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 <[email protected]> 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 <[email protected]> -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 <[email protected]> +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 <[email protected]> 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 <[email protected]> +From: Nilesh Patra <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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