[med-svn] [Git][med-team/sourmash][master] 5 commits: Update now that the upstream preferred versions of the 'md5' and 'roaring' crates are packaged.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Fri Apr 24 15:33:38 BST 2026
Michael R. Crusoe pushed to branch master at Debian Med / sourmash
Commits:
acfea08a by Michael R. Crusoe at 2026-04-24T16:13:13+02:00
Update now that the upstream preferred versions of the 'md5' and 'roaring' crates are packaged.
- - - - -
b31dcfe1 by Michael R. Crusoe at 2026-04-24T16:24:56+02:00
d/rules: respect DEB_BUILD_OPTION_PARALLEL for pytest.
- - - - -
6fc055e1 by Michael R. Crusoe at 2026-04-24T16:27:54+02:00
Standards-Version: 4.7.4 (routine-update)
- - - - -
f963b6f0 by Michael R. Crusoe at 2026-04-24T16:32:13+02:00
Use GitHub template in watch file instead of explicit Source/Matching-Pattern.
Changes-By: lintian-brush
- - - - -
3f6d9662 by Michael R. Crusoe at 2026-04-24T16:32:13+02:00
Set upstream metadata fields: Documentation.
Changes-By: lintian-brush
- - - - -
10 changed files:
- debian/changelog
- debian/control
- debian/patches/fix-testsuite.patch
- − debian/patches/older-md5
- debian/patches/series
- debian/patches/soften-deps
- debian/patches/twox-hash-2
- debian/rules
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-sourmash (4.9.4-5) unstable; urgency=medium
+sourmash (4.9.4-5) UNRELEASED; urgency=medium
* Team upload.
@@ -15,6 +15,15 @@ sourmash (4.9.4-5) unstable; urgency=medium
Closes: #1119017
* Relax cargo dependencies on itertools, md5 and roaring.
+ [ Michael R. Crusoe ]
+ * Update now that the upstream preferred versions of the 'md5' and 'roaring'
+ crates are packaged.
+ * d/rules: respect DEB_BUILD_OPTION_PARALLEL for pytest.
+ * Standards-Version: 4.7.4 (routine-update)
+ * Use GitHub template in watch file instead of explicit
+ Source/Matching-Pattern.
+ * Set upstream metadata fields: Documentation.
+
-- Andreas Tille <tille at debian.org> Sun, 22 Feb 2026 16:17:51 +0100
sourmash (4.9.4-4) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -1,5 +1,5 @@
Source: sourmash
-Standards-Version: 4.7.3
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders:
Michael R. Crusoe <crusoe at debian.org>,
@@ -30,7 +30,7 @@ Build-Depends:
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-md5-0.8+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-~~),
@@ -46,7 +46,7 @@ Build-Depends:
librust-primal-check-0.3+default-dev (>= 0.3.4-~~),
librust-rayon-dev,
librust-rkyv-dev,
- librust-roaring-0.10+default-dev,
+ librust-roaring-0.11+default-dev,
librust-rocksdb-dev,
librust-roots-0.0+default-dev (<< 0.0.9-~~),
librust-roots-0.0+default-dev (>= 0.0.8-~~),
=====================================
debian/patches/fix-testsuite.patch
=====================================
@@ -2,9 +2,9 @@ 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:
+--- sourmash.orig/tests/test_plugin_framework.py
++++ sourmash/tests/test_plugin_framework.py
+@@ -382,7 +382,7 @@
print(err)
assert "nifty: error: the following arguments are required: arg1" in err
=====================================
debian/patches/older-md5 deleted
=====================================
@@ -1,23 +0,0 @@
-Author: Michael R. Crusoe <crusoe at debian.org>
-Description: Support the older 0.7.0 interface of md5
-Forwarded: not-needed
---- sourmash.orig/src/core/src/sketch/minhash.rs
-+++ sourmash/src/core/src/sketch/minhash.rs
-@@ -310,7 +310,7 @@
- md5_ctx.consume(&buffer);
- buffer.clear();
- }
-- *data = Some(format!("{:x}", md5_ctx.finalize()));
-+ *data = Some(format!("{:x}", md5_ctx.compute()));
- }
- data.clone().unwrap()
- }
-@@ -1265,7 +1265,7 @@
- md5_ctx.consume(&buffer);
- buffer.clear();
- }
-- *data = Some(format!("{:x}", md5_ctx.finalize()));
-+ *data = Some(format!("{:x}", md5_ctx.compute()));
- }
- data.clone().unwrap()
- }
=====================================
debian/patches/series
=====================================
@@ -1,6 +1,5 @@
pytest-auto-parallel
soften-deps
-older-md5
tests-no-timeout
twox-hash-2
fix-testsuite.patch
=====================================
debian/patches/soften-deps
=====================================
@@ -2,11 +2,9 @@ Author: Michael R. Crusoe <crusoe at debian.org>
Author: Peter Michael Greem <plugwash at debian.org>
Description: soften some dependencies to match what is packaged in Debian
Forwarded: not-needed
-Index: sourmash-4.9.4/src/core/Cargo.toml
-===================================================================
---- sourmash-4.9.4.orig/src/core/Cargo.toml
-+++ sourmash-4.9.4/src/core/Cargo.toml
-@@ -31,29 +31,27 @@ byteorder = "1.4.3"
+--- sourmash.orig/src/core/Cargo.toml
++++ sourmash/src/core/Cargo.toml
+@@ -31,29 +31,27 @@
camino = { version = "1.1.10", features = ["serde1"] }
cfg-if = "1.0"
counter = "0.6.0"
@@ -47,7 +45,7 @@ Index: sourmash-4.9.4/src/core/Cargo.toml
roots = "0.0.8"
serde = { version = "1.0.219", features = ["derive"] }
serde_json = "1.0.141"
-@@ -61,13 +59,12 @@ statrs = "0.18.0"
+@@ -61,13 +59,12 @@
streaming-stats = "0.2.3"
thiserror = "2.0"
twox-hash = "1.6.0"
@@ -64,7 +62,7 @@ Index: sourmash-4.9.4/src/core/Cargo.toml
tempfile = "3.20.0"
[[bench]]
-@@ -93,26 +90,9 @@ skip_feature_sets = [
+@@ -93,26 +90,9 @@
["branchwater", "parallel"], # branchwater implies parallel
]
=====================================
debian/patches/twox-hash-2
=====================================
@@ -3,11 +3,9 @@ Bug-Debian: https://bugs.debian.org/1119017
Last-Update: 2026-01-24
Description: Upgrade to twox-hash version 2
-Index: sourmash-4.9.4/src/core/Cargo.toml
-===================================================================
---- sourmash-4.9.4.orig/src/core/Cargo.toml
-+++ sourmash-4.9.4/src/core/Cargo.toml
-@@ -58,7 +58,7 @@ serde_json = "1.0.141"
+--- sourmash.orig/src/core/Cargo.toml
++++ sourmash/src/core/Cargo.toml
+@@ -58,7 +58,7 @@
statrs = "0.18.0"
streaming-stats = "0.2.3"
thiserror = "2.0"
@@ -16,11 +14,9 @@ Index: sourmash-4.9.4/src/core/Cargo.toml
typed-builder = ">= 0.21"
vec-collections = "0.4.3"
-Index: sourmash-4.9.4/src/core/src/encodings.rs
-===================================================================
---- sourmash-4.9.4.orig/src/core/src/encodings.rs
-+++ sourmash-4.9.4/src/core/src/encodings.rs
-@@ -470,7 +470,7 @@ impl Colors {
+--- sourmash.orig/src/core/src/encodings.rs
++++ sourmash/src/core/src/encodings.rs
+@@ -470,7 +470,7 @@
}
fn compute_color(idxs: &IdxTracker) -> Color {
@@ -29,11 +25,9 @@ Index: sourmash-4.9.4/src/core/src/encodings.rs
s.hash_one(&idxs.0)
}
-Index: sourmash-4.9.4/src/core/src/index/revindex/disk_revindex.rs
-===================================================================
---- sourmash-4.9.4.orig/src/core/src/index/revindex/disk_revindex.rs
-+++ sourmash-4.9.4/src/core/src/index/revindex/disk_revindex.rs
-@@ -36,7 +36,7 @@ const VERSION: &str = "version";
+--- sourmash.orig/src/core/src/index/revindex/disk_revindex.rs
++++ sourmash/src/core/src/index/revindex/disk_revindex.rs
+@@ -36,7 +36,7 @@
const PROCESSED: &str = "processed";
fn compute_color(idxs: &Datasets) -> Color {
@@ -42,11 +36,9 @@ Index: sourmash-4.9.4/src/core/src/index/revindex/disk_revindex.rs
s.hash_one(idxs)
}
-Index: sourmash-4.9.4/src/core/src/lib.rs
-===================================================================
---- sourmash-4.9.4.orig/src/core/src/lib.rs
-+++ sourmash-4.9.4/src/core/src/lib.rs
-@@ -40,6 +40,24 @@ pub mod storage;
+--- sourmash.orig/src/core/src/lib.rs
++++ sourmash/src/core/src/lib.rs
+@@ -40,6 +40,24 @@
use cfg_if::cfg_if;
use murmurhash3::murmurhash3_x64_128;
=====================================
debian/rules
=====================================
@@ -14,7 +14,7 @@ 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=-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)'
+export PYBUILD_TEST_ARGS=$(DEB_BUILD_OPTION_PARALLEL:%=-n%) -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
=====================================
debian/upstream/metadata
=====================================
@@ -1,5 +1,6 @@
Bug-Database: https://github.com/sourmash-bio/sourmash/issues
Bug-Submit: https://github.com/sourmash-bio/sourmash/issues/new
+Documentation: https://sourmash.readthedocs.io
Repository: https://github.com/sourmash-bio/sourmash.git
Repository-Browse: https://github.com/sourmash-bio/sourmash
Reference:
=====================================
debian/watch
=====================================
@@ -1,5 +1,6 @@
Version: 5
-Source: https://github.com/sourmash-bio/@PACKAGE@/tags
-Matching-Pattern: (?:.*?/)?v?(\d[\d.]+)@ARCHIVE_EXT@
-Uversion-Mangle: s/(rc|a|b|c)/~$1/
+Source: https://api.github.com/repos/sourmash-bio/sourmash/git/matching-refs/tags/v
+Template: GitHub
+Owner: sourmash-bio
+Project: @PACKAGE@
View it on GitLab: https://salsa.debian.org/med-team/sourmash/-/compare/fdb8ccf4f7a7f49467b0f5faec1c017641c99ae2...3f6d9662b2d5987b1ed7fe40114791aa0de3be10
--
View it on GitLab: https://salsa.debian.org/med-team/sourmash/-/compare/fdb8ccf4f7a7f49467b0f5faec1c017641c99ae2...3f6d9662b2d5987b1ed7fe40114791aa0de3be10
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