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gnu: python-bioframe: Update to 0.6.4.

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* 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
This commit is contained in:
Ricardo Wurmus 2024-05-03 11:45:07 +02:00
parent 317be75d1d
commit d14d5147b1
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GPG key ID: 197A5888235FACAC
1 changed files with 14 additions and 10 deletions
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gnu/packages/bioinformatics.scm
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@ -2857,7 +2857,7 @@ telomerecat can produce an estimate in ~1 hour.")
(define-public python-bioframe (define-public python-bioframe
(package (package
(name "python-bioframe") (name "python-bioframe")
(version "0.3.3") (version "0.6.4")
(source (source
(origin (origin
(method git-fetch) (method git-fetch)
@ -2868,18 +2868,21 @@ telomerecat can produce an estimate in ~1 hour.")
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"14lvb18d4npapyi6j2zqh9q94l658dzmka5riiizw1h0zb0kp9xb")))) "1m99hgxw4cb2x4qszb2lhp1isz57sdkqbmcgisnbqxqxkv4gba7v"))))
(build-system python-build-system) (build-system pyproject-build-system)
(arguments (arguments
`(#:phases (list
(modify-phases %standard-phases #:test-flags
(replace 'check '(list "-k" (string-append "not test_fetch_chromsizes"
(lambda* (#:key tests? #:allow-other-keys) " and not test_fetch_chromsizes_local_vs_ucsc"
(setenv "MPLCONFIGDIR" "/tmp") " and not test_fetch_centromeres"))
(when tests? #:phases
(invoke "pytest" "-v"))))))) '(modify-phases %standard-phases
(add-before 'check 'pre-check
(lambda _ (setenv "MPLCONFIGDIR" "/tmp"))))))
(native-inputs (native-inputs
(list python-biopython (list python-biopython
python-hatchling
python-pysam python-pysam
python-pytest python-pytest
python-wheel)) python-wheel))
@ -2887,6 +2890,7 @@ telomerecat can produce an estimate in ~1 hour.")
(list python-matplotlib (list python-matplotlib
python-numpy python-numpy
python-pandas python-pandas
python-pyyaml
python-requests)) python-requests))
(home-page "https://github.com/open2c/bioframe") (home-page "https://github.com/open2c/bioframe")
(synopsis "Pandas utilities for tab-delimited and other genomic files") (synopsis "Pandas utilities for tab-delimited and other genomic files")