MRG: add --set-name to sig intersect and sig subtract
#3162
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## rename_sig_json_fns #3162 +/- ##
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Coverage 86.67% 86.68%
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Files 136 136
Lines 15837 15839 +2
Branches 2716 2716
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+ Hits 13727 13730 +3
+ Misses 1800 1799 -1
Partials 310 310
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Bumps [DeterminateSystems/nix-installer-action](https://github.com/determinatesystems/nix-installer-action) from 10 to 11. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/determinatesystems/nix-installer-action/releases">DeterminateSystems/nix-installer-action's releases</a>.</em></p> <blockquote> <h2>v11</h2> <h2>What's Changed</h2> <ul> <li>Rebase on top of detsys-ts for abstracting over install.determinate.systems by <a href="https://github.com/grahamc"><code>@grahamc</code></a> in <a href="https://redirect.github.com/DeterminateSystems/nix-installer-action/pull/74">DeterminateSystems/nix-installer-action#74</a></li> <li>Update detsys-ts by <a href="https://github.com/grahamc"><code>@grahamc</code></a> in <a href="https://redirect.github.com/DeterminateSystems/nix-installer-action/pull/75">DeterminateSystems/nix-installer-action#75</a></li> <li>Gracefully handle FlakeHub login failure by <a href="https://github.com/cole-h"><code>@cole-h</code></a> in <a href="https://redirect.github.com/DeterminateSystems/nix-installer-action/pull/77">DeterminateSystems/nix-installer-action#77</a></li> <li>General JS cleanup by <a href="https://github.com/lucperkins"><code>@lucperkins</code></a> in <a href="https://redirect.github.com/DeterminateSystems/nix-installer-action/pull/76">DeterminateSystems/nix-installer-action#76</a></li> <li>Fix broken CI caused by Nix reinstallation wiping out the Magic Nix Cache by <a href="https://github.com/lucperkins"><code>@lucperkins</code></a> in <a href="https://redirect.github.com/DeterminateSystems/nix-installer-action/pull/79">DeterminateSystems/nix-installer-action#79</a></li> <li>Standardize on v4 of the checkout action by <a href="https://github.com/lucperkins"><code>@lucperkins</code></a> in <a href="https://redirect.github.com/DeterminateSystems/nix-installer-action/pull/80">DeterminateSystems/nix-installer-action#80</a></li> <li>Switch to tsup for building by <a href="https://github.com/lucperkins"><code>@lucperkins</code></a> in <a href="https://redirect.github.com/DeterminateSystems/nix-installer-action/pull/82">DeterminateSystems/nix-installer-action#82</a></li> <li>Update dependencies by <a href="https://github.com/grahamc"><code>@grahamc</code></a> in <a href="https://redirect.github.com/DeterminateSystems/nix-installer-action/pull/85">DeterminateSystems/nix-installer-action#85</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/DeterminateSystems/nix-installer-action/compare/v10...v11">https://github.com/DeterminateSystems/nix-installer-action/compare/v10...v11</a></p> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/DeterminateSystems/nix-installer-action/commit/8cdf194da984e4f12b2f8c36d1fa107c1dd67f5c"><code>8cdf194</code></a> Update dependencies (<a href="https://redirect.github.com/determinatesystems/nix-installer-action/issues/85">#85</a>)</li> <li><a href="https://github.com/DeterminateSystems/nix-installer-action/commit/10f43c0d327c8599928f907a943a737cff2505f3"><code>10f43c0</code></a> Merge pull request <a href="https://redirect.github.com/determinatesystems/nix-installer-action/issues/82">#82</a> from DeterminateSystems/tsup-build</li> <li><a href="https://github.com/DeterminateSystems/nix-installer-action/commit/337589f84d8e6b91044b151577cfcf975b1b4746"><code>337589f</code></a> Switch to tsup for building</li> <li><a href="https://github.com/DeterminateSystems/nix-installer-action/commit/330a0ca1bc2730bb277470f09cb12a3e34c64693"><code>330a0ca</code></a> Merge pull request <a href="https://redirect.github.com/determinatesystems/nix-installer-action/issues/80">#80</a> from DeterminateSystems/update-checkout-action</li> <li><a href="https://github.com/DeterminateSystems/nix-installer-action/commit/2c90bb97d0414453542c4a09fd702348039ecc6f"><code>2c90bb9</code></a> Standardize on v4 of the checkout action</li> <li><a href="https://github.com/DeterminateSystems/nix-installer-action/commit/91b8eb110e4827278e9059090cbdf19592674ca3"><code>91b8eb1</code></a> Merge pull request <a href="https://redirect.github.com/determinatesystems/nix-installer-action/issues/79">#79</a> from DeterminateSystems/fix-mnc-issue</li> <li><a href="https://github.com/DeterminateSystems/nix-installer-action/commit/ff2ea37e976abaceab73fc46b55effe63e3e0204"><code>ff2ea37</code></a> Remove MNC from workflow</li> <li><a href="https://github.com/DeterminateSystems/nix-installer-action/commit/f95752164330c16e028883632a7274db3dac9c12"><code>f957521</code></a> Reinstate the MNC prior to reinstall</li> <li><a href="https://github.com/DeterminateSystems/nix-installer-action/commit/23ddac323e514704d36c8945869cfa6f09c57a50"><code>23ddac3</code></a> Remove second reinstall setting</li> <li><a href="https://github.com/DeterminateSystems/nix-installer-action/commit/3785eaaa9b5fa747cc750eafcccc6e724c86e7cb"><code>3785eaa</code></a> Fix other instance of uninstall/reinstall</li> <li>Additional commits viewable in <a href="https://github.com/determinatesystems/nix-installer-action/compare/v10...v11">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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [DeterminateSystems/magic-nix-cache-action](https://github.com/determinatesystems/magic-nix-cache-action) from 4 to 6. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/determinatesystems/magic-nix-cache-action/releases">DeterminateSystems/magic-nix-cache-action's releases</a>.</em></p> <blockquote> <h2>v6</h2> <h2>What's Changed</h2> <ul> <li>Set the default flakehub-flake-name to an empty string by <a href="https://github.com/cole-h"><code>@cole-h</code></a> in <a href="https://redirect.github.com/DeterminateSystems/magic-nix-cache-action/pull/51">DeterminateSystems/magic-nix-cache-action#51</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/DeterminateSystems/magic-nix-cache-action/compare/v5...v6">https://github.com/DeterminateSystems/magic-nix-cache-action/compare/v5...v6</a></p> <h2>v5</h2> <h2>What's Changed</h2> <ul> <li>Better Boolean handling and debug statement by <a href="https://github.com/lucperkins"><code>@lucperkins</code></a> in <a href="https://redirect.github.com/DeterminateSystems/magic-nix-cache-action/pull/39">DeterminateSystems/magic-nix-cache-action#39</a></li> <li>Cache dev shell in FlakeHub Cache by <a href="https://github.com/lucperkins"><code>@lucperkins</code></a> in <a href="https://redirect.github.com/DeterminateSystems/magic-nix-cache-action/pull/40">DeterminateSystems/magic-nix-cache-action#40</a></li> <li>Rebase on detsys-ts and get rid of bun by <a href="https://github.com/grahamc"><code>@grahamc</code></a> in <a href="https://redirect.github.com/DeterminateSystems/magic-nix-cache-action/pull/41">DeterminateSystems/magic-nix-cache-action#41</a></li> <li>Update detsys-ts by <a href="https://github.com/grahamc"><code>@grahamc</code></a> in <a href="https://redirect.github.com/DeterminateSystems/magic-nix-cache-action/pull/42">DeterminateSystems/magic-nix-cache-action#42</a></li> <li>Preflight nix, or don't fail by <a href="https://github.com/grahamc"><code>@grahamc</code></a> in <a href="https://redirect.github.com/DeterminateSystems/magic-nix-cache-action/pull/43">DeterminateSystems/magic-nix-cache-action#43</a></li> <li>Switch to tsup-based build by <a href="https://github.com/lucperkins"><code>@lucperkins</code></a> in <a href="https://redirect.github.com/DeterminateSystems/magic-nix-cache-action/pull/44">DeterminateSystems/magic-nix-cache-action#44</a></li> <li>Add prettier config by <a href="https://github.com/lucperkins"><code>@lucperkins</code></a> in <a href="https://redirect.github.com/DeterminateSystems/magic-nix-cache-action/pull/45">DeterminateSystems/magic-nix-cache-action#45</a></li> <li>Revamp logic into central class by <a href="https://github.com/lucperkins"><code>@lucperkins</code></a> in <a href="https://redirect.github.com/DeterminateSystems/magic-nix-cache-action/pull/46">DeterminateSystems/magic-nix-cache-action#46</a></li> <li>Debug daemon listen by <a href="https://github.com/grahamc"><code>@grahamc</code></a> in <a href="https://redirect.github.com/DeterminateSystems/magic-nix-cache-action/pull/47">DeterminateSystems/magic-nix-cache-action#47</a></li> <li>Gracefully handle it if a user tries to register the action twice. by <a href="https://github.com/grahamc"><code>@grahamc</code></a> in <a href="https://redirect.github.com/DeterminateSystems/magic-nix-cache-action/pull/48">DeterminateSystems/magic-nix-cache-action#48</a></li> <li>Don't mark the daemon started until after we successfully import the … by <a href="https://github.com/grahamc"><code>@grahamc</code></a> in <a href="https://redirect.github.com/DeterminateSystems/magic-nix-cache-action/pull/49">DeterminateSystems/magic-nix-cache-action#49</a></li> <li>Update deps by <a href="https://github.com/grahamc"><code>@grahamc</code></a> in <a href="https://redirect.github.com/DeterminateSystems/magic-nix-cache-action/pull/50">DeterminateSystems/magic-nix-cache-action#50</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/DeterminateSystems/magic-nix-cache-action/compare/v4...v5">https://github.com/DeterminateSystems/magic-nix-cache-action/compare/v4...v5</a></p> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/DeterminateSystems/magic-nix-cache-action/commit/87e8236f46702ab0ce5a058b605a173ec88d618e"><code>87e8236</code></a> Merge pull request <a href="https://redirect.github.com/determinatesystems/magic-nix-cache-action/issues/51">#51</a> from DeterminateSystems/lookup-project-by-token</li> <li><a href="https://github.com/DeterminateSystems/magic-nix-cache-action/commit/0cc1effd9c8fdc788f6719ca5a0417c1d189c0fb"><code>0cc1eff</code></a> Set the default flakehub-flake-name to an empty string</li> <li><a href="https://github.com/DeterminateSystems/magic-nix-cache-action/commit/15226c9b1e255d12f1e3077e7e5581b1e231ba19"><code>15226c9</code></a> Merge pull request <a href="https://redirect.github.com/determinatesystems/magic-nix-cache-action/issues/50">#50</a> from DeterminateSystems/update-deps</li> <li><a href="https://github.com/DeterminateSystems/magic-nix-cache-action/commit/bcff3c6c1ee04e13727a4da6baaa5544dd6a2703"><code>bcff3c6</code></a> Update deps</li> <li><a href="https://github.com/DeterminateSystems/magic-nix-cache-action/commit/88b25d24b9baff729576a7c81163e8684b6feb9e"><code>88b25d2</code></a> Merge pull request <a href="https://redirect.github.com/determinatesystems/magic-nix-cache-action/issues/49">#49</a> from DeterminateSystems/late-start</li> <li><a href="https://github.com/DeterminateSystems/magic-nix-cache-action/commit/ae50b12a7d781ddd0d1a460462ef98489bbd3fdc"><code>ae50b12</code></a> Set saved state later</li> <li><a href="https://github.com/DeterminateSystems/magic-nix-cache-action/commit/5a8a0e7f2cf0a2bc1f0af8520fce28c3feb68157"><code>5a8a0e7</code></a> Don't mark the daemon started until after we successfully import the closure</li> <li><a href="https://github.com/DeterminateSystems/magic-nix-cache-action/commit/c9cb2a2a7ff5cc54ee79ff176e3d01dc8bf10824"><code>c9cb2a2</code></a> Merge pull request <a href="https://redirect.github.com/determinatesystems/magic-nix-cache-action/issues/48">#48</a> from DeterminateSystems/double-action</li> <li><a href="https://github.com/DeterminateSystems/magic-nix-cache-action/commit/c4a0b3111a3cb49f947c2080191486fe18293caa"><code>c4a0b31</code></a> Move noop check to main</li> <li><a href="https://github.com/DeterminateSystems/magic-nix-cache-action/commit/f6084a76d342b5f3b063438421bb4892f35fe087"><code>f6084a7</code></a> Dedupe text</li> <li>Additional commits viewable in <a href="https://github.com/determinatesystems/magic-nix-cache-action/compare/v4...v6">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] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…h into provide_name_on_sig
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
ctb
changed the title
--name to sig intersect and sig subtract--set-name to sig intersect and sig subtract
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ready for review @sourmash-bio/devs ! |
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Note: PR into #3161
This PR cleans up and regularizes naming output on
sigsubcommands. Specifically, it:--set-nametosig intersectandsig subtractto set names on output signatures.sig inflate,sig filter,sig downsample, andsig flatten--nameto--set-nameonsig merge, and nominates--namefor deprecation and removal on v5--nameonsig extract,sig filter, andsig flattenfor deprecation and removal on v5--nameonsketch dna,sketch protein, andsketch translate- refsketch...--nameis not documented in CLI help #3152Fixes #1801
Fixes #3152
Related issues:
--nameonsigsubcommands #3173