From debbugs-submit-bounces@debbugs.gnu.org Tue Jun 06 12:16:10 2023 Received: (at submit) by debbugs.gnu.org; 6 Jun 2023 16:16:10 +0000 Received: from localhost ([127.0.0.1]:52875 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q6ZLu-0005n5-Cw for submit@debbugs.gnu.org; Tue, 06 Jun 2023 12:16:10 -0400 Received: from lists.gnu.org ([209.51.188.17]:48594) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q6ZLp-0005mt-Aq for submit@debbugs.gnu.org; Tue, 06 Jun 2023 12:16:08 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1q6ZLm-0004fy-Qc for guix-patches@gnu.org; Tue, 06 Jun 2023 12:16:03 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1q6ZLk-0008RR-3u for guix-patches@gnu.org; Tue, 06 Jun 2023 12:16:02 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1686068153; x=1687882554; bh=rX6r9Wves8pJ0Ti hjD3jm7sZzuCcM2mb+C0cUgA9jX0=; b=RTQzKVhlmpjE84+5HU/nEGxGXE1+Nee TRJp/n8a0SuA1VbBXQpeyQLTRx18JsTDHOvpM/L0F3T83SPWky0EVGyKEnpBkKX4 mO96N5HDi7oFC83XdKp3T1hYNtcHSLD6XpwxYnACd+hkkRQ9SUywydBU24vdNhn0 mn+sQ0jiqwIY= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 891BE160211 for ; Tue, 6 Jun 2023 18:15:53 +0200 (CEST) Received: from localhost (141.80.218.27) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.23; Tue, 6 Jun 2023 18:15:52 +0200 From: Navid Afkhami To: Subject: [PATCH] gnu: Add python-decoupler-py. Date: Tue, 6 Jun 2023 18:15:46 +0200 Message-ID: X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27676.000 X-TM-AS-Result: No-10--4.734500-5.000000 X-TMASE-MatchedRID: cSoPLjBYd516fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VICu qghmtWfXj5ksrE9H+lhVjdEnKZ0vVpr9F4bPByvNSHCU59h5KrH2W3gEBC4gVPt9kl8N0Ihc+jV zof0NuiOd0PCdDanA+qocp404BNkgSG5H2XkXbuoMPOZL2X19iheK/B+WKxKswi5sQ9KQ2cnUh5 yQ6tsoTL49+tcT/xuz2M9FoXSj6BDgy771S93geDuUqTPTfDTrPn/9u4K/no6XBXaJoB9JZxRFJ Jyf5BJe3QfwsVk0Ubt2gyyw2xTBhZYM8Jrj1VET3VO/BptoNtxIX6jnnaatHFRIqPcXm4Ry9b3V 6to7mC0VvIU2rtP/VjPTVWTVN9T0iM7ip/P5FW1XN/AtJ7UGU9fsYX7riG7IuOY0q66+BqahgjV 6si4Sxb6DZFmPYUrLrQKe71GYum8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.734500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27676.000 X-TM-SNTS-SMTP: E3EB02A046F4CB16A400613CB59C47F60617AA25104090FB5B7E1D1C86535E312002:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, 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: -1.4 (-) X-Debbugs-Envelope-To: submit Cc: Navid Afkhami 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: -2.4 (--) * gnu/packages/bioinformatics.scm (python-decoupler-py): New variable. --- gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 509dc3358b..12455984ed 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1549,6 +1549,64 @@ (define-public python-cmseq and sequence consensus.") (license license:expat))) +(define-public python-decoupler-py + ;; This latest commit fixes the bug in test_omnip.py file. check_if_omnipath() has changed to _check_if_omnipath() + (let ((commit "b84c524ec4a9280a56c0db963e2c7b010316ce8f") + (revision "1")) + (package + (name "python-decoupler-py") + (version (git-version "1.3.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/saezlab/decoupler-py") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0d74yr5jqc52vcxaca84kxqw7m5rbazpmvnrcp2y4xxrj6yr1sfc")))) + (build-system pyproject-build-system) + (arguments + (list #:test-flags '(list "-k" + ;; These tests require internet access + (string-append "not test_get_resource" + " and not test_show_resources" + " and not test_get_dorothea" + " and not test_get_progeny" + " and not test_plot_volcano")) + #:phases '(modify-phases %standard-phases + (add-before 'check 'set-home + ;; Some tests require a home directory to be set. + (lambda _ + (setenv "HOME" "/tmp"))) + ;; Numba needs a writable dir to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs (list python-adjusttext + python-anndata + python-ipython + python-matplotlib + python-nbsphinx + python-numba + python-numpy + python-numpydoc + python-omnipath + python-scanpy + python-scikit-learn + python-scipy + python-skranger + python-tqdm + python-typing-extensions)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/saezlab/decoupler-py") + (synopsis + "Framework for modeling, analyzing and interpreting single-cell RNA-seq data") + (description + "Different statistical methods to extract biological activities +from omics data within a unified framework.") + (license license:gpl3+)))) + (define-public python-demuxem (package (name "python-demuxem") base-commit: 9ad8b0c2ef10d8de01bad25f54337c5df35aa842 -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Jun 06 15:37:39 2023 Received: (at 63929-done) by debbugs.gnu.org; 6 Jun 2023 19:37:39 +0000 Received: from localhost ([127.0.0.1]:53084 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q6cUs-0002gE-8i for submit@debbugs.gnu.org; Tue, 06 Jun 2023 15:37:39 -0400 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21053) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q6cUm-0002g0-Nc for 63929-done@debbugs.gnu.org; Tue, 06 Jun 2023 15:37:36 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1686080248; cv=none; d=zohomail.com; s=zohoarc; b=eDdZjIeEBwiyFUSTdjg1+tJqipIYcJml7vkNj/iwEmNGYJwL/emRT+IdZ7h99ondCSNzOf16elpOHXU6v3BLkE7cfOJUSkbk9y8LgJTutqdLRCVpp2UQwg+UEBTOC8fkrwwqMbgT97TIkCuTg6/eGD1AbZA/iCmb1n/vO8hkugQ= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1686080248; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=zmzkKdK/Vv5ZevPIsqGr5Tpq4u8FClDpC18MXhU1NSo=; b=nB0il+p64+ZMk+Uedd0by6cna6Z54vkq8rQCSk0E5cDNZNHd93wHAm2qeXGvZNmx1Bg1U5GuNfTKmmqzDIMP3JsSg+fD4rvZUfQbmGQ4CueLy6S8xWLSGFk3T6KbUo+EhCBC+IyE48S0J5xI3+dIBecKqOjml1AdcrQ2hJeXKuU= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1686080248; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=zmzkKdK/Vv5ZevPIsqGr5Tpq4u8FClDpC18MXhU1NSo=; b=iOF7TwIHD0BXzdRJm/3akZ5qFxNYJoGmmOUvpGbGXKoiijSvlWrjYCyAiv7u47Aw G87TPqZxiP8Uua6tZ8sNoBZmk9xF7xCTPmEZbsSfEfWGXkcXOuOKsJqK00Z98IqqCYz ljIfsktk2ESLmPGcNe8sbp6wcXAYnj2mQ0i1D3Po= Received: from localhost (122-110-142-46.pool.kielnet.net [46.142.110.122]) by mx.zohomail.com with SMTPS id 1686080245829173.81477881601495; Tue, 6 Jun 2023 12:37:25 -0700 (PDT) User-agent: mu4e 1.10.2; emacs 28.2 From: Ricardo Wurmus To: 63929-done@debbugs.gnu.org Subject: [PATCH] gnu: Add python-decoupler-py. Date: Tue, 06 Jun 2023 21:36:59 +0200 Message-ID: <87ilc0pekt.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 63929-done 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 (-) Applied with some minor changes. Good job! -- Ricardo From unknown Sat Aug 16 21:00:08 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Wed, 05 Jul 2023 11:24:06 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator