diff options
| author | Maxim Cournoyer <maxim.cournoyer@gmail.com> | 2021-12-22 22:44:07 -0500 |
|---|---|---|
| committer | Maxim Cournoyer <maxim.cournoyer@gmail.com> | 2022-01-10 11:44:46 -0500 |
| commit | 64dac22b17f44354a990dc156ea5b88929fe52d8 (patch) | |
| tree | 0a71ee4d54ee2fe803000e188ff9d942f9b63242 /gnu/packages/bioinformatics.scm | |
| parent | 801d0ed622e0cbb8dc2b3c698cb8c2074bfe7991 (diff) | |
gnu: python-pysam: Update to 0.18.0.
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.18.0.
[source]: Add FIXME to clarify bundled libraries in use.
[phases]{check}: Streamline.
[propagated-inputs]: Use latest htslib (1.14).
[native-inputs]: Use latest samtools and bcftools (1.14). Remove python-nose.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 28 |
1 files changed, 8 insertions, 20 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3fda31a645..025c545852 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2327,7 +2327,7 @@ has several key features: (define-public python-pysam (package (name "python-pysam") - (version "0.16.0.1") + (version "0.18.0") (source (origin (method git-fetch) ;; Test data is missing on PyPi. @@ -2337,11 +2337,10 @@ has several key features: (file-name (git-file-name name version)) (sha256 (base32 - "168bwwm8c2k22m7paip8q0yajyl7xdxgnik0bgjl7rhqg0majz0f")) + "042ca27r6634xg2ixgvq1079cp714wmm6ml7bwc1snn0wxxzywfg")) (modules '((guix build utils))) (snippet '(begin - ;; Drop bundled htslib. TODO: Also remove samtools - ;; and bcftools. + ;; FIXME: Unbundle samtools and bcftools. (delete-file-recursively "htslib"))))) (build-system python-build-system) (arguments @@ -2358,35 +2357,24 @@ has several key features: (setenv "CFLAGS" "-D_CURSES_LIB=1"))) (replace 'check (lambda* (#:key tests? #:allow-other-keys) - ;; FIXME: These tests fail with "AttributeError: 'array.array' - ;; object has no attribute 'tostring'". - (delete-file "tests/AlignmentFile_test.py") (when tests? ;; Step out of source dir so python does not import from CWD. (with-directory-excursion "tests" (setenv "HOME" "/tmp") (invoke "make" "-C" "pysam_data") (invoke "make" "-C" "cbcf_data") - (invoke "pytest" "-k" - (string-append - ;; requires network access. - "not FileHTTP" - ;; bug in test suite with samtools update - ;; https://github.com/pysam-developers/pysam/issues/961 - " and not TestHeaderBAM" - " and not TestHeaderCRAM" - " and not test_text_processing"))))))))) + ;; The FileHTTP test requires network access. + (invoke "pytest" "-k" "not FileHTTP")))))))) (propagated-inputs - (list htslib-1.10)) ; Included from installed header files. + (list htslib)) ; Included from installed header files. (inputs (list ncurses curl zlib)) (native-inputs (list python-cython python-pytest ;; Dependencies below are are for tests only. - samtools-1.10 - bcftools-1.10 - python-nose)) + samtools + bcftools)) (home-page "https://github.com/pysam-developers/pysam") (synopsis "Python bindings to the SAMtools C API") (description |