diff options
| author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2021-06-07 13:53:28 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-06-08 16:35:17 +0200 |
| commit | dd3698c1ac1018ef46d9ec2da814ecab006716bc (patch) | |
| tree | 1d0aecdb795d1e40bb10fc3a2399c5314ca19b21 | |
| parent | c03da7edb0bc4bb48c2f8e00e1ef5932c399f800 (diff) | |
gnu: python-hicmatrix: Update to 15.
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15.
[arguments]: Enabled tests. Remove 'relax-requirements phase.
[native-inputs]: Add python-pytest.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 37 |
1 files changed, 18 insertions, 19 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7a47943d2d..7c4536963c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11822,29 +11822,26 @@ 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) @@ -11852,6 +11849,8 @@ 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 |