rachis 2026.10.0-1

Package Information

Description	framework for microbiome analysis (formerly QIIME 2) Rachis is a powerful, extensible, and decentralized microbiome analysis framework with a focus on data and analysis transparency. It was formerly known as the QIIME 2 Framework. Rachis enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Key features: * Integrated and automatic tracking of data provenance * Semantic type system * Plugin system for extending microbiome analysis functionality * Support for multiple types of user interfaces (e.g. API, command line, graphical) The framework provides the API and plugin architecture. Analysis functionality is made available through plugins, which are packaged separately.
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed By	Andreas Tille <tille@debian.org>
Sponsor	tille@debian.org
Distribution	experimental
Architecture	all
VCS	git: https://salsa.debian.org/med-team/qiime.git (browse)
Closes	#1076314, #1084668
Tracker	https://tracker.debian.org/pkg/rachis
Uploaded	2 hours ago

New Package Report

.changes◂

Distribution	experimental
Date	Mon, 02 Nov 2026 18:40:45 +0100
Source	rachis
Version	2026.10.0-1
Changed-By	Andreas Tille <tille@debian.org>
Architecture	source all

Changelog◂

rachis (2026.10.0-1) experimental; urgency=medium
 .
   * New upstream version which is now named rachis
     Closes: #1076314, #1084668
   * Rename remaining Debian packaging from qiime to rachis
   * Remove obsolete QIIME 1 helper scripts
   * Drop platformdirs patch, which was applied upstream
   * Use a static version instead of unpackaged versioningit
   * Fix test data lookup under hidden build directories
   * Skip tests requiring network access or unavailable parsl/dill support
   * Clean parsl test artifacts before installation
   * Drop python3.11 from explicit Test-Depends
   * Do not fail mkdir if directory just exists
   * d/watch:
      - version=5
      - Point to renamed repository
   * debputy lint --auto-fix (routine-update)
   * Build-Depends: pybuild-plugin-pyproject
   * d/copyright: Remove old FSF address
   * Standards-Version: 4.7.4
   * Set upstream metadata fields: Repository, Repository-Browse.
   * cme fix dpkg-control
   * Breaks, Provides, Replaces: qiime
   * Skip the cache multi-user test since useradd/userdel are not on PATH
   * Skip the no-missing integer round-trip test on 32-bit architectures
   * Build-Depends: dh-sequence-single-binary

.dsc◂

Section	science
Priority	optional
Component	main
Package-List	rachis deb science optional arch=all

debian/copyright◂

Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: rachis
Source: https://github.com/rachis-org/rachis/releases

Files: *
Copyright: 2016-2026 QIIME 2 and Rachis development team
License: BSD-3-clause

Files: debian/*
Copyright: 2010 Sri Girish Srinivasa Murthy <srigirish@evolbio.mpg.de>
                Steffen Moeller <moeller@debian.org>
           2011-2012 Tim Booth <tbooth@ceh.ac.uk>,
                Andreas Tille <tille@debian.org>
License: GPL-2+

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:
  .
  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.
  .
  3.  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.

License: GPL-2+
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation; either version 2 of the License, or
 (at your option) any later version.
 .
 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
 .
 For other licensing arrangements, please contact Daniel J. Schaid.
 .
 On a Debian system, the GNU GPL license version 2 is distributed in the
 file /usr/share/common-licenses/GPL-2.

DFSG Assistant LLM REVIEW 0 blocker, 1 important, 5 minor

This is an LLM based review using a Debian Inference based workflow. It was not written by a member of the DFSG team and has not been checked by one. It is not a decision on the package: it may be wrong, and it may have missed things.

Reviewed 1 hour ago.

Report◂

DFSG NEW review for rachis version 2026.10.0-1

Summary

Licensing is DFSG-compliant and debian/copyright is accurate: No
Packaging is of good quality: Yes
Issues: 0 blocker, 1 important, 5 minor
debian/watch: version 5
debian/copyright: machine-readable
Scan before the review: 4 found

Licensing

The upstream code is BSD-3-Clause throughout: one top-level LICENSE, the same four-line Copyright (c) 2016-2026, QIIME 2 development team / Modified BSD License header on every module, and no other holder or licence anywhere in the tree, so nothing here offends the DFSG; the three cite_*.zip fixtures duplicate .bib files that are in the package and rarefied_table.qza is upstream test data. debian/copyright is valid DEP-5 and describes upstream correctly, but it is not accurate about the packaging: its GPL-2+ paragraph carries an unrelated third party's contact sentence, and the Files: debian/* stanza names only the 2010-2012 packagers although most of debian/ was written later by people the file does not name.

Packaging

The packaging is conventional and in good shape: debhelper compat 14 with dh-sequence-python3 and pybuild-plugin-pyproject, Standards-Version 4.7.4 (current), a single Architecture: all binary with Breaks/Replaces/Provides for the qiime rename, DEP-3 patches with purposes tied to the Debian environment, an autopkgtest that runs the shipped suite, and a changelog consistent with the changes. What remains is clean-up rather than defects: the obsolete debian/scripts/ QIIME 1 directory the changelog says was removed is still there, platformdirs.patch is left behind out of series, four declared dependencies are imported nowhere, and one description bullet is broken by an unindented line.

Issues

important licensing 1. GPL-2+ text in debian/copyright makes an unrelated third party, Daniel J. Schaid, the contact for other licensing ◂

Files: debian/copyright:53
Basis: checked, in the package or with a reference tool
Evidence: For other licensing arrangements, please contact Daniel J. Schaid. inside the stand-alone License: GPL-2+ paragraph used by Files: debian/*
Problem: Schaid has nothing to do with rachis; the sentence is left over from another package's copyright file. It states a false fact about who may grant other terms for this packaging, in a file Policy 12.5 requires to record the actual copyright and licence.
Fix: Delete that sentence from the GPL-2+ paragraph.

minor licensing 2. Files: debian/* names only the 2010-2012 packagers and omits the authors of most of the current packaging ◂

Files: debian/copyright:10-13, debian/patches/relax-mkdir-calls.patch:5, debian/patches/platformdirs.patch:1, debian/tests/run-unit-test
Basis: checked, in the package or with a reference tool
Evidence: Copyright: 2010 Sri Girish Srinivasa Murthy ... 2011-2012 Tim Booth ..., Andreas Tille against patch headers Author: Étienne Mollier <emollier@debian.org> and From: Michael R. Crusoe <crusoe@debian.org>, and debian/tests/, debian/salsa-ci.yml and the packaging changes of 2019-2026 which are not covered by 2010-2012
Problem: The debian/* stanza understates the copyright of the packaging: Étienne Mollier, Michael R. Crusoe, Liubov Chuprikova and Nilesh Patra, and Andreas Tille's work after 2012, are not named. Policy 12.5 requires debian/copyright to record the copyright of the package.
Fix: Add those holders and their years to the debian/* Copyright field.

minor packaging 3. debian/scripts/ still holds ten unreferenced QIIME 1 helper scripts that the changelog says were removed ◂

Files: debian/scripts/qiime, debian/scripts/uclust, debian/scripts/usearch, debian/scripts/FastTree, debian/scripts/ParsInsert, debian/scripts/make_emperor.py, debian/scripts/shell/qiime_environment, debian/scripts/shell/.bashrc, debian/scripts/shell/.zshrc
Basis: checked, in the package or with a reference tool
Evidence: changelog: * Remove obsolete QIIME 1 helper scripts; no *.install, *.links or rules line refers to debian/scripts, and the scripts invoke /usr/lib/qiime/bin, a path this package does not create
Problem: Dead files from the QIIME 1 packaging (2016 and earlier) that no longer install anything, contradicting the changelog for this upload; two of them exist only to tell the user to fetch the non-free uclust/usearch binaries by hand.
Fix: Delete debian/scripts/ entirely.

minor packaging 4. debian/patches/platformdirs.patch is still shipped although series drops it and the change is upstream ◂

Files: debian/patches/platformdirs.patch, debian/patches/series
Basis: checked, in the package or with a reference tool
Evidence: debian/patches/series lists four patches and not this one; changelog: * Drop platformdirs patch, which was applied upstream; the patch still removes import appdirs, which no longer exists (src/rachis/sdk/parallel_config.py:11 imports platformdirs)
Problem: An obsolete patch fragment left in the source package, which would not even apply any more; it will mislead the next uploader.
Fix: Delete debian/patches/platformdirs.patch.

minor packaging 5. Depends and Build-Depends keep python3-decorator, python3-pyparsing, python3-notebook and python3-tornado, which nothing in the source imports ◂

Files: debian/control:17, debian/control:22, debian/control:29, debian/control:41, debian/control:50
Basis: checked, in the package or with a reference tool
Evidence: python3-decorator, python3-pyparsing, python3-notebook, python3-tornado in Build-Depends and python3-decorator, python3-pyparsing in Depends, while a search of src/rachis for those names finds them only in docstrings and in the recorded conda environments under core/archive/provenance_lib/tests/data/*/action.yaml
Problem: Stale dependencies carried over from the qiime packaging; upstream's pyproject.toml does not declare decorator, pyparsing, notebook or tornado either. They pull packages into every installation and build for nothing.
Fix: Drop those four from debian/control (keep python3-setuptools, which upstream's pyproject still declares, and python3-lxml, which pandas.read_html needs).

minor packaging 6. The description's user-interface bullet is broken by an unindented continuation line ◂

Files: debian/control:81-82
Basis: checked, in the package or with a reference tool
Evidence: * Support for multiple types of user interfaces (e.g. API, command line, followed by graphical)
Problem: Under Policy 5.6.13 a line beginning with a single space starts a paragraph, so the bullet ends after command line, and graphical) is displayed by apt as a paragraph of its own.
Fix: Indent the continuation line to line up with the bullet text (at least two spaces, e.g. graphical)).

Verified ◂

Every file under debian/ was read in full: control, rules, changelog, copyright, all five patches and series, tests/control, tests/run-unit-test, rachis.docs, rachis.README.Debian, README.test, lintian-overrides, source/format, TODO, upstream/metadata, upstream/edam, salsa-ci.yml and scripts/*.
Upstream licensing is uniform: the only LICENCE/COPYING/NOTICE file in the tree is the top-level LICENSE (BSD-3-Clause), whose text the License: BSD-3-clause paragraph of debian/copyright reproduces; all ~160 Python modules under src/rachis carry # Copyright (c) 2016-2026, QIIME 2 development team. with # Distributed under the terms of the Modified BSD License. The Files: * holder QIIME 2 and Rachis development team is that team (the prescan's QIIME 2 development team).
A grep of the whole tree (gitignore off) for Copyright, (C), ©, SPDX-License-Identifier, Licensed under, permission notices, GNU General Public, GNU Lesser, Apache License, Mozilla Public, public domain, All rights reserved, non-commercial and no-modification found no second holder and no other licence: only the root LICENSE, debian/copyright, and .github/workflows/update-copyright-headers.yaml (a sed that bumps the year in those same headers).
The three small archives the scan listed, src/rachis/core/archive/provenance_lib/tests/data/cite_many.zip, cite_one.zip and cite_none.zip, each contain exactly the .bib file of the same name that sits beside them in tests/data (cite_many.bib, cite_one.bib, cite_none.bib), so their text source is in the package; they are test fixtures.
src/rachis/core/archive/provenance_lib/tests/data/rarefied_table.qza is an 81 KB QIIME artifact used only as an input fixture by the provenance_lib parser tests; it is upstream test data in the library's own archive format, not a built program or library whose source is missing.
There are no images, fonts, sounds, PDFs, minified JS/CSS, bytecode, generated C or other built files in the tree, and no vendored third-party library: core/archive/provenance_lib (archive_parser, parse, replay, usage_drivers) is upstream's own code, not an embedded copy of a package Debian ships.
provenance_lib/assets/copyright_note.txt and python_howto.txt are upstream's own template texts (a note about the copyright of the user's input data and instructions for a generated script), not additional licence terms.
debian/copyright is DEP-5 with the exact copyright-format 1.0 URL; Files: debian/* follows Files: * and so overrides it for the packaging, and its patterns are anchored at the top of the tree as copyright-format 6.9 defines.
Standards-Version 4.7.4 against Policy 4.7.4.1 from the policy tool: the first two components match, so it is current.
Build-Depends resolve: dh-sequence-single-binary is a virtual package provided by debhelper 14.5 (apt-cache), dh-sequence-python3 comes with dh-python, and every other name is a python3-* package; test-only dependencies are marked <!nocheck>, which is right because dh skips dh_auto_test's hooks under nocheck at compat 13 and later (debhelper tool).
Compat 14 with dh $@ --buildsystem=pybuild and pybuild-plugin-pyproject; the ${python3:Depends}/${misc:Depends}/${shlibs:Depends} in Depends are harmless at this level (dh_gencontrol adds them itself).
The patches in series have DEP-3 headers (Description, Author, Forwarded, Last-Update) and each addresses a Debian-specific condition (pybuild's hidden build directory, parsl/network tests, the versioningit build dependency, mkdir in provenance capture); the tree has them applied, as .pc/ records.
autopkgtest: tests/control asks for @, python3-pytest with allow-stderr, skippable, and run-unit-test exits 77 on 32-bit, which the skippable restriction permits.
The rename is handled conventionally: source and binary rachis, Breaks: qiime (<= 2025.10.0), Replaces: qiime, Provides: qiime (Policy 7.5 read: an unversioned Provides satisfies unversioned dependencies), a continuous changelog with a higher version than the last qiime upload, and Vcs-* fields that still point at the med-team/qiime repository that holds the history.
uscan found upstream releases with debian/watch; a newer upstream version is available (upstream 2026.10.1, packaged 2026.10.0), which is not a fault of the package.
Every pointer of debian/copyright to /usr/share/common-licenses names a file that is there (GPL-2).

Not confirmed ◂

The members of src/rachis/core/archive/provenance_lib/tests/data/rarefied_table.qza could not be listed: it is binary, not UTF-8 text, and I did not open it further; judging by its role it is a QIIME artifact used as parser input.
debian/tests/run-unit-test calls dpkg-architecture while tests/control depends only on @ and python3-pytest; whether dpkg-dev is present in the autopkgtest testbed cannot be determined from the package (the call is inside a [ ... ] test, so a missing tool would not abort the script).
Build and test success was not exercised: pybuild's pytest run at build time and the autopkgtest were not executed here.

Proposed changes ◂

None.

Uploader's response to the LLM review

Waiting for the uploader's response until 2026-11-03 22:27 UTC, because the review found serious issues.

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