it is really unclear as to how to actually cite sourmash #511
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There are now instructions in README.md and on the main page, and a CITATION.cff file. I still think we should provide guidance tho - how about, Suggestion: |
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Updating over in #837. |
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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`. 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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 <bluegenes@users.noreply.github.com> Co-authored-by: N. Tessa Pierce-Ward <ntpierce@gmail.com> Co-authored-by: Katrin Leinweber <9948149+katrinleinweber@users.noreply.github.com>
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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>5.0.0 (2024-03-24)</h2> <ul> <li>Removed support for xdist rsync (now deprecated). Contributed by Matthias Reichenbach in <code>[#623](pytest-dev/pytest-cov#623) <https://github.com/pytest-dev/pytest-cov/pull/623></code>_.</li> <li>Switched docs theme to Furo.</li> <li>Various legacy Python cleanup and CI improvements. Contributed by Christian Clauss and Hugo van Kemenade in <code>[#630](pytest-dev/pytest-cov#630) <https://github.com/pytest-dev/pytest-cov/pull/630></code><em>, <code>[#631](pytest-dev/pytest-cov#631) <https://github.com/pytest-dev/pytest-cov/pull/631></code></em>, <code>[#632](pytest-dev/pytest-cov#632) <https://github.com/pytest-dev/pytest-cov/pull/632></code>_ and <code>[#633](pytest-dev/pytest-cov#633) <https://github.com/pytest-dev/pytest-cov/pull/633></code>_.</li> <li>Added a <code>pyproject.toml</code> example in the docs. Contributed by Dawn James in <code>[#626](pytest-dev/pytest-cov#626) <https://github.com/pytest-dev/pytest-cov/pull/626></code>_.</li> <li>Modernized project's pre-commit hooks to use ruff. Initial POC contributed by Christian Clauss in <code>[#584](pytest-dev/pytest-cov#584) <https://github.com/pytest-dev/pytest-cov/pull/584></code>_.</li> </ul> <h2>4.1.0 (2023-05-24)</h2> <ul> <li>Updated CI with new Pythons and dependencies.</li> <li>Removed rsyncdir support. This makes pytest-cov compatible with xdist 3.0. Contributed by Sorin Sbarnea in <code>[#558](pytest-dev/pytest-cov#558) <https://github.com/pytest-dev/pytest-cov/pull/558></code>_.</li> <li>Optimized summary generation to not be performed if no reporting is active (for example, when <code>--cov-report=''</code> is used without <code>--cov-fail-under</code>). Contributed by Jonathan Stewmon in <code>[#589](pytest-dev/pytest-cov#589) <https://github.com/pytest-dev/pytest-cov/pull/589></code>_.</li> <li>Added support for JSON reporting. Contributed by Matthew Gamble in <code>[#582](pytest-dev/pytest-cov#582) <https://github.com/pytest-dev/pytest-cov/pull/582></code>_.</li> <li>Refactored code to use f-strings. Contributed by Mark Mayo in <code>[#572](pytest-dev/pytest-cov#572) <https://github.com/pytest-dev/pytest-cov/pull/572></code>_.</li> <li>Fixed a skip in the test suite for some old xdist. Contributed by a bunch of people in <code>[#565](pytest-dev/pytest-cov#565) <https://github.com/pytest-dev/pytest-cov/pull/565></code>_.</li> </ul> <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</p> </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/5295ce01c84262cec88f31255e9ac538718f3047"><code>5295ce0</code></a> Bump version: 4.1.0 → 5.0.0</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/1181b067972bf94569f8011f3b18f271690f9ab1"><code>1181b06</code></a> Update changelog.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/9757222e2e044361e70125ebdd96e5eb87395983"><code>9757222</code></a> Fix a minor grammar error (<a href="https://redirect.github.com/pytest-dev/pytest-cov/issues/636">#636</a>)</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/9f5cd81a0dbe3fe41681efdbef516c08988fe8ff"><code>9f5cd81</code></a> Cleanup releasing instructions. Closes <a href="https://redirect.github.com/pytest-dev/pytest-cov/issues/616">#616</a>.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/93b5047ec5050d63c10a6fe16a09b671a7a03df8"><code>93b5047</code></a> Add test for pyproject.toml loading without explicit --cov-config. Ref <a href="https://redirect.github.com/pytest-dev/pytest-cov/issues/508">#508</a>.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/ff50860d7c67b920503745d92a3f0944cf41f982"><code>ff50860</code></a> docs: add config instructions for pyproject.toml.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/4a5a4b5fa4b1c63ddcab5cbc1813798c9b6f1d36"><code>4a5a4b5</code></a> Keep GitHub Actions up to date with GitHub's Dependabot</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/1d7f55963d5138f41c452a946f7cca7e0b6ee8b2"><code>1d7f559</code></a> Fix or remove URLs that are causing docs tests to fail</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/6a5af8e85b8242ac815f33e26adf9068f5f0ebc3"><code>6a5af8e</code></a> Update changelog.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/d9fe8dfed15023d3410dd299c5092e755b8981c2"><code>d9fe8df</code></a> Switch to furo. Closes <a href="https://redirect.github.com/pytest-dev/pytest-cov/issues/618">#618</a>.</li> <li>Additional commits viewable in <a href="https://github.com/pytest-dev/pytest-cov/compare/v4.0.0...v5.0.0">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`. 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someone should fix this.
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