From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 16 07:38:59 2022 Received: (at submit) by debbugs.gnu.org; 16 Mar 2022 11:38:59 +0000 Received: from localhost ([127.0.0.1]:50394 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nURzR-0008PA-NN for submit@debbugs.gnu.org; Wed, 16 Mar 2022 07:38:59 -0400 Received: from lists.gnu.org ([209.51.188.17]:41934) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nURzP-0008P2-Fr for submit@debbugs.gnu.org; Wed, 16 Mar 2022 07:38:52 -0400 Received: from eggs.gnu.org ([209.51.188.92]:41180) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nURzP-00045N-0n for guix-patches@gnu.org; Wed, 16 Mar 2022 07:38:51 -0400 Received: from flashner.co.il ([178.62.234.194]:38838) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nURzI-0000rf-M5 for guix-patches@gnu.org; Wed, 16 Mar 2022 07:38:46 -0400 Received: from localhost (unknown [31.210.181.186]) by flashner.co.il (Postfix) with ESMTPSA id 182F2400B7; Wed, 16 Mar 2022 11:38:11 +0000 (UTC) From: Efraim Flashner To: guix-patches@gnu.org Subject: [PATCH] gnu: Add python-scikit-allel. Date: Wed, 16 Mar 2022 13:37:35 +0200 Message-Id: <856daf639aa2f6dee3f09e242179ba2fccaf22d8.1647430620.git.efraim@flashner.co.il> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=178.62.234.194; envelope-from=efraim@flashner.co.il; helo=flashner.co.il X-Spam_score_int: -18 X-Spam_score: -1.9 X-Spam_bar: - X-Spam_report: (-1.9 / 5.0 requ) BAYES_00=-1.9, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: Efraim Flashner 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: -2.3 (--) * gnu/packages/python-science.scm (python-scikit-allel): New variable. --- gnu/packages/python-science.scm | 51 ++++++++++++++++++++++++++++++++- 1 file changed, 50 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index e3e874dac2..bb25386094 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015 Federico Beffa ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2016 Hartmut Goebel -;;; Copyright © 2016 Efraim Flashner +;;; Copyright © 2016, 2022 Efraim Flashner ;;; Copyright © 2016-2020, 2022 Marius Bakke ;;; Copyright © 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2021 Maxim Cournoyer @@ -35,6 +35,7 @@ (define-module (gnu packages python-science) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) #:use-module (gnu packages base) + #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages cpp) @@ -307,6 +308,54 @@ (define-public python-scikit-image "Scikit-image is a collection of algorithms for image processing.") (license license:bsd-3))) +(define-public python-scikit-allel + (package + (name "python-scikit-allel") + (version "1.3.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scikit-allel" version)) + (sha256 + (base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "setup.py" "build_ext" "--inplace") + (invoke "python" "-m" "pytest" "-v" "allel" + ;; AttributeError: 'Dataset' object has no attribute 'asstr' + "-k" (string-append + "not test_vcf_to_hdf5" + " and not test_vcf_to_hdf5_exclude" + " and not test_vcf_to_hdf5_rename" + " and not test_vcf_to_hdf5_group" + " and not test_vcf_to_hdf5_ann")))))))) + (propagated-inputs + (list python-dask + python-numpy)) + (native-inputs + (list python-cython + ;; The following are all needed for the tests + htslib + python-h5py + python-hmmlearn + python-numexpr + python-pytest + python-scipy + python-setuptools-scm + python-zarr)) + (home-page "https://github.com/cggh/scikit-allel") + (synopsis "Explore and analyze genetic variation data") + (description + "This package provides utilities for exploratory analysis of large scale +genetic variation data.") + (license license:expat))) + (define-public python-sgp4 (package (name "python-sgp4") base-commit: 53d986215f629f461651e3181af0689ef5f418a2 -- 2.34.0 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 18 09:57:17 2022 Received: (at 54419) by debbugs.gnu.org; 18 Mar 2022 13:57:17 +0000 Received: from localhost ([127.0.0.1]:57999 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nVD6S-0003mz-RR for submit@debbugs.gnu.org; Fri, 18 Mar 2022 09:57:17 -0400 Received: from eggs.gnu.org ([209.51.188.92]:47620) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nVD6R-0003mm-Ji for 54419@debbugs.gnu.org; Fri, 18 Mar 2022 09:57:15 -0400 Received: from [2001:470:142:3::e] (port=48892 helo=fencepost.gnu.org) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nVD6L-00088g-B9; Fri, 18 Mar 2022 09:57:09 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:In-Reply-To:Date:References:Subject:To: From; bh=b9eTNlri1KkzloznPT8jdb4p+k5NCywmhKXTr8p9o7Y=; b=EHipD56aF7ny10RkgDB+ 8octrprPGXrwtVPqu+7pVjfdwCao29jXZquBXfSiWlxRu5Y8zUIGRZ/lEnzTrerHJ9jNXIUbmkNSy baEki+jkJzqQ3rRtO1N9W5Be+8k3/0URem4r5J+0ARoyGWApUUM4dwJMG9tj1vz5hsRXjmUhUtSSe sLcbqDKuqZt8qWuzuCh4a3oLDYwMoEldxaOsozRx/nnDsE7XvagDoFo2W34jEjwNDac26vnvrzhKJ i5RbRpp3r1P2/UyXvnZLXLrTgWyJMMcDwmAqWnvLjmPr5TCj5UDr0vx8K/TVnZa/ZMBs8SG8PmlA3 qgoPwxlk7dK91A==; Received: from 91-160-117-201.subs.proxad.net ([91.160.117.201]:54604 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nVD6K-0001Y5-Ns; Fri, 18 Mar 2022 09:57:08 -0400 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Efraim Flashner Subject: Re: bug#54419: [PATCH] gnu: Add python-scikit-allel. References: <856daf639aa2f6dee3f09e242179ba2fccaf22d8.1647430620.git.efraim@flashner.co.il> Date: Fri, 18 Mar 2022 14:57:07 +0100 In-Reply-To: <856daf639aa2f6dee3f09e242179ba2fccaf22d8.1647430620.git.efraim@flashner.co.il> (Efraim Flashner's message of "Wed, 16 Mar 2022 13:37:35 +0200") Message-ID: <87ilsbqs7g.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 54419 Cc: 54419@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: -3.3 (---) Hello, Efraim Flashner skribis: > * gnu/packages/python-science.scm (python-scikit-allel): New variable. LGTM! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 18 10:00:56 2022 Received: (at 54419-done) by debbugs.gnu.org; 18 Mar 2022 14:00:56 +0000 Received: from localhost ([127.0.0.1]:58017 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nVDA0-0003vf-2W for submit@debbugs.gnu.org; Fri, 18 Mar 2022 10:00:56 -0400 Received: from flashner.co.il ([178.62.234.194]:59846) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nVD9x-0003vQ-Gu for 54419-done@debbugs.gnu.org; Fri, 18 Mar 2022 10:00:54 -0400 Received: from localhost (unknown [31.210.181.186]) by flashner.co.il (Postfix) with ESMTPSA id 41168401E4; Fri, 18 Mar 2022 14:00:47 +0000 (UTC) Date: Fri, 18 Mar 2022 16:00:01 +0200 From: Efraim Flashner To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: bug#54419: [PATCH] gnu: Add python-scikit-allel. Message-ID: Mail-Followup-To: Efraim Flashner , Ludovic =?utf-8?Q?Court=C3=A8s?= , 54419-done@debbugs.gnu.org References: <856daf639aa2f6dee3f09e242179ba2fccaf22d8.1647430620.git.efraim@flashner.co.il> <87ilsbqs7g.fsf@gnu.org> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="E2MDAvPMYtDbVZDU" Content-Disposition: inline In-Reply-To: <87ilsbqs7g.fsf@gnu.org> 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-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 54419-done Cc: 54419-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 (-) --E2MDAvPMYtDbVZDU Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Thanks for the review. Patch pushed! --=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 --E2MDAvPMYtDbVZDU Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCgAdFiEEoov0DD5VE3JmLRT3Qarn3Mo9g1EFAmI0kGEACgkQQarn3Mo9 g1EoYQ/7BkZ3ETTF4MM/6BD7SjAHrjJXNfqnRIXyq7GPwY+jhxRict1VPA2HQAFR ZZABlb9agS22M7FdNmfmJbCL3dN7G7fZpe5PU7IGgTqkDlsE8smp+donKiCRVKWn p5ZksUATfYrI12dmsTVKIk/t5xGQXjt//h1EXYGlh4zwt2QmHA5vRUz/2RXUcVNd 0x5Sw98AnaTPp0rzkeFnmhfVjFgJKQsI+ie/A0s+HJvscP4kbZ08ZUypCcn8u9MN WfSFZtx1TRwVDmt7dJeZed7u6Cl9QRWTJXBF9taejZLyDEp9wgii8fKIM7ZmtUUm q5aaSlu1YsEBUVMyZbowNJyWo9hpfknpAGd+IkzOlb+m8kF4hbMDKygcaOaXvQki 6MRzu4NBvtViqEGnEOn+IEg2SknexITFhlkLx4tAKwaNcuM0VakNY6ROR2MHcqOi c1M3BAImfggX7l9VcMmJoS9QECNhG2I78eX0BcCqs2KkLvDcQIYadRaagrGAWxjg qitCbW0u0Fzy4jnbWvgcsCSt+Ibg3JVklOo54sZ0gIfIloZZtWb8T+7+m+zwM4yK RLJcouIrR4F4xAbnjZxZzowCtUtHxIZwzmLz4D15ZOwomg6DWh8t3FRZodag2gP5 XNdiwDCmXFc6dwGC/g9hZztB2TjWmfGw1C+YKGA55tcmc0eJJ5o= =21eL -----END PGP SIGNATURE----- --E2MDAvPMYtDbVZDU-- From unknown Sun Jun 15 08:45:04 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. 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