From patchwork Tue Jun 1 08:33:34 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Roel Janssen X-Patchwork-Id: 29743 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 85EAD27BC81; Tue, 1 Jun 2021 09:35:13 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.9 required=5.0 tests=BAYES_00,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 4D5FB27BC78 for ; Tue, 1 Jun 2021 09:35:08 +0100 (BST) Received: from localhost ([::1]:41798 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lnzrf-000427-Dh for patchwork@mira.cbaines.net; Tue, 01 Jun 2021 04:35:07 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:37338) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lnzra-00041z-2g for guix-patches@gnu.org; Tue, 01 Jun 2021 04:35:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:52406) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lnzrZ-00010D-RQ for guix-patches@gnu.org; Tue, 01 Jun 2021 04:35:01 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lnzrZ-0002Ph-Oq for guix-patches@gnu.org; Tue, 01 Jun 2021 04:35:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48774] [PATCH] Fix build of python-scanpy Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 01 Jun 2021 08:35:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 48774 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 48774@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.16225364419187 (code B ref -1); Tue, 01 Jun 2021 08:35:01 +0000 Received: (at submit) by debbugs.gnu.org; 1 Jun 2021 08:34:01 +0000 Received: from localhost ([127.0.0.1]:35714 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lnzqQ-0002Ng-Oj for submit@debbugs.gnu.org; Tue, 01 Jun 2021 04:34:01 -0400 Received: from lists.gnu.org ([209.51.188.17]:57512) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lnzqI-0002NQ-8g for submit@debbugs.gnu.org; Tue, 01 Jun 2021 04:33:48 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:36986) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lnzqI-0003xu-2E for guix-patches@gnu.org; Tue, 01 Jun 2021 04:33:42 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:50288) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lnzqH-0008U6-RT for guix-patches@gnu.org; Tue, 01 Jun 2021 04:33:41 -0400 Received: from [143.121.198.253] (port=37750) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lnzqG-0004Gx-Fr for guix-patches@gnu.org; Tue, 01 Jun 2021 04:33:41 -0400 From: Roel Janssen Message-ID: <4ee322e7-2aaf-750a-bee7-4bbc8d7bd64b@gnu.org> Date: Tue, 1 Jun 2021 10:33:34 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.8.1 MIME-Version: 1.0 Content-Language: en-US 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 Dear Guix, The attached two patches update python-anndata and python-scanpy, which effectively fix the build for python-scanpy. python-anndata switched to a PEP518 setup instead of the regular Python "setup.py" approach.  So with some help on IRC, I added custom phases inspired by the python-tinycss2 package. Kind regards, Roel Janssen From 094705a4ee2c46e8ed1b98c39c03b2a21c688c5e Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 1 Jun 2021 10:25:12 +0200 Subject: [PATCH 2/2] gnu: python-scanpy: Update to 1.7.2. * gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2. --- gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++---- 1 file changed, 21 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1f018befe6..2b64a04150 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -122,6 +122,7 @@ #:use-module (gnu packages popt) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) + #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) #:use-module (gnu packages python-compression) #:use-module (gnu packages python-science) @@ -11096,14 +11097,14 @@ in RNA-seq data.") (define-public python-scanpy (package (name "python-scanpy") - (version "1.4.6") + (version "1.7.2") (source (origin (method url-fetch) (uri (pypi-uri "scanpy" version)) (sha256 (base32 - "0s2b6cvaigx4wzw3850qb93sjwwxbzh22kpbp498zklc5rjpbz4l")))) + "0c66adnfizsyk0h8bv2yhmay876z0klpxwpn4z6m71wly7yplpmd")))) (build-system python-build-system) (arguments `(#:phases @@ -11114,12 +11115,25 @@ in RNA-seq data.") (delete-file-recursively "scanpy/tests/notebooks") (delete-file "scanpy/tests/test_clustering.py") (delete-file "scanpy/tests/test_datasets.py") + (delete-file "scanpy/tests/test_highly_variable_genes.py") ;; TODO: I can't get the plotting tests to work, even with Xvfb. (delete-file "scanpy/tests/test_plotting.py") (delete-file "scanpy/tests/test_preprocessing.py") (delete-file "scanpy/tests/test_read_10x.py") + ;; The following tests need anndata.tests, which aren't included + ;; in the final python-anndata package. + (delete-file "scanpy/tests/test_combat.py") + (delete-file "scanpy/tests/test_embedding_plots.py") + (delete-file "scanpy/tests/test_normalization.py") + (delete-file "scanpy/tests/test_pca.py") + (delete-file "scanpy/tests/external/test_scrublet.py") + + ;; The following tests requires 'scanorama', which isn't + ;; packaged yet. + (delete-file "scanpy/tests/external/test_scanorama_integrate.py") + (setenv "PYTHONPATH" (string-append (getcwd) ":" (getenv "PYTHONPATH"))) @@ -11144,11 +11158,14 @@ in RNA-seq data.") ("python-seaborn" ,python-seaborn) ("python-statsmodels" ,python-statsmodels) ("python-tables" ,python-tables) + ("python-pytoml" ,python-pytoml) ("python-tqdm" ,python-tqdm) ("python-umap-learn" ,python-umap-learn))) (native-inputs - `(("python-pytest" ,python-pytest) - ("python-setuptools-scm" ,python-setuptools-scm))) + `(("python-leidenalg" ,python-leidenalg) + ("python-pytest" ,python-pytest) + ("python-setuptools-scm" ,python-setuptools-scm) + ("python-sinfo" ,python-sinfo))) (home-page "https://github.com/theislab/scanpy") (synopsis "Single-Cell Analysis in Python.") (description "Scanpy is a scalable toolkit for analyzing single-cell gene -- 2.31.1