MRG: update #2065 (uniquify CSV output from multigather) #2721
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* Initial commit * Added cat command details * Added describe command details * Downsample details failing * Added downsample command details * Added export command details * Added extract command details * Added filter command details * Added flatten command details * Added intersect command details * Added kmers command details * Added merge command details * Added overlap command details * Added rename command details * Added split command details * Added subtract command details * fix #2070 * minor updates Co-authored-by: C. Titus Brown <[email protected]>
* Initial commit * Added cat command details * Added describe command details * Downsample details failing * Added downsample command details * Added export command details * Added extract command details * Added filter command details * Added flatten command details * Added intersect command details * Added kmers command details * Added merge command details * Added overlap command details * Added rename command details * Added split command details * Added subtract command details * trial cleanup of sourmash sig cat usage * merge * fix sig split usage string * Update src/sourmash/cli/sig/intersect.py Co-authored-by: ccbaumler <[email protected]> Co-authored-by: keyabarve <[email protected]> Co-authored-by: ccbaumler <[email protected]>
* fix notification message about query scaled * fix tests
…omies (#2178) * add basics of sourmash tax grep command * initial implementation * fixed bug; added various args * more tests * support gzipped taxonomy files * let 'prepare' save gzip csv files, too * switch to outputting lineage; refactor * fix and test invert match * more tests * add --count * comment * upd docs * add test for tax prepare combining * test multiple, duplicate tax * finish? tests * implement --force * update usage string * Update doc/command-line.md Co-authored-by: Tessa Pierce Ward <[email protected]> Co-authored-by: Tessa Pierce Ward <[email protected]>
* add FileInputCSV * support zipfile taxonommies * rename 'default_zip_name' to 'default_csvname' * hack in support for CSVs with version info * more tests, support for ZipFile objs being passed in * sourmash sketch now accepts gzipped CSV files * picklists can now be gzipped * sig check now supports gz input file * add test for sig check with gz picklist * add delimiter support * update comment * fix comment * update comment * update comment * remove SOURMASH-TAXONOMY.csv * add explicit tests for FileOutputCSV * add gzip output tests for compare, plot, gather * change prefetch to use FileOutputCSV * fix gather --save-prefetch-csv to use FileOutputCSV * fix manifests to read/write gzip * add test for sig describe -o csv.gz * more test
* remove unnecessary exit checks * add fail-on-empty; adjust notify output * update tests * more argparse foo * re-add sys exit * construct empty db when invalid * be ok with databases with no pcklist matches * add fail-on-empty to search and multigather * adjust prefetch reporting, too * add test for new output from prefetch * simplify unnecessary code * remove more unnecessary * fix argparse foo, add test for search --no-fail-on-empty-database * add test for sourmash gather --no-fail * remove debug * more tests * even more test
* adjust search output to include threshold * add docs, fix tests * Apply suggestions from code review thanks! Co-authored-by: ccbaumler <[email protected]> * Update doc/command-line.md Co-authored-by: ccbaumler <[email protected]> Co-authored-by: ccbaumler <[email protected]>
Co-authored-by: C. Titus Brown <[email protected]>
Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.8.1 to 2.9.0. - [Release notes](https://github.com/pypa/cibuildwheel/releases) - [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md) - [Commits](pypa/cibuildwheel@v2.8.1...v2.9.0) --- updated-dependencies: - dependency-name: pypa/cibuildwheel dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: C. Titus Brown <[email protected]>
* update links to static rmd * try fix links * use full paths * punctuation typo Co-authored-by: C. Titus Brown <[email protected]>
…`runtmp` fixture instead of `utils.TempDirectory()` (#1739) * Initial commit * Fixed test * Removed comments * Made requested modification * Removed commented code * Made requested changes * minor fix Co-authored-by: C. Titus Brown <[email protected]>
* added angus tutorial to docs * update tutorial * fix images in tutorial-long.md Co-authored-by: C. Titus Brown <[email protected]>
* try switching rtd to using mamba * remove python version? * bump CI * bump up ubuntu version, too
…ation (#2215) * fix? containment direction * fix numbers * sketchcomparison tests pass 🎉 * update; tests pass * update docs with containment and ANI info * add asymmetric test for prefetch containment ANI * add test for search asymmetry * fix spacing :) * do specific compare test * Update doc/command-line.md Co-authored-by: Tessa Pierce Ward <[email protected]> Co-authored-by: Tessa Pierce Ward <[email protected]>
* fix? containment direction * fix numbers * sketchcomparison tests pass 🎉 * update; tests pass * update docs with containment and ANI info * add asymmetric test for prefetch containment ANI * add test for search asymmetry * fix spacing :) * do specific compare test * add --distance-matrix to compare * minor refactoring/cleanup/commenting of tests * add distance test; minor test refactoring * test refactoring * more test refactoring * add another --distance test * add one more test * update command line docs * rename matrix to 'matrix' in compare, to reduce confusion * Update doc/command-line.md Co-authored-by: Tessa Pierce Ward <[email protected]> Co-authored-by: Tessa Pierce Ward <[email protected]>
* add kreport output format to tax metagenome * better fn info * rm change not for this pr * upd description * add kreport to docs
* tests pass * try out into_mutable and into_frozen * use into_mutable/into_frozen * use a context manager for into_* * comment/doc, fix most tests * fix totally foreseeable bug from use of dangerous mutate() * remove dangerous to_mutable() * slight refactoring * clean up after merge * some more fixes * more fixes * cleanup * add some tests, and docs * hmm. * clean up
* use argparse extend for better list arg handling * mult tax file tests * testy tests * implement force in loading * add some more tests * add test for 'extend' in metagenome -g arg * mark places to test * add tests for argparse extend to tax annotate * add test for tax prepare * add tests for tax grep * add tests for tax genome Co-authored-by: C. Titus Brown <[email protected]>
…tiple gather files (#2244) * do not allow same query in mult gather files * do allow us to load non-duplicated queries from this csv * fail instead of ignore
* add bf to ani containment calculations * write bf a diff way * debiased containment * basic tests for debiased containment mh fns * constrain debiased containment * Update src/sourmash/minhash.py Co-authored-by: C. Titus Brown <[email protected]> Co-authored-by: C. Titus Brown <[email protected]>
* add orig_query_sum_abunds column * initial addition of n_weighted_found and sum_weighted_hashes * ok, three columns * more better * remove redundant total_abund * add total_weighted_hashes to SummarizedGatherResult * catch missing total_weighted_hashes * update kreport output * fix the things * fix final tests for scaled=2000 * Update src/sourmash/tax/tax_utils.py Co-authored-by: Tessa Pierce Ward <[email protected]> Co-authored-by: Tessa Pierce Ward <[email protected]>
…2251) * check query_abundance when gather --ignore-abund is set * check values for flat query
* version bumps for Rust dependencies * flake updates
Bumps [serde_json](https://github.com/serde-rs/json) from 1.0.100 to 1.0.103. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/serde-rs/json/releases">serde_json's releases</a>.</em></p> <blockquote> <h2>v1.0.103</h2> <ul> <li>Documentation improvements</li> </ul> <h2>v1.0.102</h2> <ul> <li>Add a way to customize the serialization of byte arrays (<a href="https://github.com/serde-rs/json/issues/1039">#1039</a>)</li> </ul> <h2>v1.0.101</h2> <ul> <li>Allow f32 and f64 as keys in maps (<a href="https://github.com/serde-rs/json/issues/1027">#1027</a>, thanks <a href="https://github.com/overdrivenpotato"><code>@overdrivenpotato</code></a>)</li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/serde-rs/json/commit/54bcb4dc94a29a0fe67ec735c5525760823a5499"><code>54bcb4d</code></a> Release 1.0.103</li> <li><a href="https://github.com/serde-rs/json/commit/9c2879a848ae3117d2c99a03d415bb77a1ac7d34"><code>9c2879a</code></a> Opt in to generate-link-to-definition when building on docs.rs</li> <li><a href="https://github.com/serde-rs/json/commit/d1a07e29f2a665e133a8bee4d58666bea8ea40ef"><code>d1a07e2</code></a> Fix rustdoc::bare_urls lint in lexical code</li> <li><a href="https://github.com/serde-rs/json/commit/658689d36bc4c4c04b6d40bca4719ee99d09a781"><code>658689d</code></a> Release 1.0.102</li> <li><a href="https://github.com/serde-rs/json/commit/42dbd000163dc8e3aa07fe9dbee3691073c10627"><code>42dbd00</code></a> Merge pull request <a href="https://github.com/serde-rs/json/issues/1039">#1039</a> from dtolnay/writebytearray</li> <li><a href="https://github.com/serde-rs/json/commit/a1ca32a5c759066b3d8a84267078869ce74df773"><code>a1ca32a</code></a> Factor out byte array serialization to a new Formatter method</li> <li><a href="https://github.com/serde-rs/json/commit/857b010ce0dd98ba37e9c7c773b72940b7605008"><code>857b010</code></a> Inline Serializer::serialize_u8 into serialize_bytes</li> <li><a href="https://github.com/serde-rs/json/commit/6ad54959060c8b87b4f7459e203d4750dcb1fd94"><code>6ad5495</code></a> Inline u8::serialize into serialize_bytes</li> <li><a href="https://github.com/serde-rs/json/commit/44b4a6c8599d8988c82e3932a7a1cf3a38f377c3"><code>44b4a6c</code></a> Simplify serialize_bytes</li> <li><a href="https://github.com/serde-rs/json/commit/0e2c949638571990059c9783cf6f06f0d77126b2"><code>0e2c949</code></a> Inline SerializeSeq::end into serialize_bytes</li> <li>Additional commits viewable in <a href="https://github.com/serde-rs/json/compare/v1.0.100...v1.0.103">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [thiserror](https://github.com/dtolnay/thiserror) from 1.0.43 to 1.0.44. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/dtolnay/thiserror/releases">thiserror's releases</a>.</em></p> <blockquote> <h2>1.0.44</h2> <ul> <li>Documentation improvements</li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/dtolnay/thiserror/commit/54b70cfe109981e6349aebae4393c62c93cccafc"><code>54b70cf</code></a> Release 1.0.44</li> <li><a href="https://github.com/dtolnay/thiserror/commit/f86e8e5881f157f115c271b9ff578867cc91ba92"><code>f86e8e5</code></a> Opt in to generate-link-to-definition when building on docs.rs</li> <li>See full diff in <a href="https://github.com/dtolnay/thiserror/compare/1.0.43...1.0.44">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [ouroboros](https://github.com/joshua-maros/ouroboros) from 0.17.0 to 0.17.2. <details> <summary>Commits</summary> <ul> <li>See full diff in <a href="https://github.com/joshua-maros/ouroboros/commits">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [tempfile](https://github.com/Stebalien/tempfile) from 3.6.0 to 3.7.0. <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/Stebalien/tempfile/blob/master/CHANGELOG.md">tempfile's changelog</a>.</em></p> <blockquote> <h2>3.7.0</h2> <p>BREAKING: This release updates the MSRV to 1.63. This isn't an API-breaking change (so no major release) but it's still a breaking change for some users.</p> <ul> <li>Update fastrand from 1.6 to 2.0</li> <li>Update rustix to 0.38</li> <li>Updates the MSRV to 1.63.</li> <li>Provide AsFd/AsRawFd on wasi.</li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/Stebalien/tempfile/commit/d258544335e040e727cde095a468416910893a2a"><code>d258544</code></a> chore: release 3.7.0</li> <li><a href="https://github.com/Stebalien/tempfile/commit/da36cd5ddd7adf84d1cacf17d6269f0597ac45f0"><code>da36cd5</code></a> Provide implementations for I/O safety traits unconditionally (<a href="https://github.com/Stebalien/tempfile/issues/244">#244</a>)</li> <li><a href="https://github.com/Stebalien/tempfile/commit/74f9fbcbe1a09c1cc25cd91b9435981d308f77f3"><code>74f9fbc</code></a> Update to rustix 0.38 and update MSRV to 1.63 (<a href="https://github.com/Stebalien/tempfile/issues/241">#241</a>)</li> <li><a href="https://github.com/Stebalien/tempfile/commit/1cff81e583ec483ca38acc7d8b46c64d292090e1"><code>1cff81e</code></a> build(deps): update fastrand requirement from 1.6.0 to 2.0.0 (<a href="https://github.com/Stebalien/tempfile/issues/240">#240</a>)</li> <li><a href="https://github.com/Stebalien/tempfile/commit/c7d9afd91144edf17b67e8459fcfe6395f55b2b5"><code>c7d9afd</code></a> Update/format changelog</li> <li>See full diff in <a href="https://github.com/Stebalien/tempfile/compare/v3.6.0...v3.7.0">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
The rs214 links are broken for the LCA files, small fix to point to the correct URL folder; the URLs for the rs214 LCA DBs did not get updated in the update of the table for those links. Currently the DBs in the LCA column of the table are 404ed. https://sourmash.readthedocs.io/en/latest/databases.html#gtdb-r08-rs214-genomic-representatives-85k Once the items above are done, and all checks pass, request a review!
Bumps [serde_json](https://github.com/serde-rs/json) from 1.0.103 to 1.0.104. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/serde-rs/json/releases">serde_json's releases</a>.</em></p> <blockquote> <h2>v1.0.104</h2> <ul> <li>Provide IntoDeserializer impl for &serde_json::Value (<a href="https://github.com/serde-rs/json/issues/1045">#1045</a>, thanks <a href="https://github.com/ZetaNumbers"><code>@ZetaNumbers</code></a>)</li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/serde-rs/json/commit/ab084832926cf7d733785c8801aa4fcf96523956"><code>ab08483</code></a> Release 1.0.104</li> <li><a href="https://github.com/serde-rs/json/commit/f6cc4f31a38228b59cc28ffc471a8d50fc20d2a3"><code>f6cc4f3</code></a> Merge pull request <a href="https://github.com/serde-rs/json/issues/1045">#1045</a> from ZetaNumbers/value-ref-into-deserializer</li> <li><a href="https://github.com/serde-rs/json/commit/8e8db8ce0cf066d8ef4cbe0167c3a97d18a49674"><code>8e8db8c</code></a> Implement IntoDeserializer for &Value</li> <li><a href="https://github.com/serde-rs/json/commit/8f90eacf6c6335fbd925b1d663e46f4a7592ebba"><code>8f90eac</code></a> Delete inline attributes throughout test suite</li> <li>See full diff in <a href="https://github.com/serde-rs/json/compare/v1.0.103...v1.0.104">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [supercharge/redis-github-action](https://github.com/supercharge/redis-github-action) from 1.5.0 to 1.6.0. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/supercharge/redis-github-action/releases">supercharge/redis-github-action's releases</a>.</em></p> <blockquote> <h2>1.6.0</h2> <p>Release 1.6.0</p> </blockquote> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/supercharge/redis-github-action/blob/main/CHANGELOG.md">supercharge/redis-github-action's changelog</a>.</em></p> <blockquote> <h1>Changelog</h1> <h2><a href="https://github.com/supercharge/redis-github-action/compare/v1.5.0...v1.66.0">1.66.0</a> - 2023-07-27</h2> <h3>Added</h3> <ul> <li>add <code>redis-remove-container</code> option adding the <code>--rm</code> flag to the resulting <code>docker run … --rm</code> command which starts the Redis container</li> </ul> <h3>Updated</h3> <ul> <li>update versions in README</li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/supercharge/redis-github-action/commit/656b0b5cf954e2f1e716731e810b839d3050577d"><code>656b0b5</code></a> prepare changelog for 1.6.0</li> <li><a href="https://github.com/supercharge/redis-github-action/commit/f14f21735302be362ede0d003ec82877f9129200"><code>f14f217</code></a> update versions</li> <li><a href="https://github.com/supercharge/redis-github-action/commit/b026ae8b2c88c1a1bde3189e91f8cae62a16608e"><code>b026ae8</code></a> Merge pull request <a href="https://github.com/supercharge/redis-github-action/issues/15">#15</a> from kien-cs/feature-add-rm-container</li> <li><a href="https://github.com/supercharge/redis-github-action/commit/9c4929a4702a620bd5a3e590bd576ae1b91b8d74"><code>9c4929a</code></a> Add option to remove container when it exits</li> <li>See full diff in <a href="https://github.com/supercharge/redis-github-action/compare/1.5.0...1.6.0">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [tempfile](https://github.com/Stebalien/tempfile) from 3.7.0 to 3.7.1. <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/Stebalien/tempfile/blob/master/CHANGELOG.md">tempfile's changelog</a>.</em></p> <blockquote> <h2>3.7.1</h2> <ul> <li>Tempfile builds on haiku again.</li> <li>Under the hood, we've switched from the unlinkat/linkat syscalls to the regular unlink/link syscalls where possible.</li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/Stebalien/tempfile/commit/bf8f7ea4362894f572935ea730a271378d7277f2"><code>bf8f7ea</code></a> chore: release 3.7.1</li> <li><a href="https://github.com/Stebalien/tempfile/commit/a5c236ca11fb06373105f65952e194323e9f2637"><code>a5c236c</code></a> Use <code>rename</code>/<code>unlink</code>/<code>etc. instead of </code>renameat<code>/</code>unlinkat`/etc. (<a href="https://github.com/Stebalien/tempfile/issues/247">#247</a>)</li> <li>See full diff in <a href="https://github.com/Stebalien/tempfile/compare/v3.7.0...v3.7.1">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
This PR adds `-E/--extension` to `sourmash sig split`, so that you can do (for example) ``` sourmash sig split -E .sig.gz database.zip ``` and get a bunch of `.sig.gz` files instead of a bunch of `.sig` files. Addresses #2703
This PR updates `test_standalone_manifest_signatures_prefix_fail` to use `runtmp.out(...)` for a directory that's not supposed to exist; the test was failing on my laptop because the directory used in the test _did_ exist on my laptop 😄
Fixes #2684 This PR adds a function that creates an `args` object for a particular sourmash command - so that you can do something like this: ```python import sourmash.commands, sourmash.cli # create args object: args = sourmash.cli.parse_args(['plot', 'cmp']) # run 'sourmash plot' sourmash.commands.plot(args) ``` For convenience, this PR also makes all of the `sourmash sig` functions available in Python via `sourmash.sig.<fn>`.
) This PR adds support for argparse `usage` and `epilog` strings, as well as `formatter_class`, per [argparse docs](https://docs.python.org/3/library/argparse.html#argparse.ArgumentParser). See sourmash-bio/sourmash_plugin_template@cb5d454 for general use in plugins, and ctb/sourmash_plugin_commonhash@3fbb4d2 for an example use in commonhash. This means that e.g. commonhash now supports pleasing output for both bad usage and `-h` flag - ``` sourmash scripts commonhash usage: sourmash scripts commonhash [ -m 2 ] *.sig.gz -o filtered.zip commonhash: error: the following arguments are required: sigfiles, -o/--output ``` and ``` == This is sourmash version 4.8.3.dev0. == == Please cite Brown and Irber (2016), doi:10.21105/joss.00027. == usage: sourmash scripts commonhash [ -m 2 ] *.sig.gz -o filtered.zip filter hashes by min occurrence across sketches Reduce 'noise' in Jaccard comparisons of sequencing data by removing hashes that are present in only a few sketches. 'commonhash' supports the full range of sourmash sketch output formats [1]. [1] https://sourmash.readthedocs.io/en/latest/command-line.html#choosing-signature-output-formats --- positional arguments: sigfiles input signatures options: -h, --help show this help message and exit -q, --quiet suppress non-error output -d, --debug provide debugging output -k KSIZE, --ksize KSIZE select this k-mer size -o OUTPUT, --output OUTPUT save sketches to this location; e.g. output.zip or ./output/ -m MIN_SAMPLES, --min-samples MIN_SAMPLES a hash must be in this many samples to be retained See https://github.com/ctb/sourmash_plugin_commonhash for more examples. Need help? Have questions? Ask at https://github.com/sourmash/issues! ```
Bumps [log](https://github.com/rust-lang/log) from 0.4.19 to 0.4.20. <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/rust-lang/log/blob/master/CHANGELOG.md">log's changelog</a>.</em></p> <blockquote> <h2>[0.4.20] - 2023-07-11</h2> <ul> <li>Remove rustversion dev-dependency by <a href="https://github.com/Thomasdezeeuw"><code>@Thomasdezeeuw</code></a> in <a href="https://github.com/rust-lang/log/pull/568">rust-lang/log#568</a></li> <li>Remove <code>local_inner_macros</code> usage by <a href="https://github.com/EFanZh"><code>@EFanZh</code></a> in <a href="https://github.com/rust-lang/log/pull/570">rust-lang/log#570</a></li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/rust-lang/log/commit/4708f1484c7e6b8d4418b571c05e613b18e57673"><code>4708f14</code></a> Merge pull request <a href="https://github.com/rust-lang/log/issues/574">#574</a> from chrysn-pull-requests/doc-log-to-defmt</li> <li><a href="https://github.com/rust-lang/log/commit/6de3cccc3670231edae0b2c86202a002aae65b2d"><code>6de3ccc</code></a> Merge pull request <a href="https://github.com/rust-lang/log/issues/571">#571</a> from rust-lang/cargo/0.4.20</li> <li><a href="https://github.com/rust-lang/log/commit/838920cf182cf7d24ff411834c85a46d92ed0463"><code>838920c</code></a> Merge pull request <a href="https://github.com/rust-lang/log/issues/575">#575</a> from EFanZh/group-target-module-path-and-file</li> <li><a href="https://github.com/rust-lang/log/commit/3985711f74bb75a6504c41f6f4b66ad5fd29ef41"><code>3985711</code></a> Group <code>target</code>, <code>module_path</code> and <code>file</code> arguments</li> <li><a href="https://github.com/rust-lang/log/commit/3f534d00e485ba7f029b9ef348385154e4e51dfd"><code>3f534d0</code></a> Move private APIs into a single module</li> <li><a href="https://github.com/rust-lang/log/commit/f5ab686e9b1ce6962dd4e02d6cc71a1d7ec48ea6"><code>f5ab686</code></a> doc: Add log-to-defmt to other-facilities section</li> <li><a href="https://github.com/rust-lang/log/commit/6d173bf94114f62217349b76bc18ed4340f12586"><code>6d173bf</code></a> prepare for 0.4.20 release</li> <li><a href="https://github.com/rust-lang/log/commit/cab10885defdf445dc730e5a22f67fcec69ca728"><code>cab1088</code></a> Merge pull request <a href="https://github.com/rust-lang/log/issues/570">#570</a> from EFanZh/remove-local-inner-macros</li> <li><a href="https://github.com/rust-lang/log/commit/9d052b17d3ddf9b5894740c6d82899c531c789ee"><code>9d052b1</code></a> Remove <code>local_inner_macros</code> usage</li> <li><a href="https://github.com/rust-lang/log/commit/e9123d6d9a62a99771bd33e43a29f67f7811eee0"><code>e9123d6</code></a> Merge pull request <a href="https://github.com/rust-lang/log/issues/568">#568</a> from Thomasdezeeuw/remove-rustversion-dep</li> <li>Additional commits viewable in <a href="https://github.com/rust-lang/log/compare/0.4.19...0.4.20">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.14.1 to 2.15.0. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p> <blockquote> <h2>v2.15.0</h2> <ul> <li>🌟 CPython 3.12 wheels are now built by default - without the CIBW_PRERELEASE_PYTHONS flag. It's time to build and upload these wheels to PyPI! This release includes CPython 3.12.0rc1, which is guaranteed to be ABI compatible with the final release. (<a href="https://github.com/pypa/cibuildwheel/issues/1565">#1565</a>)</li> <li>✨ Adds musllinux_1_2 support - this allows packagers to build for musl-based Linux distributions on a more recent Alpine image, and a newer musl libc. (<a href="https://github.com/pypa/cibuildwheel/issues/1561">#1561</a>)</li> </ul> </blockquote> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md">pypa/cibuildwheel's changelog</a>.</em></p> <blockquote> <h3>v2.15.0</h3> <p><em>8 August 2023</em></p> <ul> <li>🌟 CPython 3.12 wheels are now built by default - without the CIBW_PRERELEASE_PYTHONS flag. It's time to build and upload these wheels to PyPI! This release includes CPython 3.12.0rc1, which is guaranteed to be ABI compatible with the final release. (<a href="https://github.com/pypa/cibuildwheel/issues/1565">#1565</a>)</li> <li>✨ Adds musllinux_1_2 support - this allows packagers to build for musl-based Linux distributions on a more recent Alpine image, and a newer musl libc. (<a href="https://github.com/pypa/cibuildwheel/issues/1561">#1561</a>)</li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pypa/cibuildwheel/commit/39a63b5912f086dd459cf6fcb13dcdd3fe3bc24d"><code>39a63b5</code></a> Bump version: v2.15.0</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/47e5d3c2cdee9d5324b6abe18c380c5ee33fd8f9"><code>47e5d3c</code></a> Merge pull request <a href="https://github.com/pypa/cibuildwheel/issues/1565">#1565</a> from henryiii/henryiii/feat/312rc</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/a63e11a1c40bf45810a29b0837a72312202cb00b"><code>a63e11a</code></a> feat: build using 3.12 RC by default</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/df94b5db6769eb8c3abb164caa9ab84c763570da"><code>df94b5d</code></a> [Bot] Update dependencies (<a href="https://github.com/pypa/cibuildwheel/issues/1553">#1553</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/36049d86a2e21d74382d84d7a423e20e49a2ca91"><code>36049d8</code></a> feature: add musllinux_1_2 support (<a href="https://github.com/pypa/cibuildwheel/issues/1561">#1561</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/229f8570b497b5fa4a201f7dd28c4f52c104218e"><code>229f857</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://github.com/pypa/cibuildwheel/issues/1562">#1562</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/5b32ee7d7bcd9433f559d8b43e9f9a180288c227"><code>5b32ee7</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://github.com/pypa/cibuildwheel/issues/1559">#1559</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/3f3bd9cff62eb311ed99891cc65132731c0a1c6f"><code>3f3bd9c</code></a> Merge pull request <a href="https://github.com/pypa/cibuildwheel/issues/1554">#1554</a> from pypa/pre-commit-ci-update-config</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/8df6d59adf7f9c7876ece95d0f908b53e2014ff2"><code>8df6d59</code></a> [pre-commit.ci] pre-commit autoupdate</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/4135c0a01dc11910ce118f58acc7caf4ac5c524a"><code>4135c0a</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://github.com/pypa/cibuildwheel/issues/1546">#1546</a>)</li> <li>Additional commits viewable in <a href="https://github.com/pypa/cibuildwheel/compare/v2.14.1...v2.15.0">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…tation (#2713) Fixes #2709 Fixes #2708 For review - - [ ] updated [prefetch section](https://sourmash--2713.org.readthedocs.build/en/2713/command-line.html#caveats-and-comments) - [ ] updated [sig intersect docs](https://sourmash--2713.org.readthedocs.build/en/2713/command-line.html#sourmash-signature-intersect-intersect-two-or-more-signatures) - [ ] updated [sig inflate docs](https://sourmash--2713.org.readthedocs.build/en/2713/command-line.html#sourmash-signature-inflate-transfer-abundances-from-one-signature-to-others) - [ ] updated [sig overlap docs](https://sourmash--2713.org.readthedocs.build/en/2713/command-line.html#sourmash-signature-overlap-detailed-comparison-of-two-signatures-overlap) - [ ] updated [sig merge docs](https://sourmash--2713.org.readthedocs.build/en/2713/command-line.html#sourmash-signature-merge-merge-two-or-more-signatures-into-one) - [ ] updated [sig subtract docs](https://sourmash--2713.org.readthedocs.build/en/2713/command-line.html#sourmash-signature-subtract-subtract-other-signatures-from-a-signature) --------- Co-authored-by: Luiz Irber <[email protected]>
Per openjournals/joss#423, we are planning to make a new submission to JOSS for sourmash v4.x. The first paper from 2016 is [here](https://joss.theoj.org/papers/10.21105/joss.00027). Fixes #1321. Ref #622, #444. - [x] update authors per #1367 - [x] fix `@@@` in paper.md YAML header - [x] review [JOSS guidelines](https://joss.readthedocs.io/en/latest/submitting.html) and think about what to add, if anything. - [x] add funding acks - Moore esp - [ ] let's fix citation issue finally #511 --------- Co-authored-by: Tessa Pierce Ward <[email protected]> Co-authored-by: N. Tessa Pierce-Ward <[email protected]> Co-authored-by: Katrin Leinweber <[email protected]>
Codecov Report
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- Coverage 91.81% 85.26% -6.56%
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Files 99 133 +34
Lines 11047 15196 +4149
Branches 2178 2615 +437
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+ Hits 10143 12957 +2814
- Misses 606 1937 +1331
- Partials 298 302 +4
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This was referenced Aug 19, 2023
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…t-add-query-md5sum` (#2722) This PR: - adds documentation for `multigather` to sourmash docs! - builds on #2065 / #2721 so that tests pass. - adds an option `-U/--output-add-query-md5sum` to `sourmash multigather` - adds an option `--force-allow-overwrite-output` to `sourmash multigather` - **CHANGES BEHAVIOR** of multigather by treating `query.filename == '-'` as if `query.filename` is empty, thus replacing it with md5sum - **CHANGES BEHAVIOR** of multigather by failing loudly and clearly if output files are going to be overwritten - adds `-E/--extension` to allow output to files other than `.sig` See discussion over in [#2328: `multigather` CSV output uses signature `filename` as basename](#2328). To add: - [x] tests for `-U`; - [x] implement and test `-E/--extension` - [x] implement and test `--force-allow-overwrite-output` - [x] fix for `query_filename` being None/empty in `-U` branch - [x] documentation update for changed output behavior for multigather: '-' => using md5sum - [x] documentation update for changed output behavior for multigather: fails if overwrite happens - [x] fix multigather link in docs --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Olga Botvinnik <[email protected]> Co-authored-by: Keya Barve <[email protected]> Co-authored-by: ccbaumler <[email protected]> Co-authored-by: Tessa Pierce Ward <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Taylor Reiter <[email protected]> Co-authored-by: Erik Young <[email protected]> Co-authored-by: David Koslicki <[email protected]> Co-authored-by: Luiz Irber <[email protected]> Co-authored-by: Colton Baumler <[email protected]> Co-authored-by: Luiz Irber <[email protected]> Co-authored-by: N. Tessa Pierce-Ward <[email protected]> Co-authored-by: Peter Cock <[email protected]> Co-authored-by: Francesco Beghini <[email protected]> Co-authored-by: Jason Stajich <[email protected]> Co-authored-by: Katrin Leinweber <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Note: PR into #2065.
This PR updates #2065 with all the changes from
latest. This includes the fix & update to multigather in #2322, which:--output-dirNo functional changes are made beyond the merge, so some tests are still failing; will discuss fixes in yet a new PR :).