diff options
| author | Sharlatan Hellseher <sharlatanus@gmail.com> | 2025-09-23 12:32:19 +0100 |
|---|---|---|
| committer | Sharlatan Hellseher <sharlatanus@gmail.com> | 2025-09-25 09:36:58 +0100 |
| commit | 75fdb7a43ade40c571a33079cb0ca4701181a947 (patch) | |
| tree | c6f67af5daba8d1c44ce6d91922d1fc0cbe20859 /gnu | |
| parent | c3744a8ba14a8f54c1cc4ec3fbc49e4e6b915520 (diff) | |
gnu: python-pybbi: Update to 0.4.1.
* gnu/packages/bioinformatics.scm (python-pybbi): Update to 0.4.1. Use
G-Expressions.
[build-system]: Switch to pyproject-build-system.
[arguments] <test-flags>: Skip tests requiring network access.
<phases>: Use default 'check; add 'remove-local-bbi.
[propagated-inputs]: Remove python-cython, python-pandas, and python-six.
[native-inputs]: Add python-cython, python-pandas, and python-setuptools.
Change-Id: I580999a2aa7ba3511752ba00f3c923a26ab2c426
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 51 |
1 files changed, 32 insertions, 19 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 18352f35291..e67cc589ba7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -24323,34 +24323,47 @@ data from @file{.hic} files. This package provides Python bindings.") (define-public python-pybbi (package (name "python-pybbi") - (version "0.3.0") + (version "0.4.1") (source (origin (method url-fetch) (uri (pypi-uri "pybbi" version)) (sha256 - (base32 - "1hvy2f28i2b41l1pq15vciqbj538n0lichp8yr6413jmgg06xdsk")))) - (build-system python-build-system) + (base32 "0p1s6y9f33wzmvxdhfg9b37sas2kghnmvkfnb317aiad1p6ks6ba")))) + (build-system pyproject-build-system) (arguments - `(#:tests? #false ; tests require network access - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'set-cc - (lambda _ (setenv "CC" "gcc"))) - (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - (copy-recursively "tests" "/tmp/tests") - (with-directory-excursion "/tmp/tests" - (invoke "python" "-m" "pytest" "-v")))))))) + (list + #:test-flags + #~(list "-k" (string-join + ;; Network is required to run these tests. + (list "not test_aws_403_redirect" + "test_chromsizes" + "test_fetch_remote" + "test_fetch_remote_https" + "test_sigs") + " and not ")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-cc + (lambda _ (setenv "CC" #$(cc-for-target)))) + (add-before 'check 'remove-local-bbi + (lambda _ + ;; This would otherwise interfere with finding the installed bbi + ;; when running tests. + (delete-file-recursively "bbi")))))) (native-inputs - (list pkg-config python-pkgconfig python-pytest)) + (list pkg-config + python-cython + python-pandas + python-pkgconfig + python-pytest + python-setuptools)) (inputs - (list libpng openssl zlib)) + (list libpng + openssl + zlib)) (propagated-inputs - (list python-cython python-numpy python-pandas python-six)) + (list python-numpy)) (home-page "https://github.com/nvictus/pybbi") (synopsis "Python bindings to UCSC Big Binary file library") (description |