbnQkFsS3GU nzQn7T3n69Hpm5KFSEeRR/iHk3jEEj/fSLp8T8yNOmG7xpe/RSFwCE9A/tufpXqyPQKJ993Ee NO/YRzDm3Xgnpvkz9vE5DoiuXr1Y+Mvl/8DJTV+YXR/tNc8P5w92n6rzL4Iv6GpXneYznMsKb dzgnljk/4Y6PLWffT0nRePOsB0Nqaai9Z8kDK1+e/iRMpF5f1eUhvPYjhboUVdmkfCzgQwl4y ddO39mcH11PueB5yC2WODuFfwR+GKemcDBBgfmI77DE80M1m3Cq+mEMlV5hVvn/0QU02/llSE TUu1bvQu4CheFqftBwCwtjOLgpBvz7gz2PkQvbPqg52VZCM4W/Ytz8eqhJ4++Q7dRBm4URMwG lPExR9Hc8zFAYYLj+XBVbiaRh6gYTzk5a0DN/zM2IslGBbS3SGXfy4Lf7p3APM+zIg/kboYey UdHUAZcDRzl8e2vz2nhewUdhwMIq1k+sEsbUfHywb+BljLMVA+oOgBhJ/429Vsz7lyNmG9Xzy Kga9c2jQz5qupraO/quqP/LRvjNfJxnkMXdi70ljhtrxZqvnh0wUBqVkf5mylsk+O/ROXJqul 6Qj5EPQwgAV5xHeyUKt7lcDDMUPzu3IqsnN6mNNv2a0UbhB37YQsGjLzqZeKLeDdihj9nCYQJ DGGWdsUS4wzLhJQOwmcA8/cfiFQiLcA7g7cags2I213OUDlttKl0mZG2KO X-Spam-Score: 1.3 (+) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: This is still WIP as some things are broken like: * icons don't render * openbabel optimization is broken with DNA Content analysis details: (1.3 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 0.0 RCVD_IN_VALIDITY_RPBL_BLOCKED RBL: ADMINISTRATOR NOTICE: The query to Validity was blocked. See https://knowledge.validity.com/hc/en-us/articles/20961730681243 for more information. [212.227.17.11 listed in bl.score.senderscore.com] 0.0 RCVD_IN_VALIDITY_CERTIFIED_BLOCKED RBL: ADMINISTRATOR NOTICE: The query to Validity was blocked. See https://knowledge.validity.com/hc/en-us/articles/20961730681243 for more information. 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Fri, 07 Mar 2025 20:37:20 +0100 Date: Fri, 7 Mar 2025 20:37:17 +0100 From: Jakob Kirsch To: 76728@debbugs.gnu.org Subject: PATCH v2 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="mqscGeM6pGqux1Ck" Content-Disposition: inline X-Provags-ID: V03:K1:9r76iHWxUByGmxQNDkWobxEfw47usQMZxlO/wA8e3LvM5Ow1QsI qvz875zjqXpwQk8ynZOkcGzpR655ebclnALSRNTEEYkYYDE4zels55tdcXk8lV8IRSpjbZS VMQVnfaBWFOE2+7eHvegw35TaBJxeucOP7llMnw2xUPjVWLQeIy3BmKFOB20Vn6bXPOT3Qg LdMtW2kVTb4cn3zgOd1QQ== X-Spam-Flag: NO UI-OutboundReport: notjunk:1;M01:P0:6snBI7nf1T4=;Pr8o5+qLvR4VAv/t7Yxy0/Hl6Kp Y481hpGarBvPksqWkFv7fJ2aVduJX6F9GyYi+air2e1KV8ub31Bl0HfQoFzUpvEP8+zION89e XbV//8aErpIH2j35Xqr2gwOMYAhmMGWvzKnrVuKtd3e/Yy6lR6WFJ1dY4/9F9Z4YDp55SZYXN xru7e4vfprhtqN2PKwkKq2uDoy/ZdeBbIj3X7awjscPFhdHY/ZR/PX2WTnet9IaUdGxZsc71D Q7wPcubDGvbC+jRAnrhA4zH0uqDn71slfcS7uZYi550kO7OYQAVg54jVtZ0PKr4CcsuCKHy3F GSooJTZVX7L/xDLnvcpUyQCR5sJrmoDHtdStWuQuLyiZgnFMYp6wxlX8CN9eL27S3vWHVrv3k Jys1E3V1msK0K6AHOOjmuRx3P/OWgazCYS8yFBdCJafzJ3ocqJMIyw+X+Drmj5iQgzbcc+6J0 eTvi0RXdmbqDIcPkpWyreuCUAxpZl/KQyiSdaRnnTfP5MC4+Q/de31tSR5QPgNiNpRHQhfhea 3fWYr4N/vqfBo8/5DNsHRxgfljnARo9/Mla1yrxxJJSP9vrzZd3AtC1NVtNKUdUb3yUzxzjCl JDmqYQxbFFqBZ7+boljgTN16YMgMKi6i/OyJcf+drwlPnTCwO8etOY6BNriuF/QzGyGe3CCHH AV+Nu9QnWBHeeIYR0YaXK8XYlx0fk0m+No5lAQVtrNwm8st1MOBcG+6njdUDyV55nL4bYxmHD pqjxY0LinRxghdeaogd9rRHn+wWhWYoGdMrZkTTcZP/tCc13+vwWNMsGJEc5zu9+fnh/yq2qo on9kGilv5eJ3GL5KsXJP720IcbzN/LnwkYFhjSfxGnjqJ+CbOnVQsQRreRsoqu7HSY3r55jmL /9jwkC1jGG3B/r4PuWumN7kTzaQiXwkegWw1bYywdZr9C087TgRNpCPpxWh/qqgeUvRwjmToH lC3/Ecxh28AqWglDdFVi5+2UBRG8vN2qyXl9sGYVJyvFXua4mG6UpPLpY3Qv5xO+WREq9/v8y XMRTTmyddt7svjCWde7ajmZUXz3f+iAKg0r/bYi1GhvPYtUKj3Rqc60byaA/p4LfiBwemt2k8 8BwXkGkWguos5lTi0PyJS9VgnJBwNENxX7aUZk+VUvh2hjw8iW1lBVwudd6zGWDF/pMvyfyVL vhmuslkPBX9zmsNe1tZ4vmI3rbfYxUGD3Wc6tBXez/uhZgPLo1h9mQQQG6FqxAgKLoaH7wEDr TEpvVAOIrFjbAR6CSFLLJBvTyA8UhrOaBBc+y/acJxEp6Ml9XOQxbeemmutX5yrqGKuQ9kXFY xsY/P/McY2xKgrugUjByNStKhiYtZ7jMQXhYmNRyiHr5YBx8VrxbMiw9Aa3WUwk2w5cEOTFr2 SUB4zhH83jJMaNqqCbVaWUF1XB8hZ0+ieBgvKqsGZnQCEmDtFCFyp3sGr8tafwGL7jjd+Lbcj gq6x7tl1I0t3n0BCv080ClJZNCro= X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 76728 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --mqscGeM6pGqux1Ck Content-Type: text/plain; charset=us-ascii Content-Disposition: inline I changed some stuff (don't remember what tho). Still WIP. --mqscGeM6pGqux1Ck Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: attachment; filename="v2-0001-Update-avogadro2-to-1.100.patch" Content-Transfer-Encoding: quoted-printable =46rom 372abf8bb087488d0453cfa0ed82837636466b0e Mon Sep 17 00:00:00 2001 Message-ID: <372abf8bb087488d0453cfa0ed82837636466b0e.1741376160.git.jakob= .kirsch@web.de> From: Jakob Kirsch Date: Thu, 6 Mar 2025 15:51:33 +0100 Subject: [PATCH v2] Update avogadro2 to 1.100 Change-Id: Ia97823f9950a587b52b274b17338102cf4340e71 =2D-- gnu/packages/chemistry.scm | 211 ++++++++++++++++++++++++++++--------- 1 file changed, 164 insertions(+), 47 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index bd27bfad7a..05eefd52f4 100644 =2D-- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -7,6 +7,7 @@ ;;; Copyright =A9 2020 Vincent Legoll ;;; Copyright =A9 2021 Ricardo Wurmus ;;; Copyright =A9 2022, 2023, 2024 David Elsing +;;; Copyright =A9 2025 Jakob Kirsch ;;; ;;; This file is part of GNU Guix. ;;; @@ -67,13 +68,75 @@ (define-module (gnu packages chemistry) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (guix build-system cmake) + #:use-module (guix build-system copy) #:use-module (guix build-system gnu) #:use-module (guix build-system python)) +(define-public avogadro-molecules + (package + (name "avogadro-molecules") + (version "1.100") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openchemistry/molecules") + (commit "8a37883"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "00mfx0bwmqazbiklrvaijjd5n4wa5lp3z73291ihm78q0v9dzhl4")))= ) + (build-system copy-build-system) + (home-page "https://two.avogadro.cc/") + (synopsis "Common molecule fragments for visualization in Avogadro") + (description + "Common molecule fragments including a variety of organic functional= groups.") + (license license:bsd-3))) + +(define-public avogadro-crystals + (package + (name "avogadro-crystals") + (version "1.100") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openchemistry/crystals") + (commit "28404bd"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0kcz99q5nfl2v2qmm9cqnbb2c2qqzw79vsnv557i7x64bxsxrw1m")))= ) + (build-system copy-build-system) + (home-page "https://two.avogadro.cc/") + (synopsis + "Crystallographic files of common materials, elements, oxides, for v= isualization in Avogadro") + (description + "Crystal structures of over 500 common materials, elements, oxides."= ) + (license license:bsd-3))) + +(define-public avogadro-fragments + (package + (name "avogadro-fragments") + (version "1.100") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openchemistry/fragments") + (commit "c4943b5"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "17l6qmkc25wb0nvic708l25fxiy89b3vfs0x5d40qcnn27bid32n")))= ) + (build-system copy-build-system) + (home-page "https://two.avogadro.cc/") + (synopsis "Molecular fragments for Avogadro") + (description + "Molecular fragments and inorganic ligands for rapidly building stru= ctures") + (license license:bsd-3))) + (define-public avogadrolibs (package (name "avogadrolibs") - (version "1.93.0") + (version "1.100.0") (source (origin (method git-fetch) @@ -81,28 +144,33 @@ (define-public avogadrolibs (url "https://github.com/OpenChemistry/avogadrolibs") (commit version))) (sha256 - (base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39")) + (base32 "1l9bp3ba8yx9mk2in5v375jzi1w4y7l1xl37xqv869810drgjffc")) (file-name (git-file-name name version)))) (build-system cmake-build-system) - (native-inputs - (list eigen - mmtf-cpp - googletest - pkg-config - pybind11)) - (inputs - (list glew - libarchive - libmsym - molequeue - python - spglib - qtbase-5)) + (native-inputs (list eigen mmtf-cpp googletest pkg-config pybind11)) + (inputs (list glew + libarchive + libmsym + molequeue + python + spglib + qtbase-5 + qtsvg-5 + avogadro-molecules + avogadro-crystals + avogadro-fragments)) (arguments - '(#:configure-flags (list "-DENABLE_TESTING=3DON" - (string-append "-DSPGLIB_INCLUDE_DIR=3D" - (assoc-ref %build-inputs "s= pglib") - "/include")))) + (list + #:configure-flags + #~(list "-DENABLE_TESTING=3DON") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'symlink + (lambda _ + (begin + (symlink #$avogadro-molecules "../molecules") + (symlink #$avogadro-crystals "../crystals") + (symlink #$avogadro-fragments "../fragments"))))))) (home-page "https://www.openchemistry.org/projects/avogadro2/") (synopsis "Libraries for chemistry, bioinformatics, and related areas= ") (description @@ -111,10 +179,30 @@ (define-public avogadrolibs bioinformatics, materials science, and related areas.") (license license:bsd-3))) +(define-public avogadro-i18n + (package + (name "avogadro-i18n") + (version "1.100") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openchemistry/avogadro-i18n") + (commit "07bee85"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1vhjh0gilmm90269isrkvyzwwh1cj3bwcxls394psadw1a89mk14")))= ) + (build-system copy-build-system) + (home-page "https://two.avogadro.cc/") + (synopsis "Translations for Avogadro app and libraries") + (description + "Translations for the Avogadro app and libraries. Contributions and = edits are always welcome through Weblate.") + (license license:bsd-3))) + (define-public avogadro2 (package (name "avogadro2") - (version "1.93.0") + (version "1.100.0") (source (origin (method git-fetch) @@ -122,17 +210,28 @@ (define-public avogadro2 (url "https://github.com/OpenChemistry/avogadroapp") (commit version))) (sha256 - (base32 - "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7")) + (base32 "19cd5aqvcw6xj0x1kmzmxl0vrnbhk5ymnl9p2p4d9504ma5k6aim")) (file-name (git-file-name name version)))) (build-system cmake-build-system) - (native-inputs - (list eigen pkg-config)) - (inputs - (list avogadrolibs hdf5 molequeue qtbase-5)) + (native-inputs (list eigen pkg-config avogadro-i18n)) + (inputs (list avogadrolibs hdf5 molequeue qtbase-5)) ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag. (arguments - '(#:tests? #f)) + (list + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'symlink + (lambda _ + (begin + (symlink #$avogadro-i18n "../avogadro-i18n")))) + + (add-after 'install 'wrap-program + (lambda _ + (wrap-program (string-append #$output "/bin/avogadro2") + (list "PATH" + 'suffix + (list (string-append #$openbabel "/bin"))))))))) (home-page "https://www.openchemistry.org/projects/avogadro2/") (synopsis "Advanced molecule editor") (description @@ -481,7 +580,7 @@ (define-public openbabel (define-public spglib (package (name "spglib") - (version "1.16.0") + (version "2.5.0") (source (origin (method git-fetch) @@ -489,26 +588,44 @@ (define-public spglib (url "https://github.com/spglib/spglib") (commit (string-append "v" version)))) (sha256 - (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws")) - (file-name (git-file-name name version)))) + (base32 "0x5igrqwx7r2shysmi9sqcjg4hpb7hba3ddlwg05z6c57a3ifbqc")) + (file-name (git-file-name name version)) + (modules '((guix build utils))) + (snippet #~(begin + (substitute* "CMakeLists.txt" + (("include\\(cmake/DynamicVersion.cmake\\)") + "") + (("dynamic_version.*") + "") + (("PROJECT_PREFIX.*") + "") + (("FALLBACK_VERSION.*") + "set (PROJECT_VERSION 2.5.0") + (("\\$\\{PROJECT_VERSION_FULL\\}") + "2.5.0") + (("\\$\\{GIT_COMMIT\\}") + "\"\"")) + (substitute* "src/CMakeLists.txt" + ((".*Spglib_GitHash.*") + "")))))) (build-system cmake-build-system) (arguments - '(#:test-target "check" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-header-install-dir - (lambda _ - ;; As of the writing of this package, CMake and GNU build sy= stems - ;; install the header to two different location. This patch= makes - ;; the CMake build system's choice of header directory compa= tible - ;; with the GNU build system's choice and with what avogadro= libs - ;; expects. - ;; See https://github.com/spglib/spglib/issues/75 and the re= levant - ;; part of https://github.com/OpenChemistry/avogadroapp/issu= es/97. - (substitute* "CMakeLists.txt" - (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir) - (string-append include-dir "/spglib"))) - #t))))) + '(#:tests? #f + #:configure-flags '("-DSPGLIB_WITH_TESTS=3DOFF") + #:phases (modify-phases %standard-phases + (add-after 'unpack 'patch-header-install-dir + (lambda _ + ;; As of the writing of this package, CMake and GNU= build systems + ;; install the header to two different location. T= his patch makes + ;; the CMake build system's choice of header direct= ory compatible + ;; with the GNU build system's choice and with what= avogadrolibs + ;; expects. + ;; See https://github.com/spglib/spglib/issues/75 a= nd the relevant + ;; part of https://github.com/OpenChemistry/avogadr= oapp/issues/97. + (substitute* "CMakeLists.txt" + (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir= ) + (string-append include-dir "/spglib"))) + #t))))) (home-page "https://spglib.github.io/spglib/index.html") (synopsis "Library for crystal symmetry search") (description "Spglib is a library for finding and handling crystal base-commit: 9bc4c9f521caab8aa8d88aa948a650945bb55838 =2D- 2.48.1 --mqscGeM6pGqux1Ck-- From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 08 07:09:44 2025 Received: (at 76728) by debbugs.gnu.org; 8 Apr 2025 11:09:44 +0000 Received: from localhost ([127.0.0.1]:59347 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u26ps-0003s4-40 for submit@debbugs.gnu.org; Tue, 08 Apr 2025 07:09:44 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:41402) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u26pp-0003rC-5v for 76728@debbugs.gnu.org; Tue, 08 Apr 2025 07:09:41 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 0DA3129C; Tue, 8 Apr 2025 13:09:33 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id 3ZxtgvtLoLcz; Tue, 8 Apr 2025 13:09:32 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 905C155; Tue, 8 Apr 2025 13:09:30 +0200 (CEST) Date: Tue, 8 Apr 2025 13:09:28 +0200 From: Andreas Enge To: Jakob Kirsch Subject: Re: PATCH v2 Message-ID: References: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: X-Rspamd-Server: hera X-Spamd-Bar: +++++ X-Rspamd-Queue-Id: 0DA3129C X-Spamd-Result: default: False [5.40 / 15.00]; SPAM_FLAG(5.00)[]; NEURAL_SPAM(3.00)[1.000]; BAYES_HAM(-3.00)[99.99%]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; FREEMAIL_TO(0.00)[web.de]; ARC_NA(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; TO_DN_SOME(0.00)[]; FROM_HAS_DN(0.00)[]; FREEMAIL_ENVRCPT(0.00)[gmail.com,web.de]; RCPT_COUNT_THREE(0.00)[4]; FREEMAIL_CC(0.00)[debbugs.gnu.org,posteo.net,gmail.com] X-Spam-Level: ***** X-Rspamd-Action: greylist X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 76728 Cc: bavier@posteo.net, sharlatanus@gmail.com, 76728@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hello Jakob, Am Fri, Mar 07, 2025 at 08:37:17PM +0100 schrieb Jakob Kirsch: > I changed some stuff (don't remember what tho). Still WIP. are you still progressing, or should we close this issue? 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Thu, 10 Apr 2025 19:28:15 +0200 Date: Thu, 10 Apr 2025 19:28:13 +0200 From: Jakob Kirsch To: 76728@debbugs.gnu.org Subject: [PATCH] gnu: avogadro2: update to 1.100.0 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="GruEu5apdr3IAEeN" Content-Disposition: inline X-Provags-ID: V03:K1:kF7g48tgu52ynfpPYBooGcZFNuBRjA2ZoszSvYBNkTVF/xJkC7S Kld0epwigdhpDU0bcpsmx4WvKCisVfTgaN88MIEbNnkG2rnz3GUILZXZlgD+eFz0L5nLuvt XheK7C3oYj7wd8ZTx9fZqZq7Cb/3dlqpjhKeK4SeCKSWGOc3PSEi8gZAxVvCluYelCV464Z O+SBNv3fW8PryfdRnzhMQ== X-Spam-Flag: NO UI-OutboundReport: notjunk:1;M01:P0:U+QPTv8C+Ks=;awTMK9NcGWOxD47X0HftlbKvAyz mcrafvZ/6Se9QUrNd0gz1lnDN+89zfRQ/HnJHP3HWyCb+L3IfpIVJOD31ZRelPKyt9uxBrldZ pmIXJV1URBqIQMcy9ye53xEOosM7vcgT9LRpLdmvsiU5Zbdji1Td45p8nCivcQhM1CAdw6Yox pROuzqEs6VNP5HFeePExgLd5ON6T7oSLEN4SqL8FT5joHMGa9P+4flwCNrkriWDM6jSKf3lX0 fKKMzXkukXG76SaeMCos7VXi6W0/5cciABz4KPXCZCVOvxpAr/gKTFJRuegHRfV6vNN7h/iEH UAxjP192x2eqTY+z2AonDcgw+95ibgy/9zXmB0N3BFcnbo1TRYYGS6rbjYu+h/Q2DRYiAFDcL DzAGbCGv4Rn5ztgI6+hwdmBZ5dT7nBeXpmtVwi0r9SeN9NPvpSFyNOb5DHD4UsUOJcZX6EZKW sk8lVb4wMNzz0/L5w49maSMpmsEKN9YyNWwQaU3vV7/KDDKnKCVdab1AgejrsCXumfNS0s/1a 0UqKna7MbZ69wvAMkIUkSGWtpsgO7vP5s52E8DlRLD50jP6j0yWbccgLYRxmFC1k+a05Mdxt1 DVDFLvW3KJB2y4hbJWaWotN81zipKXVLy9mEFAy+jMjxJt/LmJaNQvot1qbAakS3nUo8/Px2c n7KobuoOq2HlQPAlrEsZZcFIUPOqLzZxc2V9L9hNzCswy4n4152lDuvfQdzz4v8IJ9NmqdYUW 63D8Ot/uwEs9EeccEDBcm9FTCT7tLbmyQ/yEpqRsiI16jc5gYpnXfhPiM2rY/RGW3OtBI9B2C 9qMEWEOuU1Lx9BaNygnJ0bYkZfTdvTR25a8BUaH9rvN8pY9pXU4Yw4+MSFdRHQBVNhY63vpJM pz14XW7lI8I+CJBCzb9DN+9MFMWD+35aSfVyFQX9BuGN1f0V+ytOcUm7/aEq9VmPVsXKzMwBx cYoywpa6yS9nOU881FPPJ9cgGgWy5mmIImui27sEw0RnylBgnLJXh175rH4sEiJCvYumqS1UE TlBHjCojS7/Mzkl5O+Y+YWPr6V19CMymTPnZAVA8brLT+iggG9b8IdV5aysQJPmD70LQkB7T1 MLSxs2gslA5YKWUcIWXabfNeTwgn932d0+yVQ+JnX8B7LkVbUg29hX4H8UzWmkoxV3FEdKJQb LNPKcHPg8sdDSvpvHgWdGeJVSfmoCemL+oyEwpXJ2YwghMBdEQ9db92L6p4F3xC3g5p3kX4tf K+d7AdONBhNTuVAsCMmTaTjZgkwWN5Dr5B42k9QCzJ/PMVTmpDff8NzuC+9uBMb9vULg7SRI7 FeFuXa2WrONk775mih1dqGUs3tx0stvZBoyrpofWCoSIeEpXkYK0ySfax3psspJe+4Uo0FeRJ DYsu6JgF6LC8+Qd/2qKrHweB4ek00jlGAAlqLMDJx7OuXrrOOX23XdxWw74d7BtP+8hZgOTau js3n6Mmsq6BVE3sbuWNZthiOxuAO7R+hZpLMt+2y21I8QT9lveq4YiOyJWr7jHq5HbybFSJbJ pZC32Rt5Xfoxg1csBWSeftj1W04icSD7Vlowf8xIrjx3sl1OF1esE6AAcsVICAbq9O1xVp/bB laJk1FlfDm+UxKfE+pStuhE2XladT0Y1HxJhRwiOkuAGhffWdhmvZP4gaI01vRBcGbPzhHkJk 09LYz/mwJrhokqo/r1TiCRVnff+WaqB51b6MrTb6fudvI6Y3nQUAtW7amrLyA41ccbx9ElS6G svYTC7io+9143IbJYsl9jsrJxl6yyw8ZsWH4wrpCNAbE+d3twsfnn1RnDi/6WcWMSg6lYPfd1 jvopBDSKy2AeU2X/9vpvm2lZVdH7Gf+kDDg7G0ym8Wpr4d8AKIMnhfK0a/pwY4avuCUxVh+sy mE/BZCS62tYaU5vlKgfN0Kh//H7vApAXaJJDzP4Mk0nO4H+oi/pCSB8EnczJbBRGgcK63Ypdg wW24xN4dXBi01ewzGwEtGaiAgUn2pDN7Y79UCVYke67wTxUTpkXmJ0+xJmF6hMVzGI7bQUoux XUeNDwFmVpPOePG6TGc97BlN1P0PtyXsd2qFs4X6b/vNKEGFDBhXNGti1t0ENG1Z/rrV39AZQ J1a7P6BMXSRCzfvpmkh9sU3uCYX7WLzxnW7b8dNMto9VMu8DaIC9tWfn6gg1D/bvHV4g4/nZl ZmZ0I50rbWf0YxY7i1sDjezJDtr38mLeMglBGWUvS4H6pEEZrN33m9ZL+5AMSNZqZi0f2P9qE WRH4zSBRi7N1y5yN//kGKxwRrwjzRK/VtaCV3OViAYnC1403OL0Qy6gco0swagoTH9RMN0Frr SLcIZUaDCuZDusG/QDEh2hVXvKFNcOio625OvPrBU4f4Lto7K9PFNIVn8fha8SK1N5ez0UwWr Vp59fi5MOJmnIhhnbxsdjsC4jGvlnUf4Zy+Tf+FvBKLA5ZfPUU++4Ha3W1zzuFDWYZXa/dIuE FudKuaqdBpaokiUOzBYZpcV7Ha0aTqR3Spj4uASvg4QtAO8qQiLQgPU4lXLBBqPx6lIQezjXM jgdG/M5jNpJD7Dd4P1ySGHKg6NlE8jYOm4a35NFKsRXC+DCN3khduWVDLkylZhh5POYXN+OZn I1XTHLsvjC6aZqXwhuc5FQfyZj0Z0RxEOlOdQm3QmROTaUj99LjbdB6jNoqREBSIFkqOD/2QJ 4PvRM5KlEyxc7GMQeJe9sw6OPXu9Fl9wuM8buav0BQ+FKQopA+N/kII0eCOvgRFwY/kf8qgFk KJl+FRcRQq1ql5XfbnwhxL6Ih5nQqCqezg/vwBD2k5yRR75rU/F4ez4NzUj+jEMLRbFScAdPD nsvfFLdNmKNz4zuf/9GOAYByinn2KYO5Bh8Zilpr+QsWB5i44scV0d8MDzbJllCQA5UwTyh7D dpzmpw+YiKSQu7YXXsvWo1CWGvyaYYD8NdUU55kDOtGNwe3ecx388iFzoVlsAoAxczsYiP+A3 CffyIsp3di05dl2+8QaQ0YGcPfvj+8C5LP6nec+3j34R2xzGhn2G+WWkUFjgNrDT4N+tGngLI byvhdeMuQb94eIcVN8+qBw3Ku/DxSKGUQN8YBcz5mklVd4jovhFnNEk/sKqVItD3CDHDBM351 v4ajplVz3okbAqJOmB5GFYKI/PEPXzYckjfrYbA3ElA79eSqwUYRvCnMH+ufNrp2UT+x5OLOQ iRVZ7evQOmhoAfPRw/tmjNO5UDzFM7yAkTtjxsFcKUuFt3g== X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 76728 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) --GruEu5apdr3IAEeN Content-Type: text/plain; charset=us-ascii Content-Disposition: inline I fixed all the issues. It's good to merge now. --GruEu5apdr3IAEeN Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename=0001-gnu-avogadro2-update-to-1.100.0.patch Content-Transfer-Encoding: quoted-printable =46rom d37b05f6d07df4bdb87ad4d210715c725ba909e5 Mon Sep 17 00:00:00 2001 Message-ID: From: Jakob Kirsch Date: Thu, 10 Apr 2025 19:24:23 +0200 Subject: [PATCH] gnu: avogadro2: update to 1.100.0 * gnu/packages/chemistry.scm (avogadro-molecules): New variable. (avogadro-crystals): New variable. (avogadro-fragments): New variable. (avogadrolibs): Update to 1.100.0 (avogadro-i18n): New variable. (avogadro2): Update to 1.100.0 (spglib): Update to 2.5.0 Change-Id: Ie6a22f21aca770d628729bd514acbea1185d89a8 =2D-- gnu/packages/chemistry.scm | 215 ++++++++++++++++++++++++++++--------- 1 file changed, 167 insertions(+), 48 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index d05792c56d..94deff34cd 100644 =2D-- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -67,13 +67,75 @@ (define-module (gnu packages chemistry) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (guix build-system cmake) + #:use-module (guix build-system copy) #:use-module (guix build-system gnu) #:use-module (guix build-system python)) +(define-public avogadro-molecules + (package + (name "avogadro-molecules") + (version "1.100") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openchemistry/molecules") + (commit "8a37883"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "00mfx0bwmqazbiklrvaijjd5n4wa5lp3z73291ihm78q0v9dzhl4")))= ) + (build-system copy-build-system) + (home-page "https://two.avogadro.cc/") + (synopsis "Common molecule fragments for visualization in Avogadro") + (description + "Common molecule fragments including a variety of organic functional= groups.") + (license license:bsd-3))) + +(define-public avogadro-crystals + (package + (name "avogadro-crystals") + (version "1.100") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openchemistry/crystals") + (commit "28404bd"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0kcz99q5nfl2v2qmm9cqnbb2c2qqzw79vsnv557i7x64bxsxrw1m")))= ) + (build-system copy-build-system) + (home-page "https://two.avogadro.cc/") + (synopsis + "Crystallographic files of common materials, elements, oxides, for v= isualization in Avogadro") + (description + "Crystal structures of over 500 common materials, elements, oxides."= ) + (license license:bsd-3))) + +(define-public avogadro-fragments + (package + (name "avogadro-fragments") + (version "1.100") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openchemistry/fragments") + (commit "c4943b5"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "17l6qmkc25wb0nvic708l25fxiy89b3vfs0x5d40qcnn27bid32n")))= ) + (build-system copy-build-system) + (home-page "https://two.avogadro.cc/") + (synopsis "Molecular fragments for Avogadro") + (description + "Molecular fragments and inorganic ligands for rapidly building stru= ctures") + (license license:bsd-3))) + (define-public avogadrolibs (package (name "avogadrolibs") - (version "1.93.0") + (version "1.100.0") (source (origin (method git-fetch) @@ -81,28 +143,34 @@ (define-public avogadrolibs (url "https://github.com/OpenChemistry/avogadrolibs") (commit version))) (sha256 - (base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39")) + (base32 "1l9bp3ba8yx9mk2in5v375jzi1w4y7l1xl37xqv869810drgjffc")) (file-name (git-file-name name version)))) (build-system cmake-build-system) - (native-inputs - (list eigen - mmtf-cpp - googletest - pkg-config - pybind11)) - (inputs - (list glew - libarchive - libmsym - molequeue - python - spglib - qtbase-5)) - (arguments - '(#:configure-flags (list "-DENABLE_TESTING=3DON" - (string-append "-DSPGLIB_INCLUDE_DIR=3D" - (assoc-ref %build-inputs "s= pglib") - "/include")))) + (native-inputs (list eigen mmtf-cpp googletest pkg-config pybind11)) + (inputs (list glew + libarchive + libmsym + molequeue + python + spglib + qtbase-5 + qtsvg-5 + avogadro-molecules + avogadro-crystals + avogadro-fragments)) + (arguments + + (list + #:configure-flags + #~(list "-DENABLE_TESTING=3DON") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'symlink + (lambda _ + (begin + (symlink #$avogadro-molecules "../molecules") + (symlink #$avogadro-crystals "../crystals") + (symlink #$avogadro-fragments "../fragments"))))))) (home-page "https://www.openchemistry.org/projects/avogadro2/") (synopsis "Libraries for chemistry, bioinformatics, and related areas= ") (description @@ -111,10 +179,30 @@ (define-public avogadrolibs bioinformatics, materials science, and related areas.") (license license:bsd-3))) +(define-public avogadro-i18n + (package + (name "avogadro-i18n") + (version "1.100") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openchemistry/avogadro-i18n") + (commit "07bee85"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1vhjh0gilmm90269isrkvyzwwh1cj3bwcxls394psadw1a89mk14")))= ) + (build-system copy-build-system) + (home-page "https://two.avogadro.cc/") + (synopsis "Translations for Avogadro app and libraries") + (description + "Translations for the Avogadro app and libraries. Contributions and = edits are always welcome through Weblate.") + (license license:bsd-3))) + (define-public avogadro2 (package (name "avogadro2") - (version "1.93.0") + (version "1.100.0") (source (origin (method git-fetch) @@ -122,17 +210,30 @@ (define-public avogadro2 (url "https://github.com/OpenChemistry/avogadroapp") (commit version))) (sha256 - (base32 - "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7")) + (base32 "19cd5aqvcw6xj0x1kmzmxl0vrnbhk5ymnl9p2p4d9504ma5k6aim")) (file-name (git-file-name name version)))) (build-system cmake-build-system) - (native-inputs - (list eigen pkg-config)) - (inputs - (list avogadrolibs hdf5 molequeue qtbase-5)) + (native-inputs (list eigen pkg-config avogadro-i18n)) + (inputs (list avogadrolibs hdf5 molequeue qtbase-5 qtsvg-5)) ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag. (arguments - '(#:tests? #f)) + (list + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'symlink + (lambda _ + (begin + (symlink #$avogadro-i18n "../avogadro-i18n")))) + (add-after 'install 'wrap-program + (lambda _ + (wrap-program (string-append #$output "/bin/avogadro2") + (list "PATH" + 'suffix + (list (string-append #$openbabel "/bin"))) + (list "QT_PLUGIN_PATH" + 'suffix + (list (string-append #$qtsvg-5 "/lib/qt5/plugins"))= ))))))) (home-page "https://www.openchemistry.org/projects/avogadro2/") (synopsis "Advanced molecule editor") (description @@ -477,7 +578,7 @@ (define-public openbabel (define-public spglib (package (name "spglib") - (version "1.16.0") + (version "2.5.0") (source (origin (method git-fetch) @@ -485,26 +586,44 @@ (define-public spglib (url "https://github.com/spglib/spglib") (commit (string-append "v" version)))) (sha256 - (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws")) - (file-name (git-file-name name version)))) + (base32 "0x5igrqwx7r2shysmi9sqcjg4hpb7hba3ddlwg05z6c57a3ifbqc")) + (file-name (git-file-name name version)) + (modules '((guix build utils))) + (snippet #~(begin + (substitute* "CMakeLists.txt" + (("include\\(cmake/DynamicVersion.cmake\\)") + "") + (("dynamic_version.*") + "") + (("PROJECT_PREFIX.*") + "") + (("FALLBACK_VERSION.*") + "set (PROJECT_VERSION 2.5.0") + (("\\$\\{PROJECT_VERSION_FULL\\}") + "2.5.0") + (("\\$\\{GIT_COMMIT\\}") + "\"\"")) + (substitute* "src/CMakeLists.txt" + ((".*Spglib_GitHash.*") + "")))))) (build-system cmake-build-system) (arguments - '(#:test-target "check" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-header-install-dir - (lambda _ - ;; As of the writing of this package, CMake and GNU build sy= stems - ;; install the header to two different location. This patch= makes - ;; the CMake build system's choice of header directory compa= tible - ;; with the GNU build system's choice and with what avogadro= libs - ;; expects. - ;; See https://github.com/spglib/spglib/issues/75 and the re= levant - ;; part of https://github.com/OpenChemistry/avogadroapp/issu= es/97. - (substitute* "CMakeLists.txt" - (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir) - (string-append include-dir "/spglib"))) - #t))))) + '(#:tests? #f + #:configure-flags '("-DSPGLIB_WITH_TESTS=3DOFF") + #:phases (modify-phases %standard-phases + (add-after 'unpack 'patch-header-install-dir + (lambda _ + ;; As of the writing of this package, CMake and GNU= build systems + ;; install the header to two different location. T= his patch makes + ;; the CMake build system's choice of header direct= ory compatible + ;; with the GNU build system's choice and with what= avogadrolibs + ;; expects. + ;; See https://github.com/spglib/spglib/issues/75 a= nd the relevant + ;; part of https://github.com/OpenChemistry/avogadr= oapp/issues/97. + (substitute* "CMakeLists.txt" + (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir= ) + (string-append include-dir "/spglib"))) + #t))))) (home-page "https://spglib.github.io/spglib/index.html") (synopsis "Library for crystal symmetry search") (description "Spglib is a library for finding and handling crystal base-commit: 6036f1f3053bc9b4f0411b5e8aeaab5bd7f4ec7b =2D- 2.49.0 --GruEu5apdr3IAEeN-- From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 11 06:59:59 2025 Received: (at 76728) by debbugs.gnu.org; 11 Apr 2025 10:59:59 +0000 Received: from localhost ([127.0.0.1]:48993 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u3C74-0001aW-V9 for submit@debbugs.gnu.org; Fri, 11 Apr 2025 06:59:59 -0400 Received: from mira.cbaines.net ([212.71.252.8]:44176) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u3C71-0001aK-So for 76728@debbugs.gnu.org; Fri, 11 Apr 2025 06:59:56 -0400 Received: from localhost (unknown [IPv6:2a02:6b67:e390:8b00::1ce5]) by mira.cbaines.net (Postfix) with ESMTPSA id E04E227BC49; Fri, 11 Apr 2025 11:59:53 +0100 (BST) Received: from fang (localhost [127.0.0.1]) by localhost (OpenSMTPD) with ESMTP id 728bdef7; Fri, 11 Apr 2025 10:59:53 +0000 (UTC) From: Christopher Baines To: Jakob Kirsch via Guix-patches via Subject: Re: [bug#76728] [PATCH] gnu: avogadro2: update to 1.100.0 In-Reply-To: (Jakob Kirsch via Guix-patches via's message of "Thu, 10 Apr 2025 19:28:13 +0200") References: User-Agent: mu4e 1.12.9; emacs 29.4 Date: Fri, 11 Apr 2025 11:59:50 +0100 Message-ID: <87a58nx8t5.fsf@cbaines.net> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 76728 Cc: Jakob Kirsch , 76728@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --=-=-= Content-Type: text/plain Jakob Kirsch via Guix-patches via writes: > I fixed all the issues. It's good to merge now. > > [2. text/plain; 0001-gnu-avogadro2-update-to-1.100.0.patch]... It would be clearer to add each new package in a separate commit/patch rather than one big commit. Alternatively, I'm unsure if these new packages should exist, why would someone install avogadro-fragments for example? If they just exist to be symlinked in avogadrolibs, you can directly pass the origin records you're using as sources for the new packages as inputs. Regarding the origin changes to spglib, doing the substitute* operations as a package build phase is preferable if doing them on the source isn't required since that results in one less derivation. Thanks, Chris --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQKlBAEBCgCPFiEEPonu50WOcg2XVOCyXiijOwuE9XcFAmf49iZfFIAAAAAALgAo aXNzdWVyLWZwckBub3RhdGlvbnMub3BlbnBncC5maWZ0aGhvcnNlbWFuLm5ldDNF ODlFRUU3NDU4RTcyMEQ5NzU0RTBCMjVFMjhBMzNCMEI4NEY1NzcRHG1haWxAY2Jh aW5lcy5uZXQACgkQXiijOwuE9XcV3w//bd1IuutvgC6gslL4S1yfvQVYim5atLR2 tApYhTt0BAKqg0kZbD1fOf/rJMw1B6AhOY1i3zg09O+AQho7eL+dp0PhfjxRkSvu qbHvStOOB5hlRsac6xY7GTTmg9EKDMnbKJIpgUcSIX/V3t2arD+JDTkTd3zACkh1 WY1oFYq/dgs8LZkLqXoBZ8M5fgmugV7zCIGyBEP+qVMHLpvW8q7yb0OOpROp/xXK WP/6wCaELA5cxW4VmR/9iobzeEfXq8hz/qKyEbnUZcrGpbkbvlOj/16mGwWQqBtx RMZs7NumVkb2ObtPn1n3zm4HV57dnibBH/ckUQu6zG/BLxPsbc1fuQsTVqtg9jK3 QlUsWYViLS2sSEjsJ0p5PtruNqs8JlMBv0EL9kFtyZODYV48VBf9tOVVn/Y3HlPt c5z/G4gjx97PS7LIRYYq+AFvO614U5J6BW3+V8DqgA6vF+FpHym/OiKrHYZBWIdG akQYXCH10ZadWLXYTayc6cU+kaxoGvN+rndCjGaJY/0Gn2j5MUNjxa6VGfGYM8GB UnLjw85Oo4N68WS4IJljmgQEVSEmOOtjYNS3iqqcYsldKMkSH2N8yPGSrEKJ7rih IWYCZSEBd0FqvBGzkxyojHPlYtDrIvgiMX1Xf1qzDmNP0EBVTRzhXv9MGi4u1NxS 6wR1D4PaUwY= =4/jw -----END PGP SIGNATURE----- --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 11 08:56:07 2025 Received: (at 76728) by debbugs.gnu.org; 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Fri, 11 Apr 2025 14:55:59 +0200 Date: Fri, 11 Apr 2025 14:55:55 +0200 From: Jakob Kirsch To: Christopher Baines Subject: Re: [bug#76728] [PATCH] gnu: avogadro2: update to 1.100.0 Message-ID: References: <87a58nx8t5.fsf@cbaines.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <87a58nx8t5.fsf@cbaines.net> X-Provags-ID: V03:K1:a09FNfKV18/DZ93n1a4yBJ6Tz/gdid6eOM/dhqnsy5yvx+5L1PX e2yYbvruTxmIo5m5OOA2HFznD398UWg3j9HeqRGSvoPgYKrzPxrgf+OgI6C4NvKlzcHlHE3 TZFMAb4zoKUP0eOnSkwKImcfg9QQet/ojWjfSkgdvsIY/r3A9arlUk68zU7k4YVVU2/lyGT 09nvSP9HlOvQSei7KJuCA== X-Spam-Flag: NO UI-OutboundReport: notjunk:1;M01:P0:5g0X/8UnZ38=;Jdo66EL4owkCLYVYGNmhl3+YCTo YgbkMKZdbI5Adx5QsqBM0ZVV+f7p+Wpy5mV1+AYYdICxNKBKsomV902nesn4TV+wOmLHBOjOx K3EuTkJGjalt+w6uqIzW1i8899pL1BtcGdLrB2SDTBQpyZeSAPePnS5KZOwN7FZryPz+c+4vV OU+rH2WFTlphPH2KcMvXE0QnjYlkJKKc2SvfRIqG7yORfvbHYZUTm0q9Y1AilpSXtarBMcjEz 5wR1MybPI9ZCw9fgdc9rRZAzkUoCkkwtZX9iA/VKeTMrf4nuVzXLYXHIAxBWqFbYWGfk/8RNW yVYYROV+Xzc2bVI7oIn0joL4L5MllIsemILJJpBbzYUfyNEc5NYrFud4u5p0raXsQj99JJT/F qJHj6/8vZC8Q9MeyVwCNlMPb4QeT0lqWw0bfZ4Ma4tmtK1EqMEadnl7pJoWC9ik8FuySDHko7 FkrIugHRB+XKmImskm4/ij3FTIAARWAPiay0fRy4xT99DwRldG1NbiV6bDhVgYhtcFg0aXpzT yjNBkf9GLngtErMi80RrKdYkHtHtav5z+/hAn6wFpIU4YDOHKMxBRlhZa0l8Ubmr7bauH6S7B bzWQRFyXxFJfLYcrLh0GSN7ZKnGrRGyxQvhsO+lIokCn3laYDTGACoWCGuKw/eA91IdHz0VOb T5bEzY8SSHX3TlhkrBSFC2j3JvSrsJZcdyRPo4N8CWGNpnbM143F/VG+OeEJOXxUtVMrqJmUr r54Gmc8Qg5ekkUCdRfFzOA26Lrhv6bWe485GU3VhPvDq5gsOT+pfyYviQfjY3HV4+f/RDlPc0 zciyV2ZQFzzZfZbu0PHiAZeulSr3jsLiEOb/s1tRxyNaXMgwU5J0IXBRG91Vl4dHhZmo1BMSo cwM2bwMZmyJGhkkXS0Mk+mC91PqC17TiPcWthSRT/4p135Jj3cro/BDElpjjMy9u1FZEie1rr dP3Wpq+nbPXa+OeOrsIBjZqARfFZj9WpRwKTJEwr4v8/pBj5M6ge6vUw7B0y5bAzSsYyo6Tl7 ejJcD/yznpQbRr6cCOeu0w0ekB5W4mIoYbXr/T/+j+7eZNqFujM6M3YshXL4amVtMGPGshQf5 +Qny/Er/sHlm8LFEa5zan8LAiy0LPR371pWCHSehXB1Yh7qaz2uFt3knatFWQbL6iTd4733HG oUWe+QHIA/jZShnqNo1Zm3YRLyicmU2MBZ/NL4CsKq7F+k4Uha0Xwmmm3VvHRBEVaW5P6ZEpz noj7Sv5hjLDJWljVZYq2Tix7No1Msf8M6xbD2lxkM7eDrN6M5oByzI34Ni8IcrGSE7IS+wpn6 IArYZL1wzemqbyC/jxN0kHt7ySwO5gMf6Q1HqVSB0ISrjEKSX2a3IO3mKgmEAKw+fpb5XXD+g pHfwl6nE0eX9HvtAOXPkkKCrtmD5+gTG4Kqc6C8rwYOmURA9rQQB9Jr9Ko+N4ANIvIGqiPbV+ dMmi7ffy7wSrCnYYinBFQx9mO9nChJ4BWHMcj8L9pg4vcgm47k+STK8dp/UtJNGWklj+PaD9a ja0YU1EcC+p8PTp+sqTb+Od3jezlerEMDhFpiarSJloasTdIxwsLQOTX5NBpAFrYYatLpADuR rvhkKWD4pY8WuCats83Zgd8E3E5j8ymXtYE/gXpspsVIXzMkN6eptgvvN3Enhd2HJt0g7h4H/ heqzdaaJs5RH6vC2/TFYAd4gjQe368bg95sI41qZPWHi9BIckyKqWJMdTQHp3m3DU4n842AXd YThqJBnP/s8a7eBhEFyCsX96yQ/JClJHzz2OUGowdyMrTEAL6V64obD/Ebejr7RJAAOkAcf95 F75phpJ0KT6YxLJn6oUn9c4nBbNwP37mW6AGyJEwuN1TQpK40N0/A6+gg6/u7h1bfokq5oQYN PoO536KkQc2s5jDnT/66q4u8P00TbrC+euHjnyIFikBZpKUrpsarV41EmZ0yUjHHv61TnQiUc Hjz847SGbO+xO57flX2CfxzdYktRjKwR0IkdtfxSCg/qzfcOrXG3vqhdiO4TG+jmPs/R2Cia3 /fVpsH2sdg+dWnHJj+DiPlXbdAm15yRLXLiOCZ5Tp8wsdHpGt/zzDSD60Uql5Upjpw2zkIYwC 98Bd1k/ETozNUFC5BxNo+jSZ+7lWYqLcwMPQIdxeh46DLUZosY5Qy8OdzQT5wk4FzzrdiCRQb WbyBqH3bNnPaD1GiM6HeJvWkt21MynZjh74ETpTKzzXj7Tg69Hh39+vGZVKeRe/d0XlCQpQgP oEpDCuiDzLInY6mfZAm13DPONUE0iOWTmM1iLEaIdCg9+d3nrK4wBO1WiiUZSlBgK4z4P9ssO kOhfrnD7BYHI6hdv2fLyH8BGxWQOBo6ik5egLL7aGaISp39monCfCN/9rq+VTe+IwHKk/Azok TmdEcdLGupV8fdZswA51FRPXMzlxF2Toegbq2JZZA/ORTeF2z44vSnmLtR17THNj7h1xpT8ae UyDD1VdsMzrqKpcr4DG+2/UGCU/TLwbXKlLv9UMkEALGL6sK4lFu1QryPlBoFMt+M21QqpshX 6QNu7jqoMcc2FF43YDNFEf2M7Rw03Ql+GCH3kZSFyGqM1sHA07AvsX44r7tX0BwM/55VhK9iW JqAG9SBKr0gNRdtb2eTl0g5iEiymY70OIh5QvXGrZ44zuK8bFw5zmC3zrkFb5OZTrx6hIITS6 hIFuLcjlgrb716fqKD5Q3m24Am2/3tR/oomGQlicarHHsArPFXQyxi/z3f7WNITj6GI/VYpIf MBmyYK945ULU9l9c4aMe82uyHf0p4MJStGkSlp1AA5aCGJcnA+MZshCyao2GZN1EnLJz/zL15 GPYST7luVeelry7CDCC9ARX5CA9eicYFWvSkL2Duks0LZYBboq6iePr4dF1Upj6vbEOkNMSOy /9W+pkuIGxNrbUWoNegi+qL9RT9qzcdIKqECHtYvpptZU2cMXBdyGVtwy5VscP7ntEhuvgAeM l4bE0qEh0g== X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 76728 Cc: 76728@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) Yeah makes sense, I'll change the things and send a patch. 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Fri, 11 Apr 2025 15:37:19 +0200 Date: Fri, 11 Apr 2025 15:37:17 +0200 From: Jakob Kirsch To: 76728@debbugs.gnu.org Subject: New patch series Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="/XY3sKa7Me8Yqnwc" Content-Disposition: inline X-Provags-ID: V03:K1:AQCqLnzsjGuIyxba1XrIp2Ndt/K1xWmeVeiwxqOUeK/CX0SxM01 iZg76/L7kM/8IVQJ8/3HeY683sxei54IPN3Jnz7K70P+2lE7NDWboTJZB9jOTeZa4UxSktQ SPD//x5qE4es1tOIbdBl3TjkomdSzkbHvepjbPtqaCABygioaJU/Y/6QJeKrDQz0pa2wDPs jFEL1dbWMpx3EMaTnYStg== X-Spam-Flag: NO UI-OutboundReport: notjunk:1;M01:P0:cnGcq33d+uI=;By4SVYd87DoYKGzlph78uJ5sR+M 0ECooL2WXthR3XKgbVE3YvbxaqeCrxerlHngZAymgDYWy4filAU7IliubSrCz50h+tUrvB69I eJ2KTCNA/Id4r9nbUvQV1vbPItI8MJx4/ml4RjnB2cjX+gIQugplqMelH7+7YKUSRZ0bfQ4rv DE5BCThIzf5qjbaudPbMrQpJtWQjmOP+JVPi2F0iZ85J0VekbURtSpNdTWHBtJ7NzCKjX8hGQ hlqyJt3BV9fsZl8K33iPbZeY0eIouaicABSYL5lkRiE/8XAb9DFQKcebzZYwcal2+bwuTH6Gc 7yJyrrVxDWytqwEG0DVXqu0sgRlJw2eSTb8i0w4ajy1CfLH2h7UhgOzBPxaJsTL4QKAmwJieO 08DsSLV2SM5lF0+7rJa+gcnwUGeQQqzZqprVfuBVKAcZxs5ZJcrxQY55ln/yWGxSuXr4MZgbl SGlIJQb8LV64woTmwLT2FqxzVFjnJxn2vbip0cQed/OoZDhm2TGosqLxktFyaU9Gb99jT2k4g QHdsaXwuf8xJSPjN+ukEDNFD6gd4nZZoSGYdtxORkhmDJiDkKSDgwyQNo4HWK2MnKnBvdWqs8 QQsE3DtaI1W65XAnbW+BFePQi735zV8Fwt2qoHQcTvxLYzKX501gSYXkyBHbQQ+iHllk1qckq ZhExrOqlgqbF9aDlfNBYalSpF2zp+dNQQXpSf2HYcwIAGHNmm4unFxs7Q6V2EMuvianFrs8nx 2jC/eLeo8MDBUNnbNRmphJjO9gr8P1XnL1w9thhFIKfyE4BR8+4+FL8hSJCKsbsv9HpSGR7Ka wr44A6T0OGnH2S2QsFKw+NKFwicz5bVr6+ugKJZBu6mr4kntYF+s47Vh2o321rGIN4APRouxd vaJtsI4Augczty/juOnm4z/qkN/FOSODWCpHuqjWEnkEQUKtPgOprmHG9z2CeR0JncRQy0Dct RHouW4fAbsoHOw2vpa7WrM/RRcJ9Ay39ivLXIAjxjN28LN3nS9BIQa+YWIjkO0tYPFFBIg2mU py4DAkNe3ElU7yLIOdKMm1QAExXy9LgmFrTxbnY+qVMUgzuzB+Mq4OOGcxho8gH97OWNias/+ uqdACV17L1oh7iDbAP8kXZYnBdXmkMv/UEd0LzJI+LmvZTc28CxcWb2OfkMUO9zf3EzE09zCw ZpsbR1wDS63wcEF9GzA2/Tx/wXdY8fEmfZMfdBmzwUycVzc+Bnto9ZPp/MAG6x61Nj4SIsNI6 wlx/cCTNHoPX5aPFkcJL0JGSxenXcBe0LoY9RbPl1Wlkc4B1Pyz8WZF+y//+r9spHaz5LhBZh xoII6K+cSI6M0T0AFj7lHqxV/q4zEg0tDtL13IXeTQ09IdMQWkjezFh+if/6HhTb+slHaNg4H jhy+aEeM+IJQR0iGFmJvAgbi+3IiNEyKDRken355Yx8vb3GOu6g1aj189axGXPHtRqnszlfzB VGrtxvCGxtZcTmzwcX1teR5UwXoKJOnCTFvy8QZgY69c9zpIvv7NeiBv9iFfbi5xzqAXqJvd2 skpiasdjHmDBtzpnbdQZOZ7ohATViwDsbLu8YueOvaegeolLnO4LxZTVQJSovEo5KfBYmzNMi z6k52MJSDVGo0/ypnfDErOuC2M929uoETKJXejK5kr4hjjkDh8Nbepql61jIGmUDc4NiFHNHE jAKmU2UF/qGO7MWxSBFP4dX90Gj02CgWc26Xti3B6CfGIkRaHxdx7IvHs1af9T+kSTuk2IoX1 JRzTk9OcrkqVBtLKUmTkRPEh+T64PXXGmgMCQys+5sEUzvqWj+VoqsuObXaT/063d21rDFD7N npKIIcMafNMGRV6NhuQqSdhlHQ9sdqIVpZwTcSHp91ELjH94jeHDOIYnbc81CTm4o2dfdgIpb bKkLf/cXsbMyyty09evxvzJOdrL/e3jvQ/g5wL6IRAtfsEoLs+SQVztZzBhWg7v1VrYRnJD+q NlpX6vNWIemuLrkZJ+ngidtt/gxmnw42I14ufUIrmSkFiKUtIX0BQxTRwwxkJ2l1C8xqzEgS6 bDzIXFpV5SKayRGwXXOsmdte+U/Z7R2oUtX0cHhk8fPMFyhOqjNSEKuDLl0oLIZUV+3mlVSDB CuIPIGw0x5ErIZiPkYO0AzjJqoHqK+/Xzs00MoL1+6bB0zFOiseiDbcAiRq9oSpMd9oklNpwg BQ08IunaSodk25bX96InxZweiXn8PzlpSkV3rdVjTFV+QmZ8KiM4boZqZsOsjj9E7JQb+Z7Ds SkNxwXoluwbeUDyd5vExhtUKIWXAuLapedEeTeQa0CfJ/VpOxYpdfI5K1NG7tZCDrbg6BQK01 2VTkleWGup7Zf0OvXJDR3Db2LH6ILQgVI9eO7VpLjzNZSOQRCe86eiKr9v0MHOrbVS03oa2/4 SfHed1t7vG3OOpVP2NesXEn8PUM7tkfiwv6G957G+X00fWehwfKIvz+DCrQKucY70aCWRQHQ4 lrk5ROkgj8Zsu9aN+BTvxsdo+xhoWf9CpwBlppcvzb6rJrwX9DcNEKbk0Uf74yg1673CWTtaY fL+lTqUTLHI1Tkrs3MlpXZtpcZtHE2krqHZkXfcgEaoFEMcsuhkgu4kaEqdHwlH+CrYfxCqv8 1v327qkb/fQpOr3QXjjIot9ibglVJKQguB/ANQmI2GTvMrpJLxGBOr31yuEPQVLAZbpQ0NnDM rUl4M2GGpOn7wyBPFl3Qghtu3YCIpSRNoX0hieoPmu9Wi8YciWd2apwI+WQn2bojUjCqxvgLE F4bXPSWZzmdl1dp38pivOhvo4YswCXsM1tvGM7jfbwkC5C5VKxaWrFfMuigAKbz8r8X5wtVpv dSK5KDffKFtwGYMW3+HfNAaTa89AipS+3UKUVlI8pLwVZFOLM5+8LfY8xb26Y9eL0NGcfZJjs V4TUlcwyUpJBA/a+Ewl126U2Z0m1UxbT1TO3OmTBKtJnuwfCfCw6FcZNwcFWTur0NsuIGrzqm FDEnvpj403Lw+Yx4bTOrOeEawB2j8scuj0JZHYj705IoYcczm7MahmFv1yFGQsQrTsGDEd6O6 1iR5U5I931sPj77RNSzELrNgt8KXRtKwd5zA3jtYIA5Seh+qe4IjUZDkJAK+KKkbHhP2ch4jz gxZCHPlRdQ6WDyX61Y9osbm026Uj5PAYHX X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 76728 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) --/XY3sKa7Me8Yqnwc Content-Type: text/plain; charset=us-ascii Content-Disposition: inline I've implemented the changes and split it into 3 commits (spglib, avogadrolibs, avogadro2). --/XY3sKa7Me8Yqnwc Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename=0001-gnu-spglib-Update-to-2.5.0.patch Content-Transfer-Encoding: quoted-printable =46rom 244dc62d6ce1787dccd45be54a17354f33ba0782 Mon Sep 17 00:00:00 2001 Message-ID: <244dc62d6ce1787dccd45be54a17354f33ba0782.1744378594.git.jakob= .kirsch@web.de> From: Jakob Kirsch Date: Fri, 11 Apr 2025 15:33:14 +0200 Subject: [PATCH 1/3] gnu: spglib: Update to 2.5.0. * gnu/packages/chemistry.scm (spglib): Update to 2.5.0. Change-Id: Ia05bb8e2f012fcf4c576db8a6e5d2f8b153493ff =2D-- gnu/packages/chemistry.scm | 52 +++++++++++++++++++++++++------------- 1 file changed, 34 insertions(+), 18 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index d05792c56d..9ef1f72b62 100644 =2D-- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -477,7 +477,7 @@ (define-public openbabel (define-public spglib (package (name "spglib") - (version "1.16.0") + (version "2.5.0") (source (origin (method git-fetch) @@ -485,26 +485,42 @@ (define-public spglib (url "https://github.com/spglib/spglib") (commit (string-append "v" version)))) (sha256 - (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws")) + (base32 "0x5igrqwx7r2shysmi9sqcjg4hpb7hba3ddlwg05z6c57a3ifbqc")) (file-name (git-file-name name version)))) (build-system cmake-build-system) (arguments - '(#:test-target "check" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-header-install-dir - (lambda _ - ;; As of the writing of this package, CMake and GNU build sy= stems - ;; install the header to two different location. This patch= makes - ;; the CMake build system's choice of header directory compa= tible - ;; with the GNU build system's choice and with what avogadro= libs - ;; expects. - ;; See https://github.com/spglib/spglib/issues/75 and the re= levant - ;; part of https://github.com/OpenChemistry/avogadroapp/issu= es/97. - (substitute* "CMakeLists.txt" - (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir) - (string-append include-dir "/spglib"))) - #t))))) + '(#:tests? #f + #:configure-flags '("-DSPGLIB_WITH_TESTS=3DOFF") + #:phases (modify-phases %standard-phases + (add-before 'configure 'patch-files (lambda _ (substitu= te* "CMakeLists.txt" + (("include\\(cmake/DynamicVersion.cmake\\)") + "") + (("dynamic_version.*") + "") + (("PROJECT_PREFIX.*") + "") + (("FALLBACK_VERSION.*") + "set (PROJECT_VERSION 2.5.0") + (("\\$\\{PROJECT_VERSION_FULL\\}") + "2.5.0") + (("\\$\\{GIT_COMMIT\\}") + "\"\"")) + (substitute* "src/CMakeLists.txt" + ((".*Spglib_GitHash.*") + "")))) + (add-after 'unpack 'patch-header-install-dir + (lambda _ + ;; As of the writing of this package, CMake and GNU= build systems + ;; install the header to two different location. T= his patch makes + ;; the CMake build system's choice of header direct= ory compatible + ;; with the GNU build system's choice and with what= avogadrolibs + ;; expects. + ;; See https://github.com/spglib/spglib/issues/75 a= nd the relevant + ;; part of https://github.com/OpenChemistry/avogadr= oapp/issues/97. + (substitute* "CMakeLists.txt" + (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir= ) + (string-append include-dir "/spglib"))) + #t))))) (home-page "https://spglib.github.io/spglib/index.html") (synopsis "Library for crystal symmetry search") (description "Spglib is a library for finding and handling crystal base-commit: 172e9a1aa1ee2ef3e557cf46a11e451aa7982983 =2D- 2.49.0 --/XY3sKa7Me8Yqnwc Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename=0002-gnu-avogadrolibs-Update-to-1.100.0.patch Content-Transfer-Encoding: quoted-printable =46rom c8899e851eb85df748f1cab13de88ab2c746fc3a Mon Sep 17 00:00:00 2001 Message-ID: In-Reply-To: <244dc62d6ce1787dccd45be54a17354f33ba0782.1744378594.git.jako= b.kirsch@web.de> References: <244dc62d6ce1787dccd45be54a17354f33ba0782.1744378594.git.jakob= .kirsch@web.de> From: Jakob Kirsch Date: Fri, 11 Apr 2025 15:34:12 +0200 Subject: [PATCH 2/3] gnu: avogadrolibs: Update to 1.100.0. * gnu/packages/chemistry.scm (avogadrolibs): Update to 1.100.0. [inputs]: Add qtsvg-5, avogadro-molecules, avogadro-crystals, avogadro-fra= gments. Change-Id: I16693aff5f986f062c4683ca9b64bb2f7321a9d1 =2D-- gnu/packages/chemistry.scm | 70 +++++++++++++++++++++++++++----------- 1 file changed, 50 insertions(+), 20 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 9ef1f72b62..c597d4736a 100644 =2D-- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -73,7 +73,7 @@ (define-module (gnu packages chemistry) (define-public avogadrolibs (package (name "avogadrolibs") - (version "1.93.0") + (version "1.100.0") (source (origin (method git-fetch) @@ -81,28 +81,58 @@ (define-public avogadrolibs (url "https://github.com/OpenChemistry/avogadrolibs") (commit version))) (sha256 - (base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39")) + (base32 "1l9bp3ba8yx9mk2in5v375jzi1w4y7l1xl37xqv869810drgjffc")) (file-name (git-file-name name version)))) (build-system cmake-build-system) - (native-inputs - (list eigen - mmtf-cpp - googletest - pkg-config - pybind11)) - (inputs - (list glew - libarchive - libmsym - molequeue - python - spglib - qtbase-5)) + (native-inputs (list eigen mmtf-cpp googletest pkg-config pybind11)) + (inputs `(("glew" ,glew) + ("libarchive" ,libarchive) + ("libmsym" ,libmsym) + ("molequeue" ,molequeue) + ("python" ,python) + ("spglib" ,spglib) + ("qtbase-5" ,qtbase-5) + ("qtsvg-5" ,qtsvg-5) + ("avogadro-molecules" ,(origin + (method git-fetch) + (uri (git-reference (url + "https://gith= ub.com/openchemistry/molecules") + (commit "8a378= 83"))) + (file-name (git-file-name name ver= sion)) + (sha256 (base32 + "00mfx0bwmqazbiklrvaijjd5= n4wa5lp3z73291ihm78q0v9dzhl4")))) + ("avogadro-crystals" ,(origin + (method git-fetch) + (uri (git-reference (url + "https://githu= b.com/openchemistry/crystals") + (commit "28404b= d"))) + (file-name (git-file-name name vers= ion)) + (sha256 (base32 + "0kcz99q5nfl2v2qmm9cqnbb2c= 2qqzw79vsnv557i7x64bxsxrw1m")))) + ("avogadro-fragments" ,(origin + (method git-fetch) + (uri (git-reference (url + "https://gith= ub.com/openchemistry/fragments") + (commit "c4943= b5"))) + (file-name (git-file-name name ver= sion)) + (sha256 (base32 + "17l6qmkc25wb0nvic708l25f= xiy89b3vfs0x5d40qcnn27bid32n")))))) (arguments - '(#:configure-flags (list "-DENABLE_TESTING=3DON" - (string-append "-DSPGLIB_INCLUDE_DIR=3D" - (assoc-ref %build-inputs "s= pglib") - "/include")))) + + (list + #:configure-flags + #~(list "-DENABLE_TESTING=3DON") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'symlink + (lambda _ + (begin + (symlink (assoc-ref %build-inputs "avogadro-molecules") + "../molecules") + (symlink (assoc-ref %build-inputs "avogadro-crystals") + "../crystals") + (symlink (assoc-ref %build-inputs "avogadro-fragments") + "../fragments"))))))) (home-page "https://www.openchemistry.org/projects/avogadro2/") (synopsis "Libraries for chemistry, bioinformatics, and related areas= ") (description =2D- 2.49.0 --/XY3sKa7Me8Yqnwc Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename=0003-gnu-avogadro2-Update-to-1.100.0.patch Content-Transfer-Encoding: quoted-printable =46rom 585bdca7666a4cc52e32baa11cdddec04cdd9552 Mon Sep 17 00:00:00 2001 Message-ID: <585bdca7666a4cc52e32baa11cdddec04cdd9552.1744378594.git.jakob= .kirsch@web.de> In-Reply-To: <244dc62d6ce1787dccd45be54a17354f33ba0782.1744378594.git.jako= b.kirsch@web.de> References: <244dc62d6ce1787dccd45be54a17354f33ba0782.1744378594.git.jakob= .kirsch@web.de> From: Jakob Kirsch Date: Fri, 11 Apr 2025 15:35:46 +0200 Subject: [PATCH 3/3] gnu: avogadro2: Update to 1.100.0. * gnu/packages/chemistry.scm (avogadro2): Update to 1.100.0. [inputs]: Add qtsvg-5. [native-inputs]: Add avogadro-i18n. Change-Id: I9577e27021ca449426d7506589939c050a5d0cfb =2D-- gnu/packages/chemistry.scm | 40 ++++++++++++++++++++++++++++++-------- 1 file changed, 32 insertions(+), 8 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index c597d4736a..d44bfd2334 100644 =2D-- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -144,7 +144,7 @@ (define-public avogadrolibs (define-public avogadro2 (package (name "avogadro2") - (version "1.93.0") + (version "1.100.0") (source (origin (method git-fetch) @@ -152,17 +152,41 @@ (define-public avogadro2 (url "https://github.com/OpenChemistry/avogadroapp") (commit version))) (sha256 - (base32 - "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7")) + (base32 "19cd5aqvcw6xj0x1kmzmxl0vrnbhk5ymnl9p2p4d9504ma5k6aim")) (file-name (git-file-name name version)))) (build-system cmake-build-system) - (native-inputs - (list eigen pkg-config)) - (inputs - (list avogadrolibs hdf5 molequeue qtbase-5)) + (native-inputs `(("eigen" ,eigen) + ("pkg-config" ,pkg-config) + ("avogadro-i18n" ,(origin + (method git-fetch) + (uri (git-reference (url + "https://gi= thub.com/openchemistry/avogadro-i18n") + (commit "07b= ee85"))) + (file-name (git-file-name name + versio= n)) + (sha256 (base32 + "1vhjh0gilmm90269isrkvy= zwwh1cj3bwcxls394psadw1a89mk14")))))) + (inputs (list avogadrolibs hdf5 molequeue qtbase-5 qtsvg-5)) ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag. (arguments - '(#:tests? #f)) + (list + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'symlink + (lambda _ + (begin + (symlink (assoc-ref %build-inputs "avogadro-i18n") + "../avogadro-i18n")))) + (add-after 'install 'wrap-program + (lambda _ + (wrap-program (string-append #$output "/bin/avogadro2") + (list "PATH" + 'suffix + (list (string-append #$openbabel "/bin"))) + (list "QT_PLUGIN_PATH" + 'suffix + (list (string-append #$qtsvg-5 "/lib/qt5/plugins"))= ))))))) (home-page "https://www.openchemistry.org/projects/avogadro2/") (synopsis "Advanced molecule editor") (description =2D- 2.49.0 --/XY3sKa7Me8Yqnwc-- From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 14 09:31:00 2025 Received: (at 76728) by debbugs.gnu.org; 14 Apr 2025 13:31:01 +0000 Received: from localhost ([127.0.0.1]:46414 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u4Jts-0004Oa-I3 for submit@debbugs.gnu.org; Mon, 14 Apr 2025 09:31:00 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:46450) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u4Jtp-0004OD-QX for 76728@debbugs.gnu.org; Mon, 14 Apr 2025 09:30:58 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 1E5C8393; Mon, 14 Apr 2025 15:30:50 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id It-gZX4481v8; Mon, 14 Apr 2025 15:30:49 +0200 (CEST) Received: from jurong (nat-eduroam-36-gw-01-bso.bordeaux.inria.fr [194.199.1.36]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 083C5BF; Mon, 14 Apr 2025 15:30:47 +0200 (CEST) Date: Mon, 14 Apr 2025 15:30:46 +0200 From: Andreas Enge To: Jakob Kirsch Subject: Re: PATCH v2 Message-ID: References: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: X-Rspamd-Queue-Id: 1E5C8393 X-Spamd-Result: default: False [5.40 / 15.00]; SPAM_FLAG(5.00)[]; NEURAL_SPAM(3.00)[1.000]; BAYES_HAM(-3.00)[99.99%]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; FREEMAIL_TO(0.00)[web.de]; ARC_NA(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCPT_COUNT_FIVE(0.00)[5]; FROM_HAS_DN(0.00)[]; FREEMAIL_ENVRCPT(0.00)[gmail.com,web.de]; TO_DN_SOME(0.00)[]; FREEMAIL_CC(0.00)[debbugs.gnu.org,posteo.net,gmail.com,cbaines.net] X-Spamd-Bar: +++++ X-Rspamd-Action: greylist X-Rspamd-Server: hera X-Spam-Level: ***** X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 76728 Cc: bavier@posteo.net, sharlatanus@gmail.com, Christopher Baines , 76728@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hello, in your spglib update, you disable the tests; this requires to add a comment to the source. In this case it is annoying since you update a package with tests to one without; is this on purpose or an oversight? Andreas From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 15 13:18:10 2025 Received: (at 76728) by debbugs.gnu.org; 15 Apr 2025 17:18:11 +0000 Received: from localhost ([127.0.0.1]:54817 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u4jvC-0003nI-JO for submit@debbugs.gnu.org; Tue, 15 Apr 2025 13:18:10 -0400 Received: from mout.web.de ([212.227.15.14]:51143) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u4jv7-0003ky-8P for 76728@debbugs.gnu.org; Tue, 15 Apr 2025 13:18:03 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=web.de; s=s29768273; t=1744737475; x=1745342275; i=jakob.kirsch@web.de; bh=nVQFPHHBYBTR6tsu94Jo1K/MrVsPrHI8raZdENvonMM=; h=X-UI-Sender-Class:Date:From:To:Subject:Message-ID:MIME-Version: Content-Type:cc:content-transfer-encoding:content-type:date:from: message-id:mime-version:reply-to:subject:to; b=igOXwGMjz1tiSdaj8Afn8J9YMUxlCDGRJSUKEowDehXHMxHZs35+CpY9/XgvBXr6 jy3ibx0IzJn9mwPBJ97a+7I3qF6ZmjMBJzYQHmypuA6SfGjLqz5jNrRbokbsChU2B 0o0CWqwWpPn3SSgkXH/JZDiYQ+jBs07a+D6O1N0sahvZWccP8ZonFpATLSh3ggMtW BQS45/pC7q/P/yacZV93JdfsO3iyLaEAqVn7a7Bsr83dTM8TpBRQS406P8XbPfZFb 2FATfYE0vh98VGG3lx89T9sIwA1FT2b03qvAQ73mP8+FuFdRgDSe1+XhP+KJhNk4E +P+ft8KnGmpRsE7b2A== X-UI-Sender-Class: 814a7b36-bfc1-4dae-8640-3722d8ec6cd6 Received: from kernelpanicroom ([134.19.24.167]) by smtp.web.de (mrweb006 [213.165.67.108]) with ESMTPSA (Nemesis) id 1N7gbW-1t08yv06Fu-00x8D9 for <76728@debbugs.gnu.org>; Tue, 15 Apr 2025 19:17:55 +0200 Date: Tue, 15 Apr 2025 19:17:53 +0200 From: Jakob Kirsch To: 76728@debbugs.gnu.org Subject: Patches with comments Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="FU7YrpezzA7M7F6M" Content-Disposition: inline X-Provags-ID: V03:K1:khDX+HSO4XA4AI0KIbAS/orCOYtnm3cU+6TJ7KFsrizJg0k2ikj OQyQXqgYbJbky7WoDm4WbprHKUazpq545NHaZKW4RJvCzHc8O+ARAQHEUmiH1BffIgnasYz tqjyH1xzkLawNoHAtR4ci2tZTrPckw1qhc+Sg4z9DCz46BpIuHJEeYXq1037Gniwd/vi0D5 bWS+7skq+LTD5ZheUAfag== X-Spam-Flag: NO UI-OutboundReport: notjunk:1;M01:P0:1T1zO3k3ybo=;epofOhq33RazY3GTm+kqS7+GQ4v W4IqsE5GIV4roOLnhSzxGcbUDpUV2dgH+G0HD4WQemPeRseCETaSu9dptq+ouh9/Tn+c9of6x MuJEhWrUVjjNVnmvY8mqsII/A5QKU9h6nQZ+9r9CG5HkH+FuRRMk4S+PDNIiX6o9uOaZcHB0K coYBZ1IsAIXLOSluwTZrAgQ+QnOJHgb1D86M4M9sTcyro/ySJoZwiQaDMOqi+H15ghLkGJupw Tp41eI3nkCMB83l89XZLEtNbREwlMTrKRKg1AHaqmawDDpZ7rLKwZfG8Tut5daeQGIF2JjKOh dGRV/k7vA0lngq0VcJis8yoHksyrFtLF+iZJ6HqdPRMVxB4TMNGg+9wzXFPRbF+u4dh7Fje6+ MV4En449/vRBTtdJ69tbFthqIoaaydIwcAUf8dPf/npGdoZoJtxwKG9fSCgYOLSaqEv2HbWR3 FfJmQel04BiSNIPIq7NLnfAe5jl91vc3iCnNB6QolEF/V65DJXiNiWuSk6zMVvBYdDAg2nKeW nDdCicdcNO9HzOsMar8hrdD20wR4rzbKwdfbDDhTKXh8nOgRkaR7O3n7zQaW3Y+K2J/OkfYwl rbdLlBYFv/DQpk8P7L4uj10id+qwWpguo9Cckm4jDVstaEF2uvlqzh0958bZnGeRR7L3Hip96 nWnAC3xGT9473EEmToZa6lidKrerOZnThD83ytYRBQtGxv/EPLmNdQNOOVBlN9VuXMgbwXZkM XvCRDOjMho/OhC0hcCzQFb9ZSlu8GgzuypswNHglJQGIvBW1QJFlCFUC33dqsrOmHhD7YmYvf yz89iCa7Iv30CQBjd63aqh+T0beVdb4HUhytI2e/pvm2OSwsRdJKce/17NxxHbHQMHpz22EYS Gmnm1Q3MH97S4AHWQMh0Tt+00EPpZZJUe65zeTNcVwB9UXLuLPXQyh8BKL74NEBLZovaVUoEi HxYcsRP6oDJWml22jvYzXBnnHtZpJrMNTYmt/PjL5SokADLRtKj57+l627vtBCQc5DiuTtvYx 0/he+otZB2GCHoeYOspDvNu3yrNpkGhQY/HF87V+0Mw84XasrhKIemGp5BOjz8ePdmchEFyUp muLbZJ6CwJHnuu3ak4eosKzvxRJcjpnbRD0EQV1I0iM/FSGvlLM6XSnCm8xkgOpGBe2GM7Y1S /XS+FX1vQB+fbUyeCMLpbI+OHqCxPSzQuBSHyVhdiTdORvJQl38uq0q/PpGI8vb3es/BXOh39 b1fuB+BsViggONJ3GaKw7939kzgpqGFiW7XbeKdYqyKpzwQfkjKlgAgozmqIkPTSI6AOwzHfV bIsTs7CR7iQeOn6JrTFf9GPp0GB/e0YsuTdbghdAkrEN9c4GRtTFZ6cECs8OjRuSnw0OHpPZF hvnbNJA3uk6o+QSqK5qlvLO20f9UYTPAQkjQMi6lxYyFwh05BUdAVy+OJ1Dcxqi6g6BMu8MBS vtUQWvx+sMlMX/jEnnfsw1SH1ZRkSZBKpiaoiTj/rUNCCAUe4q8sUDkln028P0lmn0gfVLm0f cfIK2cfDBc8wzmVDEodVFM2mnOd4TICi4eHEOvVnAZZyo+EaGW5CRTUkaQoMX3b1JwvSKAnKl LcGocLdxup0BKkL6BWCorIPektZVPgmSZS6MC9cMAToVy6YCDsA/VIbOBAGaLqH8mVnL1lTqD O4aDVD27Sg+nSnwSDHoBG31eJT6Qh5CHkPf4j16sfuhSQ0ZSDqiZltqp+qcJBW7uH8RcrFnfi coL0mJ96TPGRTkhA68l0BJsdIycRCcFva5x+tuFjdSBZ8Q4tmuZedbLL+ZIA0Jx5y7/7CcGPj kKBk6u4VkcYDSTXAT4pJnKbZFUtQ0lwnXe4LYLXC6p1PuXEILjVLL8dHVVT1IgcunHCcmwEmJ iWMvh000nfyhUo9dMYpVPiZOcap8pZ3I8kK6gxPuTMvZsbqw1DNHZG8m6YjGzB25cTbcpqBH8 SmYFDJZwPzOYsh9wD+3JfX72UEnluGmRM9OVhF6PJiRVYi4jvtSLopLWmPX6xKQhR1xv65Rqv WuxO4W9byZ4UyMt00f6rv3j1lPDwkB2eTyz2mRveXdYaZMxqzXkL5aSLeQtqYOL1h6/PHhAw1 veI05qmodHeStN6TnSrJeZ/3gibU6YdzmALapTJ4u9hWq0YiY6S5KsGTed3Xj+v0G3Pkb98NW jy3muZLshb/Qw5HBl4S7tBPxvDTLv4ALqsPUex9TXFJyV9uDm1yZTE8uVisPz04ZIoSRgICCy BZA4zHvSSGnMDPHgXb79VjJMMLDW4IavmSJLN2Lb2K+OSiVKGWwDbQt7h4Km9drT/uCb3Z0Xk LZzlLULg6xH/e0jNesnNrsYqerItvBoKTlRCAbCa+Agad37zznqSDv6hOlP5q2gthOIB8ScsE Q4DhayirvqEb8qbxY5rBJbDV9AZZ7bQkbI6TfnRcnsXR05um09PknCzfAZoTCwwmaqVIdfPWA hqxUhQPXCgtlStg62Ws5M2PAfv26aZtowN3uwL9GoggmpUqLuwrHN0jM3D6QHtwbzni3yrOGK MlRwVZCJXZH9P544jaidGWq9nzQwna7ji9aJcIq/nf4ZzsUzPQ345i3U0mDsWmgLXCUq4GPbA jSwE9elCiYId2EeqLSfSonp6hGiqn/l0STbGDUVmi7Sh/2gxwNLf9UK4tFS3as0RnYnJCuRVH H0GpXbhd5noVWtCeXiq2tKdhODopITNzZHxxAgrt8q5s8ecTIbz7ar0fmxlj/CyrRgmNUHmO7 5WR30rvmJAcJlyOT5OwATjq+dV8/XpuKptecQPzQnAzBRD5NJPZsoySDVDKMqAnDtW4EM5xJp vGuqLd4YDsbJSqj07y1GYLyVzeV5Urkk7nQdGJFYJWdythNY7W/VwVqQl7nYTtUlvAhedq+nN R4/XogfOrry8PYY/CRwx+7agHYyW9Wg/51ufd8QhdaxZHZCWH8H6EN+dM6lKrGX5Q0b5/QlfI kJCt497r6aJoOJjzpjwba6C5+O9VLKbxv1bDaMLX4Vx759iyRSq1/nROqQRXw7Wij+8K2Ni8e 3HK9mHQfsxLQ4zLFaza+JcKkX+9pQYkLoTiM2L5avDHSkinJ3Ie97gvrE8rPw+LYcu6j/Oi9M 3fZNNIdzLKQy5L3XgG9/uv/3KAD/rIF3et X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 76728 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) --FU7YrpezzA7M7F6M Content-Type: text/plain; charset=us-ascii Content-Disposition: inline spglib wants to clone a repository using git while building the tests and that won't work so I've added a comment (spglib works with avogadro2 that is its only dependant). --FU7YrpezzA7M7F6M Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename=0001-gnu-spglib-Update-to-2.5.0.patch Content-Transfer-Encoding: quoted-printable =46rom 2a366ea2a876dff391fad94fb9a7ca34b0b92850 Mon Sep 17 00:00:00 2001 Message-ID: <2a366ea2a876dff391fad94fb9a7ca34b0b92850.1744737318.git.jakob= .kirsch@web.de> From: Jakob Kirsch Date: Fri, 11 Apr 2025 15:33:14 +0200 Subject: [PATCH 1/3] gnu: spglib: Update to 2.5.0. * gnu/packages/chemistry.scm (spglib): Update to 2.5.0. Change-Id: Ia05bb8e2f012fcf4c576db8a6e5d2f8b153493ff =2D-- gnu/packages/chemistry.scm | 52 +++++++++++++++++++++++++------------- 1 file changed, 34 insertions(+), 18 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index d05792c56d..4e186e017c 100644 =2D-- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -477,7 +477,7 @@ (define-public openbabel (define-public spglib (package (name "spglib") - (version "1.16.0") + (version "2.5.0") (source (origin (method git-fetch) @@ -485,26 +485,42 @@ (define-public spglib (url "https://github.com/spglib/spglib") (commit (string-append "v" version)))) (sha256 - (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws")) + (base32 "0x5igrqwx7r2shysmi9sqcjg4hpb7hba3ddlwg05z6c57a3ifbqc")) (file-name (git-file-name name version)))) (build-system cmake-build-system) (arguments - '(#:test-target "check" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-header-install-dir - (lambda _ - ;; As of the writing of this package, CMake and GNU build sy= stems - ;; install the header to two different location. This patch= makes - ;; the CMake build system's choice of header directory compa= tible - ;; with the GNU build system's choice and with what avogadro= libs - ;; expects. - ;; See https://github.com/spglib/spglib/issues/75 and the re= levant - ;; part of https://github.com/OpenChemistry/avogadroapp/issu= es/97. - (substitute* "CMakeLists.txt" - (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir) - (string-append include-dir "/spglib"))) - #t))))) + '(#:tests? #f ; tests want to clone a git repository, which won't wo= rk + #:configure-flags '("-DSPGLIB_WITH_TESTS=3DOFF") + #:phases (modify-phases %standard-phases + (add-before 'configure 'patch-files (lambda _ (substitu= te* "CMakeLists.txt" + (("include\\(cmake/DynamicVersion.cmake\\)") + "") + (("dynamic_version.*") + "") + (("PROJECT_PREFIX.*") + "") + (("FALLBACK_VERSION.*") + "set (PROJECT_VERSION 2.5.0") + (("\\$\\{PROJECT_VERSION_FULL\\}") + "2.5.0") + (("\\$\\{GIT_COMMIT\\}") + "\"\"")) + (substitute* "src/CMakeLists.txt" + ((".*Spglib_GitHash.*") + "")))) + (add-after 'unpack 'patch-header-install-dir + (lambda _ + ;; As of the writing of this package, CMake and GNU= build systems + ;; install the header to two different location. T= his patch makes + ;; the CMake build system's choice of header direct= ory compatible + ;; with the GNU build system's choice and with what= avogadrolibs + ;; expects. + ;; See https://github.com/spglib/spglib/issues/75 a= nd the relevant + ;; part of https://github.com/OpenChemistry/avogadr= oapp/issues/97. + (substitute* "CMakeLists.txt" + (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir= ) + (string-append include-dir "/spglib"))) + #t))))) (home-page "https://spglib.github.io/spglib/index.html") (synopsis "Library for crystal symmetry search") (description "Spglib is a library for finding and handling crystal base-commit: 12a6dd40a7b88454cc8a8c930c22681fcee5b1ea =2D-=20 2.49.0 --FU7YrpezzA7M7F6M Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename=0002-gnu-avogadrolibs-Update-to-1.100.0.patch Content-Transfer-Encoding: quoted-printable =46rom 9aebea9956d9ca92da16664fae8835bf11d04eaf Mon Sep 17 00:00:00 2001 Message-ID: <9aebea9956d9ca92da16664fae8835bf11d04eaf.1744737318.git.jakob= .kirsch@web.de> In-Reply-To: <2a366ea2a876dff391fad94fb9a7ca34b0b92850.1744737318.git.jako= b.kirsch@web.de> References: <2a366ea2a876dff391fad94fb9a7ca34b0b92850.1744737318.git.jakob= .kirsch@web.de> From: Jakob Kirsch Date: Fri, 11 Apr 2025 15:34:12 +0200 Subject: [PATCH 2/3] gnu: avogadrolibs: Update to 1.100.0. * gnu/packages/chemistry.scm (avogadrolibs): Update to 1.100.0. [inputs]: Add qtsvg-5, avogadro-molecules, avogadro-crystals, avogadro-fra= gments. Change-Id: I16693aff5f986f062c4683ca9b64bb2f7321a9d1 =2D-- gnu/packages/chemistry.scm | 70 +++++++++++++++++++++++++++----------- 1 file changed, 50 insertions(+), 20 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 4e186e017c..80b55dd7d1 100644 =2D-- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -73,7 +73,7 @@ (define-module (gnu packages chemistry) (define-public avogadrolibs (package (name "avogadrolibs") - (version "1.93.0") + (version "1.100.0") (source (origin (method git-fetch) @@ -81,28 +81,58 @@ (define-public avogadrolibs (url "https://github.com/OpenChemistry/avogadrolibs") (commit version))) (sha256 - (base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39")) + (base32 "1l9bp3ba8yx9mk2in5v375jzi1w4y7l1xl37xqv869810drgjffc")) (file-name (git-file-name name version)))) (build-system cmake-build-system) - (native-inputs - (list eigen - mmtf-cpp - googletest - pkg-config - pybind11)) - (inputs - (list glew - libarchive - libmsym - molequeue - python - spglib - qtbase-5)) + (native-inputs (list eigen mmtf-cpp googletest pkg-config pybind11)) + (inputs `(("glew" ,glew) + ("libarchive" ,libarchive) + ("libmsym" ,libmsym) + ("molequeue" ,molequeue) + ("python" ,python) + ("spglib" ,spglib) + ("qtbase-5" ,qtbase-5) + ("qtsvg-5" ,qtsvg-5) + ("avogadro-molecules" ,(origin + (method git-fetch) + (uri (git-reference (url + "https://gith= ub.com/openchemistry/molecules") + (commit "8a378= 83"))) + (file-name (git-file-name name ver= sion)) + (sha256 (base32 + "00mfx0bwmqazbiklrvaijjd5= n4wa5lp3z73291ihm78q0v9dzhl4")))) + ("avogadro-crystals" ,(origin + (method git-fetch) + (uri (git-reference (url + "https://githu= b.com/openchemistry/crystals") + (commit "28404b= d"))) + (file-name (git-file-name name vers= ion)) + (sha256 (base32 + "0kcz99q5nfl2v2qmm9cqnbb2c= 2qqzw79vsnv557i7x64bxsxrw1m")))) + ("avogadro-fragments" ,(origin + (method git-fetch) + (uri (git-reference (url + "https://gith= ub.com/openchemistry/fragments") + (commit "c4943= b5"))) + (file-name (git-file-name name ver= sion)) + (sha256 (base32 + "17l6qmkc25wb0nvic708l25f= xiy89b3vfs0x5d40qcnn27bid32n")))))) (arguments - '(#:configure-flags (list "-DENABLE_TESTING=3DON" - (string-append "-DSPGLIB_INCLUDE_DIR=3D" - (assoc-ref %build-inputs "s= pglib") - "/include")))) + + (list + #:configure-flags + #~(list "-DENABLE_TESTING=3DON") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'symlink + (lambda _ + (begin + (symlink (assoc-ref %build-inputs "avogadro-molecules") + "../molecules") + (symlink (assoc-ref %build-inputs "avogadro-crystals") + "../crystals") + (symlink (assoc-ref %build-inputs "avogadro-fragments") + "../fragments"))))))) (home-page "https://www.openchemistry.org/projects/avogadro2/") (synopsis "Libraries for chemistry, bioinformatics, and related areas= ") (description =2D-=20 2.49.0 --FU7YrpezzA7M7F6M Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename=0003-gnu-avogadro2-Update-to-1.100.0.patch Content-Transfer-Encoding: quoted-printable =46rom 5589fafd03ed7dd461e9353e09a5ee2d1645ce69 Mon Sep 17 00:00:00 2001 Message-ID: <5589fafd03ed7dd461e9353e09a5ee2d1645ce69.1744737318.git.jakob= .kirsch@web.de> In-Reply-To: <2a366ea2a876dff391fad94fb9a7ca34b0b92850.1744737318.git.jako= b.kirsch@web.de> References: <2a366ea2a876dff391fad94fb9a7ca34b0b92850.1744737318.git.jakob= .kirsch@web.de> From: Jakob Kirsch Date: Fri, 11 Apr 2025 15:35:46 +0200 Subject: [PATCH 3/3] gnu: avogadro2: Update to 1.100.0. * gnu/packages/chemistry.scm (avogadro2): Update to 1.100.0. [inputs]: Add qtsvg-5. [native-inputs]: Add avogadro-i18n. Change-Id: I9577e27021ca449426d7506589939c050a5d0cfb =2D-- gnu/packages/chemistry.scm | 40 ++++++++++++++++++++++++++++++-------- 1 file changed, 32 insertions(+), 8 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 80b55dd7d1..f01dd757e1 100644 =2D-- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -144,7 +144,7 @@ (define-public avogadrolibs (define-public avogadro2 (package (name "avogadro2") - (version "1.93.0") + (version "1.100.0") (source (origin (method git-fetch) @@ -152,17 +152,41 @@ (define-public avogadro2 (url "https://github.com/OpenChemistry/avogadroapp") (commit version))) (sha256 - (base32 - "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7")) + (base32 "19cd5aqvcw6xj0x1kmzmxl0vrnbhk5ymnl9p2p4d9504ma5k6aim")) (file-name (git-file-name name version)))) (build-system cmake-build-system) - (native-inputs - (list eigen pkg-config)) - (inputs - (list avogadrolibs hdf5 molequeue qtbase-5)) + (native-inputs `(("eigen" ,eigen) + ("pkg-config" ,pkg-config) + ("avogadro-i18n" ,(origin + (method git-fetch) + (uri (git-reference (url + "https://gi= thub.com/openchemistry/avogadro-i18n") + (commit "07b= ee85"))) + (file-name (git-file-name name + versio= n)) + (sha256 (base32 + "1vhjh0gilmm90269isrkvy= zwwh1cj3bwcxls394psadw1a89mk14")))))) + (inputs (list avogadrolibs hdf5 molequeue qtbase-5 qtsvg-5)) ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag. (arguments - '(#:tests? #f)) + (list + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'symlink + (lambda _ + (begin + (symlink (assoc-ref %build-inputs "avogadro-i18n") + "../avogadro-i18n")))) + (add-after 'install 'wrap-program + (lambda _ + (wrap-program (string-append #$output "/bin/avogadro2") + (list "PATH" + 'suffix + (list (string-append #$openbabel "/bin"))) + (list "QT_PLUGIN_PATH" + 'suffix + (list (string-append #$qtsvg-5 "/lib/qt5/plugins"))= ))))))) (home-page "https://www.openchemistry.org/projects/avogadro2/") (synopsis "Advanced molecule editor") (description =2D-=20 2.49.0 --FU7YrpezzA7M7F6M-- From debbugs-submit-bounces@debbugs.gnu.org Sun May 18 07:02:41 2025 Received: (at 76728) by debbugs.gnu.org; 18 May 2025 11:02:41 +0000 Received: from localhost ([127.0.0.1]:55873 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uGbmy-0003I3-Ml for submit@debbugs.gnu.org; Sun, 18 May 2025 07:02:40 -0400 Received: from zebra.cherry.relay.mailchannels.net ([23.83.223.195]:35185) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uGbmw-0003Ht-4G for 76728@debbugs.gnu.org; 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The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: Hi, As a user of the avogadro2 program, would you say that a regular user would use openbabel as an extra program anyway? (or be aware of it) That is, is openbabel "inside the avogadro2 black box" or "outside the avogadro2 black box as its own black box" ? Content analysis details: (3.6 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 0.0 RCVD_IN_VALIDITY_CERTIFIED_BLOCKED RBL: ADMINISTRATOR NOTICE: The query to Validity was blocked. See https://knowledge.validity.com/hc/en-us/articles/20961730681243 for more information. [23.83.223.195 listed in sa-trusted.bondedsender.org] 0.0 RCVD_IN_VALIDITY_RPBL_BLOCKED RBL: ADMINISTRATOR NOTICE: The query to Validity was blocked. See https://knowledge.validity.com/hc/en-us/articles/20961730681243 for more information. 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The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: Hi, As a user of the avogadro2 program, would you say that a regular user would use openbabel as an extra program anyway? (or be aware of it) That is, is openbabel "inside the avogadro2 black box" or "outside the avogadro2 black box as its own black box" ? Content analysis details: (2.6 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 0.0 RCVD_IN_VALIDITY_CERTIFIED_BLOCKED RBL: ADMINISTRATOR NOTICE: The query to Validity was blocked. See https://knowledge.validity.com/hc/en-us/articles/20961730681243 for more information. [23.83.223.195 listed in sa-accredit.habeas.com] 3.6 RCVD_IN_SBL_CSS RBL: Received via a relay in Spamhaus SBL-CSS [84.115.226.251 listed in zen.spamhaus.org] -0.0 RCVD_IN_DNSWL_NONE RBL: Sender listed at https://www.dnswl.org/, no trust [23.83.223.195 listed in list.dnswl.org] 0.0 RCVD_IN_MSPIKE_H4 RBL: Very Good reputation (+4) [23.83.223.195 listed in wl.mailspike.net] 0.0 RCVD_IN_VALIDITY_RPBL_BLOCKED RBL: ADMINISTRATOR NOTICE: The query to Validity was blocked. See https://knowledge.validity.com/hc/en-us/articles/20961730681243 for more information. [23.83.223.195 listed in bl.score.senderscore.com] -0.0 SPF_PASS SPF: sender matches SPF record 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record 0.0 RCVD_IN_MSPIKE_WL Mailspike good senders -1.0 MAILING_LIST_MULTI Multiple indicators imply a widely-seen list manager Hi, As a user of the avogadro2 program, would you say that a regular user would use openbabel as an extra program anyway? (or be aware of it) That is, is openbabel "inside the avogadro2 black box" or "outside the avogadro2 black box as its own black box" ? For what it's worth, I've checked the avogadro2 source code, and they set the variable OBABEL_EXE to where the program "obabel" is. After that, they set BABEL_DIR relative to that, and finally they set ob_plugins to refer to some .so files within $BABEL_DIR/lib, and then: install_qt5_executable(${exe} "${plugins}" "${ob_plugins}" "${dirs}" "") So for me as not-a-user-of-avogadro2 it seems like openbabel should be inside the black box of avogadro2? What do you think? From debbugs-submit-bounces@debbugs.gnu.org Mon Jun 02 08:57:48 2025 Received: (at 76728-done) by debbugs.gnu.org; 2 Jun 2025 12:57:49 +0000 Received: from localhost ([127.0.0.1]:50140 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uM4jc-0005fp-LT for submit@debbugs.gnu.org; Mon, 02 Jun 2025 08:57:48 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:34278) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uM4jZ-0005fO-Vd for 76728-done@debbugs.gnu.org; Mon, 02 Jun 2025 08:57:46 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 2C43CC39; Mon, 2 Jun 2025 14:57:38 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id 2dhFJt5UJzCu; Mon, 2 Jun 2025 14:57:37 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 46DCE1AA; Mon, 2 Jun 2025 14:57:36 +0200 (CEST) Date: Mon, 2 Jun 2025 14:57:34 +0200 From: Andreas Enge To: Danny Milosavljevic Subject: Re: [bug#76728] [PATCH] gnu: avogadro2: fix open babel input Message-ID: References: <87plg6tc5a.fsf@friendly-machines.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <87plg6tc5a.fsf@friendly-machines.com> X-Rspamd-Server: hera X-Rspamd-Queue-Id: 2C43CC39 X-Spamd-Result: default: False [-4.78 / 15.00]; NEURAL_HAM(-2.96)[-0.986]; BAYES_HAM(-2.22)[96.28%]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; ARC_NA(0.00)[]; TO_DN_SOME(0.00)[]; FREEMAIL_ENVRCPT(0.00)[web.de]; RCVD_VIA_SMTP_AUTH(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; FREEMAIL_CC(0.00)[web.de,debbugs.gnu.org] X-Rspamd-Action: no action X-Spamd-Bar: ---- X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 76728-done Cc: Jakob Kirsch , 76728-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hello, this somehow does not pass the hurdle of being picked up by QA, so I ended up going through the patches manually. I have added openbabel as an explicit input to avogadro2; I am surprised it can be referenced without this... Danny, I do not quite get what you mean with the "blackbox" comment. I have pushed the patches as they are; please feel free to open a new issue to improve the packages or correct anything I may have broken. Thanks, Andreas