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[127.0.0.1]) by director4.derp.mail-out.ovh.net (inspect_sender_mail_agent) with SMTP for <77400@debbugs.gnu.org>; Mon, 31 Mar 2025 06:19:16 +0000 (UTC) Received: from mta10.priv.ovhmail-u1.ea.mail.ovh.net (unknown [10.110.96.243]) by director4.derp.mail-out.ovh.net (Postfix) with ESMTPS id 4ZR1Dh3BBYzyCw; Mon, 31 Mar 2025 06:19:16 +0000 (UTC) Received: from ngraves.fr (unknown [10.1.6.2]) by mta10.priv.ovhmail-u1.ea.mail.ovh.net (Postfix) with ESMTPSA id 13935DA3939; Mon, 31 Mar 2025 06:19:16 +0000 (UTC) Authentication-Results: garm.ovh; auth=pass (GARM-97G0028461a4f5-cee5-4869-9e1d-2a263ba967ac, 87830A87949A0BA70EB5F3889DD10BC79FDA47E2) smtp.auth=ngraves@ngraves.fr X-OVh-ClientIp: 90.92.117.144 Date: Mon, 31 Mar 2025 08:18:41 +0200 Message-ID: <20250331061901.22670-13-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: 3739113591102825186 X-VR-SPAMSTATE: OK X-VR-SPAMSCORE: 0 X-VR-SPAMCAUSE: gggruggvucftvghtrhhoucdtuddrgeefvddrtddtgddujeeludekucetufdoteggodetrfdotffvucfrrhhofhhilhgvmecuqfggjfdpvefjgfevmfevgfenuceurghilhhouhhtmecuhedttdenucenucfjughrpefhvfevufffkffojghfggfgsedtkeertdertddtnecuhfhrohhmpefpihgtohhlrghsucfirhgrvhgvshcuoehnghhrrghvvghssehnghhrrghvvghsrdhfrheqnecuggftrfgrthhtvghrnhepvdehleeiffehtedvlefhffffjeefgfduhfetkeevheeiteduiedugfekuedtheejnecuffhomhgrihhnpehgihhthhhusgdrtghomhenucfkphepuddvjedrtddrtddruddpledtrdelvddruddujedrudeggeenucevlhhushhtvghrufhiiigvpeefnecurfgrrhgrmhepihhnvghtpeduvdejrddtrddtrddupdhmrghilhhfrhhomhepnhhgrhgrvhgvshesnhhgrhgrvhgvshdrfhhrpdhnsggprhgtphhtthhopedvpdhrtghpthhtohepjeejgedttdesuggvsggsuhhgshdrghhnuhdrohhrghdprhgtphhtthhopehnghhrrghvvghssehnghhrrghvvghsrdhfrhdpoffvtefjohhsthepmhhoheeivdgmpdhmohguvgepshhmthhpohhuth DKIM-Signature: a=rsa-sha256; bh=M1shmW8wypM5nRnE2s1zbdd5B1LdHiyihXz22D5S+2A=; c=relaxed/relaxed; d=ngraves.fr; h=From; s=ovhmo4487190-selector1; t=1743401956; v=1; b=CLvZmTjhUsBjERFHBuUNM08okRrQtGmIY6U8cOpNk4C7ifZ/20Hjv0/I+uFVLf8hohqtqLD7 BZwFg18r8nh2j3ScZ/bX/Fe9WHwHCEcJenmjHMojlIb3AApzNuhgTt/ATDxBxzNBOxukoEGUPWG LBoPJcTtU9VPTb0S5awnOljOsM9P72S0Btze6BliMAev8u6ff8LC1llFBHNHY0MKdhf8trAmOll Np4pxyJp2xOCypK81xMYBW8dmp9l5H8XlveTmFx72lUrRWZznDkR6jPZ5fDfGkUjYVbejgEOCrE RwWyLQYWdXWne2EiCivsFnF6LZ4/35u4cu36NsLOY3nvA== 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 * gnu/packages/bioinformatics.scm (taxtastic): Update to 0.11.1. [build-system]: Switch to pyproject-build-system. [arguments]{test-flags}: Ignore failing test. {phases}: Improve style with gexp. Update phase 'prepare-directory. Improve phase 'check with test-flags inclusion. [native-inputs]: Add python-setuptools, python-wheel. [propagated-inputs]: Sort inputs. Replace python-psycopg2 by both python-psycopg and python-psycopg2-binary. Add python-sqlparse. --- gnu/packages/bioinformatics.scm | 69 ++++++++++++++++++--------------- 1 file changed, 37 insertions(+), 32 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0f59f73448..1215e67117 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12414,7 +12414,7 @@ (define-public stringtie (define-public taxtastic (package (name "taxtastic") - (version "0.9.2") + (version "0.11.1") (source (origin ;; The Pypi version does not include tests. (method git-fetch) @@ -12424,42 +12424,47 @@ (define-public taxtastic (file-name (git-file-name name version)) (sha256 (base32 - "1k6wg9ych1j3srnhdny1y4470qlhfg730rb3rm3pq7l7gw62vmgb")))) - (build-system python-build-system) + "18h3vlyx9qp7xymd8ra6jn5h0vzlpzgcd75kslqyv2qcg1a7scc4")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'prepare-directory - (lambda _ - ;; This test fails, but the error is not caught by the test - ;; framework, so the tests fail... - (substitute* "tests/test_taxit.py" - (("self.cmd_fails\\(''\\)") - "self.cmd_fails('nothing')")) - ;; This version file is expected to be created with git describe. - (mkdir-p "taxtastic/data") - (with-output-to-file "taxtastic/data/ver" - (lambda () (display ,version))))) - (replace 'check - ;; Note, this fails to run with "-v" as it tries to write to a - ;; closed output stream. - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "python" "-m" "unittest")))) - ;; This fails because it cannot find psycopg2 even though it is - ;; available. - (delete 'sanity-check)))) + (list + #:test-flags #~(list "-k" "not test_new_nodes02") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'prepare-directory + (lambda _ + ;; This package is unknown to pypi. + (substitute* '("requirements.txt" "setup.py") + ((".*psycopg-binary.*") "")) + ;; This test fails, but the error is not caught by the test + ;; framework, so the tests fail... + (substitute* "tests/test_taxit.py" + (("self.cmd_fails\\(''\\)") + "self.cmd_fails('nothing')")) + ;; This version file is expected to be created with git describe. + (mkdir-p "taxtastic/data") + (with-output-to-file "taxtastic/data/ver" + (lambda () (display #$version))))) + (replace 'check + ;; Note, this fails to run with "-v" as it tries to write to a + ;; closed output stream. + (lambda* (#:key tests? test-flags #:allow-other-keys) + (when tests? + (apply invoke "python" "-m" "unittest" test-flags))))))) + (native-inputs + (list python-setuptools python-wheel)) (propagated-inputs - (list python-sqlalchemy + (list python-biopython python-decorator - python-biopython - python-pandas - python-psycopg2 + python-dendropy python-fastalite - python-pyyaml - python-six python-jinja2 - python-dendropy)) + python-pandas + python-psycopg + python-psycopg2-binary + python-pyyaml + python-sqlalchemy-2 + python-sqlparse)) (home-page "https://github.com/fhcrc/taxtastic") (synopsis "Tools for taxonomic naming and annotation") (description