GNU bug report logs - #77400
[PATCH python-team 00/26] Some further updates

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From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77400 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [bug#77400] [PATCH 12/26] gnu: Remove python-pyfasta.
Date: Mon, 31 Mar 2025 08:18:40 +0200

This package is archived and deprecated in favor or python-pyfaidx for
7 years.

* gnu/packages/bioinformatics.scm (python-pyfasta): Delete variable.
---
 gnu/packages/bioinformatics.scm | 72 ---------------------------------
 1 file changed, 72 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 00f0e10475..0f59f73448 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6396,78 +6396,6 @@ (define-public python-pybigwig
 accessing bigWig files.")
     (license license:expat)))
 
-(define-public python-pyfasta
-  ;; The release on pypi does not contain the test data files.
-  (let ((commit "c2f0611c5311f1b1466f2d56560447898b4a8b03")
-        (revision "1"))
-    (package
-      (name "python-pyfasta")
-      (version (git-version "0.5.2" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/brentp/pyfasta")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "0a189id3fbv88gssyk6adbmz2ll1mqpmyw8vxmx3fi955gvaq9j7"))))
-      (build-system pyproject-build-system)
-      (arguments
-       (list
-        #:phases
-        '(modify-phases %standard-phases
-           (add-after 'unpack 'python3.10-compat
-             (lambda _
-               (substitute* "pyfasta/__init__.py"
-                 (("from fasta import")
-                  "from pyfasta.fasta import")
-                 (("from records import")
-                  "from pyfasta.records import")
-                 (("from split_fasta import")
-                  "from pyfasta.split_fasta import")
-                 (("in f.iteritems")
-                  "in f.items"))
-               (substitute* "pyfasta/fasta.py"
-                 (("from collections import Mapping")
-                  "from collections.abc import Mapping")
-                 (("from records import")
-                  "from pyfasta.records import"))
-               (substitute* "pyfasta/records.py"
-                 (("cPickle") "pickle")
-                 (("\\(int, long\\)")
-                  "(int, int)")
-                 ;; XXX: it's not clear if this is really correct.
-                 (("buffer\\(self\\)")
-                  "memoryview(bytes(str(self), encoding='utf-8'))")
-                 (("sys.maxint") "sys.maxsize"))
-               (substitute* "pyfasta/split_fasta.py"
-                 (("from cStringIO import")
-                  "from io import")
-                 (("in lens.iteritems") "in lens.items"))
-               (substitute* "tests/test_all.py"
-                 (("f.keys\\(\\)\\) == \\['a-extra'")
-                  "list(f.keys())) == ['a-extra'")
-                 (("f.iterkeys\\(\\)") "iter(f.keys())")
-                 (("tests/data/" m)
-                  (string-append (getcwd) "/" m))))))))
-      (propagated-inputs (list python-numpy))
-      (native-inputs (list python-nose python-setuptools python-wheel))
-      (home-page "https://github.com/brentp/pyfasta/")
-      (synopsis "Pythonic access to fasta sequence files")
-      (description
-       "This library provides fast, memory-efficient, pythonic (and
-command-line) access to fasta sequence files.  It stores a flattened version
-of a fasta sequence file without spaces or headers and uses either a
-@code{mmap} in numpy binary format or @code{fseek}/@code{fread} so the
-sequence data is never read into memory.  It saves a pickle (@code{.gdx}) of
-the start and stop (for @code{fseek}/@code{mmap}) locations of each header in
-the fasta file for internal use.
-
-Note that this package has been deprecated in favor of @code{pyfaidx}.")
-      (license license:expat))))
-
 (define-public python-schema-salad
   (package
     (name "python-schema-salad")
-- 
2.49.0

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