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Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 01 Apr 2021 15:39:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46946 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Cc: 46946@debbugs.gnu.org Received: via spool by 46946-submit@debbugs.gnu.org id=B46946.161729153613713 (code B ref 46946); Thu, 01 Apr 2021 15:39:02 +0000 Received: (at 46946) by debbugs.gnu.org; 1 Apr 2021 15:38:56 +0000 Received: from localhost ([127.0.0.1]:58347 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lRzPM-0003Z7-EI for submit@debbugs.gnu.org; Thu, 01 Apr 2021 11:38:56 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21166) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lRzPK-0003Yy-Bj for 46946@debbugs.gnu.org; Thu, 01 Apr 2021 11:38:55 -0400 ARC-Seal: i=1; a=rsa-sha256; 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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=elephly.net header.s=zoho header.b=cQsOmxX+; arc=reject ("signature check failed: fail, {[1] = sig:zohomail.com:reject}"); dmarc=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-Spam-Score: 0.57 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=elephly.net header.s=zoho header.b=cQsOmxX+; arc=reject ("signature check failed: fail, {[1] = sig:zohomail.com:reject}"); dmarc=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: 7B8FB28102 X-Spam-Score: 0.57 X-Migadu-Scanner: scn0.migadu.com X-TUID: 2IU5ZQ6BHrvD Hi M=C4=83d=C4=83lin, > * gnu/packages/bioinformatics.scm (python-bioframe): New variable. Thanks for the patch. Despite all the test inputs the test suite is not actually run: --8<---------------cut here---------------start------------->8--- starting phase `check' running "python setup.py" with command "test" and parameters () running test running egg_info writing bioframe.egg-info/PKG-INFO writing dependency_links to bioframe.egg-info/dependency_links.txt writing requirements to bioframe.egg-info/requires.txt writing top-level names to bioframe.egg-info/top_level.txt reading manifest file 'bioframe.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '__pycache__/*' found anywhe= re in distribution warning: no previously-included files matching '*.so' found anywhere in dis= tribution warning: no previously-included files matching '*.pyd' found anywhere in di= stribution warning: no previously-included files matching '*.pyc' found anywhere in di= stribution warning: no previously-included files matching '.git*' found anywhere in di= stribution warning: no previously-included files matching '.deps/*' found anywhere in = distribution warning: no previously-included files matching '.DS_Store' found anywhere i= n distribution writing manifest file 'bioframe.egg-info/SOURCES.txt' running build_ext /tmp/guix-build-python-bioframe-0.2.0.drv-0/source/bioframe/io/dask.py:47: = NumbaWarning:=20 Compilation is falling back to object mode WITH looplifting enabled because= Function "reg2bins" failed type inference due to: No conversion from list(= int64) to int32 for '$262return_value.1', defined at None File "bioframe/io/dask.py", line 79: def reg2bins(rbeg, rend): return lst ^ During: typing of assignment at /tmp/guix-build-python-bioframe-0.2.0.drv-0= /source/bioframe/io/dask.py (79) File "bioframe/io/dask.py", line 79: def reg2bins(rbeg, rend): return lst ^ @numba.jit("int32(int32, int32)") /tmp/guix-build-python-bioframe-0.2.0.drv-0/source/bioframe/io/dask.py:47: = NumbaWarning:=20 Compilation is falling back to object mode WITHOUT looplifting enabled beca= use Function "reg2bins" failed type inference due to: cannot determine Numb= a type of File "bioframe/io/dask.py", line 59: def reg2bins(rbeg, rend): k =3D 9 + (rbeg >> 23) ^ @numba.jit("int32(int32, int32)") /gnu/store/sm6k3ar46q11w77s7cc2q1hv33q8p3v0-python-numba-0.51.2/lib/python3= .8/site-packages/numba/core/object_mode_passes.py:177: NumbaWarning: Functi= on "reg2bins" was compiled in object mode without forceobj=3DTrue, but has = lifted loops. File "bioframe/io/dask.py", line 50: def reg2bins(rbeg, rend): MAX_BIN =3D ((1 << 18) - 1) // 7 ^ warnings.warn(errors.NumbaWarning(warn_msg, /gnu/store/sm6k3ar46q11w77s7cc2q1hv33q8p3v0-python-numba-0.51.2/lib/python3= .8/site-packages/numba/core/object_mode_passes.py:187: NumbaDeprecationWarn= ing:=20 Fall-back from the nopython compilation path to the object mode compilation= path has been detected, this is deprecated behaviour. For more information visit https://numba.pydata.org/numba-doc/latest/refere= nce/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-us= ing-jit File "bioframe/io/dask.py", line 50: def reg2bins(rbeg, rend): MAX_BIN =3D ((1 << 18) - 1) // 7 ^ warnings.warn(errors.NumbaDeprecationWarning(msg, ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK phase `check' succeeded after 3.1 seconds --8<---------------cut here---------------end--------------->8--- I made a couple of cosmestic changes: --8<---------------cut here---------------start------------->8--- (define-public python-bioframe (package (name "python-bioframe") (version "0.2.0") ;; Sources on pypi do not contain requirements.txt (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/open2c/bioframe") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0w5xrb93cf3hx3d1lw48a0l1ranghpj260b05b1rpk58wwwcsqfh")))) (build-system python-build-system) (propagated-inputs `(("python-click" ,python-click) ("python-numpy" ,python-numpy) ("python-pandas" ,python-pandas) ("python-requests" ,python-requests))) (native-inputs `(("python-dask" ,python-dask) ; for tests ("python-matplotlib" ,python-matplotlib) ; for tests ("python-numba" ,python-numba) ; for tests ("python-pypairix" ,python-pypairix) ; for tests ("python-pytest" ,python-pytest) ("python-wheel" ,python-wheel))) (home-page "https://github.com/open2c/bioframe") (synopsis "Framework for genomic data analysis using Pandas dataframes") (description "This package is a library to enable flexible and scalable operations = on genomic interval dataframes in Python. @code{python-bioframe} enables acce= ss; to a rich set of dataframe operations. Working in Python enables rapid visualization (e.g. matplotlib, seaborn) and iteration of genomic analyses.= ") (license license:expat))) --8<---------------cut here---------------end--------------->8--- Please note that the lack of requirements.txt on pypi shouldn=E2=80=99t be = an obstacle to use the sources from pypi. It should build just as well. --=20 Ricardo