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87/142: gnu: python-pysam: Update to 0.18.0.
From: |
guix-commits |
Subject: |
87/142: gnu: python-pysam: Update to 0.18.0. |
Date: |
Mon, 10 Jan 2022 13:07:26 -0500 (EST) |
apteryx pushed a commit to branch version-1.4.0
in repository guix.
commit 64dac22b17f44354a990dc156ea5b88929fe52d8
Author: Maxim Cournoyer <maxim.cournoyer@gmail.com>
AuthorDate: Wed Dec 22 22:44:07 2021 -0500
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.
---
gnu/packages/bioinformatics.scm | 28 ++++++++--------------------
1 file 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
- 49/142: gnu: pangomm: Add python to native inputs., (continued)
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- 58/142: gnu: glade3: Add python to native inputs., guix-commits, 2022/01/10
- 55/142: gnu: python-msgpack: Update to 1.0.3., guix-commits, 2022/01/10
- 59/142: gnu: python-curio: Disable newly failing 'test_timeout' test., guix-commits, 2022/01/10
- 07/142: gnu: python-tomli: Update to 2.0.0., guix-commits, 2022/01/10
- 22/142: gnu: cairo: Use bash-minimal unconditionally., guix-commits, 2022/01/10
- 40/142: gnu: gnome-backgrounds: Update to 41.0., guix-commits, 2022/01/10
- 43/142: gnu: epiphany: Update to 41.2., guix-commits, 2022/01/10
- 45/142: gnu: wayland-protocols: Add python to native inputs., guix-commits, 2022/01/10
- 75/142: gnu: python-matplotlib: Update to 3.5.1 and run tests in parallel., guix-commits, 2022/01/10
- 87/142: gnu: python-pysam: Update to 0.18.0.,
guix-commits <=
- 90/142: gnu: python-igraph: Update to 0.9.8., guix-commits, 2022/01/10
- 91/142: gnu: tbb-2020: Use ld.gold to work around segfaults in check phase., guix-commits, 2022/01/10
- 103/142: gnu: python-scikit-learn: Remove obsolete phase., guix-commits, 2022/01/10
- 104/142: gnu: jalv-select: Remove obsolete phase., guix-commits, 2022/01/10
- 102/142: gnu: go-ipfs: Remove obsolete phase., guix-commits, 2022/01/10
- 106/142: gnu: helm: Remove obsolete phase., guix-commits, 2022/01/10
- 113/142: gnu: meson: Update to 0.60.3., guix-commits, 2022/01/10
- 114/142: gnu: glib: Update to 2.70.2., guix-commits, 2022/01/10
- 128/142: gnu: rust: Use rust-1.57.0., guix-commits, 2022/01/10
- 127/142: gnu: simple-scan: Add python to native inputs., guix-commits, 2022/01/10