[MRG] remove lingering uses of sourmash_lib #626

ctb · 2019-01-12T16:18:32Z

This completes the removal of sourmash_lib from within the codebase. Among other things, it was causing some trouble with running tests, because test_lca.py was importing sourmash_lib and thus borking the proper type identification of objects in sbtmh.py (...don't ask).

Is it mergeable?
make test Did it pass the tests?
make coverage Is the new code covered?
Did it change the command-line interface? Only additions are allowed
without a major version increment. Changing file formats also requires a
major version number increment.
Was a spellchecker run on the source code and documentation after
changes were made?

codecov · 2019-01-12T16:24:01Z

Codecov Report

Merging #626 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #626   +/-   ##
=======================================
  Coverage   89.44%   89.44%           
=======================================
  Files          27       27           
  Lines        4227     4227           
  Branches       39       39           
=======================================
  Hits         3781     3781           
  Misses        446      446

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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>  </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://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://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://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://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`. [//]: # (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>

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>6.0.0 (2024-10-29)</h2> <ul> <li>Updated various documentation inaccuracies, especially on subprocess handling.</li> <li>Changed fail under checks to use the precision set in the coverage configuration. Now it will perform the check just like <code>coverage report</code> would.</li> <li>Added a <code>--cov-precision</code> cli option that can override the value set in your coverage configuration.</li> <li>Dropped support for now EOL Python 3.8.</li> </ul> <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><code>--cov-fail-under</code> no longer causes <code>pytest --collect-only</code> to fail</li> </ul>  </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/95404375a0e436178e012e20b8865c23c54c8a50"><code>9540437</code></a> Bump version: 5.0.0 → 6.0.0</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/9f8175467afc67db9001fb364ad1f2dfe79b51f1"><code>9f81754</code></a> Further trim down envs and drop Python 3.8.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/b12b5ec65da4c66bbc0c35918957f9f875f465c3"><code>b12b5ec</code></a> Update conf.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/23f4b27b432a54fcc3b6df7363f0e73e568233fb"><code>23f4b27</code></a> Update changelog.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/291a04f49566054bb19644aba27c3799ac8b7f42"><code>291a04f</code></a> Bump test deps and trim config.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/08f1101455ba293dda388fdb3b61e62fd95a827d"><code>08f1101</code></a> Add <code>--cov-precision</code> option. Close <a href="https://github.com/pytest-dev/pytest-cov/issues/655">#655</a>.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/76fe2a7e48e5c9c53644994c5ba5a421c84286f5"><code>76fe2a7</code></a> Move the warnings/errors in a place that doesn't import anything.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/a9ea7b71711479d4c5ccc5e21e2eb1694b259cb0"><code>a9ea7b7</code></a> Implement error/warning for the bad dynamic_context being set in config.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/c299e01b6422284a6a7f7322e6b9bf8f44aa3c25"><code>c299e01</code></a> Add explicit suffixing to make it easier to see the identify the sources/usag...</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/c87e54643ef696ed2b0e2b9a4209581da8467fcb"><code>c87e546</code></a> Add reproducer for weird xdist dynamic_context interaction. Ref <a href="https://github.com/pytest-dev/pytest-cov/issues/604">#604</a>.</li> <li>Additional commits viewable in <a href="https://github.com/pytest-dev/pytest-cov/compare/v4.0.0...v6.0.0">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 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>

remove lingering uses of sourmash_lib

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Merge branch 'master' into fix/sourmash_lib

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luizirber approved these changes Jan 13, 2019

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Merge branch 'master' into fix/sourmash_lib

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ctb merged commit 21d225f into master Jan 13, 2019

ctb deleted the fix/sourmash_lib branch January 13, 2019 17:09

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[MRG] remove lingering uses of sourmash_lib #626

[MRG] remove lingering uses of sourmash_lib #626

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[MRG] remove lingering uses of sourmash_lib #626

[MRG] remove lingering uses of sourmash_lib #626

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