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| author | Ricardo Wurmus <rekado@elephly.net> | 2024-05-03 11:45:07 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2024-05-05 22:38:18 +0200 |
| commit | d14d5147b1eb42c98591af96f05a872d9ea791ae (patch) | |
| tree | 7b2f51161cc58e491058319b9a401e48a7f7bc80 /gnu/packages/bioinformatics.scm | |
| parent | 317be75d1d70673d73f76df1dafd7fe873f365bd (diff) | |
gnu: python-bioframe: Update to 0.6.4.
* gnu/packages/bioinformatics.scm (python-bioframe): Update to 0.6.4.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom 'check phase; add 'pre-check phase. Use
#:test-flags to disable tests that require internet access.
[native-inputs]: Add python-hatchling.
[propagated-inputs]: Add python-pyyaml.
Change-Id: Iad1c8c6ef8f52886e398e9c4d2d384c5fce075c6
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 24 |
1 files changed, 14 insertions, 10 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dff8ba4d87..946898d055 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2857,7 +2857,7 @@ telomerecat can produce an estimate in ~1 hour.") (define-public python-bioframe (package (name "python-bioframe") - (version "0.3.3") + (version "0.6.4") (source (origin (method git-fetch) @@ -2868,18 +2868,21 @@ telomerecat can produce an estimate in ~1 hour.") (file-name (git-file-name name version)) (sha256 (base32 - "14lvb18d4npapyi6j2zqh9q94l658dzmka5riiizw1h0zb0kp9xb")))) - (build-system python-build-system) + "1m99hgxw4cb2x4qszb2lhp1isz57sdkqbmcgisnbqxqxkv4gba7v")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (setenv "MPLCONFIGDIR" "/tmp") - (when tests? - (invoke "pytest" "-v"))))))) + (list + #:test-flags + '(list "-k" (string-append "not test_fetch_chromsizes" + " and not test_fetch_chromsizes_local_vs_ucsc" + " and not test_fetch_centromeres")) + #:phases + '(modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ (setenv "MPLCONFIGDIR" "/tmp")))))) (native-inputs (list python-biopython + python-hatchling python-pysam python-pytest python-wheel)) @@ -2887,6 +2890,7 @@ telomerecat can produce an estimate in ~1 hour.") (list python-matplotlib python-numpy python-pandas + python-pyyaml python-requests)) (home-page "https://github.com/open2c/bioframe") (synopsis "Pandas utilities for tab-delimited and other genomic files") |