[med-svn] [Git][med-team/circlator][master] 3 commits: Replace d/patches/fix_canu_detection with upstream's solution.

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch master at Debian Med / circlator


Commits:
9f71c8f0 by Michael R. Crusoe at 2023-08-21T12:33:55+02:00
Replace d/patches/fix_canu_detection with upstream's solution.

- - - - -
be5896c1 by Michael R. Crusoe at 2023-08-21T12:41:12+02:00
Forwarded two patches to upstream.

- - - - -
fdc1be6a by Michael R. Crusoe at 2023-08-21T12:46:18+02:00
routine-update: Ready to upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/patches/fix_canu_detection.patch
- debian/patches/split_canu_tests
- debian/patches/switch-to-pytest.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+circlator (1.5.6-9) unstable; urgency=medium
+
+  * Team upload.
+  * Replace d/patches/fix_canu_detection with upstream's solution.
+  * Forwarded two patches to upstream.
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Mon, 21 Aug 2023 12:46:18 +0200
+
 circlator (1.5.6-8) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/fix_canu_detection.patch
=====================================
@@ -1,16 +1,22 @@
-Description: Fix canu detection
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 02 Dec 2017 16:44:51 +0100
-Bug-Debian: https://bugs.debian.org/880248
+From f0404184d11c67a984fe8e2b450a3854ac88b38b Mon Sep 17 00:00:00 2001
+From: Jason Stajich <jasonstajich.phd at gmail.com>
+Date: Tue, 13 Apr 2021 12:34:15 -0700
+Subject: Canu version is reported with capital
+Origin: upstream, https://github.com/sanger-pathogens/circlator/commit/3e223bee8ae581582b3b50c920aa08d94fcdc7bd
 
---- a/circlator/external_progs.py
-+++ b/circlator/external_progs.py
+canu version in 2.1.1 is 'canu 2.1.1' need to support lowercase
+---
+ circlator/external_progs.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+--- circlator.orig/circlator/external_progs.py
++++ circlator/circlator/external_progs.py
 @@ -19,7 +19,7 @@
      'prodigal': ('-v', re.compile(r'^Prodigal V([0-9\.]+):')),
      'samtools': ('', re.compile(r'Version: (\d+\.\d+[\.\d]*)')),
      'spades': ('-v', re.compile(r'v.?([0-9][0-9\.]+)')),
 -    'canu': ('-version', re.compile(r'^Canu \D*([\d][\d\.]+)')),
-+    'canu': ('-version', re.compile('^Canu.*([0-9][0-9\.]+)')),
++    'canu': ('-version', re.compile(r'^[Cc]anu \D*([\d][\d\.]+)')),
  }
  
  min_versions = {


=====================================
debian/patches/split_canu_tests
=====================================
@@ -1,5 +1,6 @@
 From: Michael R. Crusoe <crusoe at debian.org>
 Subject: Allow for testing without spades installed
+Forwarded: https://github.com/sanger-pathogens/circlator/pull/186
 
 --- circlator.orig/circlator/tests/assemble_test.py
 +++ circlator/circlator/tests/assemble_test.py


=====================================
debian/patches/switch-to-pytest.patch
=====================================
@@ -1,6 +1,8 @@
-Description: Switch from nose->pytest since the former is deprecated
-Author: Nilesh Patra <nilesh at debian.org>
+From: Nilesh Patra <nilesh at debian.org>
+Subject: Switch from nose->pytest since the former is deprecated
 Last-Updated: 2021-10-25
+Forwarded: https://github.com/sanger-pathogens/circlator/pull/186
+
 --- a/setup.py
 +++ b/setup.py
 @@ -15,8 +15,7 @@



View it on GitLab: https://salsa.debian.org/med-team/circlator/-/compare/c7e798b08104ba912ee1b0499795088c88c9bda2...fdc1be6a22ccb6efbd96436fdeca1a954ba0457d

-- 
View it on GitLab: https://salsa.debian.org/med-team/circlator/-/compare/c7e798b08104ba912ee1b0499795088c88c9bda2...fdc1be6a22ccb6efbd96436fdeca1a954ba0457d
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