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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: 0.18 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b="PB/tWKBq"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (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: 4A31620C6B X-Spam-Score: 0.18 X-Migadu-Scanner: scn0.migadu.com X-TUID: OiHHESVz1OTX Hi Guix! I changed the commit message! All the best! On 06.06.2021 10:31, Mădălin Ionel Patrașcu wrote: > * gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15. > [source]: Changed from pypi to github, pypi sources do not contain tests. > [arguments]: Removed build phase "relax-requirements" and replaced the > pahse "check". > [native-inputs]: Add python-pytest. > --- > gnu/packages/bioinformatics.scm | 37 ++++++++++++++++----------------- > 1 file changed, 18 insertions(+), 19 deletions(-) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index 2de8a59d3c..02da131fdf 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -11786,29 +11786,26 @@ such as Hi-C contact matrices.") > (define-public python-hicmatrix > (package > (name "python-hicmatrix") > - (version "12") > - (source > - (origin > - ;; Version 12 is not available on pypi. > - (method git-fetch) > - (uri (git-reference > - (url "https://github.com/deeptools/HiCMatrix") > - (commit version))) > - (file-name (git-file-name name version)) > - (sha256 > - (base32 > - "1xhdyx16f3brgxgxybixdi64ki8nbbkq5vk4h9ahi11pzpjfn1pj")))) > + (version "15") > + (source > + (origin > + ;;Pypi sources do not contain any test > + (method git-fetch) > + (uri (git-reference > + (url "https://github.com/deeptools/HiCMatrix") > + (commit version))) > + (file-name (git-file-name name version)) > + (sha256 > + (base32 > + "1dshjxgb16sdfg9k1bhw2yhyngac04k4ca7aqy8g3i3pprr068r5")))) > (build-system python-build-system) > (arguments > `(#:phases > (modify-phases %standard-phases > - (add-after 'unpack 'relax-requirements > - (lambda _ > - (substitute* '("requirements.txt" > - "setup.py") > - (("cooler *=+ *0.8.5") > - "cooler==0.8.*")) > - #t))))) > + (replace 'check > + (lambda* (#:key tests? #:allow-other-keys) > + (when tests? > + (invoke "python" "-m" "pytest" "-v"))))))) > (propagated-inputs > `(("python-cooler" ,python-cooler) > ("python-intervaltree" ,python-intervaltree) > @@ -11816,6 +11813,8 @@ such as Hi-C contact matrices.") > ("python-pandas" ,python-pandas) > ("python-scipy" ,python-scipy) > ("python-tables" ,python-tables))) > + (native-inputs > + `(("python-pytest" ,python-pytest))) > (home-page "https://github.com/deeptools/HiCMatrix/") > (synopsis "HiCMatrix class for HiCExplorer and pyGenomeTracks") > (description -- System Administrator Bioinformatics and Omics Data Science BIMSB - MDC