GNU bug report logs - #70731
[PATCH] gnu: Add python-pyrodigal.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: nafkhamdc <navid.afkhami <at> mdc-berlin.de>
Subject: bug#70731: closed ([PATCH] gnu: Add python-pyrodigal.)
Date: Mon, 06 May 2024 11:04:02 +0000

[Message part 1 (text/plain, inline)]

Your bug report

#70731: [PATCH] gnu: Add python-pyrodigal.

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 70731 <at> debbugs.gnu.org.

-- 
70731: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=70731
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: 70731-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add python-pyrodigal.
Date: Mon, 06 May 2024 13:03:21 +0200

Thanks for the patch.  I changed it to actually run the tests and pushed
it to the "master" branch.

-- 
Ricardo

[Message part 3 (message/rfc822, inline)]

From: nafkhamdc <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: nafkhamdc <navid.afkhami <at> mdc-berlin.de>
Subject: [PATCH] gnu: Add python-pyrodigal.
Date: Fri, 3 May 2024 09:53:12 +0000

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

Change-Id: Iaa0bdb4b918d93f990d5b904f1df3a3f910726b0
---
 gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b90a1c7824..bc10123a8f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -17710,6 +17710,37 @@ (define-public python-pypairix
 bgzipped text file that contains a pair of genomic coordinates per line.")
     (license license:expat)))
 
+(define-public python-pyrodigal
+  (package
+    (name "python-pyrodigal")
+    (version "3.3.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/althonos/pyrodigal")
+             (commit (string-append "v" version))
+             (recursive? #t)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "10vxbm9i33wari0ifsr78xnfn7d0yqwzqpc5pchirjflf1mmnr6w"))))
+    (build-system pyproject-build-system)
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+                  (replace 'check
+                    (lambda* (#:key tests? #:allow-other-keys)
+                      (when tests?
+                        (with-directory-excursion "/tmp"
+                          (invoke "python3" "-m" "unittest" "discover" "-vv"))))))))
+    (propagated-inputs (list python-archspec python-importlib-resources))
+    (native-inputs (list python-cython-3 python-mock python-unittest2))
+    (home-page "https://github.com/althonos/pyrodigal")
+    (synopsis "Cython bindings and Python interface for Prodigal")
+    (description
+     "This package offers Cython bindings and a Python interface for Prodigal.
+ Prodigal is an ORF finder designed for both genomes and metagenomes.")
+    (license license:gpl3)))
+
 (define-public python-pyfaidx
   (package
     (name "python-pyfaidx")

base-commit: aa9ac252206615713ab988d7068da9e14a9bccc0
prerequisite-patch-id: 68498b47732fb0359e4db6d2f1c86f44d8c700ab
prerequisite-patch-id: 8cad86329867720ca9938e551ece489b056b37ad
-- 
2.34.1

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