Michael R. Crusoe pushed to branch master at Debian Med / sourmash
Commits: 00acaf75 by Michael R. Crusoe at 2025-09-13T09:49:13+02:00 New upstream version - - - - - c61f851a by Michael R. Crusoe at 2025-09-13T09:49:15+02:00 New upstream version 4.9.4 - - - - - 8a890bc8 by Michael R. Crusoe at 2025-09-13T09:51:37+02:00 Update upstream source from tag 'upstream/4.9.4' Update to upstream version '4.9.4' with Debian dir c7fe954f54b3d45a843af69843c60c2753f8796d - - - - - fc71ad22 by Michael R. Crusoe at 2025-09-13T09:51:38+02:00 Standards-Version: 4.7.2 (routine-update) - - - - - 8c1e7224 by Michael R. Crusoe at 2025-09-13T11:47:13+02:00 Refreshed patches. Dropped "skip_from-finch_feature", upstream removed the conversion from Finch in version 4.9.0. - - - - - 94051b2a by Michael R. Crusoe at 2025-09-13T11:47:19+02:00 Added a new patch to adapt to the older version of the md5 Rust crate in Debian. - - - - - ab9c51bf by Michael R. Crusoe at 2025-09-13T11:47:19+02:00 docs: new build-dep of python3-sphinx-copybutton. - - - - - 679a5232 by Michael R. Crusoe at 2025-09-13T11:47:19+02:00 d/rules: parallelize the pytest respecting DEB_BUILD_OPTION_PARALLEL - - - - - 97dc4dfa by Michael R. Crusoe at 2025-09-13T12:00:04+02:00 Install the README - - - - - b73a81fc by Michael R. Crusoe at 2025-09-13T12:00:34+02:00 d/rules: set MPLCONFIGDIR - - - - - b620d7af by Michael R. Crusoe at 2025-09-13T12:31:45+02:00 routine-update: Ready to upload to unstable. Closes: #1114393 - - - - - 169 changed files: - .git_archival.txt - .github/dependabot.yml - .github/workflows/asv.yml - .github/workflows/build_wheel.yml - .github/workflows/build_wheel_all_archs.yml - .github/workflows/codspeed.yml - .github/workflows/dev_envs.yml - .github/workflows/hypothesis.yml - .github/workflows/python.yml - .github/workflows/rust.yml - .pre-commit-config.yaml - .readthedocs.yml - Cargo.lock - Makefile - README.md - binder/environment.yml - debian/changelog - debian/control - + debian/patches/older-md5 - + debian/patches/pytest-auto-parallel - debian/patches/series - − debian/patches/skip_from-finch_feature - debian/patches/soften-deps - debian/rules - debian/python3-sourmash.docs → debian/sourmash.docs - dev.yml - doc/classifying-signatures.md - doc/command-line.md - doc/conf.py - + doc/databases-md/gtdb220.md - + doc/databases-md/gtdb226.md - + doc/databases-md/ncbi_euks_2025_01.md - + doc/databases-md/ncbi_viruses_2025_01.md - doc/databases.md - doc/developer.md - + doc/howto-rocksdb.md - doc/index.md - doc/legacy-databases.md - + doc/release-notes/sourmash-5.0.md - doc/release.md - doc/requirements.md - doc/runtime.txt - doc/sidebar.md - doc/sourmash-sketch.md - doc/support.md - doc/toc.md - flake.lock - flake.nix - include/sourmash.h - pixi.lock - pyproject.toml - src/core/CHANGELOG.md - src/core/Cargo.toml - src/core/README.md - src/core/src/collection.rs - src/core/src/encodings.rs - src/core/src/errors.rs - src/core/src/ffi/cmd/compute.rs - src/core/src/ffi/index/mod.rs - src/core/src/ffi/index/revindex.rs - + src/core/src/ffi/manifest.rs - src/core/src/ffi/mod.rs - src/core/src/ffi/utils.rs - − src/core/src/from.rs - src/core/src/index/linear.rs - src/core/src/index/mod.rs - src/core/src/index/revindex/disk_revindex.rs - src/core/src/index/revindex/mem_revindex.rs - src/core/src/index/revindex/mod.rs - src/core/src/lib.rs - src/core/src/manifest.rs - src/core/src/signature.rs - src/core/src/sketch/minhash.rs - src/core/src/wasm.rs - src/sourmash/cli/index.py - src/sourmash/cli/sig/check.py - src/sourmash/cli/sig/collect.py - src/sourmash/cli/sig/manifest.py - src/sourmash/cli/tax/genome.py - src/sourmash/cli/tax/metagenome.py - src/sourmash/cli/utils.py - src/sourmash/command_sketch.py - src/sourmash/commands.py - src/sourmash/index/__init__.py - src/sourmash/index/revindex.py - src/sourmash/manifest.py - src/sourmash/minhash.py - src/sourmash/save_load.py - src/sourmash/sig/__main__.py - src/sourmash/signature.py - src/sourmash/tax/__main__.py - src/sourmash/tax/tax_utils.py - src/sourmash/utils.py - tests/conftest.py - tests/sourmash_tst_utils.py - + tests/test-data/2sigs.branch_0913.rocksdb/000008.log - + tests/test-data/2sigs.branch_0913.rocksdb/000009.sst - + tests/test-data/2sigs.branch_0913.rocksdb/000010.sst - + tests/test-data/2sigs.branch_0913.rocksdb/CURRENT - + tests/test-data/2sigs.branch_0913.rocksdb/IDENTITY - + tests/test-data/2sigs.branch_0913.rocksdb/LOCK - + tests/test-data/2sigs.branch_0913.rocksdb/MANIFEST-000005 - + tests/test-data/2sigs.branch_0913.rocksdb/OPTIONS-000007 - + tests/test-data/3sigs.branch_0913.rocksdb/000008.log - + tests/test-data/3sigs.branch_0913.rocksdb/000009.sst - + tests/test-data/3sigs.branch_0913.rocksdb/000010.sst - + tests/test-data/3sigs.branch_0913.rocksdb/CURRENT - + tests/test-data/3sigs.branch_0913.rocksdb/IDENTITY - + tests/test-data/3sigs.branch_0913.rocksdb/LOCK - + tests/test-data/3sigs.branch_0913.rocksdb/MANIFEST-000005 - + tests/test-data/3sigs.branch_0913.rocksdb/OPTIONS-000007 - + tests/test-data/SRR606249.sig.gz - + tests/test-data/prot/dayhoff.rocksdb/000008.log - + tests/test-data/prot/dayhoff.rocksdb/000009.sst - + tests/test-data/prot/dayhoff.rocksdb/000010.sst - + tests/test-data/prot/dayhoff.rocksdb/CURRENT - + tests/test-data/prot/dayhoff.rocksdb/IDENTITY - + tests/test-data/prot/dayhoff.rocksdb/LOCK - + tests/test-data/prot/dayhoff.rocksdb/MANIFEST-000005 - + tests/test-data/prot/dayhoff.rocksdb/OPTIONS-000007 - + tests/test-data/prot/hp.rocksdb/000008.log - + tests/test-data/prot/hp.rocksdb/000009.sst - + tests/test-data/prot/hp.rocksdb/000010.sst - + tests/test-data/prot/hp.rocksdb/CURRENT - + tests/test-data/prot/hp.rocksdb/IDENTITY - + tests/test-data/prot/hp.rocksdb/LOCK - + tests/test-data/prot/hp.rocksdb/MANIFEST-000005 - + tests/test-data/prot/hp.rocksdb/OPTIONS-000007 - + tests/test-data/prot/protein.rocksdb/000008.log - + tests/test-data/prot/protein.rocksdb/000009.sst - + tests/test-data/prot/protein.rocksdb/000010.sst - + tests/test-data/prot/protein.rocksdb/CURRENT - + tests/test-data/prot/protein.rocksdb/IDENTITY - + tests/test-data/prot/protein.rocksdb/LOCK - + tests/test-data/prot/protein.rocksdb/MANIFEST-000005 - + tests/test-data/prot/protein.rocksdb/OPTIONS-000007 - + tests/test-data/skipmers/2.skip.sig.zip - + tests/test-data/skipmers/47.skip.sig.zip - + tests/test-data/skipmers/63.skip.sig.zip - + tests/test-data/track_abund/47+63.abund.rocksdb/000008.log - + tests/test-data/track_abund/47+63.abund.rocksdb/000009.sst - + tests/test-data/track_abund/47+63.abund.rocksdb/000010.sst - + tests/test-data/track_abund/47+63.abund.rocksdb/CURRENT - + tests/test-data/track_abund/47+63.abund.rocksdb/IDENTITY - + tests/test-data/track_abund/47+63.abund.rocksdb/LOCK - + tests/test-data/track_abund/47+63.abund.rocksdb/MANIFEST-000005 - + tests/test-data/track_abund/47+63.abund.rocksdb/OPTIONS-000007 - tests/test_api.py - + tests/test_cmd_index.py - tests/test_cmd_signature.py - tests/test_cmd_signature_collect.py - tests/test_index.py - tests/test_index_protocol.py - tests/test_lca_db_protocol.py - tests/test_manifest_protocol.py - tests/test_minhash.py - + tests/test_moltypes.py - tests/test_plugin_framework.py - + tests/test_revindex.py - tests/test_sbt.py - tests/test_search.py - tests/test_sketchcomparison.py - tests/test_sourmash.py - tests/test_sourmash_args.py - tests/test_sourmash_sketch.py - tests/test_sqlite_index.py - tests/test_tax.py - tests/test_tax_utils.py - tox.ini The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/sourmash/-/compare/8589346c50966764540119ab39725904372af26d...b620d7afc05c95864d91d122fe67c996ca7d10ad -- View it on GitLab: https://salsa.debian.org/med-team/sourmash/-/compare/8589346c50966764540119ab39725904372af26d...b620d7afc05c95864d91d122fe67c996ca7d10ad You're receiving this email because of your account on salsa.debian.org.
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