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Wed, 19 May 2021 20:16:51 +0200 (CEST) Message-ID: From: Vinicius Monego Date: Wed, 19 May 2021 18:16:41 +0000 In-Reply-To: References: Content-Type: text/plain; charset="UTF-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit 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+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1621448288; h=from:from:sender:sender: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: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 guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: -1.34 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=posteo.net header.s=2017 header.b=ey+Fmbv8; dmarc=fail reason="SPF not aligned (strict)" header.from=posteo.net (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: 61DA8D5B4 X-Spam-Score: -1.34 X-Migadu-Scanner: scn1.migadu.com X-TUID: 9RnNKTDpFAUI Hi, Em seg, 2021-04-26 às 20:01 +0000, Sharlatan Hellseher escreveu: > Hi Guix team! > > Here is my attempt to pack bulky python package - > https://www.astropy.org/ > I've disabled test and add minor modification removing `_compiler.c' > file. I've tried to package AstroPy before but got stuck in the dependencies, more specifically pytest-astropy. There is a bug somewhere that pytest- filter-subpackage is not found by setup.py, even though it's listed in the inputs. I encountered that problem again here, after enabling the tests. > + ;; NOTE: (Sharlatan-20210426T204315+0100): Tests require build > astropy > + ;; module, it needs a good review on how to enable them. > + `(#:tests? #f AstroPy uses pytest, which is not listed in your native-inputs. The other dependencies I had to add are python-hypothesis, python-pytest- cov, python-pytest-astropy and python-pytest-xdist. According to the documentation, it should be as simple as running pytest to run the entire test suite: https://docs.astropy.org/en/latest/development/testguide.html#running-tests If you end up in 'ModuleNotFoundError: No module named "astropy"', you may have to update PYTHONPATH after the install phase with (add- installed-pythonpath inputs outputs). That usually happens when replacing the check phase. > + (inputs > + `(("asdf" ,python-asdf) > + ("beautifulsoup4" ,python-beautifulsoup4) > + ("bleach" ,python-bleach) > + ("bottleneck" ,python-bottleneck) > + ("cfitsio" ,cfitsio) > + ("dask" ,python-dask) > + ("expat" ,expat) > + ("graphviz" ,graphviz) > + ("h5py" ,python-h5py) > + ("html5lib" ,python-html5lib) > + ("jplephem" ,python-jplephem) > + ("matplotlib" ,python-matplotlib) > + ("mpmath" ,python-mpmath) > + ("numpy" ,python-numpy) > + ("pandas" ,python-pandas) > + ("pyerfa" ,python-pyerfa) > + ("pytz" ,python-pytz) > + ("pyyaml" ,python-pyyaml) > + ("scipy" ,python-scipy) > + ("sortedcontainers" ,python-sortedcontainers) > + ("wcslib" ,wcslib))) AstroPy is a library, its Python inputs should be propagated here. See https://guix.gnu.org/manual/en/html_node/package-Reference.html#package-Reference for reference. Also, the documentation states that the only strict requirements are PyERFA and NumPy: https://docs.astropy.org/en/stable/install.html IMO we should only propagate these, and leave the rest in native-inputs as needed by tests. Now speaking of the astropy dependencies, pytest-astropy is supposed to propagate its six dependencies. AFAIK its purpose is to be a metapackage to install these other 6 pytest modules. PyERFA should also propagate numpy (liberfa can remain as normal input). I'll take a look at this package again next week. Could you test these suggestions in the meantime? Vinicius