[med-svn] [Git][med-team/ltrsift] Pushed new tag debian/1.0.2-10
Sascha Steinbiss pushed new tag debian/1.0.2-10 at Debian Med / ltrsift -- View it on GitLab: https://salsa.debian.org/med-team/ltrsift/-/tree/debian/1.0.2-10 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ltrsift][master] dch -r
Sascha Steinbiss pushed to branch master at Debian Med / ltrsift Commits: 95e7a097 by Sascha Steinbiss at 2024-04-05T23:02:40+02:00 dch -r - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,6 +1,4 @@ -ltrsift (1.0.2-10) UNRELEASED; urgency=medium - - * Team upload. +ltrsift (1.0.2-10) unstable; urgency=medium [ Matthias Klose ] * Remove hard-coded dependencies on shared libraries. @@ -17,7 +15,7 @@ ltrsift (1.0.2-10) UNRELEASED; urgency=medium * Fix day-of-week for changelog entry 1.0.1-1. * watch file standard 4 (routine-update) - -- Sascha Steinbiss Thu, 04 Apr 2024 22:16:04 +0200 + -- Sascha Steinbiss Fri, 05 Apr 2024 22:59:43 +0200 ltrsift (1.0.2-9) unstable; urgency=medium View it on GitLab: https://salsa.debian.org/med-team/ltrsift/-/commit/95e7a09745408a9ad0b22cfc3f60da066d5bfcb7 -- View it on GitLab: https://salsa.debian.org/med-team/ltrsift/-/commit/95e7a09745408a9ad0b22cfc3f60da066d5bfcb7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ltrsift][master] 2 commits: stop mentioning autopkgtest
Sascha Steinbiss pushed to branch master at Debian Med / ltrsift Commits: a73b468a by Sascha Steinbiss at 2024-04-04T22:32:26+02:00 stop mentioning autopkgtest - - - - - 475248c0 by Sascha Steinbiss at 2024-04-04T22:32:43+02:00 remove ltrsift-encode from example data - - - - - 4 changed files: - debian/changelog - debian/control - + debian/patches/no-binary-in-examples.patch - debian/patches/series Changes: = debian/changelog = @@ -16,12 +16,9 @@ ltrsift (1.0.2-10) UNRELEASED; urgency=medium (already present in machine-readable debian/copyright). * Fix day-of-week for changelog entry 1.0.1-1. * watch file standard 4 (routine-update) - * Add new binary package ltrsift with data that can be used in -autopkgtest - TODO: remove ltrsift_encode from examples -write autopkgtest + * Add new binary package ltrsift with example data. - -- Andreas Tille Thu, 04 Apr 2024 18:40:38 +0200 + -- Sascha Steinbiss Thu, 04 Apr 2024 22:16:04 +0200 ltrsift (1.0.2-9) unstable; urgency=medium = debian/control = @@ -41,4 +41,4 @@ Description: postprocessing and classification of LTR retrotransposons (sample d sometimes large results of de novo prediction software. It also offers customizable filtering and classification functionality. . - This package contains sample data to run the autopkgtest. + This package contains example data to test the LTRsift functionality. = debian/patches/no-binary-in-examples.patch = @@ -0,0 +1,13 @@ +--- a/Makefile b/Makefile +@@ -40,10 +40,6 @@ + .PHONY: all clean cleanup dirs install + + all: dirs bin/ltrsift bin/ltrsift_encode $(STATICBIN) +- @(test -f bin/ltrsift_encode_static && \ +- cp bin/ltrsift_encode_static sample_data) \ +- || (test -f bin/ltrsift_encode && \ +- cp bin/ltrsift_encode sample_data) + dirs: bin obj obj/src + + obj/%.o: %.c = debian/patches/series = @@ -1,3 +1,4 @@ build_on_64bit use_deterministic_file_order spelling.patch +no-binary-in-examples.patch View it on GitLab: https://salsa.debian.org/med-team/ltrsift/-/compare/da191eac881fd7b461037f58e8c91b2bd98cdd4a...475248c0399f5bad08c91de67cf1bb63db521c0c -- View it on GitLab: https://salsa.debian.org/med-team/ltrsift/-/compare/da191eac881fd7b461037f58e8c91b2bd98cdd4a...475248c0399f5bad08c91de67cf1bb63db521c0c You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/aragorn] Pushed new tag debian/1.2.41-3
Sascha Steinbiss pushed new tag debian/1.2.41-3 at Debian Med / aragorn -- View it on GitLab: https://salsa.debian.org/med-team/aragorn/-/tree/debian/1.2.41-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/aragorn][master] 2 commits: update watchfile
Sascha Steinbiss pushed to branch master at Debian Med / aragorn Commits: 4b2f95ce by Sascha Steinbiss at 2024-04-02T11:14:05+02:00 update watchfile - - - - - 6c9f2f1f by Sascha Steinbiss at 2024-04-02T11:16:56+02:00 update watchfile to point to working directory again - - - - - 2 changed files: - debian/changelog - debian/watch Changes: = debian/changelog = @@ -1,3 +1,9 @@ +aragorn (1.2.41-3) unstable; urgency=medium + + * Update watchfile to point to working directory again. + + -- Sascha Steinbiss Tue, 02 Apr 2024 11:14:39 +0200 + aragorn (1.2.41-2) unstable; urgency=medium * Ensure multiple builds can be done in same directory. = debian/watch = @@ -1,2 +1,2 @@ version=4 -https://www.ansikte.se/ARAGORN/Downloads/aragorn(.*).c +https://www.trna.se/ARAGORN/Downloads/aragorn(.*).c View it on GitLab: https://salsa.debian.org/med-team/aragorn/-/compare/e3ffa7a620cf3625283bec52678555d9689154ab...6c9f2f1f94d39f89b8e9c14b2dcd196d80e66b2d -- View it on GitLab: https://salsa.debian.org/med-team/aragorn/-/compare/e3ffa7a620cf3625283bec52678555d9689154ab...6c9f2f1f94d39f89b8e9c14b2dcd196d80e66b2d You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/aegean] Pushed new tag debian/0.16.0+dfsg-4
Sascha Steinbiss pushed new tag debian/0.16.0+dfsg-4 at Debian Med / aegean -- View it on GitLab: https://salsa.debian.org/med-team/aegean/-/tree/debian/0.16.0+dfsg-4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/aegean][master] 8 commits: remove explicit runtime dependency on libgenometools0
Sascha Steinbiss pushed to branch master at Debian Med / aegean
Commits:
5f1e8f0f by Sascha Steinbiss at 2024-04-01T20:16:44+02:00
remove explicit runtime dependency on libgenometools0
- - - - -
f1a37fcb by Sascha Steinbiss at 2024-04-01T20:18:43+02:00
add d/copyright information for debian/ directory
- - - - -
38ff6b88 by Sascha Steinbiss at 2024-04-01T20:18:43+02:00
bump Standards-Version
- - - - -
8b8c0f0b by Sascha Steinbiss at 2024-04-01T20:18:43+02:00
add Rules-Requires-Root: no
- - - - -
c1d3cbb3 by Sascha Steinbiss at 2024-04-01T20:18:43+02:00
update debhelper compat level to 13
- - - - -
364d9ef6 by Sascha Steinbiss at 2024-04-01T20:18:43+02:00
only list files not installed
- - - - -
4ad2b23c by Sascha Steinbiss at 2024-04-01T20:18:43+02:00
adjust renamed lintian tag overrides
- - - - -
396cf939 by Sascha Steinbiss at 2024-04-01T20:18:43+02:00
bump watchfile version to 4
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/rules
- debian/source/lintian-overrides
- debian/watch
Changes:
=
debian/changelog
=
@@ -1,3 +1,17 @@
+aegean (0.16.0+dfsg-4) unstable; urgency=medium
+
+ * Remove explicit runtime dependency on libgenometools0.
+Closes: #1068178
+ * Add d/copyright information for debian/ directory.
+ * Bump Standards-Version.
+ * Add Rules-Requires-Root: no.
+ * Update debhelper compat level to 13.
+ * Only list files not installed.
+ * Adjust renamed lintian tag overrides.
+ * Bump watchfile version to 4.
+
+ -- Sascha Steinbiss Mon, 01 Apr 2024 19:49:51 +0200
+
aegean (0.16.0+dfsg-3) unstable; urgency=medium
* Ensure multiple builds can be done in same directory.
=
debian/control
=
@@ -3,11 +3,12 @@ Maintainer: Debian Med Packaging Team
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
libcairo2-dev,
libgenometools0-dev,
python3
-Standards-Version: 4.4.0
+Standards-Version: 4.6.2
+Rules-Requires-Root: no
Vcs-Browser: https://salsa.debian.org/med-team/aegean
Vcs-Git: https://salsa.debian.org/med-team/aegean.git
Homepage: https://standage.github.io/AEGeAn
@@ -18,8 +19,7 @@ Depends: ${shlibs:Depends},
${misc:Depends},
libjs-jquery,
libjs-jquery-datatables,
- libjs-mootools,
- libgenometools0
+ libjs-mootools
Description: integrated genome analysis toolkit
The AEGeAn Toolkit is designed for the Analysis and Evaluation of Genome
Annotations. The toolkit includes a variety of analysis programs, e.g. for
=
debian/copyright
=
@@ -8,6 +8,8 @@ Files:
*
Copyright:
2010-2015, Daniel S. Standage and CONTRIBUTORS
+License: ISC
+
License: ISC
Permission to use, copy, modify, and/or distribute this software for any
purpose with or without fee is hereby granted, provided that the above
@@ -20,3 +22,7 @@ License: ISC
WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+
+Files: debian/*
+Copyright: 2016-2024 Sascha Steinbiss
+License: ISC
=
debian/rules
=
@@ -35,3 +35,6 @@ override_dh_installdocs:
override_dh_auto_clean:
dh_auto_clean
rm -f $(CURDIR)/README
+
+override_dh_missing:
+ dh_missing --list-missing
=
debian/source/lintian-overrides
=
@@ -1,2 +1,2 @@
# Upstream does not provide signed tarballs.
-aegean source: debian-watch-does-not-check-gpg-signature
+aegean source: debian-watch-does-not-check-openpgp-signature
=
debian/watch
=
@@ -1,4 +1,4 @@
-version=3
+version=4
opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
https://github.com/BrendelGroup/AEGeAn/tags
.*/v?(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz))
View it on GitLab:
https://salsa.debian.org/med-team/aegean/-/compare/7e866348e7f485b380e9d8c2060608df5cd5c68d...396cf93986b221ad5ff88d367c269559f147b9d6
--
View it on GitLab:
https://salsa.debian.org/med-team/aegean/-/compare/7e866348e7f485b380e9d8c2060608df5cd5c68d...396cf93986b221ad5ff88d367c269559f147b9d6
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[med-svn] [Git][med-team/tantan][master] 3 commits: change d/watch to use Git instead of tarballs
Sascha Steinbiss pushed to branch master at Debian Med / tantan Commits: bf20bad2 by Sascha Steinbiss at 2024-04-01T11:16:28+02:00 change d/watch to use Git instead of tarballs - - - - - d5aa16fa by Sascha Steinbiss at 2024-04-01T11:16:57+02:00 update d/copyright after reviewing source - - - - - fef1d7c2 by Sascha Steinbiss at 2024-04-01T11:17:06+02:00 bump copyright date for debian/ directory - - - - - 3 changed files: - debian/changelog - debian/copyright - debian/watch Changes: = debian/changelog = @@ -1,3 +1,11 @@ +tantan (49-2) unstable; urgency=medium + + * Change d/watch to use Git instead of tarballs. + * Update d/copyright after reviewing source. + * Bump copyright date for debian/ directory. + + -- Sascha Steinbiss Mon, 01 Apr 2024 11:04:08 +0200 + tantan (49-1) unstable; urgency=medium * New upstream version 49. = debian/copyright = @@ -3,14 +3,19 @@ Upstream-Name: tantan Source: https://gitlab.com/mcfrith/tantan Files: * -Copyright: © 2010 Martin Frith - © 2008 Michiaki Hamada - © Stephen Altschul - © Yi-Kuo Yu +Copyright: 2010-2018 Martin Frith +License: GPL-3+ + +Files: src/LambdaCalculator.cc +Copyright: 2015 Yutaro Konta +License: GPL-3+ + +Files: src/LambdaCalculator.hh +Copyright: 2008 Michiaki Hamada License: GPL-3+ Files: debian/* -Copyright: © 2015-2023 Sascha Steinbiss +Copyright: © 2015-2024 Sascha Steinbiss License: GPL-3+ License: GPL-3+ = debian/watch = @@ -1,2 +1,3 @@ version=4 - https://gitlab.com/mcfrith/tantan/-/tags?sort=updated_desc .*/archive/(\d\S+)/.*\.tar\.gz +opts="mode=git, gitmode=full, pgpmode=none" \ +https://gitlab.com/mcfrith/tantan.git refs/tags/v?@ANY_VERSION@ View it on GitLab: https://salsa.debian.org/med-team/tantan/-/compare/f55bae9908d63e53b5e7190514726923669e4962...fef1d7c20559e28346d3bb53cc805bd29111cc73 -- View it on GitLab: https://salsa.debian.org/med-team/tantan/-/compare/f55bae9908d63e53b5e7190514726923669e4962...fef1d7c20559e28346d3bb53cc805bd29111cc73 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/tantan] Pushed new tag debian/49-2
Sascha Steinbiss pushed new tag debian/49-2 at Debian Med / tantan -- View it on GitLab: https://salsa.debian.org/med-team/tantan/-/tree/debian/49-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-awkward][master] 3 commits: use dh_python3 correctly
Sascha Steinbiss pushed to branch master at Debian Med / python-awkward
Commits:
fcddb40b by Sascha Steinbiss at 2024-02-19T21:18:52+01:00
use dh_python3 correctly
- - - - -
3206deb6 by Sascha Steinbiss at 2024-02-19T21:18:58+01:00
add hardening flags
- - - - -
b81bbd73 by Sascha Steinbiss at 2024-02-19T21:19:02+01:00
dch -r
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,5 +1,6 @@
-python-awkward (2.6.1-1) UNRELEASED; urgency=medium
+python-awkward (2.6.1-1) unstable; urgency=medium
- * Initial release (Closes: #)
+ [ Andreas Tille ]
+ * Initial release (Closes: #1064291)
- -- Andreas Tille Sat, 17 Feb 2024 19:13:57 +0100
+ -- Sascha Steinbiss Mon, 19 Feb 2024 18:28:57 +0100
=
debian/control
=
@@ -31,12 +31,7 @@ Package: python3-awkward
Architecture: any
Depends: ${misc:Depends},
${shlibs:Depends},
- ${python3:Depends},
- python3-packaging,
- python3-numpy,
- python3-fsspec,
- python3-typing-extensions,
- python3-importlib-metadata
+ ${python3:Depends}
Description: manipulate JSON-like data with NumPy-like idioms
Awkward Array is a library for nested, variable-sized data, including
arbitrary-length lists, records, mixed types, and missing data, using
@@ -45,4 +40,3 @@ Description: manipulate JSON-like data with NumPy-like idioms
Arrays are dynamically typed, but operations on them are compiled and fast.
Their behavior coincides with NumPy when array dimensions are regular and
generalizes when they're not.
-
=
debian/rules
=
@@ -3,6 +3,7 @@
export PYBUILD_DESTDIR = debian/tmp_i_mean_it
export PYBUILD_TEST_ARGS=-v
export PY_IGNORE_IMPORTMISMATCH=1
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
%:
dh $@ --buildsystem=pybuild
@@ -22,7 +23,7 @@ override_dh_install:
dh_install --sourcedir=debian/tmp_i_mean_it
override_dh_python3:
- dh_python3 --no-ext-rename
/usr/lib/python3/dist-packages/awkward_cpp/lib/*
+ dh_python3 --no-ext-rename
override_dh_auto_test:
# pass
View it on GitLab:
https://salsa.debian.org/med-team/python-awkward/-/compare/b53d7cd6d377ac201cb28c1567ca8863c1ef3f69...b81bbd73b08d6bb984db011bb93d46cc34c5ab27
--
View it on GitLab:
https://salsa.debian.org/med-team/python-awkward/-/compare/b53d7cd6d377ac201cb28c1567ca8863c1ef3f69...b81bbd73b08d6bb984db011bb93d46cc34c5ab27
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[med-svn] [Git][med-team/python-awkward][master] 4 commits: add myself to d/copyright
Sascha Steinbiss pushed to branch master at Debian Med / python-awkward
Commits:
9b3d7a70 by Sascha Steinbiss at 2024-02-19T18:52:48+01:00
add myself to d/copyright
- - - - -
e4525de5 by Sascha Steinbiss at 2024-02-19T18:52:54+01:00
complete dependencies
- - - - -
1a8caecf by Sascha Steinbiss at 2024-02-19T18:53:01+01:00
add upstream metadata
- - - - -
b53d7cd6 by Sascha Steinbiss at 2024-02-19T18:53:13+01:00
add minimal autopkgtest
- - - - -
5 changed files:
- debian/control
- debian/copyright
- + debian/tests/control
- + debian/tests/python-test
- + debian/upstream/metadata
Changes:
=
debian/control
=
@@ -31,7 +31,12 @@ Package: python3-awkward
Architecture: any
Depends: ${misc:Depends},
${shlibs:Depends},
- ${python3:Depends}
+ ${python3:Depends},
+ python3-packaging,
+ python3-numpy,
+ python3-fsspec,
+ python3-typing-extensions,
+ python3-importlib-metadata
Description: manipulate JSON-like data with NumPy-like idioms
Awkward Array is a library for nested, variable-sized data, including
arbitrary-length lists, records, mixed types, and missing data, using
=
debian/copyright
=
@@ -8,6 +8,7 @@ License: BSD-3-Clause
Files: debian/*
Copyright: 2024 Andreas Tille
+ 2024 Sascha Steinbiss
License: BSD-3-Clause
Files: src/awkward/_operators.py
=
debian/tests/control
=
@@ -0,0 +1,3 @@
+Tests: python-test
+Depends: python3-awkward, python3-numpy
+Restrictions: allow-stderr, skip-not-installable
=
debian/tests/python-test
=
@@ -0,0 +1,12 @@
+#!/usr/bin/env python3
+# autopkgtest check: Check whether awkward module is importable
+# and does basic tasks
+# Author: Sascha Steinbiss
+
+import awkward
+
+array = awkward.Array([[{"x": 1.1, "y": [1]}, {"x": 2.2, "y": [1, 2]}, {"x":
3.3, "y": [1, 2, 3]}], [], [{"x": 4.4, "y": [1, 2, 3, 4]}, {"x": 5.5, "y": [1,
2, 3, 4, 5]}]])
+
+import numpy as np
+
+output = np.square(array["y", ..., 1:])
=
debian/upstream/metadata
=
@@ -0,0 +1,14 @@
+Bug-Database: https://github.com/scikit-hep/awkward
+Bug-Submit: https://github.com/scikit-hep/awkward/issues/new
+Repository: https://github.com/scikit-hep/awkward.git
+Repository-Browse: https://github.com/scikit-hep/awkward
+Reference:
+ Author: >
+Jim Pivarski and Peter Elmer and David Lange
+ Title: >
+Awkward Arrays in Python, C++, and Numba
+ Journal: EPJ Web Conf.
+ Year: 2018
+ Volume: 245
+ DOI: 10.1051/epjconf/202024505023
+ URL:
https://www.epj-conferences.org/articles/epjconf/abs/2020/21/epjconf_chep2020_05023/epjconf_chep2020_05023.html
View it on GitLab:
https://salsa.debian.org/med-team/python-awkward/-/compare/1de0f0d72b215785340b6078f40c721a09f9aa1d...b53d7cd6d377ac201cb28c1567ca8863c1ef3f69
--
View it on GitLab:
https://salsa.debian.org/med-team/python-awkward/-/compare/1de0f0d72b215785340b6078f40c721a09f9aa1d...b53d7cd6d377ac201cb28c1567ca8863c1ef3f69
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[med-svn] [Git][med-team/python-awkward][master] do not rename object files
Sascha Steinbiss pushed to branch master at Debian Med / python-awkward Commits: 1de0f0d7 by Sascha Steinbiss at 2024-02-19T15:56:48+01:00 do not rename object files - - - - - 1 changed file: - debian/rules Changes: = debian/rules = @@ -21,5 +21,8 @@ override_dh_auto_build: override_dh_install: dh_install --sourcedir=debian/tmp_i_mean_it +override_dh_python3: + dh_python3 --no-ext-rename /usr/lib/python3/dist-packages/awkward_cpp/lib/* + override_dh_auto_test: # pass View it on GitLab: https://salsa.debian.org/med-team/python-awkward/-/commit/1de0f0d72b215785340b6078f40c721a09f9aa1d -- View it on GitLab: https://salsa.debian.org/med-team/python-awkward/-/commit/1de0f0d72b215785340b6078f40c721a09f9aa1d You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/python-awkward][master] 2 commits: get package to build (but not importable)
Sascha Steinbiss pushed to branch master at Debian Med / python-awkward
Commits:
4876079d by Sascha Steinbiss at 2024-02-18T18:15:06+01:00
get package to build (but not importable)
- - - - -
a44515b0 by Sascha Steinbiss at 2024-02-18T18:39:20+01:00
add install file
- - - - -
3 changed files:
- debian/control
- + debian/python3-awkward.install
- debian/rules
Changes:
=
debian/control
=
@@ -1,17 +1,26 @@
Source: python-awkward
Maintainer: Debian Med Packaging Team
-Uploaders: Andreas Tille
-Section: science
+Uploaders: Sascha Steinbiss
+Section: python
Priority: optional
-Build-Depends: debhelper-compat (= 13),
- dh-sequence-python3,
+Build-Depends: dh-sequence-python3,
+ python3-setuptools,
+ debhelper-compat (= 13),
pybuild-plugin-pyproject,
- cmake,
- python3-all,
python3-hatchling,
python3-hatch-fancy-pypi-readme,
- python3-pytest ,
- python3-numpy
+ python3-all,
+ python3-fsspec,
+ python3-typing-extensions,
+ python3-numpy,
+ python3-pytest,
+ python3-scikit-build-core,
+ python3-pyproject-metadata,
+ cmake,
+ libpython3-all-dev,
+ pybind11-dev,
+ rapidjson-dev,
+ nox
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/python-awkward
Vcs-Git: https://salsa.debian.org/med-team/python-awkward.git
@@ -20,14 +29,15 @@ Rules-Requires-Root: no
Package: python3-awkward
Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends},
+Depends: ${misc:Depends},
+ ${shlibs:Depends},
${python3:Depends}
-Description: Python3 library for nested, variable-sized data
+Description: manipulate JSON-like data with NumPy-like idioms
Awkward Array is a library for nested, variable-sized data, including
arbitrary-length lists, records, mixed types, and missing data, using
NumPy-like idioms.
.
- Arrays are dynamically typed, but operations on them are compiled and
- fast. Their behavior coincides with NumPy when array dimensions are
- regular and generalizes when they're not.
+ Arrays are dynamically typed, but operations on them are compiled and fast.
+ Their behavior coincides with NumPy when array dimensions are regular and
+ generalizes when they're not.
+
=
debian/python3-awkward.install
=
@@ -0,0 +1 @@
+usr/lib/python3*
=
debian/rules
=
@@ -1,21 +1,25 @@
#!/usr/bin/make -f
-# DH_VERBOSE := 1
-
-export PYBUILD_NAME=awkward
-
-include /usr/share/dpkg/default.mk
-
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export PYBUILD_DESTDIR = debian/tmp_i_mean_it
+export PYBUILD_TEST_ARGS=-v
+export PY_IGNORE_IMPORTMISMATCH=1
%:
dh $@ --buildsystem=pybuild
-override_dh_auto_configure:
- dh_auto_configure --sourcedir=awkward-cpp --buildsystem=cmake
-DSKBUILD_PROJECT_VERSION=$(DEB_VERSION_UPSTREAM)
- dh_auto_configure
+override_dh_auto_clean \
+override_dh_auto_configure \
+override_dh_auto_install: override_%:
+ PYBUILD_NAME=awkward_cpp $* --buildsystem=pybuild
--sourcedirectory=awkward-cpp
+ PYBUILD_NAME=awkward $* --buildsystem=pybuild --sourcedirectory=.
override_dh_auto_build:
- dh_auto_build --sourcedir=awkward-cpp --buildsystem=cmake
- dh_auto_build
+ nox -s prepare
+ PYBUILD_NAME=awkward_cpp dh_auto_build --sourcedirectory=awkward-cpp
--buildsystem=pybuild
+ PYBUILD_NAME=awkward dh_auto_build --sourcedirectory=.
--buildsystem=pybuild
+
+override_dh_install:
+ dh_install --sourcedir=debian/tmp_i_mean_it
+
+override_dh_auto_test:
+ # pass
View it on GitLab:
https://salsa.debian.org/med-team/python-awkward/-/compare/5b9cffb2d2ea0df57fe992263b0937ffa60262cf...a44515b004452c9de4b305dfce2b9b36c3c6f986
--
View it on GitLab:
https://salsa.debian.org/med-team/python-awkward/-/compare/5b9cffb2d2ea0df57fe992263b0937ffa60262cf...a44515b004452c9de4b305dfce2b9b36c3c6f986
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[med-svn] [Git][med-team/libtabixpp] Pushed new tag debian/1.1.2-2
Sascha Steinbiss pushed new tag debian/1.1.2-2 at Debian Med / libtabixpp -- View it on GitLab: https://salsa.debian.org/med-team/libtabixpp/-/tree/debian/1.1.2-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libtabixpp][master] 2 commits: enable building twice in a row
Sascha Steinbiss pushed to branch master at Debian Med / libtabixpp Commits: 4de23de1 by Sascha Steinbiss at 2024-02-17T16:05:02+01:00 enable building twice in a row - - - - - 66cdd439 by Sascha Steinbiss at 2024-02-17T16:05:13+01:00 fix LTO issue - - - - - 3 changed files: - debian/changelog - debian/libtabixpp0.symbols - debian/rules Changes: = debian/changelog = @@ -1,3 +1,12 @@ +libtabixpp (1.1.2-2) unstable; urgency=medium + + * Enable building twice in a row. +Closes: #1049726 + * Update symbols file and enable LTO. +Closes: #1015526 + + -- Sascha Steinbiss Sat, 17 Feb 2024 15:40:37 +0100 + libtabixpp (1.1.2-1) unstable; urgency=medium * New upstream version = debian/libtabixpp0.symbols = @@ -11,5 +11,3 @@ libtabixpp.so.0 libtabixpp0 #MINVER# _ZN5TabixC2Ev@Base 1.0.0 _ZN5TabixD1Ev@Base 1.0.0 _ZN5TabixD2Ev@Base 1.0.0 - _ZNKSt5ctypeIcE8do_widenEc@Base 1.1.0 - (optional)_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base 1.0.0 = debian/rules = @@ -1,7 +1,7 @@ #!/usr/bin/make -f # DH_VERBOSE := 1 -export DEB_BUILD_MAINT_OPTIONS = hardening=+all +export DEB_BUILD_MAINT_OPTIONS = hardening=+all optimize=+lto DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH) %: @@ -12,9 +12,11 @@ override_dh_auto_clean: override_dh_auto_install: ln -s libtabixpp.so.* libtabixpp.so + cp tabix.hpp debian/tabix.hpp d-shlibmove --commit \ --multiarch \ --devunversioned \ --movedev "*.hpp" usr/include/ \ libtabixpp.so find debian -name "lib*.la" -delete + mv debian/tabix.hpp . View it on GitLab: https://salsa.debian.org/med-team/libtabixpp/-/compare/cf0740413b2f665f910c29243604d290e671b674...66cdd43923632af2a85755f99e51899b0b10a0a5 -- View it on GitLab: https://salsa.debian.org/med-team/libtabixpp/-/compare/cf0740413b2f665f910c29243604d290e671b674...66cdd43923632af2a85755f99e51899b0b10a0a5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/kmc] Pushed new tag upstream/3.2.4+dfsg
Sascha Steinbiss pushed new tag upstream/3.2.4+dfsg at Debian Med / kmc -- View it on GitLab: https://salsa.debian.org/med-team/kmc/-/tree/upstream/3.2.4+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/kmc] Pushed new tag debian/3.2.4+dfsg-1
Sascha Steinbiss pushed new tag debian/3.2.4+dfsg-1 at Debian Med / kmc -- View it on GitLab: https://salsa.debian.org/med-team/kmc/-/tree/debian/3.2.4+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/kmc][upstream] New upstream version 3.2.4+dfsg
Sascha Steinbiss pushed to branch upstream at Debian Med / kmc Commits: 7c58f582 by Sascha Steinbiss at 2024-02-17T14:57:32+01:00 New upstream version 3.2.4+dfsg - - - - - 30 changed files: - Makefile - kmc_api/kmc_file.cpp - kmc_api/kmc_file.h - kmc_api/kmer_api.cpp - kmc_api/kmer_api.h - kmc_api/kmer_defs.h - kmc_api/mmer.cpp - kmc_api/mmer.h - kmc_core/bam_utils.h - kmc_core/binary_reader.h - kmc_core/bkb_merger.h - kmc_core/bkb_reader.cpp - kmc_core/bkb_reader.h - kmc_core/bkb_sorter.h - kmc_core/bkb_subbin.h - kmc_core/bkb_uncompactor.h - kmc_core/bkb_writer.cpp - kmc_core/bkb_writer.h - kmc_core/cpu_info.cpp - kmc_core/cpu_info.h - kmc_core/defs.h - kmc_core/fastq_reader.cpp - kmc_core/fastq_reader.h - kmc_core/first_dispatch.h - kmc_core/intr_copy.h - kmc_core/kb_collector.cpp - kmc_core/kb_collector.h - kmc_core/kb_completer.cpp - kmc_core/kb_completer.h - kmc_core/kb_reader.h The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/kmc/-/commit/7c58f582434066feee4f0424efa0de3d97b3fa6a -- View it on GitLab: https://salsa.debian.org/med-team/kmc/-/commit/7c58f582434066feee4f0424efa0de3d97b3fa6a You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/kmc][master] 4 commits: New upstream version 3.2.4+dfsg
Sascha Steinbiss pushed to branch master at Debian Med / kmc Commits: 7c58f582 by Sascha Steinbiss at 2024-02-17T14:57:32+01:00 New upstream version 3.2.4+dfsg - - - - - 4fed9ee3 by Sascha Steinbiss at 2024-02-17T14:57:33+01:00 Update upstream source from tag upstream/3.2.4+dfsg Update to upstream version 3.2.4+dfsg with Debian dir b39787855c18ec31f61380a342809d239b7f8ef7 - - - - - 06edbf57 by Sascha Steinbiss at 2024-02-17T15:08:21+01:00 refresh patches - - - - - 5b7a731c by Sascha Steinbiss at 2024-02-17T15:08:27+01:00 new upstream version - - - - - 30 changed files: - Makefile - debian/changelog - debian/patches/0005-Add-static-library-target-to-makefile.patch - debian/patches/disable-python-bindings.patch - debian/patches/gcc-13.patch - debian/patches/makefile.patch - debian/patches/simde - debian/patches/spelling.patch - debian/patches/support-mixed-march.patch - kmc_api/kmc_file.cpp - kmc_api/kmc_file.h - kmc_api/kmer_api.cpp - kmc_api/kmer_api.h - kmc_api/kmer_defs.h - kmc_api/mmer.cpp - kmc_api/mmer.h - kmc_core/bam_utils.h - kmc_core/binary_reader.h - kmc_core/bkb_merger.h - kmc_core/bkb_reader.cpp - kmc_core/bkb_reader.h - kmc_core/bkb_sorter.h - kmc_core/bkb_subbin.h - kmc_core/bkb_uncompactor.h - kmc_core/bkb_writer.cpp - kmc_core/bkb_writer.h - kmc_core/cpu_info.cpp - kmc_core/cpu_info.h - kmc_core/defs.h - kmc_core/fastq_reader.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/kmc/-/compare/057286347bbda4644e9429f68035702aabafe46e...5b7a731caad652a3276d5a501bb342c07147c5f7 -- View it on GitLab: https://salsa.debian.org/med-team/kmc/-/compare/057286347bbda4644e9429f68035702aabafe46e...5b7a731caad652a3276d5a501bb342c07147c5f7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/kmc][pristine-tar] pristine-tar data for kmc_3.2.4+dfsg.orig.tar.xz
Sascha Steinbiss pushed to branch pristine-tar at Debian Med / kmc Commits: f263730c by Sascha Steinbiss at 2024-02-17T14:57:33+01:00 pristine-tar data for kmc_3.2.4+dfsg.orig.tar.xz - - - - - 2 changed files: - + kmc_3.2.4+dfsg.orig.tar.xz.delta - + kmc_3.2.4+dfsg.orig.tar.xz.id Changes: = kmc_3.2.4+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/kmc_3.2.4+dfsg.orig.tar.xz.delta differ = kmc_3.2.4+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +c354ceed6f35a30122f0ae003ee5c02a087bb317 View it on GitLab: https://salsa.debian.org/med-team/kmc/-/commit/f263730c1b3d9defbdebb70996f3eeb3e3f33d3b -- View it on GitLab: https://salsa.debian.org/med-team/kmc/-/commit/f263730c1b3d9defbdebb70996f3eeb3e3f33d3b You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libhat-trie] Deleted tag upstream/0.6.0
Sascha Steinbiss deleted tag upstream/0.6.0 at Debian Med / libhat-trie -- You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libhat-trie] Pushed new tag debian/0.1.2-3
Sascha Steinbiss pushed new tag debian/0.1.2-3 at Debian Med / libhat-trie -- View it on GitLab: https://salsa.debian.org/med-team/libhat-trie/-/tree/debian/0.1.2-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libhat-trie][upstream] Deleted 1 commit: New upstream version 0.6.0
Sascha Steinbiss pushed to branch upstream at Debian Med / libhat-trie WARNING: The push did not contain any new commits, but force pushed to delete the commits and changes below. Deleted commits: 83476364 by Michael R. Crusoe at 2020-01-01T11:07:54+01:00 New upstream version 0.6.0 - - - - - 12 changed files: - + .codecov.yml - − .gitignore - .travis.yml - + CMakeLists.txt - COPYING → LICENSE - − Makefile.am - README.md - − TODO - + appveyor.yml - − configure.ac - + doxygen.conf - − hat-trie-0.1.pc.in The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/libhat-trie/-/commit/8347636442e3ea2174203182900f4bbb49ac6c0e -- View it on GitLab: https://salsa.debian.org/med-team/libhat-trie/-/commit/8347636442e3ea2174203182900f4bbb49ac6c0e You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libhat-trie][pristine-tar] Deleted 1 commit: pristine-tar data for libhat-trie_0.6.0.orig.tar.gz
Sascha Steinbiss pushed to branch pristine-tar at Debian Med / libhat-trie WARNING: The push did not contain any new commits, but force pushed to delete the commits and changes below. Deleted commits: 6b43f2c4 by Michael R. Crusoe at 2020-01-01T11:07:54+01:00 pristine-tar data for libhat-trie_0.6.0.orig.tar.gz - - - - - 2 changed files: - + libhat-trie_0.6.0.orig.tar.gz.delta - + libhat-trie_0.6.0.orig.tar.gz.id Changes: = libhat-trie_0.6.0.orig.tar.gz.delta = Binary files /dev/null and b/libhat-trie_0.6.0.orig.tar.gz.delta differ = libhat-trie_0.6.0.orig.tar.gz.id = @@ -0,0 +1 @@ +dec100e21596784fe243c5131b5e8eecb15eb59a View it on GitLab: https://salsa.debian.org/med-team/libhat-trie/-/commit/6b43f2c4825d4cdf2827318e71ab48fb1005b1a4 -- View it on GitLab: https://salsa.debian.org/med-team/libhat-trie/-/commit/6b43f2c4825d4cdf2827318e71ab48fb1005b1a4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libhat-trie][master] 5 commits: enable building twice in a row
Sascha Steinbiss pushed to branch master at Debian Med / libhat-trie Commits: 4c4178b8 by Sascha Steinbiss at 2024-02-17T14:35:12+01:00 enable building twice in a row - - - - - 5cfa80c7 by Sascha Steinbiss at 2024-02-17T14:35:25+01:00 bump d/copyright data - - - - - 716a37b1 by Sascha Steinbiss at 2024-02-17T14:35:41+01:00 dh 13 - - - - - bcd43dab by Sascha Steinbiss at 2024-02-17T14:35:53+01:00 bump Standards-Version - - - - - 1eff9142 by Sascha Steinbiss at 2024-02-17T14:36:06+01:00 set Rules-Requires-Root: no - - - - - 5 changed files: - debian/changelog - − debian/compat - debian/control - debian/copyright - debian/rules Changes: = debian/changelog = @@ -1,3 +1,10 @@ +libhat-trie (0.1.2-3) unstable; urgency=medium + + * Enable building twice in a row by fixing clean target. +Closes: #1047138 + + -- Sascha Steinbiss Sat, 17 Feb 2024 11:21:02 +0100 + libhat-trie (0.1.2-2) unstable; urgency=medium * Team upload. = debian/compat deleted = @@ -1 +0,0 @@ -11 = debian/control = @@ -3,9 +3,11 @@ Maintainer: Debian Med Packaging Team Section: science Priority: optional -Build-Depends: debhelper (>= 11~), +Build-Depends: debhelper (>= 13~), + debhelper-compat (= 13), d-shlibs -Standards-Version: 4.3.0 +Standards-Version: 4.6.2 +Rules-Requires-Root: no Vcs-Browser: https://salsa.debian.org/med-team/libhat-trie Vcs-Git: https://salsa.debian.org/med-team/libhat-trie.git Homepage: https://github.com/dcjones/hat-trie = debian/copyright = @@ -8,7 +8,7 @@ Copyright: © 2011 Daniel C. Jones License: MIT Files: debian/* -Copyright: © 2016 Sascha Steinbiss +Copyright: © 2016-2024 Sascha Steinbiss License: MIT Files: src/murmurhash3.* = debian/rules = @@ -6,6 +6,10 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow %: dh $@ +override_dh_auto_clean: + dh_auto_clean + rm -f test/test.aht + override_dh_auto_configure: dh_auto_configure -- --enable-debugging --enable-shared=yes @@ -14,8 +18,6 @@ override_dh_install: d-shlibmove --commit \ --multiarch \ --devunversioned \ ---exclude-la \ --movedev "debian/tmp/usr/include/*" usr/include \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*" usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \ debian/tmp/usr/lib/*/lib*.so - View it on GitLab: https://salsa.debian.org/med-team/libhat-trie/-/compare/10b24568bd334ef7f73c920a338c72a568377fbf...1eff914257915608f7e9165d2d4f0558cd0c3d6d -- View it on GitLab: https://salsa.debian.org/med-team/libhat-trie/-/compare/10b24568bd334ef7f73c920a338c72a568377fbf...1eff914257915608f7e9165d2d4f0558cd0c3d6d You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libhat-trie][master] fix clean target
Sascha Steinbiss pushed to branch master at Debian Med / libhat-trie Commits: 10b24568 by Sascha Steinbiss at 2024-01-08T11:43:04+01:00 fix clean target - - - - - 2 changed files: - debian/changelog - debian/rules Changes: = debian/changelog = @@ -1,11 +1,15 @@ libhat-trie (0.6.0-1) UNRELEASED; urgency=medium + [ Michael R. Crusoe ] * Team upload. * New upstream location. * debhelper-compat 12 * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target - -- Michael R. Crusoe Wed, 01 Jan 2020 11:07:54 +0100 + [ Sascha Steinbiss ] + * Enable building twice in a row by fixing clean target. + + -- Sascha Steinbiss Mon, 08 Jan 2024 11:42:10 +0100 libhat-trie (0.1.2-2) unstable; urgency=medium = debian/rules = @@ -10,6 +10,10 @@ override_dh_auto_build: dh_auto_build doxygen doxygen.conf +override_dh_auto_clean: + dh_auto_clean + rm -rf doc test/test.aht + override_dh_auto_test: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) dh_auto_test && cd obj-* && ./tsl_hat_trie_tests View it on GitLab: https://salsa.debian.org/med-team/libhat-trie/-/commit/10b24568bd334ef7f73c920a338c72a568377fbf -- View it on GitLab: https://salsa.debian.org/med-team/libhat-trie/-/commit/10b24568bd334ef7f73c920a338c72a568377fbf You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/tantan] Pushed new tag debian/49-1
Sascha Steinbiss pushed new tag debian/49-1 at Debian Med / tantan -- View it on GitLab: https://salsa.debian.org/med-team/tantan/-/tree/debian/49-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/tantan] Pushed new tag upstream/49
Sascha Steinbiss pushed new tag upstream/49 at Debian Med / tantan -- View it on GitLab: https://salsa.debian.org/med-team/tantan/-/tree/upstream/49 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/tantan][pristine-tar] pristine-tar data for tantan_49.orig.tar.gz
Sascha Steinbiss pushed to branch pristine-tar at Debian Med / tantan Commits: 3832decf by Sascha Steinbiss at 2023-12-23T23:03:16+01:00 pristine-tar data for tantan_49.orig.tar.gz - - - - - 2 changed files: - + tantan_49.orig.tar.gz.delta - + tantan_49.orig.tar.gz.id Changes: = tantan_49.orig.tar.gz.delta = Binary files /dev/null and b/tantan_49.orig.tar.gz.delta differ = tantan_49.orig.tar.gz.id = @@ -0,0 +1 @@ +fabfba13e83970f62dc5b04bdd9a31698d9dba5e View it on GitLab: https://salsa.debian.org/med-team/tantan/-/commit/3832decf668b37eddc8f9e8b6d574b9c10c319f6 -- View it on GitLab: https://salsa.debian.org/med-team/tantan/-/commit/3832decf668b37eddc8f9e8b6d574b9c10c319f6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/tantan] Pushed new tag debian/40-2
Sascha Steinbiss pushed new tag debian/40-2 at Debian Med / tantan -- View it on GitLab: https://salsa.debian.org/med-team/tantan/-/tree/debian/40-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/tantan][master] 4 commits: enable building twice in a row
Sascha Steinbiss pushed to branch master at Debian Med / tantan Commits: d5a3d210 by Sascha Steinbiss at 2023-12-23T11:57:31+01:00 enable building twice in a row - - - - - e8604f2b by Sascha Steinbiss at 2023-12-23T11:59:41+01:00 bump Standards-Version - - - - - 24eb7ffd by Sascha Steinbiss at 2023-12-23T11:59:56+01:00 bump copyright date for debian directory - - - - - f65e99fc by Sascha Steinbiss at 2023-12-23T12:00:15+01:00 update renamed lintian override tag - - - - - 5 changed files: - debian/changelog - debian/control - debian/copyright - debian/rules - debian/source/lintian-overrides Changes: = debian/changelog = @@ -1,3 +1,13 @@ +tantan (40-2) unstable; urgency=medium + + * Enable building twice in a row. +Closes: #1045561 + * Bump Standards-Version. + * Bump copyright date for debian directory. + * Update renamed lintian override tag. + + -- Sascha Steinbiss Sat, 23 Dec 2023 11:43:26 +0100 + tantan (40-1) unstable; urgency=medium * New upstream version 40. = debian/control = @@ -5,7 +5,7 @@ Section: science Priority: optional Build-Depends: debhelper-compat (= 13), zlib1g-dev -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/tantan Vcs-Git: https://salsa.debian.org/med-team/tantan.git Homepage: https://gitlab.com/mcfrith/tantan = debian/copyright = @@ -10,7 +10,7 @@ Copyright: © 2010 Martin Frith License: GPL-3+ Files: debian/* -Copyright: © 2015-2022 Sascha Steinbiss +Copyright: © 2015-2023 Sascha Steinbiss License: GPL-3+ License: GPL-3+ = debian/rules = @@ -10,3 +10,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all override_dh_auto_install: make prefix=$(DESTDIR) install + +override_dh_auto_clean: + dh_auto_clean + rm -f src/version.hh = debian/source/lintian-overrides = @@ -1,2 +1,2 @@ # Upstream does not provide signed tarballs. -tantan source: debian-watch-does-not-check-gpg-signature +tantan source: debian-watch-does-not-check-openpgp-signature View it on GitLab: https://salsa.debian.org/med-team/tantan/-/compare/4d52be29354ddb14794edcfe91e43f6873141e1b...f65e99fcbc714d6a540ce12744473e27ab2a3474 -- View it on GitLab: https://salsa.debian.org/med-team/tantan/-/compare/4d52be29354ddb14794edcfe91e43f6873141e1b...f65e99fcbc714d6a540ce12744473e27ab2a3474 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/snpomatic][master] enable building twice in a row
Sascha Steinbiss pushed to branch master at Debian Med / snpomatic Commits: a73a6736 by Sascha Steinbiss at 2023-12-23T09:20:04+01:00 enable building twice in a row - - - - - 2 changed files: - debian/changelog - debian/rules Changes: = debian/changelog = @@ -1,3 +1,10 @@ +snpomatic (1.0-7) unstable; urgency=medium + + * Enable building twice in a row by cleaning antiword output. +Closes: #1046157 + + -- Sascha Steinbiss Sat, 23 Dec 2023 09:19:24 +0100 + snpomatic (1.0-6) unstable; urgency=medium * Team upload. = debian/rules = @@ -16,6 +16,7 @@ override_dh_auto_clean: rm -rf debian/findknownsnps.1 rm -rf debian/findknownsnps.1.html rm -f mapcontigs reassemble ungap + rm -f doc/Manual.txt dh_auto_clean -- override_dh_installdocs: View it on GitLab: https://salsa.debian.org/med-team/snpomatic/-/commit/a73a67360cb25dd94834f130716eb93024ee457b -- View it on GitLab: https://salsa.debian.org/med-team/snpomatic/-/commit/a73a67360cb25dd94834f130716eb93024ee457b You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/snpomatic] Pushed new tag debian/1.0-7
Sascha Steinbiss pushed new tag debian/1.0-7 at Debian Med / snpomatic -- View it on GitLab: https://salsa.debian.org/med-team/snpomatic/-/tree/debian/1.0-7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mash] Pushed new tag debian/2.3+dfsg-6
Sascha Steinbiss pushed new tag debian/2.3+dfsg-6 at Debian Med / mash -- View it on GitLab: https://salsa.debian.org/med-team/mash/-/tree/debian/2.3+dfsg-6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mash][master] 3 commits: enable building twice in a row
Sascha Steinbiss pushed to branch master at Debian Med / mash
Commits:
b7d64728 by Sascha Steinbiss at 2023-12-18T22:53:50+01:00
enable building twice in a row
- - - - -
380f1303 by Sascha Steinbiss at 2023-12-18T22:53:50+01:00
bump copyright date for debian directory
- - - - -
a081b37f by Sascha Steinbiss at 2023-12-18T22:53:50+01:00
remove unnecessary Built-Using from mash-doc package
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,3 +1,12 @@
+mash (2.3+dfsg-6) unstable; urgency=medium
+
+ * Enable building twice in a row.
+Closes: #1046553
+ * Bump copyright date for debian directory.
+ * Remove unnecessary Built-Using from mash-doc package.
+
+ -- Sascha Steinbiss Mon, 18 Dec 2023 22:42:16 +0100
+
mash (2.3+dfsg-5) unstable; urgency=medium
* Team upload
=
debian/control
=
@@ -51,7 +51,6 @@ Section: doc
Depends: ${misc:Depends},
${sphinxdoc:Depends},
libjs-mathjax
-Built-Using: ${sphinxdoc:Built-Using}
Description: documentation for Mash
This package contains further documentation (tutorials, explanations,
etc.) for Mash, a MinHash based genome distance estimator. The documentation
=
debian/copyright
=
@@ -13,7 +13,7 @@ Copyright: © 2015 Brian Ondov, Todd Treangen, Adam Phillippy
License: BSD-3-clause
Files: debian/*
-Copyright: © 2016-2022 Sascha Steinbiss
+Copyright: © 2016-2023 Sascha Steinbiss
License: BSD-3-clause
License: BSD-3-clause
=
debian/rules
=
@@ -15,7 +15,9 @@ export DEB_CPPFLAGS_MAINT_APPEND
override_dh_auto_clean:
dh_auto_clean
- rm -rf $(CURDIR)/debian/sphinxdoc $(CURDIR)/debian/man
+ rm -rf $(CURDIR)/debian/sphinxdoc $(CURDIR)/debian/man
$(CURDIR)/test/*.msh \
+ $(CURDIR)/test/*.dist $(CURDIR)/test/*.json $(CURDIR)/Makefile \
+ $(CURDIR)/config.log $(CURDIR)/config.status
$(CURDIR)/test/screen
override_dh_auto_configure:
dh_auto_configure -- --with-capnp=/usr --with-gsl=/usr
--prefix=$(CURDIR)/debian/tmp/usr
View it on GitLab:
https://salsa.debian.org/med-team/mash/-/compare/25ca3cc5f3a6ab825b26a3ad017078a70d23ab89...a081b37fb9af215db3c7a1cde3865292e1e0f476
--
View it on GitLab:
https://salsa.debian.org/med-team/mash/-/compare/25ca3cc5f3a6ab825b26a3ad017078a70d23ab89...a081b37fb9af215db3c7a1cde3865292e1e0f476
You're receiving this email because of your account on salsa.debian.org.
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[med-svn] [Git][med-team/genomethreader] Pushed new tag debian/1.7.3+dfsg-8
Sascha Steinbiss pushed new tag debian/1.7.3+dfsg-8 at Debian Med / genomethreader -- View it on GitLab: https://salsa.debian.org/med-team/genomethreader/-/tree/debian/1.7.3+dfsg-8 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/iva] Pushed new tag debian/1.0.11+ds-4
Sascha Steinbiss pushed new tag debian/1.0.11+ds-4 at Debian Med / iva -- View it on GitLab: https://salsa.debian.org/med-team/iva/-/tree/debian/1.0.11+ds-4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/iva][master] 3 commits: enable building twice in a row
Sascha Steinbiss pushed to branch master at Debian Med / iva Commits: cb0f88cd by Sascha Steinbiss at 2023-12-18T22:30:48+01:00 enable building twice in a row - - - - - cbb2c6b1 by Sascha Steinbiss at 2023-12-18T22:30:57+01:00 bump Standards-Version - - - - - ba7045a3 by Sascha Steinbiss at 2023-12-18T22:31:09+01:00 bump debian directory copyright date - - - - - 4 changed files: - debian/changelog - debian/control - debian/copyright - debian/rules Changes: = debian/changelog = @@ -1,3 +1,12 @@ +iva (1.0.11+ds-4) unstable; urgency=medium + + * Enable building twice in a row. +Closes: #1045886 + * Bump Standards-Version. + * Bump debian directory copyright date. + + -- Sascha Steinbiss Mon, 18 Dec 2023 22:00:38 +0100 + iva (1.0.11+ds-3) unstable; urgency=medium * Team upload. = debian/control = @@ -23,7 +23,7 @@ Build-Depends: debhelper-compat (= 13), samtools, smalt, default-jdk-headless -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/iva Vcs-Git: https://salsa.debian.org/med-team/iva.git Homepage: https://github.com/sanger-pathogens/iva = debian/copyright = @@ -9,7 +9,7 @@ Copyright: © 2014-2015 Genome Research Limited License: GPL-3+ Files: debian/* -Copyright: © 2015-2022 Debian Med Packaging Team +Copyright: © 2015-2023 Debian Med Packaging Team License: GPL-3+ Files: iva/gage/* = debian/rules = @@ -34,7 +34,7 @@ override_dh_installman: dh_installman -- override_dh_auto_clean: - rm -rf .pybuild + rm -rf .pybuild *.egg-info .pytest_cache build rm -f iva/gage/*.class rm -rf $(mandir) find . -name __pycache__ | xargs rm -rf View it on GitLab: https://salsa.debian.org/med-team/iva/-/compare/1ba279d7bd41fa895cae3622ea87a5f6a665e054...ba7045a3e74e1ad521ede6b6feea3607677a7c23 -- View it on GitLab: https://salsa.debian.org/med-team/iva/-/compare/1ba279d7bd41fa895cae3622ea87a5f6a665e054...ba7045a3e74e1ad521ede6b6feea3607677a7c23 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genomethreader][master] 3 commits: enable building twice in a row
Sascha Steinbiss pushed to branch master at Debian Med / genomethreader Commits: f8935256 by Sascha Steinbiss at 2023-12-18T18:29:58+01:00 enable building twice in a row - - - - - 8e427f10 by Sascha Steinbiss at 2023-12-18T18:30:06+01:00 bump Standards-Version - - - - - 9e23f017 by Sascha Steinbiss at 2023-12-18T18:30:19+01:00 add d/copyright section for debian/ directory - - - - - 6 changed files: - debian/changelog - debian/control - debian/copyright - + debian/patches/extend-clean.patch - debian/patches/series - debian/rules Changes: = debian/changelog = @@ -1,3 +1,12 @@ +genomethreader (1.7.3+dfsg-8) unstable; urgency=medium + + * Enable building twice in a row. +Closes: #1044585, #1049675 + * Bump Standards-Version. + * Add d/copyright section for debian/ directory. + + -- Sascha Steinbiss Mon, 18 Dec 2023 18:19:28 +0100 + genomethreader (1.7.3+dfsg-7) unstable; urgency=medium * Fix watchfile to detect new versions on github = debian/control = @@ -13,7 +13,7 @@ Build-Depends: debhelper-compat (= 13), liblua5.1-0-dev, libtre-dev, asciidoctor -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Rules-Requires-Root: no Vcs-Browser: https://salsa.debian.org/med-team/genomethreader Vcs-Git: https://salsa.debian.org/med-team/genomethreader.git = debian/copyright = @@ -9,6 +9,10 @@ Copyright: © 2003-2019 Gordon Gremme 2003-2008 Center for Bioinformatics, University of Hamburg License: ISC +Files: debian/* +Copyright: © 2020-2023 Debian Med Packaging Team +License: ISC + Files: src/gth/bssm_param.c Copyright: (c) 2003-2013 Gordon Gremme (c) 2003-2005 Michael E Sparks = debian/patches/extend-clean.patch = @@ -0,0 +1,33 @@ +--- a/Makefile b/Makefile +@@ -490,6 +490,30 @@ + find gthdata -name '*.md5' | xargs rm -f + find gthdata -name '*.ois' | xargs rm -f + find gthdata -name '*.sds' | xargs rm -f ++ find gthdata -name '*.suf' | xargs rm -f ++ find gthdata -name '*.bck' | xargs rm -f ++ find gthdata -name '*.llv' | xargs rm -f ++ find gthdata -name '*.bwt' | xargs rm -f ++ find gthdata -name '*.tis' | xargs rm -f ++ find gthdata -name '*.ssp' | xargs rm -f ++ find gthdata -name '*.lcp' | xargs rm -f ++ find gthdata -name '*.sti1' | xargs rm -f ++ find testdata -name '*.des' | xargs rm -f ++ find testdata -name '*.esq' | xargs rm -f ++ find testdata -name '*.md5' | xargs rm -f ++ find testdata -name '*.ois' | xargs rm -f ++ find testdata -name '*.sds' | xargs rm -f ++ find testdata -name '*.suf' | xargs rm -f ++ find testdata -name '*.bck' | xargs rm -f ++ find testdata -name '*.llv' | xargs rm -f ++ find testdata -name '*.bwt' | xargs rm -f ++ find testdata -name '*.tis' | xargs rm -f ++ find testdata -name '*.ssp' | xargs rm -f ++ find testdata -name '*.lcp' | xargs rm -f ++ find testdata -name '*.sti1' | xargs rm -f ++ find testdata -name '*.al1' | xargs rm -f ++ find testdata -name '*.prj' | xargs rm -f ++ find testdata -name '*.polya*' | xargs rm -f + + obj/train: bin/gthbssmbuild + @mkdir -p bin/bssm = debian/patches/series = @@ -5,3 +5,4 @@ search-paths.patch m32-m64-ignore.patch reproducible.patch disable-fastdp-tests.patch +extend-clean.patch = debian/rules = @@ -27,6 +27,7 @@ endif override_dh_auto_clean: dh_clean + make licensemanager=no opt=yes 64bit=$(64BIT) cleanup rm -rf bin/bssm debian/bssm bin/gthdata debian/gthdata rm -rf $(CURDIR)/debian/man rm -f debian/*substvars View it on GitLab: https://salsa.debian.org/med-team/genomethreader/-/compare/4d8152c6200dba82fbee661b4df787a0bc5b02c5...9e23f0173f59b15983805709630745b58ab932de -- View it on GitLab: https://salsa.debian.org/med-team/genomethreader/-/compare/4d8152c6200dba82fbee661b4df787a0bc5b02c5...9e23f0173f59b15983805709630745b58ab932de You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/fastaq] Pushed new tag debian/3.17.0-6
Sascha Steinbiss pushed new tag debian/3.17.0-6 at Debian Med / fastaq -- View it on GitLab: https://salsa.debian.org/med-team/fastaq/-/tree/debian/3.17.0-6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/fastaq][master] 3 commits: enable building twice in a row
Sascha Steinbiss pushed to branch master at Debian Med / fastaq Commits: 4e62b68f by Sascha Steinbiss at 2023-12-18T17:57:02+01:00 enable building twice in a row - - - - - 15d6a03d by Sascha Steinbiss at 2023-12-18T17:57:12+01:00 bump Standards-Version - - - - - ed01b895 by Sascha Steinbiss at 2023-12-18T17:57:22+01:00 update d/copyright - - - - - 4 changed files: - debian/changelog - debian/control - debian/copyright - debian/rules Changes: = debian/changelog = @@ -1,3 +1,13 @@ +fastaq (3.17.0-6) unstable; urgency=medium + + * Enable building twice in a row. +Closes: #1044289 + * Bump Standards-Version. + * Bump copyright dates. + * Update copyright info in d/copyright. + + -- Sascha Steinbiss Mon, 18 Dec 2023 17:18:28 +0100 + fastaq (3.17.0-5) unstable; urgency=medium * Actually fix watchfile. = debian/control = @@ -13,7 +13,7 @@ Build-Depends: debhelper-compat (= 13), python3-pytest, samtools, help2man -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/fastaq Vcs-Git: https://salsa.debian.org/med-team/fastaq.git Homepage: https://github.com/sanger-pathogens/Fastaq = debian/copyright = @@ -4,11 +4,12 @@ Source: https://github.com/sanger-pathogens/Fastaq Files: * Copyright: © 2012-2015 Martin Hunt + © 2013-2017 by Genome Research Ltd. License: GPL-3 Files: debian/* Copyright: © 2014 Jorge Soares - © 2015-2022 Sascha Steinbiss + © 2015-2023 Sascha Steinbiss License: GPL-3 License: GPL-3 = debian/rules = @@ -17,7 +17,7 @@ override_dh_auto_build: cd $(CURDIR)/doc override_dh_auto_clean: - rm -rf build .pybuild doc pyfastaq.egg-info + rm -rf build .pybuild doc pyfastaq.egg-info .pytest_cache find . -name __pycache__ | xargs rm -rf rm -rf $(mandir) View it on GitLab: https://salsa.debian.org/med-team/fastaq/-/compare/004855f2fcd676a1b8f46ffda98e1ab305174e07...ed01b8955a41e9aef51850fd7cbe757e7a610352 -- View it on GitLab: https://salsa.debian.org/med-team/fastaq/-/compare/004855f2fcd676a1b8f46ffda98e1ab305174e07...ed01b8955a41e9aef51850fd7cbe757e7a610352 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/vmatch][master] 2 commits: enable building twice in a row
Sascha Steinbiss pushed to branch master at Debian Med / vmatch Commits: 33e4b669 by Sascha Steinbiss at 2023-12-15T13:16:28+01:00 enable building twice in a row - - - - - 3d277903 by Sascha Steinbiss at 2023-12-15T13:41:57+01:00 bump Standards-Version - - - - - 3 changed files: - debian/changelog - debian/control - debian/rules Changes: = debian/changelog = @@ -1,3 +1,11 @@ +vmatch (2.3.1+dfsg-9) unstable; urgency=medium + + * Fix clean step of build to enable building twice in a row. +Closes: #1045627 + * Bump Standards-Version. + + -- Sascha Steinbiss Wed, 13 Dec 2023 10:12:23 +0100 + vmatch (2.3.1+dfsg-8) unstable; urgency=medium [ Andreas Tille ] = debian/control = @@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, asciidoctor -Standards-Version: 4.6.0 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/vmatch Vcs-Git: https://salsa.debian.org/med-team/vmatch.git Homepage: http://www.vmatch.de = debian/rules = @@ -10,7 +10,19 @@ export WORKVSTREESRC=$(CURDIR)/src dh $@ override_dh_auto_clean: - rm -rf debian/man src/Makedef-debian + cd src && make cleanup + test ! -e src/Vmatch/SELECT/Shareddef || (cd src/Vmatch/SELECT && make clean) + test ! -e src/Makedef || (cd src/Mkvtree && make clean) + find $(CURDIR) -name "*.x" -delete + find $(CURDIR) -name "*.d" -delete + find $(CURDIR) -name "*.so" -delete + rm -rf debian/man \ + src/Makedef-debian \ + src/dist \ + src/Vmatch/SELECT/Shareddef \ + src/include/vmrelease.h \ + src/Makedef \ + src/Vmatch/virtualexp.h override_dh_auto_build: cp debian/Makedef-debian src/Makedef-debian View it on GitLab: https://salsa.debian.org/med-team/vmatch/-/compare/d3c660f5e869c989efd4fc55e39cdb53a47b1a7b...3d277903c6872620dc0d173cad764251da486f5b -- View it on GitLab: https://salsa.debian.org/med-team/vmatch/-/compare/d3c660f5e869c989efd4fc55e39cdb53a47b1a7b...3d277903c6872620dc0d173cad764251da486f5b You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/vmatch] Pushed new tag debian/2.3.1+dfsg-9
Sascha Steinbiss pushed new tag debian/2.3.1+dfsg-9 at Debian Med / vmatch -- View it on GitLab: https://salsa.debian.org/med-team/vmatch/-/tree/debian/2.3.1+dfsg-9 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/minimap] Pushed new tag debian/0.2-8
Sascha Steinbiss pushed new tag debian/0.2-8 at Debian Med / minimap -- View it on GitLab: https://salsa.debian.org/med-team/minimap/-/tree/debian/0.2-8 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/minimap][master] 3 commits: enable building twice in a row
Sascha Steinbiss pushed to branch master at Debian Med / minimap Commits: c02a9360 by Sascha Steinbiss at 2023-12-12T16:02:51+01:00 enable building twice in a row - - - - - 4254d505 by Sascha Steinbiss at 2023-12-12T16:03:00+01:00 bump Standards-Version - - - - - 05e513c0 by Sascha Steinbiss at 2023-12-12T16:03:10+01:00 bump d/copyright date - - - - - 4 changed files: - debian/changelog - debian/control - debian/copyright - debian/rules Changes: = debian/changelog = @@ -1,3 +1,12 @@ +minimap (0.2-8) unstable; urgency=medium + + * Enable building twice in a row. +Closes: #1049859 + * Bump Standards-Version. + * Bump d/copyright date. + + -- Sascha Steinbiss Tue, 12 Dec 2023 15:57:39 +0100 + minimap (0.2-7) unstable; urgency=medium * Bump Standards-Version. = debian/control = @@ -6,7 +6,7 @@ Priority: optional Build-Depends: debhelper-compat (= 13), d-shlibs, zlib1g-dev -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/minimap Vcs-Git: https://salsa.debian.org/med-team/minimap.git Homepage: https://github.com/lh3/minimap = debian/copyright = @@ -7,7 +7,7 @@ Copyright: © 2015 Broad Institute License: MIT Files: debian/* -Copyright: © 2015-2022 Debian Med Packaging Team +Copyright: © 2015-2023 Debian Med Packaging Team License: GPL-3+ License: MIT = debian/rules = @@ -5,6 +5,11 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow %: dh $@ + +override_dh_auto_build: + cp $(CURDIR)/*.h debian/ + dh_auto_build + override_dh_auto_install: ln -s libminimap.so.* libminimap.so d-shlibmove --commit \ @@ -12,3 +17,8 @@ override_dh_auto_install: --devunversioned \ --movedev "*.h" /usr/include/minimap \ libminimap.so + test ! -e debian/bseq.h || mv debian/*.h $(CURDIR) + +override_dh_auto_clean: + dh_auto_clean + test ! -e debian/bseq.h || mv debian/*.h $(CURDIR) View it on GitLab: https://salsa.debian.org/med-team/minimap/-/compare/26b6716e2b08e3dbd37340448889151ee8613827...05e513c0ecb95b70a1dbb519fecc532c33222a64 -- View it on GitLab: https://salsa.debian.org/med-team/minimap/-/compare/26b6716e2b08e3dbd37340448889151ee8613827...05e513c0ecb95b70a1dbb519fecc532c33222a64 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus] Pushed new tag debian/3.5.0+dfsg-4
Sascha Steinbiss pushed new tag debian/3.5.0+dfsg-4 at Debian Med / augustus -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/tree/debian/3.5.0+dfsg-4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus][master] fix multiple builds in same directory
Sascha Steinbiss pushed to branch master at Debian Med / augustus Commits: 627c2334 by Sascha Steinbiss at 2023-11-18T09:12:14+01:00 fix multiple builds in same directory - - - - - 2 changed files: - debian/changelog - debian/rules Changes: = debian/changelog = @@ -1,3 +1,11 @@ +augustus (3.5.0+dfsg-4) unstable; urgency=medium + + * Ensure multiple builds can be done in same directory. +Done by ensuring the directory is cleaned correctly. +Closes: #1043915 + + -- Sascha Steinbiss Sat, 18 Nov 2023 08:21:25 +0100 + augustus (3.5.0+dfsg-3) unstable; urgency=medium * Add patch to fix building with GCC 13. = debian/rules = @@ -39,13 +39,28 @@ override_dh_auto_clean: $(MAKE) -C auxprogs/bam2wig clean $(MAKE) -C auxprogs/compileSpliceCands clean $(MAKE) -C auxprogs/filterBam clean + $(MAKE) -C auxprogs/utrrnaseq clean rm -rf bin rm -f debian/*substvars rm -f debian/mansrc/*.1 find . -name "__pycache__" | xargs -r rm -r find src -name "*.o" | xargs -r rm + find tests -name "*.sam.bam" | xargs -r rm find auxprogs -name "*.o" | xargs -r rm - rm -f auxprogs/utrrnaseq/Debug/utrrnaseq src/augustus src/etraining src/fastBlockSearch src/getSeq src/load2db src/load2sqlitedb src/pp_simScore src/prepareAlign + rm -rf tests/short/examples/results \ + tests/short/auxprogs/bam2hints/tmp/ \ + tests/short/auxprogs/bam2hints/result_files/ \ + tests/short/auxprogs/filterbam/result_files/ + rm -f auxprogs/utrrnaseq/Debug/utrrnaseq \ + src/augustus \ + src/cxxflags \ + src/etraining \ + src/fastBlockSearch \ + src/getSeq \ + src/load2db \ + src/load2sqlitedb \ + src/pp_simScore \ + src/prepareAlign override_dh_auto_build: aln2wig bam2hints bam2wig compileSpliceCands filterBam homGeneMapping joingenes dh_auto_build View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/627c2334566ffdf60c35432101828c8e1d4bab4f -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/627c2334566ffdf60c35432101828c8e1d4bab4f You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/aragorn] Pushed new tag debian/1.2.41-2
Sascha Steinbiss pushed new tag debian/1.2.41-2 at Debian Med / aragorn -- View it on GitLab: https://salsa.debian.org/med-team/aragorn/-/tree/debian/1.2.41-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/aragorn][master] fix cleaning
Sascha Steinbiss pushed to branch master at Debian Med / aragorn Commits: e3ffa7a6 by Sascha Steinbiss at 2023-11-15T13:36:42+01:00 fix cleaning - - - - - 2 changed files: - debian/changelog - debian/rules Changes: = debian/changelog = @@ -1,3 +1,11 @@ +aragorn (1.2.41-2) unstable; urgency=medium + + * Ensure multiple builds can be done in same directory. +Done by ensuring the directory is cleaned correctly. +Closes: #1043665 + + -- Sascha Steinbiss Wed, 15 Nov 2023 11:42:55 +0100 + aragorn (1.2.41-1) unstable; urgency=medium * Update watchfile. = debian/rules = @@ -14,6 +14,10 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all override_dh_auto_build: $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -Os -o aragorn *.c +override_dh_auto_clean: + dh_auto_clean + rm -f aragorn + override_dh_auto_install: mkdir -p $(DESTDIR)/usr/bin cp aragorn $(DESTDIR)/usr/bin View it on GitLab: https://salsa.debian.org/med-team/aragorn/-/commit/e3ffa7a620cf3625283bec52678555d9689154ab -- View it on GitLab: https://salsa.debian.org/med-team/aragorn/-/commit/e3ffa7a620cf3625283bec52678555d9689154ab You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/aegean][master] fix clean behaviour
Sascha Steinbiss pushed to branch master at Debian Med / aegean Commits: 7e866348 by Sascha Steinbiss at 2023-11-15T11:36:07+01:00 fix clean behaviour - - - - - 2 changed files: - debian/changelog - debian/rules Changes: = debian/changelog = @@ -1,3 +1,11 @@ +aegean (0.16.0+dfsg-3) unstable; urgency=medium + + * Ensure multiple builds can be done in same directory. +Done by ensuring the directory is cleaned correctly. +Closes: #1043943 + + -- Sascha Steinbiss Wed, 15 Nov 2023 11:32:13 +0100 + aegean (0.16.0+dfsg-2) unstable; urgency=medium [ Jelmer Vernooij ] = debian/rules = @@ -31,3 +31,7 @@ override_dh_auto_install: override_dh_installdocs: cp $(CURDIR)/README.md $(CURDIR)/README dh_installdocs + +override_dh_auto_clean: + dh_auto_clean + rm -f $(CURDIR)/README View it on GitLab: https://salsa.debian.org/med-team/aegean/-/commit/7e866348e7f485b380e9d8c2060608df5cd5c68d -- View it on GitLab: https://salsa.debian.org/med-team/aegean/-/commit/7e866348e7f485b380e9d8c2060608df5cd5c68d You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/aegean] Pushed new tag debian/0.16.0+dfsg-3
Sascha Steinbiss pushed new tag debian/0.16.0+dfsg-3 at Debian Med / aegean -- View it on GitLab: https://salsa.debian.org/med-team/aegean/-/tree/debian/0.16.0+dfsg-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools] Pushed new branch debian/bookworm-backports
Sascha Steinbiss pushed new branch debian/bookworm-backports at Debian Med / genometools -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/tree/debian/bookworm-backports You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools] Pushed new branch debian/bullseye-backports-sloppy
Sascha Steinbiss pushed new branch debian/bullseye-backports-sloppy at Debian Med / genometools -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/tree/debian/bullseye-backports-sloppy You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools] Pushed new tag debian/1.6.5+ds-2_bpo12+1
Sascha Steinbiss pushed new tag debian/1.6.5+ds-2_bpo12+1 at Debian Med / genometools -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/tree/debian/1.6.5+ds-2_bpo12+1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools] Pushed new tag debian/1.6.5+ds-2_bpo11+1
Sascha Steinbiss pushed new tag debian/1.6.5+ds-2_bpo11+1 at Debian Med / genometools -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/tree/debian/1.6.5+ds-2_bpo11+1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools] Pushed new tag debian/1.6.5+ds-2
Sascha Steinbiss pushed new tag debian/1.6.5+ds-2 at Debian Med / genometools -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/tree/debian/1.6.5+ds-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools][master] make code build twice from same directory
Sascha Steinbiss pushed to branch master at Debian Med / genometools Commits: cc3a3800 by Sascha Steinbiss at 2023-10-26T00:09:36+02:00 make code build twice from same directory - - - - - 2 changed files: - debian/changelog - debian/rules Changes: = debian/changelog = @@ -1,3 +1,10 @@ +genometools (1.6.5+ds-2) unstable; urgency=medium + + * Facilitate building twice from the same source directory. +Closes: #1044467 + + -- Sascha Steinbiss Thu, 26 Oct 2023 00:08:09 +0200 + genometools (1.6.5+ds-1) unstable; urgency=medium * New upstream release. = debian/rules = @@ -51,11 +51,13 @@ override_dh_auto_clean: doc/manuals/annotationsketch.pdf rm -f www/genometools.org/htdocs/examples.html \ www/genometools.org/htdocs/libgenometools.html - rm -rf gtpython/build + rm -rf gtpython/build .pybuild gtpython/GenomeTools.egg-info + if test -f "debian/docs.html"; then mv debian/docs.html www/genometools.org/htdocs/; fi rm -rf obj override_dh_auto_build: cp debian/doc-imgs/*png www/genometools.org/htdocs/images + cp www/genometools.org/htdocs/docs.html debian/ $(FAKETIME) dh_auto_build -- verbose=yes useshared=yes x32=$(X32) 64bit=$(64BIT) errorcheck=no all docs manuals override_dh_auto_test: View it on GitLab: https://salsa.debian.org/med-team/genometools/-/commit/cc3a3800539cf9795b4753f54ceba4bb7b6d0669 -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/commit/cc3a3800539cf9795b4753f54ceba4bb7b6d0669 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools] Pushed new tag upstream/1.6.5+ds
Sascha Steinbiss pushed new tag upstream/1.6.5+ds at Debian Med / genometools -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/tree/upstream/1.6.5+ds You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools] Pushed new tag debian/1.6.5+ds-1
Sascha Steinbiss pushed new tag debian/1.6.5+ds-1 at Debian Med / genometools -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/tree/debian/1.6.5+ds-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools][pristine-tar] pristine-tar data for genometools_1.6.5+ds.orig.tar.xz
Sascha Steinbiss pushed to branch pristine-tar at Debian Med / genometools Commits: 5fa5a2e9 by Sascha Steinbiss at 2023-10-24T13:28:12+02:00 pristine-tar data for genometools_1.6.5+ds.orig.tar.xz - - - - - 2 changed files: - + genometools_1.6.5+ds.orig.tar.xz.delta - + genometools_1.6.5+ds.orig.tar.xz.id Changes: = genometools_1.6.5+ds.orig.tar.xz.delta = Binary files /dev/null and b/genometools_1.6.5+ds.orig.tar.xz.delta differ = genometools_1.6.5+ds.orig.tar.xz.id = @@ -0,0 +1 @@ +149300ab2a52f99eb59b97e3ec54d5697d873d8e View it on GitLab: https://salsa.debian.org/med-team/genometools/-/commit/5fa5a2e998d502c05640d8ae70e6280870b170df -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/commit/5fa5a2e998d502c05640d8ae70e6280870b170df You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools] Pushed new tag debian/1.6.4+ds-1
Sascha Steinbiss pushed new tag debian/1.6.4+ds-1 at Debian Med / genometools -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/tree/debian/1.6.4+ds-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools] Pushed new tag upstream/1.6.4+ds
Sascha Steinbiss pushed new tag upstream/1.6.4+ds at Debian Med / genometools -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/tree/upstream/1.6.4+ds You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools][upstream] New upstream version 1.6.4+ds
Sascha Steinbiss pushed to branch upstream at Debian Med / genometools Commits: a8fff127 by Sascha Steinbiss at 2023-10-08T22:57:33+02:00 New upstream version 1.6.4+ds - - - - - 30 changed files: - CHANGELOG - CONTRIBUTORS - LICENSE - Makefile - − README - README.md - VERSION - doc/RELEASE - gtruby/core/alphabet.rb - gtruby/core/encseq.rb - − scripts/Vagrantfile - scripts/add_revcmp.rb - scripts/appendsuffix.rb - − scripts/build_dists.sh - − scripts/build_windows.sh - scripts/cmp-seex-iter.rb - scripts/codegen - scripts/ctags.sh - scripts/dwmake.rb - scripts/rdj-checkcontigs.rb - scripts/rdj-parsetranscript.rb - scripts/sensitivity-test.rb - scripts/skmake.rb - scripts/sktest.sh - src/annotationsketch/custom_track_script_wrapper.h - src/core/csvline_reader.c - src/core/encseq.c - src/core/md5_tab.c - src/core/versionfunc.c - src/extended/editscript.c The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/genometools/-/commit/a8fff127f8686500289dd4dbe19c7a2b211c030b -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/commit/a8fff127f8686500289dd4dbe19c7a2b211c030b You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools][pristine-tar] pristine-tar data for genometools_1.6.4+ds.orig.tar.xz
Sascha Steinbiss pushed to branch pristine-tar at Debian Med / genometools Commits: 8bb8ca53 by Sascha Steinbiss at 2023-10-08T22:57:49+02:00 pristine-tar data for genometools_1.6.4+ds.orig.tar.xz - - - - - 2 changed files: - + genometools_1.6.4+ds.orig.tar.xz.delta - + genometools_1.6.4+ds.orig.tar.xz.id Changes: = genometools_1.6.4+ds.orig.tar.xz.delta = Binary files /dev/null and b/genometools_1.6.4+ds.orig.tar.xz.delta differ = genometools_1.6.4+ds.orig.tar.xz.id = @@ -0,0 +1 @@ +749b6dbff09bfda58b67ecb5ac174792e115a7ff View it on GitLab: https://salsa.debian.org/med-team/genometools/-/commit/8bb8ca533284084e7f710686b03420e017927ac8 -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/commit/8bb8ca533284084e7f710686b03420e017927ac8 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools][master] 5 commits: New upstream version 1.6.4+ds
Sascha Steinbiss pushed to branch master at Debian Med / genometools Commits: a8fff127 by Sascha Steinbiss at 2023-10-08T22:57:33+02:00 New upstream version 1.6.4+ds - - - - - 945f8648 by Sascha Steinbiss at 2023-10-08T22:57:49+02:00 Update upstream source from tag upstream/1.6.4+ds Update to upstream version 1.6.4+ds with Debian dir 02728a9c1c7e87f40baf817c130b3765198a3f6b - - - - - e8e3c2bc by Sascha Steinbiss at 2023-10-09T09:58:23+02:00 new upstream release - - - - - f736fb01 by Sascha Steinbiss at 2023-10-09T09:58:35+02:00 refresh patches - - - - - 7ed4d1a8 by Sascha Steinbiss at 2023-10-09T09:58:48+02:00 drop README from docs (removed upstream) - - - - - 30 changed files: - CHANGELOG - CONTRIBUTORS - LICENSE - Makefile - − README - README.md - VERSION - debian/changelog - debian/genometools.docs - debian/patches/ignore-m32-m64.patch - doc/RELEASE - gtruby/core/alphabet.rb - gtruby/core/encseq.rb - − scripts/Vagrantfile - scripts/add_revcmp.rb - scripts/appendsuffix.rb - − scripts/build_dists.sh - − scripts/build_windows.sh - scripts/cmp-seex-iter.rb - scripts/codegen - scripts/ctags.sh - scripts/dwmake.rb - scripts/rdj-checkcontigs.rb - scripts/rdj-parsetranscript.rb - scripts/sensitivity-test.rb - scripts/skmake.rb - scripts/sktest.sh - src/annotationsketch/custom_track_script_wrapper.h - src/core/csvline_reader.c - src/core/encseq.c The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/genometools/-/compare/e6faaf7a7cb0994594963c381220072cf5131d09...7ed4d1a83144ef49994ccb30097610f4b9cb60a7 -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/compare/e6faaf7a7cb0994594963c381220072cf5131d09...7ed4d1a83144ef49994ccb30097610f4b9cb60a7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools] Pushed new tag upstream/1.6.3+ds
Sascha Steinbiss pushed new tag upstream/1.6.3+ds at Debian Med / genometools -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/tree/upstream/1.6.3+ds You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools] Pushed new tag debian/1.6.3+ds-1
Sascha Steinbiss pushed new tag debian/1.6.3+ds-1 at Debian Med / genometools -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/tree/debian/1.6.3+ds-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools][upstream] New upstream version 1.6.3+ds
Sascha Steinbiss pushed to branch upstream at Debian Med / genometools Commits: c8687af0 by Sascha Steinbiss at 2023-09-19T23:26:37+02:00 New upstream version 1.6.3+ds - - - - - 30 changed files: - .github/workflows/build.yaml - + .github/workflows/release.yaml - CHANGELOG - INSTALL - LICENSE - Makefile - README - README.md - VERSION - gtpython/gt/annotationsketch/diagram.py - gtpython/gt/annotationsketch/graphics.py - gtpython/gt/annotationsketch/style.py - + gtpython/gt/bytes.py - gtpython/gt/core/alphabet.py - gtpython/gt/core/encseq.py - gtpython/gt/core/error.py - gtpython/gt/core/gtstr.py - gtpython/gt/core/str_array.py - gtpython/gt/extended/comment_node.py - gtpython/gt/extended/dup_feature_stream.py - gtpython/gt/extended/feature_index.py - gtpython/gt/extended/feature_node.py - gtpython/gt/extended/gff3_in_stream.py - gtpython/gt/extended/inter_feature_stream.py - gtpython/gt/extended/meta_node.py - gtpython/gt/extended/sequence_node.py - scripts/calltestcase.sh - scripts/spmcheck.sh - src/core/bsearch.c - src/core/qsort_r.c The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/genometools/-/commit/c8687af00efaf485605b2e72eef515b0136d0b8a -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/commit/c8687af00efaf485605b2e72eef515b0136d0b8a You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools][master] 4 commits: New upstream version 1.6.3+ds
Sascha Steinbiss pushed to branch master at Debian Med / genometools Commits: c8687af0 by Sascha Steinbiss at 2023-09-19T23:26:37+02:00 New upstream version 1.6.3+ds - - - - - 1fcc71cb by Sascha Steinbiss at 2023-09-19T23:26:55+02:00 Update upstream source from tag upstream/1.6.3+ds Update to upstream version 1.6.3+ds with Debian dir b4a53d06763332dcdbd9cb0ac7159d5a0b9f403e - - - - - 76683ee6 by Sascha Steinbiss at 2023-09-20T00:08:08+02:00 new upstream release - - - - - e6faaf7a by Sascha Steinbiss at 2023-09-20T00:08:19+02:00 refresh patches - - - - - 30 changed files: - .github/workflows/build.yaml - + .github/workflows/release.yaml - CHANGELOG - INSTALL - LICENSE - Makefile - README - README.md - VERSION - debian/changelog - debian/patches/adding_soname - debian/patches/libbam-fix - debian/patches/use-mx32 - gtpython/gt/annotationsketch/diagram.py - gtpython/gt/annotationsketch/graphics.py - gtpython/gt/annotationsketch/style.py - + gtpython/gt/bytes.py - gtpython/gt/core/alphabet.py - gtpython/gt/core/encseq.py - gtpython/gt/core/error.py - gtpython/gt/core/gtstr.py - gtpython/gt/core/str_array.py - gtpython/gt/extended/comment_node.py - gtpython/gt/extended/dup_feature_stream.py - gtpython/gt/extended/feature_index.py - gtpython/gt/extended/feature_node.py - gtpython/gt/extended/gff3_in_stream.py - gtpython/gt/extended/inter_feature_stream.py - gtpython/gt/extended/meta_node.py - gtpython/gt/extended/sequence_node.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/genometools/-/compare/a3c59c810af15a5ae927b904864f57088097a70c...e6faaf7a7cb0994594963c381220072cf5131d09 -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/compare/a3c59c810af15a5ae927b904864f57088097a70c...e6faaf7a7cb0994594963c381220072cf5131d09 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools][pristine-tar] pristine-tar data for genometools_1.6.3+ds.orig.tar.xz
Sascha Steinbiss pushed to branch pristine-tar at Debian Med / genometools Commits: 4f1de981 by Sascha Steinbiss at 2023-09-19T23:26:54+02:00 pristine-tar data for genometools_1.6.3+ds.orig.tar.xz - - - - - 2 changed files: - + genometools_1.6.3+ds.orig.tar.xz.delta - + genometools_1.6.3+ds.orig.tar.xz.id Changes: = genometools_1.6.3+ds.orig.tar.xz.delta = Binary files /dev/null and b/genometools_1.6.3+ds.orig.tar.xz.delta differ = genometools_1.6.3+ds.orig.tar.xz.id = @@ -0,0 +1 @@ +783a28652e6b33f245c0b18c95f730f4a99c4934 View it on GitLab: https://salsa.debian.org/med-team/genometools/-/commit/4f1de981c8dd8372deceeb20ffeeae96d1ac0bc5 -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/commit/4f1de981c8dd8372deceeb20ffeeae96d1ac0bc5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/mmseqs2] Pushed new tag debian/14-7e284+ds-2
Sascha Steinbiss pushed new tag debian/14-7e284+ds-2 at Debian Med / mmseqs2 -- View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/-/tree/debian/14-7e284+ds-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/lambda-align2] Pushed new tag debian/2.0.1-1
Sascha Steinbiss pushed new tag debian/2.0.1-1 at Debian Med / lambda-align2 -- View it on GitLab: https://salsa.debian.org/med-team/lambda-align2/-/tree/debian/2.0.1-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/lambda-align2] Pushed new tag upstream/2.0.1
Sascha Steinbiss pushed new tag upstream/2.0.1 at Debian Med / lambda-align2 -- View it on GitLab: https://salsa.debian.org/med-team/lambda-align2/-/tree/upstream/2.0.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/lambda-align2][pristine-tar] pristine-tar data for lambda-align2_2.0.1.orig.tar.gz
Sascha Steinbiss pushed to branch pristine-tar at Debian Med / lambda-align2 Commits: 833b01a7 by Sascha Steinbiss at 2023-07-21T11:31:01+02:00 pristine-tar data for lambda-align2_2.0.1.orig.tar.gz - - - - - 2 changed files: - + lambda-align2_2.0.1.orig.tar.gz.delta - + lambda-align2_2.0.1.orig.tar.gz.id Changes: = lambda-align2_2.0.1.orig.tar.gz.delta = Binary files /dev/null and b/lambda-align2_2.0.1.orig.tar.gz.delta differ = lambda-align2_2.0.1.orig.tar.gz.id = @@ -0,0 +1 @@ +9a51f11b44638659ae1047ee8ae6969a6bb22115 View it on GitLab: https://salsa.debian.org/med-team/lambda-align2/-/commit/833b01a7e204889fc98a9ad0765af1ec7681724a -- View it on GitLab: https://salsa.debian.org/med-team/lambda-align2/-/commit/833b01a7e204889fc98a9ad0765af1ec7681724a You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus][master] fix bug number
Sascha Steinbiss pushed to branch master at Debian Med / augustus Commits: 65db13b0 by Sascha Steinbiss at 2023-06-18T11:18:56+02:00 fix bug number - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,7 +1,7 @@ augustus (3.5.0+dfsg-3) unstable; urgency=medium * Add patch to fix building with GCC 13. -Addresses: #1037821 +Addresses: #1037585 -- Sascha Steinbiss Sat, 17 Jun 2023 18:33:10 +0200 View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/65db13b033abb51cc15da63d6d14a96e9b456c68 -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/65db13b033abb51cc15da63d6d14a96e9b456c68 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus] Pushed new tag debian/3.5.0+dfsg-3
Sascha Steinbiss pushed new tag debian/3.5.0+dfsg-3 at Debian Med / augustus -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/tree/debian/3.5.0+dfsg-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus][master] enable building with GCC 13
Sascha Steinbiss pushed to branch master at Debian Med / augustus Commits: 49f81775 by Sascha Steinbiss at 2023-06-17T18:35:07+02:00 enable building with GCC 13 - - - - - 3 changed files: - debian/changelog - + debian/patches/cstdint.patch - debian/patches/series Changes: = debian/changelog = @@ -1,3 +1,10 @@ +augustus (3.5.0+dfsg-3) unstable; urgency=medium + + * Add patch to fix building with GCC 13. +Addresses: #1037821 + + -- Sascha Steinbiss Sat, 17 Jun 2023 18:33:10 +0200 + augustus (3.5.0+dfsg-2) unstable; urgency=medium * Skip filterBam auxprogs test on s390x. = debian/patches/cstdint.patch = @@ -0,0 +1,24 @@ +Description: enable building with GCC 13 +Author: Sascha Steinbiss +Forwarded: https://github.com/Gaius-Augustus/Augustus/pull/395 +Last-Update: 2023-06-17 +--- a/auxprogs/homGeneMapping/include/sqliteDB.hh b/auxprogs/homGeneMapping/include/sqliteDB.hh +@@ -13,6 +13,7 @@ + #include + #include + #include ++#include + + using namespace std; + +--- a/include/sqliteDB.hh b/include/sqliteDB.hh +@@ -11,6 +11,7 @@ + #include + #include + #include ++#include + + using namespace std; + = debian/patches/series = @@ -4,3 +4,4 @@ interpreter_paths.patch switch_cgp_testing_off.patch disable-compare.patch s390x-disable-filterbam-tests.patch +cstdint.patch View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/49f81775abe3dc4c34557bf1384209f8405e27df -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/49f81775abe3dc4c34557bf1384209f8405e27df You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/aragorn] Pushed new tag debian/1.2.41-1
Sascha Steinbiss pushed new tag debian/1.2.41-1 at Debian Med / aragorn -- View it on GitLab: https://salsa.debian.org/med-team/aragorn/-/tree/debian/1.2.41-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/aragorn] Pushed new tag upstream/1.2.41
Sascha Steinbiss pushed new tag upstream/1.2.41 at Debian Med / aragorn -- View it on GitLab: https://salsa.debian.org/med-team/aragorn/-/tree/upstream/1.2.41 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/aragorn][pristine-tar] pristine-tar data for aragorn_1.2.41.orig.tar.gz
Sascha Steinbiss pushed to branch pristine-tar at Debian Med / aragorn Commits: e5414f91 by Sascha Steinbiss at 2023-06-17T02:31:45+02:00 pristine-tar data for aragorn_1.2.41.orig.tar.gz - - - - - 2 changed files: - + aragorn_1.2.41.orig.tar.gz.delta - + aragorn_1.2.41.orig.tar.gz.id Changes: = aragorn_1.2.41.orig.tar.gz.delta = Binary files /dev/null and b/aragorn_1.2.41.orig.tar.gz.delta differ = aragorn_1.2.41.orig.tar.gz.id = @@ -0,0 +1 @@ +4d775a84a39a8ac08ac205f70a256f90dd3844cf View it on GitLab: https://salsa.debian.org/med-team/aragorn/-/commit/e5414f917e791f5df225632cb1f573a9a13cc535 -- View it on GitLab: https://salsa.debian.org/med-team/aragorn/-/commit/e5414f917e791f5df225632cb1f573a9a13cc535 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/kissplice] Pushed new tag debian/2.6.2-2
Sascha Steinbiss pushed new tag debian/2.6.2-2 at Debian Med / kissplice -- View it on GitLab: https://salsa.debian.org/med-team/kissplice/-/tree/debian/2.6.2-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/kissplice][master] enable riscv64
Sascha Steinbiss pushed to branch master at Debian Med / kissplice
Commits:
58a37101 by Sascha Steinbiss at 2023-01-20T20:11:56+01:00
enable riscv64
- - - - -
2 changed files:
- debian/changelog
- debian/control
Changes:
=
debian/changelog
=
@@ -1,3 +1,13 @@
+kissplice (2.6.2-2) unstable; urgency=medium
+
+ * Team upload.
+
+ [ Eric Long ]
+ * Add build target for riscv64.
+Closes: #1027357
+
+ -- Sascha Steinbiss Fri, 20 Jan 2023 19:37:26 +0100
+
kissplice (2.6.2-1) unstable; urgency=medium
* New upstream version
=
debian/control
=
@@ -19,7 +19,7 @@ Homepage: http://kissplice.prabi.fr/
Rules-Requires-Root: no
Package: kissplice
-Architecture: any-amd64 any-arm64 any-mips64 any-mips64el any-ia64 any-ppc64
any-ppc64el any-sparc64
+Architecture: any-amd64 any-arm64 any-mips64 any-mips64el any-ia64 any-ppc64
any-ppc64el any-sparc64 riscv64
Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
View it on GitLab:
https://salsa.debian.org/med-team/kissplice/-/commit/58a3710118e9cfce4a21b0a54ccd16998ddc16a4
--
View it on GitLab:
https://salsa.debian.org/med-team/kissplice/-/commit/58a3710118e9cfce4a21b0a54ccd16998ddc16a4
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[med-svn] [Git][med-team/rna-star] Pushed new tag upstream/2.7.10b+dfsg
Sascha Steinbiss pushed new tag upstream/2.7.10b+dfsg at Debian Med / rna-star -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/tree/upstream/2.7.10b+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star][pristine-tar] pristine-tar data for rna-star_2.7.10b+dfsg.orig.tar.xz
Sascha Steinbiss pushed to branch pristine-tar at Debian Med / rna-star Commits: bdf38bf7 by Sascha Steinbiss at 2022-12-27T02:18:29+01:00 pristine-tar data for rna-star_2.7.10b+dfsg.orig.tar.xz - - - - - 2 changed files: - + rna-star_2.7.10b+dfsg.orig.tar.xz.delta - + rna-star_2.7.10b+dfsg.orig.tar.xz.id Changes: = rna-star_2.7.10b+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/rna-star_2.7.10b+dfsg.orig.tar.xz.delta differ = rna-star_2.7.10b+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +6953f562f0b5e9a15c6d2d5310f9a4553fb9769e View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/bdf38bf7fcc8053b475f0888159459aa1f2805c7 -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/bdf38bf7fcc8053b475f0888159459aa1f2805c7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star][upstream] New upstream version 2.7.10b+dfsg
Sascha Steinbiss pushed to branch upstream at Debian Med / rna-star Commits: 89e51161 by Sascha Steinbiss at 2022-12-27T02:18:28+01:00 New upstream version 2.7.10b+dfsg - - - - - 30 changed files: - + .travis.yml - CHANGES.md - README.md - RELEASEnotes.md - doc/STARmanual.pdf - docs/STARsolo.md - extras/doc-latex/STARmanual.tex - extras/docker/Dockerfile - extras/scripts/sjFromSAMcollapseUandM.awk - extras/scripts/sjFromSAMcollapseUandM_inclOverlaps.awk - source/Genome.cpp - source/Makefile - source/OutSJ.cpp - source/OutSJ.h - source/ParametersClip_initialize.cpp - source/ParametersSolo.cpp - source/ParametersSolo.h - source/ReadAlignChunk_mapChunk.cpp - source/STAR.cpp - source/SharedMemory.cpp - source/Solo.cpp - source/SoloCommon.h - source/SoloFeature.cpp - source/SoloFeature.h - source/SoloFeature_cellFiltering.cpp - source/SoloFeature_collapseUMIall_multiMappers.cpp → source/SoloFeature_collapseUMIall.cpp - source/SoloFeature_countCBgeneUMI.cpp - source/SoloFeature_countVelocyto.cpp - source/SoloFeature_outputResults.cpp - source/SoloFeature_processRecords.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/89e511619950f991efd95a5a581ee65a840673d3 -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/89e511619950f991efd95a5a581ee65a840673d3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star][master] 3 commits: New upstream version 2.7.10b+dfsg
Sascha Steinbiss pushed to branch master at Debian Med / rna-star Commits: 89e51161 by Sascha Steinbiss at 2022-12-27T02:18:28+01:00 New upstream version 2.7.10b+dfsg - - - - - af3a5b71 by Sascha Steinbiss at 2022-12-27T02:18:29+01:00 Update upstream source from tag upstream/2.7.10b+dfsg Update to upstream version 2.7.10b+dfsg with Debian dir e281a7aa9f9d83781a8e3d2760edf7c9507d642f - - - - - a880cfe0 by Sascha Steinbiss at 2022-12-27T10:15:44+01:00 new upstream release - - - - - 30 changed files: - + .travis.yml - CHANGES.md - README.md - RELEASEnotes.md - debian/changelog - debian/patches/gcc-12.patch - doc/STARmanual.pdf - docs/STARsolo.md - extras/doc-latex/STARmanual.tex - extras/docker/Dockerfile - extras/scripts/sjFromSAMcollapseUandM.awk - extras/scripts/sjFromSAMcollapseUandM_inclOverlaps.awk - source/Genome.cpp - source/Makefile - source/OutSJ.cpp - source/OutSJ.h - source/ParametersClip_initialize.cpp - source/ParametersSolo.cpp - source/ParametersSolo.h - source/ReadAlignChunk_mapChunk.cpp - source/STAR.cpp - source/SharedMemory.cpp - source/Solo.cpp - source/SoloCommon.h - source/SoloFeature.cpp - source/SoloFeature.h - source/SoloFeature_cellFiltering.cpp - source/SoloFeature_collapseUMIall_multiMappers.cpp → source/SoloFeature_collapseUMIall.cpp - source/SoloFeature_countCBgeneUMI.cpp - source/SoloFeature_countVelocyto.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/compare/8e58df5c0e2332e38b9ecf159d06fcf28ac99aea...a880cfe0460e2d53a0f6861b8bcbad3794c2ac8f -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/compare/8e58df5c0e2332e38b9ecf159d06fcf28ac99aea...a880cfe0460e2d53a0f6861b8bcbad3794c2ac8f You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star] Pushed new tag debian/2.7.10b+dfsg-1
Sascha Steinbiss pushed new tag debian/2.7.10b+dfsg-1 at Debian Med / rna-star -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/tree/debian/2.7.10b+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus] Pushed new tag debian/3.5.0+dfsg-2
Sascha Steinbiss pushed new tag debian/3.5.0+dfsg-2 at Debian Med / augustus -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/tree/debian/3.5.0+dfsg-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus][master] skip filterBam auxprogs test on s390x
Sascha Steinbiss pushed to branch master at Debian Med / augustus
Commits:
b29db016 by Sascha Steinbiss at 2022-11-21T00:32:03+01:00
skip filterBam auxprogs test on s390x
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/s390x-disable-filterbam-tests.patch
- debian/patches/series
Changes:
=
debian/changelog
=
@@ -1,3 +1,9 @@
+augustus (3.5.0+dfsg-2) unstable; urgency=medium
+
+ * Skip filterBam auxprogs test on s390x.
+
+ -- Sascha Steinbiss Mon, 21 Nov 2022 00:11:53 +0100
+
augustus (3.5.0+dfsg-1) unstable; urgency=medium
* Team upload.
=
debian/patches/s390x-disable-filterbam-tests.patch
=
@@ -0,0 +1,34 @@
+Index: augustus/Makefile
+===
+--- augustus.orig/Makefile
augustus/Makefile
+@@ -64,17 +64,21 @@ check-python3:
+
+ test: check-python3 all
+ ifeq ("$(shell uname -s -m)","Linux x86_64")
+- $(eval TEST_COMPARE := )
+- $(eval TEST_HTML := --html)
++ cd tests/short && ./execute_test.py --html examples
++ cd tests/short && ./execute_test.py --html bam2hints
++ cd tests/short && ./execute_test.py --html bam2wig
++ cd tests/short && ./execute_test.py --html filterbam
++else ifeq ("$(shell uname -s -m)", "Linux s390x")
++ cd tests/short && ./execute_test.py examples
++ cd tests/short && ./execute_test.py --html bam2hints
++ cd tests/short && ./execute_test.py --html bam2wig
+ else
+ $(info If you run make test on a non-AMD64 architecture or a non-Linux
system (like macOS), most tests will run without the --compare option!)
+- $(eval TEST_COMPARE := )
+- $(eval TEST_HTML := )
++ cd tests/short && ./execute_test.py examples
++ cd tests/short && ./execute_test.py --html bam2hints
++ cd tests/short && ./execute_test.py --html bam2wig
++ cd tests/short && ./execute_test.py --html filterbam
+ endif
+- cd tests/short && ./execute_test.py $(TEST_COMPARE) $(TEST_HTML)
examples
+- cd tests/short && ./execute_test.py --html bam2hints
+- cd tests/short && ./execute_test.py --html bam2wig
+- cd tests/short && ./execute_test.py --html filterbam
+
+ unit_test:
+ cd src && ${MAKE} unittest
=
debian/patches/series
=
@@ -3,3 +3,4 @@ set_installdir
interpreter_paths.patch
switch_cgp_testing_off.patch
disable-compare.patch
+s390x-disable-filterbam-tests.patch
View it on GitLab:
https://salsa.debian.org/med-team/augustus/-/commit/b29db016a53cace78ec452766c240dedb630c482
--
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[med-svn] [Git][med-team/hhsuite] Pushed new tag debian/3.3.0+ds-7
Sascha Steinbiss pushed new tag debian/3.3.0+ds-7 at Debian Med / hhsuite -- View it on GitLab: https://salsa.debian.org/med-team/hhsuite/-/tree/debian/3.3.0+ds-7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/hhsuite][master] 3 commits: fix watchfile
Sascha Steinbiss pushed to branch master at Debian Med / hhsuite Commits: 4d365cad by Sascha Steinbiss at 2022-10-25T15:37:52+02:00 fix watchfile - - - - - e698c420 by Sascha Steinbiss at 2022-10-25T15:38:01+02:00 bump Standards-Version - - - - - f65de93a by Sascha Steinbiss at 2022-10-25T15:38:10+02:00 update date in d/copyright - - - - - 4 changed files: - debian/changelog - debian/control - debian/copyright - debian/watch Changes: = debian/changelog = @@ -1,3 +1,11 @@ +hhsuite (3.3.0+ds-7) unstable; urgency=medium + + * Fix watchfile. + * Bump Standards-Version. + * Update date in d/copyright. + + -- Sascha Steinbiss Tue, 25 Oct 2022 15:17:24 +0200 + hhsuite (3.3.0+ds-6) unstable; urgency=medium * Adjust patch to not overwrite example files in tests. = debian/control = @@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 13), cmake, imagemagick, help2man -Standards-Version: 4.6.0 +Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/hhsuite Vcs-Git: https://salsa.debian.org/med-team/hhsuite.git Homepage: https://toolkit.tuebingen.mpg.de/ = debian/copyright = @@ -36,6 +36,7 @@ License: Expat Files: debian/* Copyright: 2012 Laszlo Kajan 2019 Michael R. Crusoe + 2022 Sascha Steinbiss License: GPL-3.0+ Files: cmake/xxdi.pl = debian/watch = @@ -1,4 +1,3 @@ version=4 - opts="uversionmangle=s/-beta\.(\d)/~beta$1/;s/-beta/~beta/,repacksuffix=+ds,dversionmangle=auto,repack,compression=xz" \ -https://github.com/soedinglab/hh-suite/releases .*/v(\d[-\d.beta]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) +https://github.com/soedinglab/hh-suite/tags .*/v(\d[-\d.beta]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) View it on GitLab: https://salsa.debian.org/med-team/hhsuite/-/compare/16fa1f43d782043b71be26fa283c48806ede25e0...f65de93ae6c4daf9ff3174d27d0bc557f75717b4 -- View it on GitLab: https://salsa.debian.org/med-team/hhsuite/-/compare/16fa1f43d782043b71be26fa283c48806ede25e0...f65de93ae6c4daf9ff3174d27d0bc557f75717b4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/tantan] Pushed new tag debian/40-1
Sascha Steinbiss pushed new tag debian/40-1 at Debian Med / tantan -- View it on GitLab: https://salsa.debian.org/med-team/tantan/-/tree/debian/40-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/tantan] Pushed new tag upstream/40
Sascha Steinbiss pushed new tag upstream/40 at Debian Med / tantan -- View it on GitLab: https://salsa.debian.org/med-team/tantan/-/tree/upstream/40 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/tantan][pristine-tar] pristine-tar data for tantan_40.orig.tar.gz
Sascha Steinbiss pushed to branch pristine-tar at Debian Med / tantan Commits: 3859bf62 by Sascha Steinbiss at 2022-10-24T22:30:21+02:00 pristine-tar data for tantan_40.orig.tar.gz - - - - - 2 changed files: - + tantan_40.orig.tar.gz.delta - + tantan_40.orig.tar.gz.id Changes: = tantan_40.orig.tar.gz.delta = Binary files /dev/null and b/tantan_40.orig.tar.gz.delta differ = tantan_40.orig.tar.gz.id = @@ -0,0 +1 @@ +f055833a1d3e4b1a638803e9a56135f719a32d44 View it on GitLab: https://salsa.debian.org/med-team/tantan/-/commit/3859bf624bbc5a38982fde33bb220b96cdb20ddf -- View it on GitLab: https://salsa.debian.org/med-team/tantan/-/commit/3859bf624bbc5a38982fde33bb220b96cdb20ddf You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sspace] Pushed new tag debian/2.1.1+dfsg-7
Sascha Steinbiss pushed new tag debian/2.1.1+dfsg-7 at Debian Med / sspace -- View it on GitLab: https://salsa.debian.org/med-team/sspace/-/tree/debian/2.1.1+dfsg-7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/sspace][master] 3 commits: fix watchfile
Sascha Steinbiss pushed to branch master at Debian Med / sspace Commits: 5401d14f by Sascha Steinbiss at 2022-10-24T15:21:50+02:00 fix watchfile - - - - - 3107ff62 by Sascha Steinbiss at 2022-10-24T15:22:01+02:00 bump Standards-Version - - - - - 0881de05 by Sascha Steinbiss at 2022-10-24T15:22:09+02:00 update email and dates in d/copyright - - - - - 4 changed files: - debian/changelog - debian/control - debian/copyright - debian/watch Changes: = debian/changelog = @@ -1,3 +1,11 @@ +sspace (2.1.1+dfsg-7) unstable; urgency=medium + + * Bump Standards-Version. + * Update email and dates in d/copyright. + * Fix watchfile. + + -- Sascha Steinbiss Mon, 24 Oct 2022 15:08:39 +0200 + sspace (2.1.1+dfsg-6) unstable; urgency=medium * Fix watchfile to detect new versions on github = debian/control = @@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13), python3, asciidoctor, bowtie -Standards-Version: 4.6.0 +Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/sspace Vcs-Git: https://salsa.debian.org/med-team/sspace.git Homepage: https://github.com/nsoranzo/sspace_basic = debian/copyright = @@ -19,8 +19,8 @@ Copyright: 2007 Canada's Michael Smith Genome Science Centre License: GPL-2+ Files: debian/* -Copyright: 2016 Andreas Tille - 2016 Sascha Steinbiss +Copyright: 2016-2021 Andreas Tille + 2016-2022 Sascha Steinbiss License: GPL-2+ License: GPL-2+ = debian/watch = @@ -1,4 +1,4 @@ version=4 opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \ - https://github.com/nsoranzo/sspace_basic/releases .*/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) +https://github.com/nsoranzo/sspace_basic/tags .*/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) View it on GitLab: https://salsa.debian.org/med-team/sspace/-/compare/35ca8b863649e4c4365175111b5c82b0feb28730...0881de05c55ebd26619e4ddcbbfee5c1e463fda9 -- View it on GitLab: https://salsa.debian.org/med-team/sspace/-/compare/35ca8b863649e4c4365175111b5c82b0feb28730...0881de05c55ebd26619e4ddcbbfee5c1e463fda9 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/minimap] Pushed new tag debian/0.2-7
Sascha Steinbiss pushed new tag debian/0.2-7 at Debian Med / minimap -- View it on GitLab: https://salsa.debian.org/med-team/minimap/-/tree/debian/0.2-7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/minimap][master] 3 commits: fix watchfile format
Sascha Steinbiss pushed to branch master at Debian Med / minimap Commits: b4223eef by Sascha Steinbiss at 2022-10-19T16:32:09+02:00 fix watchfile format - - - - - 994126d9 by Sascha Steinbiss at 2022-10-19T16:32:20+02:00 bump Standards-Version - - - - - 26b6716e by Sascha Steinbiss at 2022-10-19T16:32:27+02:00 bump d/copyright date - - - - - 4 changed files: - debian/changelog - debian/control - debian/copyright - debian/watch Changes: = debian/changelog = @@ -1,3 +1,11 @@ +minimap (0.2-7) unstable; urgency=medium + + * Bump Standards-Version. + * Fix watchfile format. + * Bump d/copyright date. + + -- Sascha Steinbiss Wed, 19 Oct 2022 16:29:56 +0200 + minimap (0.2-6) unstable; urgency=medium * Team upload = debian/control = @@ -6,7 +6,7 @@ Priority: optional Build-Depends: debhelper-compat (= 13), d-shlibs, zlib1g-dev -Standards-Version: 4.6.0 +Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/minimap Vcs-Git: https://salsa.debian.org/med-team/minimap.git Homepage: https://github.com/lh3/minimap = debian/copyright = @@ -7,7 +7,7 @@ Copyright: © 2015 Broad Institute License: MIT Files: debian/* -Copyright: © 2015-2020 Debian Med Packaging Team +Copyright: © 2015-2022 Debian Med Packaging Team License: GPL-3+ License: MIT = debian/watch = @@ -1,2 +1,2 @@ version=4 -https://github.com/lh3/minimap/releases .*/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) +https://github.com/lh3/minimap/tags .*/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) View it on GitLab: https://salsa.debian.org/med-team/minimap/-/compare/519bccbefd3bb75948f41175f149382f426b6309...26b6716e2b08e3dbd37340448889151ee8613827 -- View it on GitLab: https://salsa.debian.org/med-team/minimap/-/compare/519bccbefd3bb75948f41175f149382f426b6309...26b6716e2b08e3dbd37340448889151ee8613827 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/miniasm] Pushed new tag debian/0.3+dfsg-4
Sascha Steinbiss pushed new tag debian/0.3+dfsg-4 at Debian Med / miniasm -- View it on GitLab: https://salsa.debian.org/med-team/miniasm/-/tree/debian/0.3+dfsg-4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/miniasm][master] 3 commits: fix watchfile format
Sascha Steinbiss pushed to branch master at Debian Med / miniasm Commits: 7f66ecb1 by Sascha Steinbiss at 2022-10-19T13:50:27+02:00 fix watchfile format - - - - - 43c3385d by Sascha Steinbiss at 2022-10-19T13:50:35+02:00 bump d/copyright date - - - - - 22aba22d by Sascha Steinbiss at 2022-10-19T13:50:42+02:00 bump Standards-Version - - - - - 4 changed files: - debian/changelog - debian/control - debian/copyright - debian/watch Changes: = debian/changelog = @@ -1,3 +1,11 @@ +miniasm (0.3+dfsg-4) unstable; urgency=medium + + * Bump Standards-Version. + * Fix watchfile format. + * Bump d/copyright date. + + -- Sascha Steinbiss Wed, 19 Oct 2022 10:10:44 +0200 + miniasm (0.3+dfsg-3) unstable; urgency=medium * Team upload. = debian/control = @@ -5,7 +5,7 @@ Section: science Priority: optional Build-Depends: debhelper-compat (= 13), zlib1g-dev -Standards-Version: 4.6.0 +Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/miniasm Vcs-Git: https://salsa.debian.org/med-team/miniasm.git Homepage: https://github.com/lh3/miniasm = debian/copyright = @@ -12,7 +12,7 @@ Copyright: © 2008, 2009, 2011 Attractive Chaos License: MIT Files: debian/* -Copyright: © 2015 Debian Med Packaging Team +Copyright: © 20152-2022 Debian Med Packaging Team License: GPL-3+ License: MIT = debian/watch = @@ -1,4 +1,4 @@ version=4 opts=repacksuffix=+dfsg,dversionmangle=s/\+(debian|dfsg|ds|deb)(\.\d+)?$// \ -https://github.com/lh3/miniasm/releases .*/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) +https://github.com/lh3/miniasm/tags .*/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) View it on GitLab: https://salsa.debian.org/med-team/miniasm/-/compare/a094ce2ade1d1aca6a9deaf5b11e2f777388b174...22aba22da7166ba840a38b5a8529bb013d9b80ac -- View it on GitLab: https://salsa.debian.org/med-team/miniasm/-/compare/a094ce2ade1d1aca6a9deaf5b11e2f777388b174...22aba22da7166ba840a38b5a8529bb013d9b80ac You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
