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consider adding dendrogram clustering/cut code into sourmash #459

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ctb opened this issue Mar 21, 2018 · 3 comments
Open

consider adding dendrogram clustering/cut code into sourmash #459

ctb opened this issue Mar 21, 2018 · 3 comments
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@ctb
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ctb commented Mar 21, 2018

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.
@ctb ctb mentioned this issue Jul 20, 2019
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ctb commented Apr 4, 2020

Ref #469 too.

@ctb ctb changed the title add dendrogram clustering/cut code into sourmash consider adding dendrogram clustering/cut code into sourmash Jan 10, 2021
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ctb commented Mar 4, 2021

cluster and cocluster #700

ctb pushed a commit that referenced this issue Oct 28, 2022
@dependabot
Update pytest-cov requirement from <4.0,>=2.12 to >=2.12,<5.0 (#2346)
4dc2ef4 
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)
&lt;https://github.com/pytest-dev/pytest-cov/pull/511&gt;</code>_.</p>
</li>
<li>
<p>Dropped support for multiprocessing (mostly because <code>issue 82408
&lt;https://github.com/python/cpython/issues/82408&gt;</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)
&lt;https://github.com/pytest-dev/pytest-cov/pull/545&gt;</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)
&lt;https://github.com/pytest-dev/pytest-cov/pull/540&gt;</code>_.</p>
</li>
<li>
<p>Documentation fixes.
Contributed by Andre Brisco in
<code>[#543](pytest-dev/pytest-cov#543)
&lt;https://github.com/pytest-dev/pytest-cov/pull/543&gt;</code>_
and Colin O'Dell in
<code>[#525](pytest-dev/pytest-cov#525)
&lt;https://github.com/pytest-dev/pytest-cov/pull/525&gt;</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)
&lt;https://github.com/pytest-dev/pytest-cov/issues/536&gt;</code>_.</p>
</li>
<li>
<p>Modernized pytest hook implementation.
Contributed by Bruno Oliveira in
<code>[#549](pytest-dev/pytest-cov#549)
&lt;https://github.com/pytest-dev/pytest-cov/pull/549&gt;</code>_
and Ronny Pfannschmidt in
<code>[#550](pytest-dev/pytest-cov#550)
&lt;https://github.com/pytest-dev/pytest-cov/pull/550&gt;</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)
&lt;https://github.com/pytest-dev/pytest-cov/pull/500&gt;</code>_.</li>
<li>Switched from Travis CI to GitHub Actions. Contributed by Hugo van
Kemenade in
<code>[#494](pytest-dev/pytest-cov#494)
&lt;https://github.com/pytest-dev/pytest-cov/pull/494&gt;</code>_ and
<code>[#495](pytest-dev/pytest-cov#495)
&lt;https://github.com/pytest-dev/pytest-cov/pull/495&gt;</code>_.</li>
<li>Add a <code>--cov-reset</code> CLI option.
Contributed by Danilo Šegan in
<code>[#459](pytest-dev/pytest-cov#459)
&lt;https://github.com/pytest-dev/pytest-cov/pull/459&gt;</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)
&lt;https://github.com/pytest-dev/pytest-cov/pull/480&gt;</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 />


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@ctb ctb mentioned this issue Jul 31, 2023
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@ctb ctb added the plugin_todo Write a plugin for this! label Sep 23, 2023
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ctb commented May 17, 2024

see sourmash_plugin_betterplot for some functioning command-line code.

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