From 08392478de5493f947e944bc2ed728a797a6407d Mon Sep 17 00:00:00 2001
From: Andreas Enge <andreas@enge.fr>
Date: Thu, 23 Oct 2025 17:57:08 +0200
Subject: [PATCH] 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 41a0ead9d0e19c0ef07d2e1b32523f249cdad0a6..2e706c80e2cce037032e296412c041002f657747 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")