[med-svn] [Git][med-team/sourmash][master] 3 commits: cme fix dpkg-control
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sun Feb 22 15:26:43 GMT 2026
Andreas Tille pushed to branch master at Debian Med / sourmash
Commits:
d7294e54 by Andreas Tille at 2026-02-22T16:17:31+01:00
cme fix dpkg-control
- - - - -
61155f34 by Andreas Tille at 2026-02-22T16:17:40+01:00
Fix testsuite
- - - - -
5537eead by Andreas Tille at 2026-02-22T16:25:28+01:00
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/fix-testsuite.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-sourmash (4.9.4-5) UNRELEASED; urgency=medium
+sourmash (4.9.4-5) unstable; urgency=medium
* Team upload.
@@ -8,13 +8,14 @@ sourmash (4.9.4-5) UNRELEASED; urgency=medium
* More generic Build-Depends
* Update Homepage
* d/watch: version=5
+ * cme fix dpkg-control
[ Peter Michael Green ]
* Use thiserror 2, thiserror 1 is legacy.
Closes: #1119017
* Relax cargo dependencies on itertools, md5 and roaring.
- -- Andreas Tille <tille at debian.org> Tue, 09 Dec 2025 16:19:59 +0100
+ -- Andreas Tille <tille at debian.org> Sun, 22 Feb 2026 16:17:51 +0100
sourmash (4.9.4-4) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -1,101 +1,105 @@
Source: sourmash
-Section: python
+Standards-Version: 4.7.3
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Michael R. Crusoe <crusoe at debian.org>,
- Debian Rust Maintainers <pkg-rust-maintainers at alioth-lists.debian.net>
-Build-Depends: debhelper-compat (= 13),
- dh-cargo,
- dh-sequence-python3,
- dh-sequence-sphinxdoc <!nodoc>,
- architecture-is-64-bit,
- architecture-is-little-endian,
- cargo,
- cargo:native,
- librust-az-1+default-dev,
- librust-byteorder-1+default-dev (>= 1.4.3-~~),
- librust-camino-1+default-dev (>= 1.1.10-~~),
- librust-camino-1+serde1-dev (>= 1.1.10-~~),
- librust-cfg-if-1+default-dev,
- librust-chrono-dev,
- librust-counter-0.6+default-dev,
- librust-counter-dev,
- librust-csv-1+default-dev (>= 1.3-~~),
- librust-enum-dispatch-0.3+default-dev (>= 0.3.13-~~),
- librust-fixedbitset-0.4+default-dev,
- librust-getset-0.1+default-dev,
- librust-histogram-0.11+default-dev,
- librust-itertools-dev,
- librust-log-0.4+default-dev (>= 0.4.27-~~),
- librust-md5-0.7+default-dev,
- librust-memmap2-0.9+default-dev,
- librust-murmurhash3-0.0+default-dev (<< 0.0.6-~~),
- librust-murmurhash3-0.0+default-dev (>= 0.0.5-~~),
- librust-needletail-0.6-dev,
- librust-niffler-2+gz-dev (>= 2.6-~~),
- librust-niffler-2+lzma-dev (>= 2.6-~~),
- librust-niffler-2+zstd-dev (>= 2.6-~~),
- librust-nohash-hasher-0.2+default-dev,
- librust-num-iter-0.1+default-dev (>= 0.1.45-~~),
- librust-once-cell-1+default-dev (>= 1.18.0-~~),
- librust-ouroboros+default-dev (>= 0.15-~~),
- librust-piz-0.5+default-dev,
- librust-primal-check-0.3+default-dev (>= 0.3.4-~~),
- librust-rayon-dev,
- librust-rkyv-dev,
- librust-roaring-0.10+default-dev,
- librust-rocksdb-dev,
- librust-roots-0.0+default-dev (<< 0.0.9-~~),
- librust-roots-0.0+default-dev (>= 0.0.8-~~),
- librust-serde+serde-derive-dev,
- librust-serde-1+default-dev (>= 1.0.219-~~),
- librust-serde-1+derive-dev (>= 1.0.219-~~),
- librust-serde-json-1+default-dev (>= 1.0.141-~~),
- librust-statrs-0.18+default-dev,
- librust-streaming-stats-0.2+default-dev (>= 0.2.3-~~),
- librust-streaming-stats-dev,
- librust-thiserror-dev,
- librust-twox-hash-2-dev,
- librust-typed-builder-dev,
- librust-vec-collections-0.4+default-dev (>= 0.4.3-~~),
- libstd-rust-dev,
- pandoc <!nodoc>,
- pybuild-plugin-pyproject,
- python3-all-dev,
- python3-bitstring,
- python3-cachetools,
- python3-cffi,
- python3-deprecation,
- python3-hypothesis <!nocheck>,
- python3-ijson,
- python3-ipython <!nodoc>,
- python3-matplotlib,
- python3-maturin,
- python3-myst-parser <!nodoc>,
- python3-nbsphinx <!nodoc>,
- python3-numpy,
- python3-pytest <!nocheck>,
- python3-pytest-xdist <!nocheck>,
- python3-scipy,
- python3-screed,
- python3-setuptools,
- python3-setuptools-scm,
- python3-sphinx,
- python3-sphinx-copybutton <!nodoc>,
- python3-sphinx-design <!nodoc>,
- python3-yaml,
- rustc:native (>= 1.74.0)
-Standards-Version: 4.7.2
+Uploaders:
+ Michael R. Crusoe <crusoe at debian.org>,
+ Debian Rust Maintainers <pkg-rust-maintainers at alioth-lists.debian.net>,
+Section: python
+Testsuite: autopkgtest-pkg-pybuild
+Build-Depends:
+ debhelper-compat (= 13),
+ dh-cargo,
+ dh-sequence-python3,
+ dh-sequence-sphinxdoc <!nodoc>,
+ architecture-is-64-bit,
+ architecture-is-little-endian,
+ cargo,
+ cargo:native,
+ librust-az-1+default-dev,
+ librust-byteorder-1+default-dev (>= 1.4.3-~~),
+ librust-camino-1+default-dev (>= 1.1.10-~~),
+ librust-camino-1+serde1-dev (>= 1.1.10-~~),
+ librust-cfg-if-1+default-dev,
+ librust-chrono-dev,
+ librust-counter-0.6+default-dev,
+ librust-counter-dev,
+ librust-csv-1+default-dev (>= 1.3-~~),
+ librust-enum-dispatch-0.3+default-dev (>= 0.3.13-~~),
+ librust-fixedbitset-0.4+default-dev,
+ librust-getset-0.1+default-dev,
+ librust-histogram-0.11+default-dev,
+ librust-itertools-dev,
+ librust-log-0.4+default-dev (>= 0.4.27-~~),
+ librust-md5-0.7+default-dev,
+ librust-memmap2-0.9+default-dev,
+ librust-murmurhash3-0.0+default-dev (<< 0.0.6-~~),
+ librust-murmurhash3-0.0+default-dev (>= 0.0.5-~~),
+ librust-needletail-0.6-dev,
+ librust-niffler-2+gz-dev (>= 2.6-~~),
+ librust-niffler-2+lzma-dev (>= 2.6-~~),
+ librust-niffler-2+zstd-dev (>= 2.6-~~),
+ librust-nohash-hasher-0.2+default-dev,
+ librust-num-iter-0.1+default-dev (>= 0.1.45-~~),
+ librust-once-cell-1+default-dev (>= 1.18.0-~~),
+ librust-ouroboros+default-dev (>= 0.15-~~),
+ librust-piz-0.5+default-dev,
+ librust-primal-check-0.3+default-dev (>= 0.3.4-~~),
+ librust-rayon-dev,
+ librust-rkyv-dev,
+ librust-roaring-0.10+default-dev,
+ librust-rocksdb-dev,
+ librust-roots-0.0+default-dev (<< 0.0.9-~~),
+ librust-roots-0.0+default-dev (>= 0.0.8-~~),
+ librust-serde+serde-derive-dev,
+ librust-serde-1+default-dev (>= 1.0.219-~~),
+ librust-serde-1+derive-dev (>= 1.0.219-~~),
+ librust-serde-json-1+default-dev (>= 1.0.141-~~),
+ librust-statrs-0.18+default-dev,
+ librust-streaming-stats-0.2+default-dev (>= 0.2.3-~~),
+ librust-streaming-stats-dev,
+ librust-thiserror-dev,
+ librust-twox-hash-2-dev,
+ librust-typed-builder-dev,
+ librust-vec-collections-0.4+default-dev (>= 0.4.3-~~),
+ libstd-rust-dev,
+ pandoc <!nodoc>,
+ pybuild-plugin-pyproject,
+ python3-all-dev,
+ python3-bitstring,
+ python3-cachetools,
+ python3-cffi,
+ python3-deprecation,
+ python3-hypothesis <!nocheck>,
+ python3-ijson,
+ python3-ipython <!nodoc>,
+ python3-matplotlib,
+ python3-maturin,
+ python3-myst-parser <!nodoc>,
+ python3-nbsphinx <!nodoc>,
+ python3-numpy,
+ python3-pytest <!nocheck>,
+ python3-pytest-xdist <!nocheck>,
+ python3-scipy,
+ python3-screed,
+ python3-setuptools,
+ python3-setuptools-scm,
+ python3-sphinx,
+ python3-sphinx-copybutton <!nodoc>,
+ python3-sphinx-design <!nodoc>,
+ python3-yaml,
+ rustc:native (>= 1.74.0),
Vcs-Browser: https://salsa.debian.org/med-team/sourmash
Vcs-Git: https://salsa.debian.org/med-team/sourmash.git
Homepage: https://github.com/sourmash-bio/sourmash
-Testsuite: autopkgtest-pkg-pybuild
Package: sourmash
Architecture: any
-Depends: ${misc:Depends}, ${python3:Depends}, ${shlibs:Depends}
-Built-Using: ${cargo:Built-Using}
-X-Cargo-Built-Using: ${cargo:X-Cargo-Built-Using}
-Static-Built-Using: ${cargo:Static-Built-Using}
+Depends:
+ ${misc:Depends},
+ ${python3:Depends},
+ ${shlibs:Depends},
+Built-Using:
+ ${cargo:Built-Using},
Description: tools for comparing DNA sequences with MinHash sketches
Compute MinHash signatures for nucleotide (DNA/RNA) and protein sequences.
.
@@ -109,3 +113,5 @@ Description: tools for comparing DNA sequences with MinHash sketches
module for MinHash sketches.
.
These tools provide functionality previously handled by the 'khmer' package.
+Static-Built-Using: ${cargo:Static-Built-Using}
+X-Cargo-Built-Using: ${cargo:X-Cargo-Built-Using}
=====================================
debian/patches/fix-testsuite.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-02-22
+Description: Make sure test will work with Python3.1[34]
+
+--- a/tests/test_plugin_framework.py
++++ b/tests/test_plugin_framework.py
+@@ -382,7 +382,7 @@ class Test_EntryPointBasics_Command:
+ print(err)
+
+ assert "nifty: error: the following arguments are required: arg1" in err
+- assert "usage: nifty [-h] [-q] [-d] [--other] [--do-fail] arg1" in err
++ assert "nifty [-h] [-q] [-d] [--other] [--do-fail] arg1" in err
+
+ def test_cmd_4(self, runtmp):
+ # test basic argument parsing etc
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ soften-deps
older-md5
tests-no-timeout
twox-hash-2
+fix-testsuite.patch
=====================================
debian/rules
=====================================
@@ -14,13 +14,12 @@ export CARGO_HOME=$(CURDIR)/debian/cargo_home
export CARGO_REGISTRY=$(CURDIR)/debian/cargo_registry
export DEB_CARGO_CRATE=$(DEB_SOURCE)_$(DEB_VERSION_UPSTREAM)
export DEB_BUILD_MAINT_OPTIONS=hardening=+bindnow
-export PYBUILD_TEST_ARGS=-k 'not (test_sqlite_lca_db_create_readonly or test_compare_no_such_file or test_metagenome_kreport_out_fail or test_do_sourmash_index_multiscaled_rescale_fail)'
+export PYBUILD_TEST_ARGS=-n 4 -k 'not (test_sqlite_lca_db_create_readonly or test_compare_no_such_file or test_metagenome_kreport_out_fail or test_do_sourmash_index_multiscaled_rescale_fail)'
# test_sqlite_lca_db_create_readonly, fails when building as root
# test_compare_no_such_file. due to the ValueError being swallowed (?)
# test_metagenome_kreport_out_fail, same as test_compare_no_such_file
# test_do_sourmash_index_multiscaled_rescale_fail, same as above
-
%:
dh $@ --buildsystem=pybuild
@@ -42,3 +41,8 @@ execute_after_dh_auto_install:
override_dh_python3:
dh_python3 --no-ext-rename
+
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ ulimit -n 65536; dh_auto_test
+endif
View it on GitLab: https://salsa.debian.org/med-team/sourmash/-/compare/4912a13970c7ab9d0bd9615c5dbaea7a0cba4218...5537eead4d9d9e78740f8cb12639acc7b8374366
--
View it on GitLab: https://salsa.debian.org/med-team/sourmash/-/compare/4912a13970c7ab9d0bd9615c5dbaea7a0cba4218...5537eead4d9d9e78740f8cb12639acc7b8374366
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