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[127.0.0.1]) by director2.derp.mail-out.ovh.net (inspect_sender_mail_agent) with SMTP for <77400@debbugs.gnu.org>; Mon, 31 Mar 2025 06:19:15 +0000 (UTC) Received: from mta10.priv.ovhmail-u1.ea.mail.ovh.net (unknown [10.110.164.155]) by director2.derp.mail-out.ovh.net (Postfix) with ESMTPS id 4ZR1Dg53Bqzy9r; Mon, 31 Mar 2025 06:19:15 +0000 (UTC) Received: from ngraves.fr (unknown [10.1.6.1]) by mta10.priv.ovhmail-u1.ea.mail.ovh.net (Postfix) with ESMTPSA id 48C9CDA393B; Mon, 31 Mar 2025 06:19:15 +0000 (UTC) Authentication-Results: garm.ovh; auth=pass (GARM-102R00426cf6dd6-4c7b-43fc-a119-ac4fa4babda7, 87830A87949A0BA70EB5F3889DD10BC79FDA47E2) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 31 Mar 2025 08:18:40 +0200 Message-ID: <20250331061901.22670-12-ngraves@ngraves.fr> X-Mailer: git-send-email 2.49.0 In-Reply-To: <20250331061901.22670-1-ngraves@ngraves.fr> References: <20250331061901.22670-1-ngraves@ngraves.fr> MIME-Version: 1.0 X-Ovh-Tracer-Id: 3738832119011861218 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgddujeeludekucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepvdehleeiffehtedvlefhffffjeefgfduhfetkeevheeiteduiedugfekuedtheejnecuffhomhgrihhnpehgihhthhhusgdrtghomhenucfkphepuddvjedrtddrtddruddpledtrdelvddruddujedrudeggeenucevlhhushhtvghrufhiiigvpeefnecurfgrrhgrmhepihhnvghtpeduvdejrddtrddtrddupdhmrghilhhfrhhomhepnhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrpdhnsggprhgtphhtthhopedvpdhrtghpthhtohepjeejgedttdesuggvsggsuhhgshdrghhnuhdrohhrghdprhgtphhtthhopehnghhrrghvvghssehnghhrrghvvghsrdhfrhdpoffvtefjohhsthepmhhoheeivdgmpdhmohguvgepshhmthhpohhuth DKIM-Signature: a=rsa-sha256; bh=1YHI8DJ4wLg0HWjPT1ff4vy8tW2FqGy/jTu70STc5T8=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1743401956; v=1; b=cxerSLCr4M41DAr7rMOnbVQ44dVD1q0NnqzaKb5POD2H0OJksAJHG2fIZhX3p8mc9glT/jv4 DQq9WVIwVM+wBDQccnMd2N/pAKS0GvCSowvqAmUazdvoTbRkPJSUEO+oFBsrs75ChqO9aviJOAK nL9Ll9++tM82s1BDmZodwm82dAhADQOf0iUZrntdi8WCU60W0ZgAGxFAvy/vxkUmNFaLE6dsCZk g/aEfYpSChQ+M/uk3aLYQgjtKXH2KKIxkAW16UcOuuuFedPX0ZuIqn3Q6DvN+syKqQ4beCwY0wE 5Fx8MF1Y4f8+zVjLKwnjluky/hI2hQhYl25fW9NihRA/A== 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: , Reply-to: Nicolas Graves X-ACL-Warn: , Nicolas Graves via Guix-patches X-Patchwork-Original-From: Nicolas Graves via Guix-patches via From: Nicolas Graves Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches This package is archived and deprecated in favor or python-pyfaidx for 7 years. * gnu/packages/bioinformatics.scm (python-pyfasta): Delete variable. --- gnu/packages/bioinformatics.scm | 72 --------------------------------- 1 file changed, 72 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 00f0e10475..0f59f73448 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6396,78 +6396,6 @@ (define-public python-pybigwig accessing bigWig files.") (license license:expat))) -(define-public python-pyfasta - ;; The release on pypi does not contain the test data files. - (let ((commit "c2f0611c5311f1b1466f2d56560447898b4a8b03") - (revision "1")) - (package - (name "python-pyfasta") - (version (git-version "0.5.2" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/brentp/pyfasta") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0a189id3fbv88gssyk6adbmz2ll1mqpmyw8vxmx3fi955gvaq9j7")))) - (build-system pyproject-build-system) - (arguments - (list - #:phases - '(modify-phases %standard-phases - (add-after 'unpack 'python3.10-compat - (lambda _ - (substitute* "pyfasta/__init__.py" - (("from fasta import") - "from pyfasta.fasta import") - (("from records import") - "from pyfasta.records import") - (("from split_fasta import") - "from pyfasta.split_fasta import") - (("in f.iteritems") - "in f.items")) - (substitute* "pyfasta/fasta.py" - (("from collections import Mapping") - "from collections.abc import Mapping") - (("from records import") - "from pyfasta.records import")) - (substitute* "pyfasta/records.py" - (("cPickle") "pickle") - (("\\(int, long\\)") - "(int, int)") - ;; XXX: it's not clear if this is really correct. - (("buffer\\(self\\)") - "memoryview(bytes(str(self), encoding='utf-8'))") - (("sys.maxint") "sys.maxsize")) - (substitute* "pyfasta/split_fasta.py" - (("from cStringIO import") - "from io import") - (("in lens.iteritems") "in lens.items")) - (substitute* "tests/test_all.py" - (("f.keys\\(\\)\\) == \\['a-extra'") - "list(f.keys())) == ['a-extra'") - (("f.iterkeys\\(\\)") "iter(f.keys())") - (("tests/data/" m) - (string-append (getcwd) "/" m)))))))) - (propagated-inputs (list python-numpy)) - (native-inputs (list python-nose python-setuptools python-wheel)) - (home-page "https://github.com/brentp/pyfasta/") - (synopsis "Pythonic access to fasta sequence files") - (description - "This library provides fast, memory-efficient, pythonic (and -command-line) access to fasta sequence files. It stores a flattened version -of a fasta sequence file without spaces or headers and uses either a -@code{mmap} in numpy binary format or @code{fseek}/@code{fread} so the -sequence data is never read into memory. It saves a pickle (@code{.gdx}) of -the start and stop (for @code{fseek}/@code{mmap}) locations of each header in -the fasta file for internal use. - -Note that this package has been deprecated in favor of @code{pyfaidx}.") - (license license:expat)))) - (define-public python-schema-salad (package (name "python-schema-salad")