consider adding dendrogram clustering/cut code into sourmash #459
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Ref #469 too. |
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cluster and cocluster #700 |
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Oct 28, 2022
Updates the requirements on [pytest-cov](https://github.com/pytest-dev/pytest-cov) to permit the latest version. <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst">pytest-cov's changelog</a>.</em></p> <blockquote> <h2>4.0.0 (2022-09-28)</h2> <p><strong>Note that this release drops support for multiprocessing.</strong></p> <ul> <li> <p><code>--cov-fail-under</code> no longer causes <code>pytest --collect-only</code> to fail Contributed by Zac Hatfield-Dodds in <code>[#511](pytest-dev/pytest-cov#511) <https://github.com/pytest-dev/pytest-cov/pull/511></code>_.</p> </li> <li> <p>Dropped support for multiprocessing (mostly because <code>issue 82408 <https://github.com/python/cpython/issues/82408></code>_). This feature was mostly working but very broken in certain scenarios and made the test suite very flaky and slow.</p> <p>There is builtin multiprocessing support in coverage and you can migrate to that. All you need is this in your <code>.coveragerc</code>::</p> <p>[run] concurrency = multiprocessing parallel = true sigterm = true</p> </li> <li> <p>Fixed deprecation in <code>setup.py</code> by trying to import setuptools before distutils. Contributed by Ben Greiner in <code>[#545](pytest-dev/pytest-cov#545) <https://github.com/pytest-dev/pytest-cov/pull/545></code>_.</p> </li> <li> <p>Removed undesirable new lines that were displayed while reporting was disabled. Contributed by Delgan in <code>[#540](pytest-dev/pytest-cov#540) <https://github.com/pytest-dev/pytest-cov/pull/540></code>_.</p> </li> <li> <p>Documentation fixes. Contributed by Andre Brisco in <code>[#543](pytest-dev/pytest-cov#543) <https://github.com/pytest-dev/pytest-cov/pull/543></code>_ and Colin O'Dell in <code>[#525](pytest-dev/pytest-cov#525) <https://github.com/pytest-dev/pytest-cov/pull/525></code>_.</p> </li> <li> <p>Added support for LCOV output format via <code>--cov-report=lcov</code>. Only works with coverage 6.3+. Contributed by Christian Fetzer in <code>[#536](pytest-dev/pytest-cov#536) <https://github.com/pytest-dev/pytest-cov/issues/536></code>_.</p> </li> <li> <p>Modernized pytest hook implementation. Contributed by Bruno Oliveira in <code>[#549](pytest-dev/pytest-cov#549) <https://github.com/pytest-dev/pytest-cov/pull/549></code>_ and Ronny Pfannschmidt in <code>[#550](pytest-dev/pytest-cov#550) <https://github.com/pytest-dev/pytest-cov/pull/550></code>_.</p> </li> </ul> <h2>3.0.0 (2021-10-04)</h2> <p><strong>Note that this release drops support for Python 2.7 and Python 3.5.</strong></p> <ul> <li>Added support for Python 3.10 and updated various test dependencies. Contributed by Hugo van Kemenade in <code>[#500](pytest-dev/pytest-cov#500) <https://github.com/pytest-dev/pytest-cov/pull/500></code>_.</li> <li>Switched from Travis CI to GitHub Actions. Contributed by Hugo van Kemenade in <code>[#494](pytest-dev/pytest-cov#494) <https://github.com/pytest-dev/pytest-cov/pull/494></code>_ and <code>[#495](pytest-dev/pytest-cov#495) <https://github.com/pytest-dev/pytest-cov/pull/495></code>_.</li> <li>Add a <code>--cov-reset</code> CLI option. Contributed by Danilo Šegan in <code>[#459](pytest-dev/pytest-cov#459) <https://github.com/pytest-dev/pytest-cov/pull/459></code>_.</li> <li>Improved validation of <code>--cov-fail-under</code> CLI option. Contributed by ... Ronny Pfannschmidt's desire for skark in <code>[#480](pytest-dev/pytest-cov#480) <https://github.com/pytest-dev/pytest-cov/pull/480></code>_.</li> <li>Dropped Python 2.7 support.</li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/28db055bebbf3ee016a2144c8b69dd7b80b48cc5"><code>28db055</code></a> Bump version: 3.0.0 → 4.0.0</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/57e9354a86f658556fe6f15f07625c4b9a9ddf53"><code>57e9354</code></a> Really update the changelog.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/56b810b91c9ae15d1462633c6a8a1b522ebf8e65"><code>56b810b</code></a> Update chagelog.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/f7fced579e36b72b57e14768026467e4c4511a40"><code>f7fced5</code></a> Add support for LCOV output</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/1211d3134bb74abb7b00c3c2209091aaab440417"><code>1211d31</code></a> Fix flake8 error</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/b077753f5d9d200815fe500d0ef23e306784e65b"><code>b077753</code></a> Use modern approach to specify hook options</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/00713b3fec90cb8c98a9e4bfb3212e574c08e67b"><code>00713b3</code></a> removed incorrect docs on <code>data_file</code>.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/b3dda36fddd3ca75689bb3645cd320aa8392aaf3"><code>b3dda36</code></a> Improve workflow with a collecting status check. (<a href="https://github-redirect.dependabot.com/pytest-dev/pytest-cov/issues/548">#548</a>)</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/218419f665229d61356f1eea3ddc8e18aa21f87c"><code>218419f</code></a> Prevent undesirable new lines to be displayed when report is disabled</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/60b73ec673c60942a3cf052ee8a1fdc442840558"><code>60b73ec</code></a> migrate build command from distutils to setuptools</li> <li>Additional commits viewable in <a href="https://github.com/pytest-dev/pytest-cov/compare/v2.12.0...v4.0.0">compare view</a></li> </ul> </details> <br /> 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>
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see sourmash_plugin_betterplot for some functioning command-line code. |
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the dendrogram annotation, display, and cut code here is proving to be both robust and useful; should probably just add it in to base sourmash.
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