From patchwork Sun Oct 10 15:04:28 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Felix Gruber X-Patchwork-Id: 367 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 A3CB127BBE3; Sun, 10 Oct 2021 16:06:12 +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=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS,T_DKIM_INVALID, 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 2890827BBE1 for ; Sun, 10 Oct 2021 16:06:12 +0100 (BST) Received: from localhost ([::1]:38476 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1mZaOx-0001y1-3l for patchwork@mira.cbaines.net; Sun, 10 Oct 2021 11:06:11 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:32792) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1mZaOo-0001xk-Pp for guix-patches@gnu.org; Sun, 10 Oct 2021 11:06:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:44103) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1mZaOo-00034w-G8 for guix-patches@gnu.org; Sun, 10 Oct 2021 11:06:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1mZaOo-0006aR-8e for guix-patches@gnu.org; Sun, 10 Oct 2021 11:06:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#50813] [PATCH v2 0/6] gnu: python-pandas: Update to 1.3.3. Resent-From: Felix Gruber Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 10 Oct 2021 15:06:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 50813 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 50813@debbugs.gnu.org, Ludovic =?utf-8?q?Court=C3=A8s?= Cc: Felix Gruber Received: via spool by 50813-submit@debbugs.gnu.org id=B50813.163387834925282 (code B ref 50813); Sun, 10 Oct 2021 15:06:02 +0000 Received: (at 50813) by debbugs.gnu.org; 10 Oct 2021 15:05:49 +0000 Received: from localhost ([127.0.0.1]:55646 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mZaOa-0006Zi-Ub for submit@debbugs.gnu.org; Sun, 10 Oct 2021 11:05:49 -0400 Received: from mout01.posteo.de ([185.67.36.65]:44649) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mZaOX-0006ZS-QZ for 50813@debbugs.gnu.org; Sun, 10 Oct 2021 11:05:47 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 7735224002D for <50813@debbugs.gnu.org>; Sun, 10 Oct 2021 17:05:39 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1633878339; bh=kkk4jVNEjlGaHRu95ufJMiV6B9au1ZOTyeQzl0YIhZA=; h=From:To:Cc:Subject:Date:From; b=McuO5WTJxS/AYXgUHFVa8f8XdbdrEzbMykcCEPQXoZeoIFHQDY1eyT1SuT+Y6UpYT KbsbFRq3Hh6/lzjVwXxVlxauDQgitEBJ4xU05gxHOffe+yW+Fz6C5ev57E+QLbhzxD 6hoWYGYC8WHMFU4pVUi9uPETB7Nry2vVhUcEnvMzwhgSZZFkBRJBOKN6rNdD2KfoEw FNIS94PbiZzgi9fsFOhg7gOdNwy2kfwshVrlFPCJ5ipXlsiAefkPyiFVDCN7fOXx11 9yu4UEHpXohHU1lgEJFCjYob0aLuWA3yfUy8pZA3QF86sayEZQEtJpKKQ164EYlq9X MEucIx365Ca7g== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4HS4xG3pRnz9rxP; Sun, 10 Oct 2021 17:05:38 +0200 (CEST) From: Felix Gruber Date: Sun, 10 Oct 2021 15:04:28 +0000 Message-Id: <20211010150434.1966-1-felgru@posteo.net> In-Reply-To: <87zgrldwzk.fsf@gnu.org> References: <87zgrldwzk.fsf@gnu.org> MIME-Version: 1.0 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 Hi Ludo’, On 10/7/21 11:07 AM, Ludovic Courtès wrote: > > Felix Gruber skribis: > >> * gnu/packages/python-science.scm (python-pandas): Update to 1.3.3. > > The upgrade appears to cause build failures for python-dask and > pigx-rnaseq (via snakemake) among other things. > > Could you take a look? I could not reproduce the build failure in pigx-rnaseq. For python-dask the build failure could be fixed by upgrading it to 2021.9.1, whose changelog mentioned that they've deactivated a failing test when building against Pandas >= 1.3.3. After updating dask, its dependent packages python-distributed and python-eliot failed to build. I've fixed both by updating them to their latest releases and disabling failing tests. I've also took the oppurtunity to update the synapse package which was the only package depending on python-eliot. > For the record, I tried to build everything reported by ‘guix refresh -l > python-pandas’ though some of them (ocaml4.07-re, etc.) would already > fail to build before the upgrade. Of the remaining packages reported by `guix refresh -l python-pandas`, I've identified the following packages with build failures: * clipper@2.0 sometimes fails due to nondeterministic test `test_get_FDR_cutoff_mean`. The docstring of this test already says "Difficult to test because of random sampling" followed by a TODO. I've thus deactivated this test, to make it build deterministically. * pplacer@1.1.alpha19 already failed on master due to unbuildable ocaml4.07-re@1.10.3. * python-scikit-rebate@0.6 Already failed on master in test `skrebate`: ModuleNotFoundError: No module named 'sklearn.externals.joblib' (A guix refresh -u python-scikit-rebate would update it to 0.62 which was buildable, but this version seemed to come without any tests, so I'm not sure if this is the right solution.) * orange@3.28.0 Already failed to build on mater, because its dependency python-orange-canvas-core. I've looked into updating both to their latest version, but that would require updating python-pygments to >= 2.8.0 which would entail rebuilding 561 dependent packages. * imp@2.13.0 I was running out of memory while building imp, which in the end killed the build process. It seems that my 8GB of RAM are not sufficient to build imp, so I cannot tell if the update of python-pandas might break imp. * tadbit@1.0.1 depends on imp, so I couldn't build it either. I've prepared patches for those packages that I was able to fix. Best, Felix Felix Gruber (6): gnu: python-pandas: Update to 1.3.3. gnu: python-dask: Update to 2021.9.1. gnu: python-distributed: Update to 2021.09.1. gnu: python-eliot: Update to 1.13.0. gnu: synapse: Update to 1.44.0. gnu: clipper: Disable non-deterministic test. gnu/packages/bioinformatics.scm | 9 ++++++++- gnu/packages/matrix.scm | 5 +++-- gnu/packages/python-science.scm | 15 +++++++++------ gnu/packages/python-xyz.scm | 19 +++++++++++++++---- 4 files changed, 35 insertions(+), 13 deletions(-)