From patchwork Sun Jul 23 10:41:46 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 52065 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id BA37527BBEA; Sun, 23 Jul 2023 11:43:23 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 7B53C27BBE2 for ; Sun, 23 Jul 2023 11:43:20 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qNWYJ-0005fg-Hw; Sun, 23 Jul 2023 06:43:03 -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 1qNWYI-0005fV-Ks for guix-patches@gnu.org; Sun, 23 Jul 2023 06:43:02 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qNWYI-0006Rw-CV for guix-patches@gnu.org; Sun, 23 Jul 2023 06:43:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qNWYI-0001hp-7w for guix-patches@gnu.org; Sun, 23 Jul 2023 06:43:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#64801] [PATCH 1/2] gnu: Add python-liana-py. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 23 Jul 2023 10:43:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 64801 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 64801@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.16901089476496 (code B ref -1); Sun, 23 Jul 2023 10:43:02 +0000 Received: (at submit) by debbugs.gnu.org; 23 Jul 2023 10:42:27 +0000 Received: from localhost ([127.0.0.1]:38585 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qNWXj-0001gi-D0 for submit@debbugs.gnu.org; Sun, 23 Jul 2023 06:42:27 -0400 Received: from lists.gnu.org ([2001:470:142::17]:46118) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qNWXf-0001gQ-AL for submit@debbugs.gnu.org; Sun, 23 Jul 2023 06:42:25 -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 1qNWXZ-0005YQ-Dr for guix-patches@gnu.org; Sun, 23 Jul 2023 06:42:17 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qNWXV-0006JL-Du for guix-patches@gnu.org; Sun, 23 Jul 2023 06:42:15 -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=1690108921; x=1691923322; bh=AQkB1ZoccwYmmwv OEZpn29z5fj9WeyudTE4t4iQmVDE=; b=ZLGsaPJ8nzpEkxH6r9gAEmZYyZ2T2qN ZC/qpxx1Ughy7FcIVFHbgmCRi2H8/K9V6Ce8SXqViNDDgZrTafHtCBjec3aFLUwL msDKXLQpMynde9B0QQy+mOr4ujDsel1UJF0Fal7sw1wOnZprwu7EUMZb1Cx+AHIz xRKGwCswsDdk= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 376DA3001B5 for ; Sun, 23 Jul 2023 12:42:01 +0200 (CEST) Received: from localhost.localdomain (89.247.175.74) 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 15.1.2507.27; Sun, 23 Jul 2023 12:41:59 +0200 From: Navid Afkhami Date: Sun, 23 Jul 2023 12:41:46 +0200 Message-ID: X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 X-Originating-IP: [89.247.175.74] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27768.006 X-TM-AS-Result: No-10--4.201500-5.000000 X-TMASE-MatchedRID: cSoPLjBYd516fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VL6p xbTOjavycW3/J21vqoVXOLTjXPci/yq+GZ9ZHxIhuW77/y896sj4qCLIu0mtIKILsEPieIGYuJE UmdYPGSVwVOG1EkyuRvuZJosCQMU/9c0SSBk6D85IcJTn2HkqscXSSNhWWhyhyIKHzIGoT63C1R bOIHkz7iZtHzNT1dY9+Eit+61jcZfgy771S93geDuUqTPTfDTrPn/9u4K/no6XBXaJoB9JZxRFJ Jyf5BJe3QfwsVk0Ubt2gyyw2xTBhVt+R1BFsVYDUd7jzT33+eRRGW81/9tlnkOcAsVOZbJvqhtO pxuGOdlGIFihOVVF46kQHkPC+VWMvmzMxRv6F9vdhlUrvLKnJMel4d1cuMtvjvdbOxcC5/MQtmu xiADqhvKHck16UKN1GR8AXHcOfjI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.201500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27768.006 X-TM-SNTS-SMTP: B1BD961538D6DDCB6C9E1C80BE15F9DE0A33978D6BDA93514AC3E2BF5C16599A2000:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=c2062.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-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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (python-liana-py): New variable. --- gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) base-commit: 445a0359083388b5ee686e6e855f94a3aac5f79c diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 864c200707..a0ae298a2c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1863,6 +1863,64 @@ (define-public python-htsget servers supporting the protocol.") (license license:asl2.0))) +(define-public python-liana-py + (package + (name "python-liana-py") + (version "0.1.9") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/saezlab/liana-py") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00lqrmi38wmdpjlcafgmrnkwsbp0yvm2rya6qs8y6jfizww9ff8i")))) + (build-system pyproject-build-system) + (arguments + (list #:test-flags '(list "-k" + ;; These tests require internet access. + (string-append "not test_generate_lr_resource" + " and not test_generate_nondefault_lr_resource")) + #:phases '(modify-phases %standard-phases + (add-before 'check 'set-home + ;; Some tests require home directory to be set. + (lambda _ + (setenv "HOME" "/tmp"))) + ;; Numba needs a writable directory to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs (list python-anndata + python-black + python-cell2cell + python-decoupler-py + python-hypothesis + python-ipykernel + python-ipython + python-mofax + python-mudata + python-nbconvert + python-nbsphinx + python-numpydoc + python-omnipath + python-pandas + python-plotnine + python-pypandoc + python-scipy + python-requests + python-scanpy + python-statsmodels + python-tqdm + tzdata)) + (native-inputs (list python-pytest python-pytest-cov python-numpy)) + (home-page "https://github.com/saezlab/liana-py") + (synopsis "LIANA is a ligand-receptor analysis framework") + (description "This is a Ligand-Receptor inference framework. +The framework enables the use of any LR method +with any resources.") + (license license:gpl3+))) + (define-public python-logomaker (package (name "python-logomaker") From patchwork Sun Jul 23 10:41:47 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: nafkhamdc X-Patchwork-Id: 52066 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 21D4727BBEA; Sun, 23 Jul 2023 11:43:52 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 291EB27BBE2 for ; Sun, 23 Jul 2023 11:43:51 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qNWYL-0005gH-DF; Sun, 23 Jul 2023 06:43:05 -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 1qNWYJ-0005ff-FC for guix-patches@gnu.org; Sun, 23 Jul 2023 06:43:03 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qNWYJ-0006S4-7Z for guix-patches@gnu.org; Sun, 23 Jul 2023 06:43:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qNWYJ-0001i4-0n for guix-patches@gnu.org; Sun, 23 Jul 2023 06:43:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#64802] [PATCH 2/2] gnu: python-decoupler-py: Update to (git-version 1.5.0 revision commit). 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Sun, 23 Jul 2023 12:41:59 +0200 From: Navid Afkhami Date: Sun, 23 Jul 2023 12:41:47 +0200 Message-ID: <914170d63926798e3b1090818e38051bfadf7684.1690108906.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 In-Reply-To: References: MIME-Version: 1.0 X-Originating-IP: [89.247.175.74] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27768.006 X-TM-AS-Result: No-10--2.251000-5.000000 X-TMASE-MatchedRID: jtEPcQmLSaYexiL4/gRNNVCxqE4whnXlyiKgKtIyB4rAuQ0xDMaXkH4q tYI9sRE/Vztt14qydosKRuKRI67R4BDITYD8arnZutvHF25zoU8xVUWGXs3C8zkP5NCGuROodVd Df+p3DnL2gpsjdbRHZ2xOxKzHW3IX3BPrPGHYpyMMPOZL2X19inoCBx19i+GM33Nl3elSfspbwd TNmhmeEt0atarVue7jCMO3A8admEcLEf6dMNnU0zuUqTPTfDTrEOS/art35UOXBXaJoB9JZxRFJ Jyf5BJe3QfwsVk0Ubt2gyyw2xTBhT2aGYaJo52FSKw8Z/Qk1fzr6Ywzxk+aFWvd0fZWYCXh2Zwv E3ItVg5OUaLxPl5FXK72I/k+Qy8bPnj+oAbmWG7gv400vgqqxcel4d1cuMtvjvdbOxcC5/MQtmu xiADqhvKHck16UKN1GR8AXHcOfjI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.251000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27768.006 X-TM-SNTS-SMTP: 3A187DB890D134498088E401CEF5EB20F0D76AFF97D09D6B15CFA4F07BE5F4642000:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=c2062.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-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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (python-decoupler-py): Update to (git-version 1.5.0 revision commit). --- gnu/packages/bioinformatics.scm | 49 +++++++++++++++++---------------- 1 file changed, 25 insertions(+), 24 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a0ae298a2c..d39a47d694 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1680,11 +1680,11 @@ (define-public python-cmseq (define-public python-decoupler-py ;; This latest commit fixes a bug in test_omnip.py. - (let ((commit "b84c524ec4a9280a56c0db963e2c7b010316ce8f") + (let ((commit "459b235348ddd9135217a3722d9dd1caa9a14ace") (revision "1")) (package (name "python-decoupler-py") - (version (git-version "1.3.1" revision commit)) + (version (git-version "1.5.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -1693,30 +1693,31 @@ (define-public python-decoupler-py (file-name (git-file-name name version)) (sha256 (base32 - "0d74yr5jqc52vcxaca84kxqw7m5rbazpmvnrcp2y4xxrj6yr1sfc")))) + "1c0xk006iilyffdaqar2d05qdhik22fbkny387zx0bndkgqifxhl")))) (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" - ;; XXX This one fails because the "texts" list - ;; is empty, so there are no texts to adjust. - ;; It is not clear whether this a compatibility - ;; problem with our adjusttext package. - " 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")))))) + (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_get_collectri" + " and not test_get_ksn_omnipath" + ;; XXX This one fails because the "texts" list + ;; is empty, so there are no texts to adjust. + ;; It is not clear whether this a compatibility + ;; problem with our adjusttext package. + " 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