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Tue, 04 Jan 2022 17:46:12 -0500 Received: from eggs.gnu.org ([209.51.188.92]:42928) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sZ9-0005wz-O5 for guix-patches@gnu.org; Tue, 04 Jan 2022 17:46:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55688) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sZ9-0006cM-EW for guix-patches@gnu.org; Tue, 04 Jan 2022 17:46:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sZ8-0003fW-JG; Tue, 04 Jan 2022 17:46:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 00/17] Add julia-biosequences and julia-bioalignments Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: efraim@flashner.co.il, guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:46:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: zimoun , Efraim Flashner X-Debbugs-Original-To: guix-patches@gnu.org X-Debbugs-Original-Xcc: Efraim Flashner Received: via spool by submit@debbugs.gnu.org id=B.164133632514050 (code B ref -1); 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Tue, 04 Jan 2022 14:45:15 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id d4sm38830429wrx.102.2022.01.04.14.45.14 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:45:15 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:45:02 +0100 Message-Id: <20220104224502.1142878-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 MIME-Version: 1.0 X-Host-Lookup-Failed: Reverse DNS lookup failed for 2a00:1450:4864:20::32b (failed) Received-SPF: pass client-ip=2a00:1450:4864:20::32b; envelope-from=zimon.toutoune@gmail.com; helo=mail-wm1-x32b.google.com X-Spam_score_int: 6 X-Spam_score: 0.6 X-Spam_bar: / X-Spam_report: (0.6 / 5.0 requ) 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_NONE=-0.0001, RDNS_NONE=0.793, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=no autolearn_force=no X-Spam_action: no action 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+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches Hi, This series adds two useful packages for bioinformatics. The first patch sets one inputs per line. It is justified because a) Julia package name can be long and often similar and b) uniformity helps. For instance of a) --8<---------------cut here---------------start------------->8--- - (list julia-arraylayouts julia-bandedmatrices julia-blockarrays - julia-fillarrays julia-matrixfactorizations)) + (list julia-arraylayouts + julia-bandedmatrices + julia-blockarrays + julia-fillarrays --8<---------------cut here---------------end--------------->8--- and this first patch does not trigger any rebuild. The 3 other "adjust style" triggers some rebuild. The second patch fixes packages without Project.toml file which are then propagated. Sadly, it implies the rebuild of all Julia packages for only one problematic package: julia-indexablebitvectors. Last, the tests of the package julia-biosymbols are still failing and I have no clue why. Therefore, they are turned off. The package is correct because used by julia-sequences and julia-alignments, both passing their test suite. Cheers, simon zimoun (17): gnu: julia-xyz: Adjust style. build: julia-build-system: Create 'Project.toml' file when missing. gnu: julia-zygote: Adjust style. gnu: julia-documentertools: Adjust style. gnu: julia-documenter: Adjust style. gnu: Add julia-biogenerics. gnu: Add julia-indexablebitvectors. gnu: Add julia-twiddle. gnu: Add julia-simd. gnu: Add julia-scanbyte. gnu: Add julia-automa. gnu: Add julia-stringencodings. gnu: Add julia-yaml. gnu: Add julia-biosymbols. gnu: Add julia-biosequences. gnu: Add julia-intervaltrees. gnu: Add julia-bioalignments. doc/guix.texi | 19 +- gnu/packages/julia-xyz.scm | 690 +++++++++++++++++++++++++----- guix/build/julia-build-system.scm | 33 +- 3 files changed, 607 insertions(+), 135 deletions(-) base-commit: b9c5dff57ff961a16c8fc24843a4535ea817e732