From unknown Sun Jun 22 08:07:23 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#71670] [PATCH 0/2] bioinformatics: Add python-muon Resent-From: guix@mawumag.com Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 20 Jun 2024 08:46:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 71670 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 71670@debbugs.gnu.org Cc: tanguy@bioneland.org, me@bonfacemunyoki.com, lars@6xq.net, Ricardo Wurmus , jgart@dismail.de, marius@gnu.org, sharlatanus@gmail.com X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.17188731568559 (code B ref -1); Thu, 20 Jun 2024 08:46:02 +0000 Received: (at submit) by debbugs.gnu.org; 20 Jun 2024 08:45:56 +0000 Received: from localhost ([127.0.0.1]:48957 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sKDQa-0002Dz-0a for submit@debbugs.gnu.org; Thu, 20 Jun 2024 04:45:56 -0400 Received: from lists.gnu.org ([209.51.188.17]:60198) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sKDQX-0002Dq-RI for submit@debbugs.gnu.org; Thu, 20 Jun 2024 04:45:54 -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 1sKDQT-0000UT-J3 for guix-patches@gnu.org; Thu, 20 Jun 2024 04:45:49 -0400 Received: from mail-200161.simplelogin.co ([176.119.200.161]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sKDQP-0008Jw-Ro for guix-patches@gnu.org; Thu, 20 Jun 2024 04:45:49 -0400 ARC-Seal: i=1; a=rsa-sha256; d=simplelogin.co; s=arc-20230626; t=1718873131; cv=none; b=R53Ts+DQUTn8pTbpp6JwkIaim3L+VxH3Xms9nPm4c8JdqK8I+UUP+csw57hfZpsYGvJEfzT+Aa4ElN4/4YRPy2xL9/oqLHnXsiU8TSTViDiUlFfVKYP9LvmHTe8XiBo9OEr5Y776DbgQ6iIkriqCgLNZrd5kdyaQKad0aEweap7CvJDBNMDa22lKlDyKFJP4Mpq/PwVzEN2Gq7KMr/WfFheyKQDbIjyPSUUd0+tWnq4Gmvv9GR+r7mXDd76h4lBQTGo1CzFXrSpa8E0cjZVif+UAIw3bdqcN3dXWLsKcAbSZ5JrQVNhtZ8OFALim3B6HDl+73muv5xH485HRjjjosA== ARC-Message-Signature: i=1; a=rsa-sha256; d=simplelogin.co; s=arc-20230626; t=1718873131; c=relaxed/simple; bh=Lz2C5VURKjGGQEFker/9GTqDHMFM5y2Rd54pguiy8A8=; h=Date:Subject:From:To:Cc; b=wzGfgktapsiKts0O9E46Z2pCR/VEGvXdbQ8uryHD5sTsgcYzemQ/Hjc+KeScg8ZkvizaB+cySOMVvpoBG6C/yBJCSiKKHdbMand+rCjxIuEOqLEOI87oaPSu+Tk6+bn27/eeSZ7ygXBreaQ+ge2rhEPp/dt7ePQZPv7/7RfKgzijzMhVrsiFXuWcIqR6+kjMfUJ4RCluxS1GeYdy0SRle1rUldWp1GKo2rtRIs8gnDUKvd3WECcoXp908nj8dyw93WGTl5eUyQBxi8OHQQ96feGXgKpkVfUqPU8uvcMIc6gTLhC9jLCTYyDdk/nZVO40MjI0HFJo+s/wKeHekcSNDw== ARC-Authentication-Results: i=1; mail.protonmail.ch DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=mawumag.com; s=dkim; t=1718873131; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=KKmtl9SwldSz5/SFSzf6718RWgZk8NSV4tVXuDv85HY=; b=b2SYWLNvOMj+wAPFDfc6ZZl166xg2ExmaaZSRwAc9awIZ9zifjjkl2gufM/s0s3gy9co9X cSijZiuISUSg7k88ByaRFcwons4HFtidOEBESyFIGT1W3ykCQd/jSVxlHMP6m00/V0k5/c Ez9p9udcTO/3dcFKMl0yTPI0j58WfmA= Date: Thu, 20 Jun 2024 08:45:24 +0000 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable From: guix@mawumag.com Message-ID: <171887312984.7.12976181484130280866.359654925@mawumag.com> X-SimpleLogin-Type: Reply X-SimpleLogin-EmailLog-ID: 359654936 X-SimpleLogin-Want-Signing: yes Received-SPF: pass client-ip=176.119.200.161; envelope-from=sl.lmysyibtgu4tmnjuheztmlbagezdsnzzgy2v2.geznxjnsy4kfi@mawumag.com; helo=mail-200161.simplelogin.co X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 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, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=unavailable autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) 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: -2.3 (--) I am adding the packages python-muon and python-mofapy2 (as a muon dependency). Muon is a multi-omics analysis framework and is part of the scverse. I had to modify a couple of tests slightly (explained in the comments). Marco Baggio (2): bioinformatics: Add python-mofapy2 bioinformatics: Add python-muon gnu/packages/bioinformatics.scm | 93 +++++++++++++++++++++++++++++++++ 1 file changed, 93 insertions(+) base-commit: e32e3d0a03dc17c4c54a91aad053c9036998b601 -- 2.45.1 From unknown Sun Jun 22 08:07:23 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#71670] [PATCH 1/2] bioinformatics: Add python-mofapy2 References: <171887312984.7.12976181484130280866.359654925@mawumag.com> In-Reply-To: <171887312984.7.12976181484130280866.359654925@mawumag.com> Resent-From: guix@mawumag.com Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 20 Jun 2024 08:51:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 71670 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 71670@debbugs.gnu.org Cc: tanguy@bioneland.org, me@bonfacemunyoki.com, lars@6xq.net, Ricardo Wurmus , jgart@dismail.de, marius@gnu.org, sharlatanus@gmail.com Received: via spool by 71670-submit@debbugs.gnu.org id=B71670.17188734239086 (code B ref 71670); Thu, 20 Jun 2024 08:51:02 +0000 Received: (at 71670) by debbugs.gnu.org; 20 Jun 2024 08:50:23 +0000 Received: from localhost ([127.0.0.1]:49049 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sKDUs-0002MU-KF for submit@debbugs.gnu.org; Thu, 20 Jun 2024 04:50:22 -0400 Received: from mail-200167.simplelogin.co ([176.119.200.167]:25983) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sKDUp-0002MH-M2 for 71670@debbugs.gnu.org; Thu, 20 Jun 2024 04:50:20 -0400 ARC-Seal: i=1; a=rsa-sha256; d=simplelogin.co; s=arc-20230626; t=1718873410; cv=none; b=VU8/X60QyMM6e3fSM41J+RmUP3V8pyOLogao3Wviu19oqIc89ZLQy/xWM5+eGXkT72PUVpA6ITEb267uqQhZ/DbowAELHL2+weakqSPDLwdHoGKXldzs9Eh0UHH1brV5HyZ7fgde/gs2UHpwija0Sqaq0jAhzTQ6QOkMJlP1a4xgZLcTEtlRusLq6SrW/aEZOoHs9UmpyfmNU7L0dWzfaYJ1CsQDHZ6RaAivXBTZvLfU+oNoho0FJCWeBjstbewYTiDEqAx3xyg6VhPzY8HtkYxUU8LcvRN+wuRd3khSBVeHf9sTsyEp9343GjP9mlcf3/4QSaYPw41da+MFlawpmA== ARC-Message-Signature: i=1; a=rsa-sha256; d=simplelogin.co; s=arc-20230626; t=1718873410; c=relaxed/simple; bh=UTST4WTbBijO65RhsO+QO+8VYD+p5eOhhixBBtbjLgE=; h=Date:Subject:From:To:Cc; b=i5i1CODRIzsuBv5YvNgdmrDqteOJhxiMFNMhhMlvXB1YZ1btoUI0hh6MIokF4dsa5SZLcDQ2sg8t/cWCeMiV7kpryeeBU2aFOqpof4jClqhPESiNSMXP8W8thSMK4Zg8FOqZvTLbHoNKyhJS17ujZkFZfnBn39had0lx1z3lXteFLkh51j8xO42diE4YX61vSETDrKXYguh2Dr2oSVy7rqUxpfTZKkjTvI3t61mrAysh/ZLcYkpIE7xkB+EKKMt5fGUNV4v/eYlkc20GKik9B+M4C4B22lWWyuWNM/LffamfDHQM3ZoX9hX1XBQHJhiVMxrSF9TVo2JGHQRsPEG0pA== ARC-Authentication-Results: i=1; mail.protonmail.ch DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=mawumag.com; s=dkim; t=1718873409; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=5AI0TZWiigXK1xFKohF5S01G+ExDCQM7+PUrRb66r2A=; b=jAT4+NrIuVjmH3AS24wKut5pDNsAJCwdOQhLkQfV/9FHBlBnf1NgTQoqyBCbWbN+3qHY0d BvPfxg6uT9IpgpfLbR1ECTmaoSfDUbPT0tk7NeYmIIRqE2Sv0veXzItV+Ibg/Nsku6YvDj MFQJYvyqtOaU6H9ggfp4YmRCtKhqqMo= Date: Thu, 20 Jun 2024 08:50:03 +0000 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable From: guix@mawumag.com Message-ID: <171887340881.9.8063638923661902508.359656723@mawumag.com> X-SimpleLogin-Type: Reply X-SimpleLogin-EmailLog-ID: 359656734 X-SimpleLogin-Want-Signing: yes X-Spam-Score: 1.7 (+) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: Change-Id: Ide92878258511b3daf4e56d5faa94d190fdee62f --- gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cdda029809..37fa1727cb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4443, [...] Content analysis details: (1.7 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.0 SPF_PASS SPF: sender matches SPF record -0.0 SPF_HELO_PASS SPF: HELO matches SPF record 1.7 URIBL_BLACK Contains an URL listed in the URIBL blacklist [URIs: github.io] -0.0 T_SCC_BODY_TEXT_LINE No description available. 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: 0.7 (/) Change-Id: Ide92878258511b3daf4e56d5faa94d190fdee62f --- gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.= scm index cdda029809..37fa1727cb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4443,6 +4443,44 @@ (define-public python-mudata omics data.") (license license:bsd-3))) =20 +(define-public python-mofapy2 + (package + (name "python-mofapy2") + (version "0.7.1") + (source + (origin + ;; The tarball from PyPi doesn't include tests. + (method git-fetch) + (uri (git-reference + (url "https://github.com/bioFAM/mofapy2") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ahhnqk6gjrhyq286mrd5n7mxcv8l6040ffsawbjx9maqx8wbam0")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'disable-failing-tests + (lambda _ + ;; cupy is an optional dependency, which + ;; itself has nonfree dependencies (CUDA) + (delete-file "mofapy2/notebooks/test_cupy.py")))))) + (propagated-inputs (list python-anndata + python-pandas + python-scipy + python-numpy + python-scikit-learn + python-h5py)) + (native-inputs (list python-poetry-core + python-pytest)) + (home-page "https:/biofam.github.io/MOFA2/") + (synopsis "Multi-omics factor analysis") + (description "Multi-omics factor analysis.") + (license license:lgpl3))) + (define-public python-pyega3 (deprecated-package "python-pyega3" python-ega-download-client)) =20 --=20 2.45.1 From unknown Sun Jun 22 08:07:23 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#71670] [PATCH 2/2] bioinformatics: Add python-muon References: <171887312984.7.12976181484130280866.359654925@mawumag.com> In-Reply-To: <171887312984.7.12976181484130280866.359654925@mawumag.com> Resent-From: guix@mawumag.com Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 20 Jun 2024 08:52:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 71670 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 71670@debbugs.gnu.org Cc: sharlatanus@gmail.com, me@bonfacemunyoki.com, lars@6xq.net, Ricardo Wurmus , jgart@dismail.de, marius@gnu.org, tanguy@bioneland.org Received: via spool by 71670-submit@debbugs.gnu.org id=B71670.17188734899225 (code B ref 71670); 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charset=utf-8 Content-Transfer-Encoding: quoted-printable From: guix@mawumag.com Message-ID: <171887347750.7.17381680002823190276.359657180@mawumag.com> X-SimpleLogin-Type: Reply X-SimpleLogin-EmailLog-ID: 359657180 X-SimpleLogin-Want-Signing: yes X-Spam-Score: -0.0 (/) 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 (-) Change-Id: I21431b089d1f404828b78d79124d96e7d36d5a2d --- gnu/packages/bioinformatics.scm | 55 +++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.= scm index 37fa1727cb..b3fe67cae7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4481,6 +4481,61 @@ (define-public python-mofapy2 (description "Multi-omics factor analysis.") (license license:lgpl3))) =20 +(define-public python-muon + (package + (name "python-muon") + (version "0.1.6") + (source + (origin + ;; The tarball from PyPi doesn't include tests. + (method git-fetch) + (uri (git-reference + (url "https://github.com/scverse/muon") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1kd3flgy41dc0sc71wfnirh8vk1psxgyjxkbx1zx9yskkh6anbgw")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; Numba needs a writable dir to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp"))) + (add-before 'check 'disable-failing-tests + (lambda _ + ;; even providing a random seed, scipy.sparse.rand + ;; produces inconsistent results across scipy versions + (substitute* "tests/test_atac_preproc.py" + (("^class TestTFIDFSparse.*" m) + (string-append "@unittest.skip(reason=3D\"\")\n" m)))))))) + (propagated-inputs (list python-anndata + python-h5py + python-matplotlib + python-mofapy2 + python-mudata + python-numba + python-numpy + python-pandas + python-protobuf + python-pybedtools + python-pysam + python-scanpy + python-scikit-learn + python-seaborn + python-tqdm + python-umap-learn)) + (native-inputs (list python-flit-core-bootstrap + python-pytest + python-pytest-flake8)) + (home-page "https://github.com/scverse/muon") + (synopsis "Multimodal omics analysis framework") + (description "Multimodal omics analysis framework.") + (license license:bsd-3))) + (define-public python-pyega3 (deprecated-package "python-pyega3" python-ega-download-client)) =20 --=20 2.45.1 From unknown Sun Jun 22 08:07:23 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: guix@mawumag.com Subject: bug#71670: closed (Re: [PATCH 2/2] bioinformatics: Add python-muon) Message-ID: References: <87plrxtcpt.fsf@elephly.net> <171887312984.7.12976181484130280866.359654925@mawumag.com> X-Gnu-PR-Message: they-closed 71670 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 71670@debbugs.gnu.org Date: Mon, 01 Jul 2024 14:22:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1719843722-21706-1" This is a multi-part message in MIME format... ------------=_1719843722-21706-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #71670: [PATCH 0/2] bioinformatics: Add python-muon which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 71670@debbugs.gnu.org. --=20 71670: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D71670 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1719843722-21706-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 71670-done) by debbugs.gnu.org; 1 Jul 2024 14:21:41 +0000 Received: from localhost ([127.0.0.1]:33448 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sOHuX-0005dV-HR for submit@debbugs.gnu.org; Mon, 01 Jul 2024 10:21:41 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21124) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sOHuV-0005d8-Gk for 71670-done@debbugs.gnu.org; Mon, 01 Jul 2024 10:21:40 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1719843684; cv=none; d=zohomail.com; s=zohoarc; b=RC8sHwT9i15Z/XMzcFwnQ+TY1v7H8hbE1d1IddSKQ3x4ZL9v4FTX5vzvwmu8DF7WKs7NXOfGU+Ub3+kB6UDFk6MKdt8Bho9dZlosT3xviw3VjqZn5T0+wU0Z9nzmYVSE2pKZy4GeH+lABp+7ObnE2Js1nuC5q1TeRH03WP7xWls= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1719843684; h=Content-Type:Cc:Cc:Date:Date:From:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:Subject:To:To:Message-Id:Reply-To; bh=w4w7bnMDuXjUD4HHNSNrXIMpHsdofvFNo6XmRMfIK74=; b=WKizmDqRSIeePAzoNHXUlqmZJE4cztKP4l3JJ+2jVElLLFPUszq8vO7ASKWsU8dMPU8Fat9WYsRD+cvtqSxNsqOxdk2U5zaHWKwd5rEN0Glfv6rK9p/nE9piuuQr5hZk/gSCviM42yjFVN18HliBVZA+G2KE9SBzgt5B9WvOzSw= 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=1719843684; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:In-Reply-To:References:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To; bh=w4w7bnMDuXjUD4HHNSNrXIMpHsdofvFNo6XmRMfIK74=; b=Cqr1ARw2zTdtnRR8ZWHpWowM/jo7LYxp7GzFKiojrhwPEYQMdQsLH2FBOvY30bsr mOE/lhQIVPfcZO01AhU3KbCF4IgQJTkcR/uDnR9tusKGcCLGb5/zrcurT+ai4HSvlWZ 9RFtJZWD8d4iEqmd8wRO86rnyPrJHsPhG6NFOpyI= Received: by mx.zohomail.com with SMTPS id 1719843681889510.00753732030466; Mon, 1 Jul 2024 07:21:21 -0700 (PDT) From: Ricardo Wurmus To: guix@mawumag.com Subject: Re: [PATCH 2/2] bioinformatics: Add python-muon In-Reply-To: <171887347750.7.17381680002823190276.359657180@mawumag.com> (guix@mawumag.com's message of "Thu, 20 Jun 2024 08:51:12 +0000") References: <171887347750.7.17381680002823190276.359657180@mawumag.com> Date: Mon, 01 Jul 2024 16:21:18 +0200 Message-ID: <87plrxtcpt.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 71670-done Cc: tanguy@bioneland.org, me@bonfacemunyoki.com, lars@6xq.net, jgart@dismail.de, marius@gnu.org, sharlatanus@gmail.com, 71670-done@debbugs.gnu.org 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 (-) guix@mawumag.com writes: > +(define-public python-muon Thank you for the patches! I've applied them with minor changes. (Commit ddce6b2303dc6064ca50b4fbd53389e50faa115d.) -- Ricardo ------------=_1719843722-21706-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 20 Jun 2024 08:45:56 +0000 Received: from localhost ([127.0.0.1]:48957 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sKDQa-0002Dz-0a for submit@debbugs.gnu.org; Thu, 20 Jun 2024 04:45:56 -0400 Received: from lists.gnu.org ([209.51.188.17]:60198) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1sKDQX-0002Dq-RI for submit@debbugs.gnu.org; Thu, 20 Jun 2024 04:45:54 -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 1sKDQT-0000UT-J3 for guix-patches@gnu.org; Thu, 20 Jun 2024 04:45:49 -0400 Received: from mail-200161.simplelogin.co ([176.119.200.161]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1sKDQP-0008Jw-Ro for guix-patches@gnu.org; Thu, 20 Jun 2024 04:45:49 -0400 ARC-Seal: i=1; a=rsa-sha256; d=simplelogin.co; s=arc-20230626; t=1718873131; cv=none; b=R53Ts+DQUTn8pTbpp6JwkIaim3L+VxH3Xms9nPm4c8JdqK8I+UUP+csw57hfZpsYGvJEfzT+Aa4ElN4/4YRPy2xL9/oqLHnXsiU8TSTViDiUlFfVKYP9LvmHTe8XiBo9OEr5Y776DbgQ6iIkriqCgLNZrd5kdyaQKad0aEweap7CvJDBNMDa22lKlDyKFJP4Mpq/PwVzEN2Gq7KMr/WfFheyKQDbIjyPSUUd0+tWnq4Gmvv9GR+r7mXDd76h4lBQTGo1CzFXrSpa8E0cjZVif+UAIw3bdqcN3dXWLsKcAbSZ5JrQVNhtZ8OFALim3B6HDl+73muv5xH485HRjjjosA== ARC-Message-Signature: i=1; a=rsa-sha256; d=simplelogin.co; s=arc-20230626; t=1718873131; c=relaxed/simple; bh=Lz2C5VURKjGGQEFker/9GTqDHMFM5y2Rd54pguiy8A8=; h=Date:Subject:From:To:Cc; b=wzGfgktapsiKts0O9E46Z2pCR/VEGvXdbQ8uryHD5sTsgcYzemQ/Hjc+KeScg8ZkvizaB+cySOMVvpoBG6C/yBJCSiKKHdbMand+rCjxIuEOqLEOI87oaPSu+Tk6+bn27/eeSZ7ygXBreaQ+ge2rhEPp/dt7ePQZPv7/7RfKgzijzMhVrsiFXuWcIqR6+kjMfUJ4RCluxS1GeYdy0SRle1rUldWp1GKo2rtRIs8gnDUKvd3WECcoXp908nj8dyw93WGTl5eUyQBxi8OHQQ96feGXgKpkVfUqPU8uvcMIc6gTLhC9jLCTYyDdk/nZVO40MjI0HFJo+s/wKeHekcSNDw== ARC-Authentication-Results: i=1; mail.protonmail.ch DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=mawumag.com; s=dkim; t=1718873131; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=KKmtl9SwldSz5/SFSzf6718RWgZk8NSV4tVXuDv85HY=; b=b2SYWLNvOMj+wAPFDfc6ZZl166xg2ExmaaZSRwAc9awIZ9zifjjkl2gufM/s0s3gy9co9X cSijZiuISUSg7k88ByaRFcwons4HFtidOEBESyFIGT1W3ykCQd/jSVxlHMP6m00/V0k5/c Ez9p9udcTO/3dcFKMl0yTPI0j58WfmA= Date: Thu, 20 Jun 2024 08:45:24 +0000 Subject: [PATCH 0/2] bioinformatics: Add python-muon MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable From: guix@mawumag.com To: guix-patches@gnu.org Message-ID: <171887312984.7.12976181484130280866.359654925@mawumag.com> X-SimpleLogin-Type: Reply X-SimpleLogin-EmailLog-ID: 359654936 X-SimpleLogin-Want-Signing: yes Received-SPF: pass client-ip=176.119.200.161; envelope-from=sl.lmysyibtgu4tmnjuheztmlbagezdsnzzgy2v2.geznxjnsy4kfi@mawumag.com; helo=mail-200161.simplelogin.co X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 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, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=unavailable autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: tanguy@bioneland.org, me@bonfacemunyoki.com, lars@6xq.net, Ricardo Wurmus , jgart@dismail.de, marius@gnu.org, sharlatanus@gmail.com 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: -2.3 (--) I am adding the packages python-muon and python-mofapy2 (as a muon dependency). Muon is a multi-omics analysis framework and is part of the scverse. I had to modify a couple of tests slightly (explained in the comments). Marco Baggio (2): bioinformatics: Add python-mofapy2 bioinformatics: Add python-muon gnu/packages/bioinformatics.scm | 93 +++++++++++++++++++++++++++++++++ 1 file changed, 93 insertions(+) base-commit: e32e3d0a03dc17c4c54a91aad053c9036998b601 -- 2.45.1 ------------=_1719843722-21706-1--