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25 Aug 2022 13:14:13 +0200 Message-ID: Date: Thu, 25 Aug 2022 13:14:13 +0200 MIME-Version: 1.0 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:91.0) Gecko/20100101 Thunderbird/91.12.0 Content-Language: en-US From: Matthieu Simonin Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Mailman-Approved-At: Thu, 25 Aug 2022 11:35:14 -0400 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Mailman-Approved-At: Fri, 26 Aug 2022 10:00:01 -0400 X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1661522440; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; 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spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 6.39 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=inria.fr header.s=dc header.b=uPYtMITg; dmarc=fail reason="SPF not aligned (relaxed)" header.from=inria.fr (policy=none); spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: DA5F6390E4 X-Spam-Score: 6.39 X-Migadu-Scanner: scn0.migadu.com X-TUID: 0qYAwBuiZ9XK Hi there, I've taken a stab at using it and restoring the patch as Konrad pointed seems the way to go. But I also found that the package definition doesn't follow the guidelines[1] regarding the inputs definition. One should use `propagated-inputs` instead of `inputs` for a python package. In the current situation we can't invoke `snakemake` as a module: `python -m snakemake` fails as the input dependencies aren't linked in the guix profile. This way of invoking snakemake is used internally by snakemake here and there (for instance when calling the unit tests generated by `snakemake --generate-unit-tests`[2][3]. [1]: https://guix.gnu.org/manual/en/html_node/package-Reference.html [2]: https://snakemake.readthedocs.io/en/stable/snakefiles/testing.html [3]: https://github.com/snakemake/snakemake/blob/v7.7.0/snakemake/unit_tests/templates/ruletest.py.jinja2