[med-svn] [Git][med-team/bali-phy][master] 5 commits: Build-Depends: libcli11-dev, libutf8proc-dev, libxxhash-dev and libzstd-dev
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Oct 20 10:28:47 BST 2026
Andreas Tille pushed to branch master at Debian Med / bali-phy
Commits:
b1d20f1d by Andreas Tille at 2026-10-20T07:50:25+02:00
Build-Depends: libcli11-dev, libutf8proc-dev, libxxhash-dev and libzstd-dev
- - - - -
45382b04 by Andreas Tille at 2026-10-20T07:52:59+02:00
Update autopkgtest for the reworked upstream command line (--iterations instead of --iter, bpy-summarize instead of bp-analyze).
- - - - -
67a2ea4a by Andreas Tille at 2026-10-20T09:49:29+02:00
Update d/copyright; add d/lrc.config
- - - - -
c99ecbc3 by Andreas Tille at 2026-10-20T10:55:35+02:00
Do not ship extra license files
- - - - -
c6f0c0ff by Andreas Tille at 2026-10-20T11:28:03+02:00
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/lrc.config
- debian/rules
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,14 +1,20 @@
-bali-phy (4.3+dfsg-1) UNRELEASED; urgency=medium
+bali-phy (4.3+dfsg-1) unstable; urgency=medium
* Team upload.
- * d/copyright: Use Github as Source location
* New upstream version
+ Closes: #1150961
+ * Build-Depends: libcli11-dev, libutf8proc-dev, libxxhash-dev and libzstd-dev
+ * d/copyright: Use Github as Source location
* Standards-Version: 4.7.4 (routine-update)
* Reflow Uploaders field (cme)
* Drop 'Rules-Requires-Root: no' from d/control (routine-update)
* Use secure URI in Homepage field.
+ * Update autopkgtest for the reworked upstream command line
+ (--iterations instead of --iter, bpy-summarize instead of bp-analyze).
+ * Update d/copyright; add d/lrc.config
+ * Do not ship extra license files
- -- Andreas Tille <tille at debian.org> Mon, 19 Oct 2026 21:30:38 +0200
+ -- Andreas Tille <tille at debian.org> Tue, 20 Oct 2026 10:55:41 +0200
bali-phy (4.1+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -16,9 +16,13 @@ Build-Depends:
libboost-random-dev,
libcairo2-dev,
libcereal-dev,
+ libcli11-dev,
libeigen3-dev,
libfmt-dev,
librange-v3-dev,
+ libutf8proc-dev,
+ libxxhash-dev,
+ libzstd-dev,
meson,
nlohmann-json3-dev,
pandoc,
=====================================
debian/copyright
=====================================
@@ -7,17 +7,35 @@ Upstream-Contact: https://groups.google.com/forum/#!forum/bali-phy-users
Files: *
Copyright: 2004-2024 Benjamin Redelings <benjamin.redelings at gmail.com>
-License: GPL-2.0+
+License: GPL-2+
Files: external/immer/*
Copyright: 2016-2020 Juan Pedro Bolivar Puente <raskolnikov at gnu.org>
License: BSL-1.0
+Files: scripts/bpy-summarize-assets/*
+Copyright: 2006, Ivan Sagalaev.
+License: BSD-3-Clause
+
+Files: scripts/bpy-summarize-assets/x3dom-1.8.3/*
+Copyright: 2009-2020 X3DOM
+License: MIT or GPL-3+
+
+Files: external/re-flex/*
+Copyright: 2016, Robert van Engelen, Genivia Inc.
+License: BSD-3-clause
+
+Files: src/computation/parser/*
+ src/models/location.hh
+ src/models/parser.*
+Copyright: 2002-2021 Free Software Foundation, Inc.
+License: GPL-3+ with Bison-2.2 exception
+
Files: debian/*
Copyright: 2018 Benjamin Redelings <benjamin.redelings at gmail.com>
-License: GPL-2.0+
+License: GPL-2+
-License: GPL-2.0+
+License: GPL-2+
On Debian systems, the complete text of the GNU General
Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
@@ -45,3 +63,52 @@ License: BSL-1.0
FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
+License: GPL-3+
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
+License: BSD-3-Clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ * Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+ .
+ * Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ .
+ * Neither the name of the copyright holder nor the names of its
+ contributors may be used to endorse or promote products derived from
+ this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
=====================================
debian/lrc.config
=====================================
@@ -0,0 +1,5 @@
+meson.build
+ARCHITECTURE.md
+scripts/bpy-summarize-assets/x3dom-1.8.3/LICENSE.md
+scripts/bpy-summarize-assets/x3dom-1.8.3/x3dom.css
+scripts/git_version.sh
=====================================
debian/rules
=====================================
@@ -35,3 +35,9 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
dh_auto_test
rm -rf tests; mv tests.bak tests
endif
+
+execute_after_dh_install:
+ find debian/*/usr/lib/bali-phy/libexec -iname "LICENSE*" -delete
+
+execute_after_dh_installdocs:
+ rm -rf debian/*/usr/share/doc/bali-phy/licenses
=====================================
debian/tests/run-unit-test
=====================================
@@ -18,7 +18,7 @@ bali-phy --version
bali-phy --help
bali-phy 5S-rRNA/5d.fasta --test --seed=0
-bali-phy 5S-rRNA/5d.fasta --iter=50 --seed=0
-bali-phy 5S-rRNA/5d.fasta --iter=200 -I rs07 --seed=0
-bali-phy 5S-rRNA/5d.fasta --iter=100
-bp-analyze 5d-1
+bali-phy 5S-rRNA/5d.fasta --iterations=50 --seed=0
+bali-phy 5S-rRNA/5d.fasta --iterations=200 -I RS07 --seed=0
+bali-phy 5S-rRNA/5d.fasta --iterations=100
+bpy-summarize 5d-1
View it on GitLab: https://salsa.debian.org/med-team/bali-phy/-/compare/f632d5ad4f5bee451612948c8acb510d783b6d45...c6f0c0ffff4e9a7ab8242818583f1f4957ba5aad
--
View it on GitLab: https://salsa.debian.org/med-team/bali-phy/-/compare/f632d5ad4f5bee451612948c8acb510d783b6d45...c6f0c0ffff4e9a7ab8242818583f1f4957ba5aad
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