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DFSG, Licensing & New Packages Team

Review: python-galaxy-tool-util 25.1.1-1

New Package Report

.changes
DateWed, 25 Feb 2026 13:17:44 +0100
Sourcepython-galaxy-tool-util
Version25.1.1-1
Changed-ByMichael R. Crusoe
Architecturesource all
Distributionunstable
Changelog
python-galaxy-tool-util (25.1.1-1) unstable; urgency=medium
 .
   * Initial release. (Closes: #1129299)
.dsc
Sectionpython
Priorityoptional
Componentmain
Package-Listpython3-galaxy-tool-util deb python optional arch=all
debian/copyright
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: galaxy-tool-util 
Source: https://pypi.org/project/galaxy-tool-util/#files

Files: galaxy/tool-util/version.py
Copyright: Donald Stufft and individual contributors
License: BSD-2-clause
 Redistribution and use in source and binary forms, with or without            
 modification, are permitted provided that the following conditions are met:   
     1. Redistributions of source code must retain the above copyright notice, 
        this list of conditions and the following disclaimer.                  
     2. 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.   
 .                                                                                  
 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.

Files: *
Copyright: 2005-2022, Galaxy Contributors
           2011-2016 John Chilton, Jean-Frédéric Berthelot, Pierre Lindenbaum
License: expat
Comment: Codebase was relicensed to only MIT/expat on 2026-02-25. See https://github.com/galaxyproject/galaxy/pull/16970

Files: debian/*
Copyright: 2026 Michael R. Crusoe <crusoe@debian.org>
License: expat

License: expat
 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.

Review Information

rejected — allocated to awm 13 days ago, started 13 days ago, completed 13 days ago.

Final Comment

Please review the notes and make the recommended fixes to your debian/copyright
and debian/control files.

Thanks!

Public Notes

13 days ago ● public

Lintian

Command: lintian -Iiv -L '>=warning' --show-overrides --color=never ../$(basename $PWD)_*.changes
Exit code: 0

N:
W: python-galaxy-tool-util source: global-files-wildcard-not-first-paragraph-in-dep5-copyright [debian/copyright:27]
N: 
N:   The specified paragraph in the machine readable copyright file references
N:   all possible files but is not the first paragraph. For example:
N:   
N:    Files: filea
N:    Copyright: 2009, ...
N:   
N:    Files: *
N:    Copyright: 2010, ...
N:   
N:   As the paragraphs is matched on a "last match wins" principle, all
N:   proceeding paragraphs are overridden.
N: 
N:   Please refer to
N:   https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ for
N:   details.
N: 
N:   Visibility: warning
N:   Show-Always: no
N:   Check: debian/copyright/dep5
N: 
N:
W: python3-galaxy-tool-util: no-manual-page [usr/bin/galaxy-tool-test-case-validation]
N: 
N:   Each binary in /usr/bin, /usr/sbin, /bin, /sbin or /usr/games should have
N:   a manual page
N:   
N:   Note that though the man program has the capability to check for several
N:   program names in the NAMES section, each of these programs should have its
N:   own manual page (a symbolic link to the appropriate manual page is
N:   sufficient) because other manual page viewers such as xman or tkman don't
N:   support this.
N:   
N:   If the name of the manual page differs from the binary by case, man may be
N:   able to find it anyway; however, it is still best practice to match the
N:   exact capitalization of the executable in the manual page.
N:   
N:   If the manual pages are provided by another package on which this package
N:   depends, Lintian may not be able to determine that manual pages are
N:   available. In this case, after confirming that all binaries do have manual
N:   pages after this package and its dependencies are installed, please add a
N:   Lintian override.
N: 
N:   Please refer to Manual pages (Section 12.1) in the Debian Policy Manual
N:   for details.
N: 
N:   Visibility: warning
N:   Show-Always: no
N:   Check: documentation/manual
N:   Renamed from: binary-without-manpage
N: 
N:
W: python3-galaxy-tool-util: no-manual-page [usr/bin/galaxy-tool-test]
N:
W: python3-galaxy-tool-util: no-manual-page [usr/bin/galaxy-tool-upgrade-advisor]
N:
W: python3-galaxy-tool-util: no-manual-page [usr/bin/mulled-build-channel]
N:
W: python3-galaxy-tool-util: no-manual-page [usr/bin/mulled-build-files]
N:
W: python3-galaxy-tool-util: no-manual-page [usr/bin/mulled-build-tool]
N:
W: python3-galaxy-tool-util: no-manual-page [usr/bin/mulled-build]
N:
W: python3-galaxy-tool-util: no-manual-page [usr/bin/mulled-hash]
N:
W: python3-galaxy-tool-util: no-manual-page [usr/bin/mulled-list]
N:
W: python3-galaxy-tool-util: no-manual-page [usr/bin/mulled-search]
N:
W: python3-galaxy-tool-util: no-manual-page [usr/bin/mulled-update-singularity-containers]
N:
W: python3-galaxy-tool-util: no-manual-page [usr/bin/validate-test-format]
N:
W: python-galaxy-tool-util source: superfluous-file-pattern galaxy/tool-util/version.py [debian/copyright:5]
N: 
N:   The wildcard that was specified matches no file in the source tree. This
N:   either indicates that you should fix the wildcard so that it matches the
N:   intended file or that you can remove the wildcard. Notice that in contrast
N:   to shell globs, the "*" (star or asterisk) matches slashes and leading
N:   dots.
N: 
N:   Please refer to
N:   https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ for
N:   details.
N: 
N:   Visibility: warning
N:   Show-Always: no
N:   Check: debian/copyright/dep5
N: 
13 days ago ● public

vulture

Command: vulture --min-confidence 80 .
Exit code: 3

debian/tests/tool_util/data/test_tool_data_bundles.py:92: unused variable 'sync_cache' (100% confidence)
debian/tests/tool_util/test_tool_loader.py:29: unused variable 'tb' (100% confidence)
galaxy/tool_util/client/staging.py:37: unused import 'ApiTestInteractor' (90% confidence)
galaxy/tool_util/cwl/cwltool_deps.py:50: unused import 'command_line_tool' (90% confidence)
galaxy/tool_util/cwl/runtime_actions.py:162: unused variable 'output_key' (100% confidence)
galaxy/tool_util/data/__init__.py:915: unused variable 'sync_cache' (100% confidence)
galaxy/tool_util/data/__init__.py:928: unused variable 'tool_data_table_config_path_set' (100% confidence)
galaxy/tool_util/deps/container_classes.py:37: unused import 'JobInfo' (90% confidence)
galaxy/tool_util/deps/containers.py:44: unused import 'Cache' (90% confidence)
galaxy/tool_util/deps/containers.py:48: unused import 'JobInfo' (90% confidence)
galaxy/tool_util/deps/mulled/util.py:470: unused variable 'exc_tb' (100% confidence)
galaxy/tool_util/deps/mulled/util.py:470: unused variable 'exc_type' (100% confidence)
galaxy/tool_util/deps/mulled/util.py:470: unused variable 'exc_val' (100% confidence)
galaxy/tool_util/deps/requirements.py:270: unused variable 'js_evaluator' (100% confidence)
galaxy/tool_util/deps/requirements.py:270: unused variable 'runtime' (100% confidence)
galaxy/tool_util/deps/views.py:27: unused import 'StructuredApp' (90% confidence)
galaxy/tool_util/linters/datatypes.py:22: unused import 'Traversable' (90% confidence)
galaxy/tool_util/parser/interface.py:52: unused import 'ToolResourceRequirement' (90% confidence)
galaxy/tool_util/parser/output_objects.py:40: unused import 'TypeIs' (90% confidence)
galaxy/tool_util/toolbox/base.py:68: unused import 'DynamicTool' (90% confidence)
galaxy/tool_util/toolbox/base.py:68: unused import 'User' (90% confidence)
galaxy/tool_util/toolbox/base.py:142: unused variable 'tool_definition_source' (100% confidence)
galaxy/tool_util/toolbox/base.py:150: unused variable 'tool_definition_source' (100% confidence)
13 days ago ● public

Licenserecon

Command: lrc -s
Exit code: 3

en: Versions: licenserecon '12.0'  licensecheck '3.3.9-1'

Parsing Source Tree  ....
Reading d/copyright  ....
** Superfluous file pattern galaxy/tool-util/version.py
Running licensecheck ....

d/copyright      | licensecheck

expat            | AFL and/or Expat  galaxy_tool_util.egg-info/PKG-INFO
expat            | BSD-2-clause      galaxy/tool_util/version.py
expat            | CC-BY-2.5 and/or CC-BY-3.0 and/or Expat LICENSE
expat            | AFL               PKG-INFO

Short option in use. Not all differences shown

13 days ago ● public

CME fix

Command: cme fix --verbose dpkg
Exit code: 0


Reading package lists... 0%

Reading package lists... 100%

Reading package lists... Done

Building dependency tree... 0%

Building dependency tree... 0%

Building dependency tree... 50%

Building dependency tree... 50%

Building dependency tree... Done

Reading state information... 0% 

Reading state information... 0%

Reading state information... Done
cme: running fix on dpkg configuration...
Connecting to api.ftp-master.debian.org to check 16 package versions. Please wait...
Got info from api.ftp-master.debian.org for 15 packages.
Warning in 'control source Standards-Version': Current standards version is '4.7.3'. Please read https://www.debian.org/doc/debian-policy/upgrading-checklist.html for the changes that may be needed on your package
to upgrade it from standard version '4.6.2' to '4.7.3'.

Offending value: '4.6.2'
Warning in 'control source Build-Depends:7': package python3-galaxy-util is unknown. Check for typos if not a virtual package.
Offending value: 'python3-galaxy-util'

Changes applied to dpkg configuration:
- control source Standards-Version: '4.6.2' -> '4.7.3' # applied fix for :Current standards version is '4.7.3'. Please read https://www.debian.org/doc/debian-policy/upgrading-checklist.html for the changes that may be needed on your package
to upgrade it from standard version '4.6.2' to '4.7.3'.

Connecting to api.ftp-master.debian.org to check python3-galaxy-util versions. Please wait...
got no info for python3-galaxy-util

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