From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id oJ7MHNnNvWDfqQAAgWs5BA (envelope-from ) for ; Mon, 07 Jun 2021 09:42:17 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id YCQOGNnNvWB2MwAA1q6Kng (envelope-from ) for ; Mon, 07 Jun 2021 07:42:17 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id AC0C613FAB for ; Mon, 7 Jun 2021 09:42:16 +0200 (CEST) Received: from localhost ([::1]:53090 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lq9tn-0002v9-Hi for larch@yhetil.org; Mon, 07 Jun 2021 03:42:15 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:43638) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lq9tb-0002gl-Cd for guix-patches@gnu.org; Mon, 07 Jun 2021 03:42:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:42838) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lq9tb-00033L-5t for guix-patches@gnu.org; Mon, 07 Jun 2021 03:42:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lq9tb-00010E-4J for guix-patches@gnu.org; Mon, 07 Jun 2021 03:42:03 -0400 Subject: bug#48862: [PATCH] gnu: python-hic2cool: Update to 0.8.3. Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-To: guix-patches@gnu.org Resent-Date: Mon, 07 Jun 2021 07:42:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: cc-closed 48862 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Cc: rekado@elephly.net, 48862-done@debbugs.gnu.org Received: via spool by 48862-done@debbugs.gnu.org id=D48862.16230516973794 (code D ref 48862); Mon, 07 Jun 2021 07:42:02 +0000 Received: (at 48862-done) by debbugs.gnu.org; 7 Jun 2021 07:41:37 +0000 Received: from localhost ([127.0.0.1]:54378 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lq9tA-0000z8-Un for submit@debbugs.gnu.org; Mon, 07 Jun 2021 03:41:37 -0400 Received: from flashner.co.il ([178.62.234.194]:39408) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lq9t8-0000yu-Qk for 48862-done@debbugs.gnu.org; Mon, 07 Jun 2021 03:41:35 -0400 Received: from localhost (unknown [31.210.177.125]) by flashner.co.il (Postfix) with ESMTPSA id 13C9140845; Mon, 7 Jun 2021 07:41:28 +0000 (UTC) Date: Mon, 7 Jun 2021 10:40:08 +0300 From: Efraim Flashner Message-ID: Mail-Followup-To: Efraim Flashner , =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= , 48862-done@debbugs.gnu.org, rekado@elephly.net References: <20210606051407.6535-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="DqbXn2Mu7kyn+vwH" Content-Disposition: inline In-Reply-To: <20210606051407.6535-1-madalinionel.patrascu@mdc-berlin.de> X-PGP-Key-ID: 0x41AAE7DCCA3D8351 X-PGP-Key: https://flashner.co.il/~efraim/efraim_flashner.asc X-PGP-Fingerprint: A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1623051737; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type:resent-to:resent-from:resent-sender: resent-message-id:in-reply-to:in-reply-to:references:references: list-id:list-help:list-unsubscribe:list-subscribe:list-post; bh=Oe5oshFJls+ur/btCZKe2cPkLS6p6cq15Squd+oIPVI=; b=e+LtiMaQwNpw+dXxgrekUbvs2i9eK9mLpADvvCRKDas4I5Rs8l+5xkzUGrIxUeMzjC/Q/0 uyy9Uh4Q6TpRY/y1GR5wnLygDd5oeUPQUN6jSw1UNHZRI26LiRfLPsOLYy9l6Gqu5EeSpg ax5WiG5r5pRANw7g3T52Kek2deu1Cho6UkDwfXxJwmfZ9Z8f6u9uzD2FdXt/8K4rU/X8Qn 9kkjAFcq8uOPfoKM3u+Z/KuowwmhVg/iZqQVEocqRfqP007eknYHJ/GnLRCmorrVjgH7Lm vqVsr7Jm4Qq4mveAde4nXvX4xhjvaBC5MYlFHonidThyehbmZlryKks4sW6sbA== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1623051737; a=rsa-sha256; cv=none; b=WA0wMT6+Cikv0QKxB/QQe3eihW8Gj4P2ki3Wb8ls8hVyi8GaQH0EVSOP9JY8/jUSnhAsZw 5xeC6afgIaagAu6agH6WWUn7UXKQ3QK1qNGGsRwWPoPycj3Rc5Jc2uhfD9BBOidwDrCCiq lOWw9zWI5RCx617aODelRAttXmEfS5znA3vb/4NqE1+TiZibSyvEvhzhl2pVyUoMNdE2/g xpRoGC2azaSV5BrEAUihbBGASEEJBhcZcVYK0cnjZgmG2WbviyN3TlkViPndcLOWormkzL /lhm7tgrD1R1FTuLwk9y+kyLsdtFfueBjqt07Nx8HS5aaMiXmIFESDxy0JN2EA== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=none; dmarc=none; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: -2.52 Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=none; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: AC0C613FAB X-Spam-Score: -2.52 X-Migadu-Scanner: scn1.migadu.com X-TUID: oyutQOQ5hd0Y --DqbXn2Mu7kyn+vwH Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable I made a few changes before pushing the patch. On Sun, Jun 06, 2021 at 07:14:07AM +0200, M=C4=83d=C4=83lin Ionel Patra=C8= =99cu wrote: > * gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3. I mentioned that the download changed to use git-fetch, the added phase and enabled tests, and the added inputs. > --- > gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++------ > 1 file changed, 22 insertions(+), 6 deletions(-) >=20 > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatic= s.scm > index dab097381a..66e69ff2c8 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -11892,18 +11892,34 @@ pyGenomeTracks can make plots with or without H= i-C data.") > (define-public python-hic2cool > (package > (name "python-hic2cool") > - (version "0.4.2") > + (version "0.8.3") > + ;; pypi sources do not contain the test_data directory and no test c= an be > + ;; run > (source > (origin > - (method url-fetch) > - (uri (pypi-uri "hic2cool" version)) > + (method git-fetch) > + (uri (git-reference > + (url "https://github.com/4dn-dcic/hic2cool") > + (commit version))) > + (file-name (git-file-name name version)) > (sha256 > (base32 > - "0xy6mhfns2lzib1kcr6419jjp6pmh0qx8z8na55lmiwn0ds8q9cl")))) > + "0dlnf0qfcp4jrc1nyya32a035c13xicyq16bwfnwhbb9s47mz7gl")))) > (build-system python-build-system) > - (arguments '(#:tests? #f)) ; no tests included > + (arguments > + `(#:phases > + (modify-phases %standard-phases > + ;;two of the test-data files need to be writable > + (add-after 'unpack 'patch-test-data > + (lambda* (#:key inputs outputs #:allow-other-keys) > + (chmod "test_data/hic2cool_0.4.2_single_res.cool" #o600) > + (chmod "test_data/hic2cool_0.7.0_multi_res.mcool" #o600))))= )) I changed this one to be 'lambda _' and I changed the chmods to make-file-writable. > (propagated-inputs > - `(("python-cooler" ,python-cooler))) > + `(("python-cooler" ,python-cooler) > + ("python-h5py" ,python-h5py) > + ("python-numpy" ,python-numpy) > + ("python-pandas" ,python-pandas) > + ("python-scipy" ,python-scipy))) > (home-page "https://github.com/4dn-dcic/hic2cool") > (synopsis "Converter for .hic and .cool files") > (description > --=20 > 2.31.1 >=20 >=20 >=20 >=20 --=20 Efraim Flashner =D7=90=D7=A4=D7=A8=D7=99=D7=9D = =D7=A4=D7=9C=D7=A9=D7=A0=D7=A8 GPG key =3D A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted --DqbXn2Mu7kyn+vwH Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCgAdFiEEoov0DD5VE3JmLRT3Qarn3Mo9g1EFAmC9zVgACgkQQarn3Mo9 g1H8ZBAAmzLQ0055EzTDCZ5W6Sr9uMx2ufas5+r7HWpIlQHN38t9rpSxkK/mtnqH yZvlC/ZPPMh2ZVAw6BJo8qw1nAZUuMU6LsCGOCYxMhPRn9xIRvfpWx8s3BQzY/2f kNNoGG5TMAiCai867sTIQ13fsBQmiDV7vYS8RnqOOIUHp8AQbn4Dlwn15ndD4UTR jRmt3DPkcrFhVB2T9ejuMbc788leu1YWgJS6unOaqKmGXPXK0CEDKx0rSzIZf0rC 16bItC41e1vZZlNy+6ptZOomuom8zfT1gLxeBQiPeHxhmuDuck3Z6VYwoExbgZy3 dnUjddGfKpRO5dejXmA6F5P8CTLuUk6DECkm+va7whsIwQe3SaEqI7zVyEpXcswF dJhl4AdMq9LZVhfb6TsaekO8Z3A6PjWCCZ7NuGRuJVSNBqmNASknrLkRBbSIKkN1 aEJLB4ZL0wQj9GT26zUj0jY8qZtOuyRJJC3qNf5gj52L6M14xhJHyKsUWzlD4yt8 Wa9JwuDp7fa+CnG2RULSMUXjB7rk6W1Ppo471LUxvkewS64VbCrjP4oBKvPyAjO2 k2Nokth4Y9DKNtzdubhtTCF4OZjmHrP4GtlP8brhz+4UTIxzq7oYWQveok3aKOly /FSXeHj6BjbyoMlLSVHIYVYCx12QjoN44NfK9IVFB8+Ix/YXzjM= =DLfN -----END PGP SIGNATURE----- --DqbXn2Mu7kyn+vwH--