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Mon, 6 Jan 2025 12:44:15 +0100 (CET) Received: from localhost (dhcp-67-68.ixxi.ens-lyon.fr [140.77.67.68]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange ECDHE (P-256) server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by lxc-smtp2.ens-lyon.fr (Postfix) with ESMTPSA id A1ECC140388 for ; Mon, 6 Jan 2025 12:44:14 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=simple/simple; d=ens-lyon.fr; s=2024; t=1736163855; bh=xiH7Or9P6TmV/BrfpZjd9jWbpdUE4ifwaUDp03NiWV0=; h=Date:From:To:Subject:From; b=p78L9txsGxDuSC9p5d86F/oeiSYM6UyydRYEF4K75NY/cibAAza6WWi+aK0I/Kgoe sv7yEZgfZVxn2LVsxc1av8uR+Gi7Oh78Y1GzTCBrcUGlEGYx5hj5t0GvXZrQ4vUp8p e+fQHQ+U3hySmJ2VliUQqJAr4fhh5Y3TmI3LA/xIRNmW8g353BUM6+LrBzUMc9hRGX UeExDjajQzr+8mttqiXTb1xRPu0C29eUlj/swWUrhyOsSOuoadYw5GxXADBXdzuHn3 5MEUGsQUgzq/y8VrLrEzRL2TcyUYKSqKGmeUZa/44TRBeySV9LHvxxetIZJG3OeX6D 6wlo9axm3930Q== Date: Mon, 6 Jan 2025 12:44:14 +0100 From: Alice BRENON Message-ID: <20250106124414.7861f9b8@ens-lyon.fr> X-Mailer: Claws Mail 4.3.0 (GTK 3.24.41; x86_64-pc-linux-gnu) MIME-Version: 1.0 Received-SPF: pass client-ip=140.77.167.81; envelope-from=alice.brenon@ens-lyon.fr; helo=lxc-smtp2.ens-lyon.fr X-Spam_score_int: -27 X-Spam_score: -2.8 X-Spam_bar: -- X-Spam_report: (-2.8 / 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_LOW=-0.7, RCVD_IN_MSPIKE_H2=-0.001, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, RCVD_IN_VALIDITY_SAFE_BLOCKED=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 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 Hi all, The package `python-spacy` seems to have been broken at least partially by the recent changes in python tooling. The attached patch is a very short first step into fixing it. This message doesn't hope to get it accepted but is rather meant to open the discussion on the topic. - the first issue is naturally the new required dependencies in `native-inputs` mentioned in bdde278dc9c565d8e9d11427c3a670ba86808af5 an visible in many python packages commit these past weeks. Surprisingly, I managed to compile `python-spacy` by adding only `python-wheel`, without `python-setuptools`. What makes both required? Are we sure that both were required in each and every python package recently modified? - the second issue which I can't link with the changes in our tooling is caused by two packages which tests have broken: `python-aws-xray-sdk` and `python-jose`. First one seems to have a problem in sqlalchemy version (it seems to be using too recent a syntax; which is weird considering the fact that it uses version 2 and that it used to work — `python-aws-xray-sdk` hasn't been modified since cec543e7 on april the 27th 2023!). Second one now has trouble checking several certificates for mere formatting reasons (expected and actual PEMs are almost the same, only newlines are different; fixing the code of the test itself, another one breaks somewhere else. It seems that these source codes aren't sturdy enough and don't work at all in the package environment guix provides. - these packages are dependencies of `python-moto`. Removing them from the dependencies, many tests break as expected for lack of these modules, but disabling them isn't enough: I played a game of whack-a-mole yesterday trying to get the tests to pass. Strangely, whereas testing with hypothesis runs all the tests and then reports all that have failed, fixing the one reported and running the tests again doesn't help: new tests break in different files that were apparently fine before… I had three iterations of this process, each one consuming half and hour on my machine. As far as I am concerned, these tests are unreliable and don't bring any additional confidence to the package. I have disabled them to test the fix for `python-spacy` and have been able to compile it and use the package. Appart from that, everything looks ok. `python-moto` appears as a dependency of `python-smart-open` which itself is both a direct dependency of `python-spacy` and a dependency of `python-pathy` which is also a dependency of `python-spacy`. python-smart-open -> python-moto python-pathy -> python-smart-open python-spacy -> python-smart-open, python-pathy I understand that disabling the tests on a package entirely isn't a very sound practice for a distribution so I doubt this is an acceptable fix. As I understand the situation the next steps will be to sort things between `python-aws-xray-sdk` and `python-sqlalchemy` and to understand why the tests in `python-jose` have suddenly broken so bad. Best, Alice From 9a349ac01cec33fc1e49ba7f80ae18ef5cfdf922 Mon Sep 17 00:00:00 2001 Message-ID: <9a349ac01cec33fc1e49ba7f80ae18ef5cfdf922.1736155491.git.alice.brenon@ens-lyon.fr> From: Alice BRENON Date: Sat, 4 Jan 2025 23:01:50 +0100 Subject: [PATCH] gnu: python-spacy: Fix build. * gnu/packages/machine-learning.scm (python-spacy): Fix build. [native-inputs]: Add python-wheel Change-Id: I6550f6dc0cb1fb88fc733f6471f1831c4ba95977 --- gnu/packages/machine-learning.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index c7d336b8b3..1617ef917e 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1282,7 +1282,7 @@ (define-public python-spacy python-typing-extensions python-wasabi)) (native-inputs - (list python-cython python-pytest python-mock)) + (list python-cython python-pytest python-mock python-wheel)) (home-page "https://spacy.io") (synopsis "Natural Language Processing (NLP) in Python") (description base-commit: 7a7c01b393ecb20dff142b9ea9bf8317e994bef2 -- 2.47.1