Simplified implementation of label_annotations.#641
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jesper-friis merged 3 commits intoget_by_label_ni_imported_ontologiesfrom Aug 23, 2023
Merged
Simplified implementation of label_annotations.#641jesper-friis merged 3 commits intoget_by_label_ni_imported_ontologiesfrom
jesper-friis merged 3 commits intoget_by_label_ni_imported_ontologiesfrom
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## get_by_label_ni_imported_ontologies #641 +/- ##
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Coverage ? 68.32%
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Files ? 16
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francescalb
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francescalb
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Approved - this is a PR into another devlopemnt branch. The docstring error can be fixed there.
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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>7.1.0 (2026-03-21)</h2> <ul> <li> <p>Fixed total coverage computation to always be consistent, regardless of reporting settings. Previously some reports could produce different total counts, and consequently can make --cov-fail-under behave different depending on reporting options. See <code>[#641](pytest-dev/pytest-cov#641) <https://github.com/pytest-dev/pytest-cov/issues/641></code>_.</p> </li> <li> <p>Improve handling of ResourceWarning from sqlite3.</p> <p>The plugin adds warning filter for sqlite3 <code>ResourceWarning</code> unclosed database (since 6.2.0). It checks if there is already existing plugin for this message by comparing filter regular expression. When filter is specified on command line the message is escaped and does not match an expected message. A check for an escaped regular expression is added to handle this case.</p> <p>With this fix one can suppress <code>ResourceWarning</code> from sqlite3 from command line::</p> <p>pytest -W "ignore:unclosed database in <sqlite3.Connection object at:ResourceWarning" ...</p> </li> <li> <p>Various improvements to documentation. Contributed by Art Pelling in <code>[#718](pytest-dev/pytest-cov#718) <https://github.com/pytest-dev/pytest-cov/pull/718></code>_ and "vivodi" in <code>[#738](pytest-dev/pytest-cov#738) <https://github.com/pytest-dev/pytest-cov/pull/738></code><em>. Also closed <code>[#736](pytest-dev/pytest-cov#736) <https://github.com/pytest-dev/pytest-cov/issues/736></code></em>.</p> </li> <li> <p>Fixed some assertions in tests. Contributed by in Markéta Machová in <code>[#722](pytest-dev/pytest-cov#722) <https://github.com/pytest-dev/pytest-cov/pull/722></code>_.</p> </li> <li> <p>Removed unnecessary coverage configuration copying (meant as a backup because reporting commands had configuration side-effects before coverage 5.0).</p> </li> </ul> <h2>7.0.0 (2025-09-09)</h2> <ul> <li> <p>Dropped support for subprocesses measurement.</p> <p>It was a feature added long time ago when coverage lacked a nice way to measure subprocesses created in tests. It relied on a <code>.pth</code> file, there was no way to opt-out and it created bad interations with <code>coverage's new patch system <https://coverage.readthedocs.io/en/latest/config.html#run-patch></code>_ added in <code>7.10 <https://coverage.readthedocs.io/en/7.10.6/changes.html#version-7-10-0-2025-07-24></code>_.</p> <p>To migrate to this release you might need to enable the suprocess patch, example for <code>.coveragerc</code>:</p> <p>.. code-block:: ini</p> <p>[run] patch = subprocess</p> <p>This release also requires at least coverage 7.10.6.</p> </li> <li> <p>Switched packaging to have metadata completely in <code>pyproject.toml</code> and use <code>hatchling <https://pypi.org/project/hatchling/></code>_ for building. Contributed by Ofek Lev in <code>[#551](pytest-dev/pytest-cov#551) <https://github.com/pytest-dev/pytest-cov/pull/551></code>_ with some extras in <code>[#716](pytest-dev/pytest-cov#716) <https://github.com/pytest-dev/pytest-cov/pull/716></code>_.</p> </li> <li> <p>Removed some not really necessary testing deps like <code>six</code>.</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/66c8a526b1246b5eb8fb1bc218878131bc628622"><code>66c8a52</code></a> Bump version: 7.0.0 → 7.1.0</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/f7076624784332594aa4cb3585d4757d295db15e"><code>f707662</code></a> Make the examples use pypy 3.11.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/6049a7847872e3139e6c82e93787123df5dc8672"><code>6049a78</code></a> Make context test use the old ctracer (seems the new sysmon tracer behaves di...</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/8ebf20bbbc73478b3f8fd36d30237d9ea083f06b"><code>8ebf20b</code></a> Update changelog.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/861d30e60d571f97259c6b718b71c819d5dbc3b9"><code>861d30e</code></a> Remove the backup context manager - shouldn't be needed since coverage 5.0, ...</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/fd4c956014035527f0c3c8d7faef3f8cfdadac7f"><code>fd4c956</code></a> Pass the precision on the nulled total (seems that there's some caching goion...</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/78c9c4ecb005faf4962fd86ff7bf9c9cce9554d6"><code>78c9c4e</code></a> Only run the 3.9 on older deps.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/4849a922e8be725c662a3d9175da571ace6545dc"><code>4849a92</code></a> Punctuation.</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/197c35e2f37031fd1927715307ab6eed7cb3d2b7"><code>197c35e</code></a> Update changelog and hopefully I don't forget to publish release again :))</li> <li><a href="https://github.com/pytest-dev/pytest-cov/commit/14dc1c92d44108384e39803888635fdbfc578b7f"><code>14dc1c9</code></a> Update examples to use 3.11 and make the adhoc layout example look a bit more...</li> <li>Additional commits viewable in <a href="https://github.com/pytest-dev/pytest-cov/compare/v7.0.0...v7.1.0">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 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>
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Description
Simplified the implementation of
label_annotations. Thelabel_annotationsproperty is now a list of full IRI's to label annotations that will be used byget_by_label()given that the IRI is in the world of the ontology.Hence, if the ontology doesn't define
skos:prefLabelit will not be used byget_by_label()even though that "http://www.w3.org/2004/02/skos/core#prefLabel" may be included inonto.label_annotations.I think this make things behave as expected in common cases without the user having to fickle with
label_annotations.The label annotations that are currently used by
get_by_label()can be listed withI also deprecated some functions that I only think increases the complexity without providing any real value.
See also comments IN CAPITALS. They should be removed before merging to master.
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