guix_mirror_bot pushed a commit to branch master
in repository guix.
commit 08392478de5493f947e944bc2ed728a797a6407d
Author: Andreas Enge <[email protected]>
AuthorDate: Thu Oct 23 17:57:08 2025 +0200
gnu: Remove python-plastid.
* gnu/packages/bioinformatics.scm (python-plastid): Delete variable.
Fixes: guix/guix#2897
Change-Id: I72a38912c7c89997add49d08a01f8522acaa46d1
---
gnu/packages/bioinformatics.scm | 73 -----------------------------------------
1 file changed, 73 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 41a0ead9d0..2e706c80e2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6121,79 +6121,6 @@ also includes an interface for tabix.")
UCSC genome browser.")
(license license:artistic2.0)))
-(define-public python-plastid
- (package
- (name "python-plastid")
- (version "0.6.1")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/joshuagryphon/plastid";)
- (commit "d97f239d73b3a7c2eff46f71928b777431891f90")))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0iccpywlpf1ws46279z9rl0l29pil0rj0g2j5nvqq7jfbnq581cf"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:test-flags
- '(list "plastid/test"
- ;; These four failures look like errors in the test wrapper
- ;; class.
- "-k" (string-append "not test_chrom_sizes"
- " and not test_no_crash_if_file_not_exist"
- " and not test_fiveprime_variable"
- " and not test_fiveprime_variable_from_file"))
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'unpack-test-data
- (lambda* (#:key inputs #:allow-other-keys)
- (invoke "tar" "-C" "plastid/test"
- "-xf" (assoc-ref inputs "test-data"))
- ;; This one requires bowtie-build
- (delete-file "plastid/test/functional/test_crossmap.py")))
- (add-after 'unpack 'patch-for-python-3.10
- (lambda _
- ;; Some classes were moved from collections to collections.abc
- ;; in Python 3.10.
- (substitute* "plastid/readers/bigbed.pyx"
- ((", Iterable")
- "\nfrom collections.abc import Iterable"))))
- (add-before 'check 'build-extensions
- (lambda _
- ;; Cython extensions have to be built before running the tests.
- (invoke "python3" "setup.py" "build_ext" "--inplace"))))))
- (propagated-inputs
- (list python-numpy
- python-scipy
- python-pandas
- python-pysam
- python-matplotlib
- python-biopython
- python-twobitreader
- python-termcolor))
- (inputs
- (list openssl))
- (native-inputs
- `(("python-cython" ,python-cython)
- ("python-pytest" ,python-pytest)
- ("python-setuptools" ,python-setuptools)
- ("python-wheel" ,python-wheel)
- ("test-data"
- ,(origin
- (method url-fetch)
- (uri
"https://www.dropbox.com/s/np3wlfvp6gx8tb8/2022-05-04.plastid-test-data.tar.bz2?dl=1";)
- (file-name "plastid-test-data-2022-05-04.tar.bz2")
- (sha256
- (base32
"1szsji06m2r21flnvxg84jnj5zmlk6z10c9651v9ag71nxj9rbzn"))))))
- (home-page "https://github.com/joshuagryphon/plastid";)
- (synopsis "Python library for genomic analysis")
- (description
- "plastid is a Python library for genomic analysis – in particular,
-high-throughput sequencing data – with an emphasis on simplicity.")
- (license license:bsd-3)))
-
(define-public tetoolkit
(package
(name "tetoolkit")
