MRG: start writing v4->v5 migration docs #3721
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## latest #3721 +/- ##
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- Coverage 88.19% 88.17% -0.02%
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Lines 22552 22552
Branches 2298 2298
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ready for review @sourmash-bio/devs |
luizirber
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Aug 4, 2025
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| **sourmash v5 breaking change:** In sourmash v5.0 and later, | ||
| `--no-rebuild-manifest` will become default. You can specify `--v4` to | ||
| keep the old behavior, or `--v5` to support the new default behavior, | ||
| or simply specify `--no-rebuild-manifest` to override the default. See | ||
| [Migrating from sourmash v4.x to sourmash v5.x](support.md#migrating-from-sourmash-v4x-to-sourmash-v5x) for more | ||
| details. | ||
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Maybe use a github-compatible admonition for these breaking changes? https://mystmd.org/guide/admonitions
Suggested change
| **sourmash v5 breaking change:** In sourmash v5.0 and later, | |
| `--no-rebuild-manifest` will become default. You can specify `--v4` to | |
| keep the old behavior, or `--v5` to support the new default behavior, | |
| or simply specify `--no-rebuild-manifest` to override the default. See | |
| [Migrating from sourmash v4.x to sourmash v5.x](support.md#migrating-from-sourmash-v4x-to-sourmash-v5x) for more | |
| details. | |
| > [!WARNING] | |
| > **sourmash v5 breaking change:** In sourmash v5.0 and later, | |
| > `--no-rebuild-manifest` will become default. You can specify `--v4` to | |
| > keep the old behavior, or `--v5` to support the new default behavior, | |
| > or simply specify `--no-rebuild-manifest` to override the default. See | |
| > [Migrating from sourmash v4.x to sourmash v5.x](support.md#migrating-from-sourmash-v4x-to-sourmash-v5x) for more details. | |
This was referenced Aug 5, 2025
ctb
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Aug 7, 2025
Major new features: * start writing v4->v5 migration docs (#3721) * adjust warnings around tax abund and provide v5 upgrades to `tax metagenome` (#3711) Minor new features: * try setting up --v4 and --v5 behavior differences for `sig check` (#3072) * update `sig manifest` default rebuilding behavior for v5. (#3074) * handle (ignore) empty taxids for `bioboxes` format (#3748) * improve summary_csv for lingroups (#3758) Cleanup and documentation updates: * use auto-generated database list (#3754) Developer updates: * CI: fix dependabot config syntax, and clippy beta lints (#3762) * CI: update to cibuildwheel 3.1.1 (#3738) * ci: group dependabot updates by language (#3749) * Remove docutils dep (#3769) * bump version to 4.9.4-dev (#3715) * disable WebAssembly builds, for now (#3724) Dependabot updates: * Build(ci): Bump actions/download-artifact from 4 to 5 (#3766) * Build(deps): Bump DeterminateSystems/nix-installer-action from 17 to 18 (#3727) * Build(deps): Bump DeterminateSystems/nix-installer-action from 18 to 19 (#3746) * Build(deps): Bump criterion from 0.6.0 to 0.7.0 (#3741) * Build(deps): Bump md5 from 0.7.0 to 0.8.0 (#3719) * Build(deps): Bump memmap2 from 0.9.5 to 0.9.7 (#3732) * Build(deps): Bump prefix-dev/setup-pixi from 0.8.10 to 0.8.11 (#3733) * Build(deps): Bump prefix-dev/setup-pixi from 0.8.11 to 0.8.14 (#3747) * Build(deps): Bump rand from 0.9.1 to 0.9.2 (#3743) * Build(deps): Bump serde_json from 1.0.140 to 1.0.141 (#3742) * [pre-commit.ci] pre-commit autoupdate (#3718) * [pre-commit.ci] pre-commit autoupdate (#3725) * [pre-commit.ci] pre-commit autoupdate (#3731) * [pre-commit.ci] pre-commit autoupdate (#3737) * [pre-commit.ci] pre-commit autoupdate (#3740) * [pre-commit.ci] pre-commit autoupdate (#3756)
ctb
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Aug 10, 2025
In #3721 (review), @luizirber suggested using `[!WARNING]` to mark v5 breaking changes: >Maybe use a github-compatible admonition for these breaking changes? https://mystmd.org/guide/admonitions I couldn't get `[!WARNING]` to work for me, so I put `:::{warning}` blocks in. This PR also fixes a few minor doc nits that I noticed when building. Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
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This PR starts to rejigger the sourmash docs to discuss how to experiment with v5 features per #3076, and creates spaces to place various types of breaking changes. Breaking changes are also added to the relevant sections in the command-line docs.
It also moves the sourmash v3 migration docs into an appendix, since they are now 4 years old (!!)