Re: packaging python-cyvcf2

[Ricardo Wurmus <rekado@elephly.net>]

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Hi,

> I've abandoned running the tests though, I'm hitting a module not
> found error. pytest doesn't manage to load the just built module,
> probably an issue with the paths.

It's an actual problem with the build.  You need to build the cython
extension first.  I've attached the working package definition.

I'd like to add this to gnu/packages/bioinformatics.scm.  I'd like to
set authorship of the commit to you.  Is the name and email address I
used for attribution correct?  (See the attached commit.)

-- 
Ricardo



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From 12af58e7f29c5a96888ecba7d264669940f1f259 Mon Sep 17 00:00:00 2001
Message-ID: <12af58e7f29c5a96888ecba7d264669940f1f259.1713431532.git.rekado@elephly.net>
From: Alexis Simon <alexis.simon@runbox.com>
Date: Thu, 18 Apr 2024 11:10:22 +0200
Subject: [PATCH] gnu: Add python-cyvcf2.

* gnu/packages/bioinformatics.scm (python-cyvcf2): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I0db07e7b5840f5c1f5c68512ffabb3d6b39ab95c
---
 gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 448ea5d6de..d2e0656435 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -25,6 +25,7 @@
 ;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
 ;;; Copyright © 2022, 2023 Navid Afkhami <navid.afkhami@mdc-berlin.de>
 ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org>
+;;; Copyright © 2024 Alexis Simon <alexis.simon@runbox.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1916,6 +1917,58 @@ (define-public python-cmseq
 and sequence consensus.")
     (license license:expat)))
 
+(define-public python-cyvcf2
+  (package
+    (name "python-cyvcf2")
+    (version "0.30.28")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/brentp/cyvcf2")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "16yhfax509zyip8kkq2b0lflx5bdq5why7d785ayrqyzzq2rxqkk"))
+       (modules '((guix build utils)))
+       (snippet
+        ;; Delete bundled library
+        '(delete-file-recursively "htslib"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'build-extensions
+            (lambda _
+              ;; Cython extensions have to be built before running the tests.
+              (invoke "python" "setup.py" "build_ext" "--inplace")))
+          (add-after 'unpack 'fix-setup
+            (lambda* (#:key inputs #:allow-other-keys)
+              (substitute* "setup.py"
+                (("^htslib_include_dirs =.*")
+                 (string-append "htslib_include_dirs = [\""
+                                #$(this-package-input "htslib") "/include\"]\n"))
+                (("lib_name = \"libhts.so\"")
+                 (string-append "lib_name = \""
+                                (search-input-file inputs "lib/libhts.so.3")
+                                "\"\n")))))
+          (add-before 'build 'use-system-htslib-package
+            (lambda _
+              (setenv "CYTHONIZE" "1")
+              (setenv "CYVCF2_HTSLIB_MODE" "EXTERNAL"))))))
+    (inputs (list curl htslib libdeflate openssl zlib))
+    (native-inputs (list python-cython python-pytest))
+    (propagated-inputs
+     (list python-click
+           python-coloredlogs
+           python-numpy))
+    (home-page "https://github.com/brentp/cyvcf2/")
+    (synopsis "Fast vcf file parsing with Cython and htslib")
+    (description "Cyvcf2 is a Cython wrapper around htslib built for fast
+parsing of Variant Call Format (VCF) files.")
+    (license license:expat)))
+
 (define-public python-decoupler-py
   ;; This latest commit fixes a bug in test_omnip.py.
   (let ((commit "459b235348ddd9135217a3722d9dd1caa9a14ace")

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