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first contribution in <a\r\nhref=\"https://redirect.github.com/actions/cache/pull/1284\">actions/cache#1284</a></li>\r\n<li><a href=\"https://github.com/to-s\"><code>@​to-s</code></a> made their\r\nfirst contribution in <a\r\nhref=\"https://redirect.github.com/actions/cache/pull/1242\">actions/cache#1242</a></li>\r\n</ul>\r\n<p><strong>Full Changelog</strong>: <a\r\nhref=\"https://github.com/actions/cache/compare/v3...v4.0.0\">https://github.com/actions/cache/compare/v3...v4.0.0</a></p>\r\n<h2>v3.3.3</h2>\r\n<h2>What's Changed</h2>\r\n<ul>\r\n<li>Cache v3.3.3 by <a\r\nhref=\"https://github.com/robherley\"><code>@​robherley</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/cache/pull/1302\">actions/cache#1302</a></li>\r\n</ul>\r\n<h2>New Contributors</h2>\r\n<ul>\r\n<li><a href=\"https://github.com/robherley\"><code>@​robherley</code></a>\r\nmade their first contribution in <a\r\nhref=\"https://redirect.github.com/actions/cache/pull/1302\">actions/cache#1302</a></li>\r\n</ul>\r\n<p><strong>Full Changelog</strong>: <a\r\nhref=\"https://github.com/actions/cache/compare/v3...v3.3.3\">https://github.com/actions/cache/compare/v3...v3.3.3</a></p>\r\n<h2>v3.3.2</h2>\r\n<h2>What's Changed</h2>\r\n<ul>\r\n<li>Fixed readme with new segment timeout values by <a\r\nhref=\"https://github.com/kotewar\"><code>@​kotewar</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/cache/pull/1133\">actions/cache#1133</a></li>\r\n<li>Readme fixes by <a\r\nhref=\"https://github.com/kotewar\"><code>@​kotewar</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/cache/pull/1134\">actions/cache#1134</a></li>\r\n<li>Updated description of the lookup-only input for main action by <a\r\nhref=\"https://github.com/kotewar\"><code>@​kotewar</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/cache/pull/1130\">actions/cache#1130</a></li>\r\n<li>Change two new actions mention as quoted text by <a\r\nhref=\"https://github.com/bishal-pdMSFT\"><code>@​bishal-pdMSFT</code></a>\r\nin <a\r\nhref=\"https://redirect.github.com/actions/cache/pull/1131\">actions/cache#1131</a></li>\r\n<li>Update Cross-OS Caching tips by <a\r\nhref=\"https://github.com/pdotl\"><code>@​pdotl</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/cache/pull/1122\">actions/cache#1122</a></li>\r\n<li>Bazel example (Take <a\r\nhref=\"https://redirect.github.com/actions/cache/issues/2\">#2</a>️⃣) by\r\n<a href=\"https://github.com/vorburger\"><code>@​vorburger</code></a> in\r\n<a\r\nhref=\"https://redirect.github.com/actions/cache/pull/1132\">actions/cache#1132</a></li>\r\n<li>Remove actions to add new PRs and issues to a project board by <a\r\nhref=\"https://github.com/jorendorff\"><code>@​jorendorff</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/cache/pull/1187\">actions/cache#1187</a></li>\r\n<li>Consume latest toolkit and fix dangling promise bug 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Changed</h2>\r\n<ul>\r\n<li>Bug: Permission is missing in cache delete example by <a\r\nhref=\"https://github.com/kotokaze\"><code>@​kotokaze</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/cache/pull/1123\">actions/cache#1123</a></li>\r\n</ul>\r\n<!-- raw HTML omitted -->\r\n</blockquote>\r\n<p>... (truncated)</p>\r\n</details>\r\n<details>\r\n<summary>Changelog</summary>\r\n<p><em>Sourced from <a\r\nhref=\"https://github.com/actions/cache/blob/main/RELEASES.md\">actions/cache's\r\nchangelog</a>.</em></p>\r\n<blockquote>\r\n<h1>Releases</h1>\r\n<h3>3.0.0</h3>\r\n<ul>\r\n<li>Updated minimum runner version support from node 12 -&gt; node\r\n16</li>\r\n</ul>\r\n<h3>3.0.1</h3>\r\n<ul>\r\n<li>Added support for caching from GHES 3.5.</li>\r\n<li>Fixed download issue for files &gt; 2GB during restore.</li>\r\n</ul>\r\n<h3>3.0.2</h3>\r\n<ul>\r\n<li>Added support for dynamic cache size cap on GHES.</li>\r\n</ul>\r\n<h3>3.0.3</h3>\r\n<ul>\r\n<li>Fixed avoiding empty cache save when no files are available for\r\ncaching. (<a\r\nhref=\"https://redirect.github.com/actions/cache/issues/624\">issue</a>)</li>\r\n</ul>\r\n<h3>3.0.4</h3>\r\n<ul>\r\n<li>Fixed tar creation error while trying to create tar with path as\r\n<code>~/</code> home folder on <code>ubuntu-latest</code>. 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(truncated)</p>\r\n</details>\r\n<details>\r\n<summary>Commits</summary>\r\n<ul>\r\n<li><a\r\nhref=\"https://github.com/actions/cache/commit/13aacd865c20de90d75de3b17ebe84f7a17d57d2\"><code>13aacd8</code></a>\r\nMerge pull request <a\r\nhref=\"https://redirect.github.com/actions/cache/issues/1242\">#1242</a>\r\nfrom to-s/main</li>\r\n<li><a\r\nhref=\"https://github.com/actions/cache/commit/53b35c543921fe2e8b288765ff817de9de8d906f\"><code>53b35c5</code></a>\r\nMerge branch 'main' into main</li>\r\n<li><a\r\nhref=\"https://github.com/actions/cache/commit/65b8989fab3bb394817bdb845a453dff480c2b51\"><code>65b8989</code></a>\r\nMerge pull request <a\r\nhref=\"https://redirect.github.com/actions/cache/issues/1284\">#1284</a>\r\nfrom takost/update-to-node-20</li>\r\n<li><a\r\nhref=\"https://github.com/actions/cache/commit/d0be34d54485f31ca2ccbe66e6ea3d96544a807b\"><code>d0be34d</code></a>\r\nFix dist</li>\r\n<li><a\r\nhref=\"https://github.com/actions/cache/commit/66cf064d47313d2cccf392d01bd10925da2bd072\"><code>66cf064</code></a>\r\nMerge branch 'main' into update-to-node-20</li>\r\n<li><a\r\nhref=\"https://github.com/actions/cache/commit/1326563738ddb735c5f2ce85cba8c79f33b728cd\"><code>1326563</code></a>\r\nMerge branch 'main' into main</li>\r\n<li><a\r\nhref=\"https://github.com/actions/cache/commit/e71876755e268d6cc25a5d3e3c46ae447e35290a\"><code>e718767</code></a>\r\nFix format</li>\r\n<li><a\r\nhref=\"https://github.com/actions/cache/commit/01229828ffa049a8dee4db27bcb23ed33f2b451f\"><code>0122982</code></a>\r\nApply workaround for earlyExit</li>\r\n<li><a\r\nhref=\"https://github.com/actions/cache/commit/3185ecfd6135856ca6d904ae032cff4f39b8b365\"><code>3185ecf</code></a>\r\nUpdate &quot;only-&quot; actions to node20</li>\r\n<li><a\r\nhref=\"https://github.com/actions/cache/commit/25618a0a675e8447e5ffc8ed9b7ddb2aaf927f65\"><code>25618a0</code></a>\r\nBump version</li>\r\n<li>Additional commits viewable in <a\r\nhref=\"https://github.com/actions/cache/compare/v3...v4\">compare\r\nview</a></li>\r\n</ul>\r\n</details>\r\n<br />\r\n\r\n\r\n[![Dependabot compatibility\r\nscore](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/cache&package-manager=github_actions&previous-version=3&new-version=4)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)\r\n\r\nDependabot will resolve any conflicts with this PR as long as you don't\r\nalter it yourself. You can also trigger a rebase manually by commenting\r\n`@dependabot rebase`.\r\n\r\n[//]: # (dependabot-automerge-start)\r\n[//]: # (dependabot-automerge-end)\r\n\r\n---\r\n\r\n<details>\r\n<summary>Dependabot commands and options</summary>\r\n<br />\r\n\r\nYou can trigger Dependabot actions by commenting on this PR:\r\n- `@dependabot rebase` will rebase this PR\r\n- `@dependabot recreate` will recreate this PR, overwriting any edits\r\nthat have been made to it\r\n- `@dependabot merge` will merge this PR after your CI passes on it\r\n- `@dependabot squash and merge` will squash and merge this PR after\r\nyour CI passes on it\r\n- `@dependabot cancel merge` will cancel a previously requested merge\r\nand block automerging\r\n- `@dependabot reopen` will reopen this PR if it is closed\r\n- `@dependabot close` will close this PR and stop Dependabot recreating\r\nit. You can achieve the same result by closing it manually\r\n- `@dependabot show <dependency name> ignore conditions` will show all\r\nof the ignore conditions of the specified dependency\r\n- `@dependabot ignore this major version` will close this PR and stop\r\nDependabot creating any more for this major version (unless you reopen\r\nthe PR or upgrade to it yourself)\r\n- `@dependabot ignore this minor version` will close this PR and stop\r\nDependabot creating any more for this minor version (unless you reopen\r\nthe PR or upgrade to it yourself)\r\n- `@dependabot ignore this dependency` will close this PR and stop\r\nDependabot creating any more for this dependency (unless you reopen the\r\nPR or upgrade to it yourself)\r\n\r\n\r\n</details>\r\n\r\nSigned-off-by: dependabot[bot] <support@github.com>\r\nCo-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>","shortMessageHtmlLink":"Bump actions/cache from 3 to 4 (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2087582164\" data-permission-text=\"Title is private\" data-url=\"https://github.com/dib-lab/screed/issues/109\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/dib-lab/screed/pull/109/hovercard\" href=\"https://github.com/dib-lab/screed/pull/109\">#109</a>)"}},{"before":null,"after":"c436d49810688559d486df98d81c2c50697a85d0","ref":"refs/heads/dependabot/github_actions/actions/cache-4","pushedAt":"2024-01-18T06:09:59.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"dependabot[bot]","name":null,"path":"/apps/dependabot","primaryAvatarUrl":"https://avatars.githubusercontent.com/in/29110?s=80&v=4"},"commit":{"message":"Bump actions/cache from 3 to 4\n\nBumps [actions/cache](https://github.com/actions/cache) from 3 to 4.\n- [Release notes](https://github.com/actions/cache/releases)\n- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)\n- [Commits](https://github.com/actions/cache/compare/v3...v4)\n\n---\nupdated-dependencies:\n- dependency-name: actions/cache\n  dependency-type: direct:production\n  update-type: version-update:semver-major\n...\n\nSigned-off-by: dependabot[bot] <support@github.com>","shortMessageHtmlLink":"Bump actions/cache from 3 to 4"}},{"before":"5b7dfbb4b17e1437d9b39be9452c5eb987d58c98","after":null,"ref":"refs/heads/dependabot/github_actions/actions/setup-python-5","pushedAt":"2023-12-07T14:22:34.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"ctb","name":"C. 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Changed</h2>\r\n<p>In scope of this release we added support for GraalPy (<a\r\nhref=\"https://redirect.github.com/actions/setup-python/pull/694\">actions/setup-python#694</a>).\r\nYou can use this snippet to set up GraalPy:</p>\r\n<pre lang=\"yaml\"><code>steps:\r\n- uses: actions/checkout@v4\r\n- uses: actions/setup-python@v4 \r\n  with:\r\n    python-version: 'graalpy-22.3' \r\n- run: python my_script.py\r\n</code></pre>\r\n<p>Besides, the release contains such changes as:</p>\r\n<ul>\r\n<li>Trim python version when reading from file by <a\r\nhref=\"https://github.com/FerranPares\"><code>@​FerranPares</code></a> in\r\n<a\r\nhref=\"https://redirect.github.com/actions/setup-python/pull/628\">actions/setup-python#628</a></li>\r\n<li>Use non-deprecated versions in examples by <a\r\nhref=\"https://github.com/jeffwidman\"><code>@​jeffwidman</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/setup-python/pull/724\">actions/setup-python#724</a></li>\r\n<li>Change deprecation comment to past tense by <a\r\nhref=\"https://github.com/jeffwidman\"><code>@​jeffwidman</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/setup-python/pull/723\">actions/setup-python#723</a></li>\r\n<li>Bump <code>@​babel/traverse</code> from 7.9.0 to 7.23.2 by <a\r\nhref=\"https://github.com/dependabot\"><code>@​dependabot</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/setup-python/pull/743\">actions/setup-python#743</a></li>\r\n<li>advanced-usage.md: Encourage the use actions/checkout@v4 by <a\r\nhref=\"https://github.com/cclauss\"><code>@​cclauss</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/setup-python/pull/729\">actions/setup-python#729</a></li>\r\n<li>Examples now use checkout@v4 by <a\r\nhref=\"https://github.com/simonw\"><code>@​simonw</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/setup-python/pull/738\">actions/setup-python#738</a></li>\r\n<li>Update actions/checkout to v4 by <a\r\nhref=\"https://github.com/dmitry-shibanov\"><code>@​dmitry-shibanov</code></a>\r\nin <a\r\nhref=\"https://redirect.github.com/actions/setup-python/pull/761\">actions/setup-python#761</a></li>\r\n</ul>\r\n<h2>New Contributors</h2>\r\n<ul>\r\n<li><a\r\nhref=\"https://github.com/FerranPares\"><code>@​FerranPares</code></a>\r\nmade their first contribution in <a\r\nhref=\"https://redirect.github.com/actions/setup-python/pull/628\">actions/setup-python#628</a></li>\r\n<li><a href=\"https://github.com/timfel\"><code>@​timfel</code></a> made\r\ntheir first contribution in <a\r\nhref=\"https://redirect.github.com/actions/setup-python/pull/694\">actions/setup-python#694</a></li>\r\n<li><a\r\nhref=\"https://github.com/jeffwidman\"><code>@​jeffwidman</code></a> made\r\ntheir first contribution in <a\r\nhref=\"https://redirect.github.com/actions/setup-python/pull/724\">actions/setup-python#724</a></li>\r\n</ul>\r\n<p><strong>Full Changelog</strong>: <a\r\nhref=\"https://github.com/actions/setup-python/compare/v4...v4.8.0\">https://github.com/actions/setup-python/compare/v4...v4.8.0</a></p>\r\n<h2>v4.7.1</h2>\r\n<h2>What's Changed</h2>\r\n<ul>\r\n<li>Bump word-wrap from 1.2.3 to 1.2.4 by <a\r\nhref=\"https://github.com/dependabot\"><code>@​dependabot</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/setup-python/pull/702\">actions/setup-python#702</a></li>\r\n<li>Add range validation for toml files by <a\r\nhref=\"https://github.com/dmitry-shibanov\"><code>@​dmitry-shibanov</code></a>\r\nin <a\r\nhref=\"https://redirect.github.com/actions/setup-python/pull/726\">actions/setup-python#726</a></li>\r\n</ul>\r\n<p><strong>Full Changelog</strong>: <a\r\nhref=\"https://github.com/actions/setup-python/compare/v4...v4.7.1\">https://github.com/actions/setup-python/compare/v4...v4.7.1</a></p>\r\n<h2>v4.7.0</h2>\r\n<p>In scope of this release, the support for reading python version from\r\npyproject.toml was added (<a\r\nhref=\"https://redirect.github.com/actions/setup-python/pull/669\">actions/setup-python#669</a>).</p>\r\n<pre lang=\"yaml\"><code>      - name: Setup Python\r\n        uses: actions/setup-python@v4\r\n&lt;/tr&gt;&lt;/table&gt; \r\n</code></pre>\r\n</blockquote>\r\n<p>... (truncated)</p>\r\n</details>\r\n<details>\r\n<summary>Commits</summary>\r\n<ul>\r\n<li><a\r\nhref=\"https://github.com/actions/setup-python/commit/0a5c61591373683505ea898e09a3ea4f39ef2b9c\"><code>0a5c615</code></a>\r\nUpdate action to node20 (<a\r\nhref=\"https://redirect.github.com/actions/setup-python/issues/772\">#772</a>)</li>\r\n<li><a\r\nhref=\"https://github.com/actions/setup-python/commit/0ae58361cdfd39e2950bed97a1e26aa20c3d8955\"><code>0ae5836</code></a>\r\nAdd example of GraalPy to docs (<a\r\nhref=\"https://redirect.github.com/actions/setup-python/issues/773\">#773</a>)</li>\r\n<li><a\r\nhref=\"https://github.com/actions/setup-python/commit/b64ffcaf5b410884ad320a9cfac8866006a109aa\"><code>b64ffca</code></a>\r\nupdate actions/checkout to v4 (<a\r\nhref=\"https://redirect.github.com/actions/setup-python/issues/761\">#761</a>)</li>\r\n<li><a\r\nhref=\"https://github.com/actions/setup-python/commit/8d2896179abf658742de432b3f203d2c2d86a587\"><code>8d28961</code></a>\r\nExamples now use checkout@v4 (<a\r\nhref=\"https://redirect.github.com/actions/setup-python/issues/738\">#738</a>)</li>\r\n<li><a\r\nhref=\"https://github.com/actions/setup-python/commit/7bc6abb01e0555719edc2dbca70a2fde309e5e56\"><code>7bc6abb</code></a>\r\nadvanced-usage.md: Encourage the use actions/checkout@v4 (<a\r\nhref=\"https://redirect.github.com/actions/setup-python/issues/729\">#729</a>)</li>\r\n<li><a\r\nhref=\"https://github.com/actions/setup-python/commit/e8111cec9d3dc15220d8a3b638f08419f57b906a\"><code>e8111ce</code></a>\r\nBump <code>@​babel/traverse</code> from 7.9.0 to 7.23.2 (<a\r\nhref=\"https://redirect.github.com/actions/setup-python/issues/743\">#743</a>)</li>\r\n<li><a\r\nhref=\"https://github.com/actions/setup-python/commit/a00ea43da65e7c04d2bdae58b3afecd77057eb9e\"><code>a00ea43</code></a>\r\nadd fix for graalpy ci (<a\r\nhref=\"https://redirect.github.com/actions/setup-python/issues/741\">#741</a>)</li>\r\n<li><a\r\nhref=\"https://github.com/actions/setup-python/commit/8635b1ccc5934e73ed3510980fd2e7790b85839b\"><code>8635b1c</code></a>\r\nChange deprecation comment to past tense (<a\r\nhref=\"https://redirect.github.com/actions/setup-python/issues/723\">#723</a>)</li>\r\n<li><a\r\nhref=\"https://github.com/actions/setup-python/commit/f6cc428f535856f9c23558d01765a42a4d6cf758\"><code>f6cc428</code></a>\r\nUse non-deprecated versions in examples (<a\r\nhref=\"https://redirect.github.com/actions/setup-python/issues/724\">#724</a>)</li>\r\n<li><a\r\nhref=\"https://github.com/actions/setup-python/commit/5f2af211d616f86005883b44826180b21abb4060\"><code>5f2af21</code></a>\r\nAdd GraalPy support (<a\r\nhref=\"https://redirect.github.com/actions/setup-python/issues/694\">#694</a>)</li>\r\n<li>Additional commits viewable in <a\r\nhref=\"https://github.com/actions/setup-python/compare/v4...v5\">compare\r\nview</a></li>\r\n</ul>\r\n</details>\r\n<br />\r\n\r\n\r\n[![Dependabot compatibility\r\nscore](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/setup-python&package-manager=github_actions&previous-version=4&new-version=5)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)\r\n\r\nDependabot will resolve any conflicts with this PR as long as you don't\r\nalter it yourself. You can also trigger a rebase manually by commenting\r\n`@dependabot rebase`.\r\n\r\n[//]: # (dependabot-automerge-start)\r\n[//]: # (dependabot-automerge-end)\r\n\r\n---\r\n\r\n<details>\r\n<summary>Dependabot commands and options</summary>\r\n<br />\r\n\r\nYou can trigger Dependabot actions by commenting on this PR:\r\n- `@dependabot rebase` will rebase this PR\r\n- `@dependabot recreate` will recreate this PR, overwriting any edits\r\nthat have been made to it\r\n- `@dependabot merge` will merge this PR after your CI passes on it\r\n- `@dependabot squash and merge` will squash and merge this PR after\r\nyour CI passes on it\r\n- `@dependabot cancel merge` will cancel a previously requested merge\r\nand block automerging\r\n- `@dependabot reopen` will reopen this PR if it is closed\r\n- `@dependabot close` will close this PR and stop Dependabot recreating\r\nit. You can achieve the same result by closing it manually\r\n- `@dependabot show <dependency name> ignore conditions` will show all\r\nof the ignore conditions of the specified dependency\r\n- `@dependabot ignore this major version` will close this PR and stop\r\nDependabot creating any more for this major version (unless you reopen\r\nthe PR or upgrade to it yourself)\r\n- `@dependabot ignore this minor version` will close this PR and stop\r\nDependabot creating any more for this minor version (unless you reopen\r\nthe PR or upgrade to it yourself)\r\n- `@dependabot ignore this dependency` will close this PR and stop\r\nDependabot creating any more for this dependency (unless you reopen the\r\nPR or upgrade to it yourself)\r\n\r\n\r\n</details>\r\n\r\nSigned-off-by: dependabot[bot] <support@github.com>\r\nCo-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>","shortMessageHtmlLink":"Bump actions/setup-python from 4 to 5 (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2029987074\" data-permission-text=\"Title is private\" data-url=\"https://github.com/dib-lab/screed/issues/108\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/dib-lab/screed/pull/108/hovercard\" href=\"https://github.com/dib-lab/screed/pull/108\">#108</a>)"}},{"before":null,"after":"5b7dfbb4b17e1437d9b39be9452c5eb987d58c98","ref":"refs/heads/dependabot/github_actions/actions/setup-python-5","pushedAt":"2023-12-07T06:15:40.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"dependabot[bot]","name":null,"path":"/apps/dependabot","primaryAvatarUrl":"https://avatars.githubusercontent.com/in/29110?s=80&v=4"},"commit":{"message":"Bump actions/setup-python from 4 to 5\n\nBumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.\n- [Release notes](https://github.com/actions/setup-python/releases)\n- [Commits](https://github.com/actions/setup-python/compare/v4...v5)\n\n---\nupdated-dependencies:\n- dependency-name: actions/setup-python\n  dependency-type: direct:production\n  update-type: version-update:semver-major\n...\n\nSigned-off-by: dependabot[bot] <support@github.com>","shortMessageHtmlLink":"Bump actions/setup-python from 4 to 5"}},{"before":"aa64720a8e68870df6df3989a36d812b9ea3b5a0","after":null,"ref":"refs/heads/lirber/close_reader","pushedAt":"2023-11-25T17:37:40.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"luizirber","name":"Luiz Irber","path":"/luizirber","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6642?s=80&v=4"}},{"before":"12bfb9528e99c83b6564606f5e0cd8466c64a807","after":"53f29eb6a68597310b1f4581aab67bf6eab7327b","ref":"refs/heads/latest","pushedAt":"2023-11-25T17:37:39.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"luizirber","name":"Luiz Irber","path":"/luizirber","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6642?s=80&v=4"},"commit":{"message":"Close sequencefile if an error happens in open_reader (#106)\n\nWhen running downstream projects with\r\n[`PYTHONDEVMODE=1`](https://docs.python.org/3/library/devmode.html)\r\nthere is a `ResourceWarning` for unclosed files:\r\n\r\n```\r\ntests/test_cmd_signature.py::test_sig_kmers_1_dna_empty_seq                                                                                                                                    \r\n  sourmash/.tox/py310/lib/python3.10/site-packages/screed/openscreed.py:35: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/nix-shell.7nFxtp/so\r\nurmashtest_f12d2h09/query.fa'>                                                                                                                                                                 \r\n    self.iter_fn = self.open_reader(filename, *args, **kwargs)                                                                                                                                 \r\n                                                                                                                                                                                               \r\n  Object allocated at:                                                                                                                                                                         \r\n    File \"sourmash/.tox/py310/lib/python3.10/site-packages/screed/openscreed.py\", line 35                                                                    \r\n      self.iter_fn = self.open_reader(filename, *args, **kwargs)   \r\n```\r\n\r\nTurns out we didn't close the `sequencefile` in the `open_reader` method\r\nof `screed.openscreed.Open` for two error cases before raising an\r\nexception, and with the fix in this PR the warnings disappear.","shortMessageHtmlLink":"Close sequencefile if an error happens in open_reader (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2010176228\" data-permission-text=\"Title is private\" data-url=\"https://github.com/dib-lab/screed/issues/106\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/dib-lab/screed/pull/106/hovercard\" href=\"https://github.com/dib-lab/screed/pull/106\">#106</a>)"}},{"before":"d1638236784816062914d23daffe8df2c628a8c7","after":"aa64720a8e68870df6df3989a36d812b9ea3b5a0","ref":"refs/heads/lirber/close_reader","pushedAt":"2023-11-25T17:35:39.000Z","pushType":"push","commitsCount":3,"pusher":{"login":"luizirber","name":"Luiz Irber","path":"/luizirber","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6642?s=80&v=4"},"commit":{"message":"Merge branch 'latest' into lirber/close_reader","shortMessageHtmlLink":"Merge branch 'latest' into 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Titus Brown","path":"/ctb","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/51016?s=80&v=4"}},{"before":"efaef6aae922018ce71546c19fcbe47b1af77d2e","after":"12bfb9528e99c83b6564606f5e0cd8466c64a807","ref":"refs/heads/latest","pushedAt":"2023-11-25T13:34:40.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"ctb","name":"C. Titus Brown","path":"/ctb","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/51016?s=80&v=4"},"commit":{"message":"Bump actions/checkout from 3 to 4 (#104)\n\nBumps [actions/checkout](https://github.com/actions/checkout) from 3 to\r\n4.\r\n<details>\r\n<summary>Release notes</summary>\r\n<p><em>Sourced from <a\r\nhref=\"https://github.com/actions/checkout/releases\">actions/checkout's\r\nreleases</a>.</em></p>\r\n<blockquote>\r\n<h2>v4.0.0</h2>\r\n<h2>What's Changed</h2>\r\n<ul>\r\n<li>Update default runtime to node20 by <a\r\nhref=\"https://github.com/takost\"><code>@​takost</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1436\">actions/checkout#1436</a></li>\r\n<li>Support fetching without the --progress option by <a\r\nhref=\"https://github.com/simonbaird\"><code>@​simonbaird</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1067\">actions/checkout#1067</a></li>\r\n<li>Release 4.0.0 by <a\r\nhref=\"https://github.com/takost\"><code>@​takost</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1447\">actions/checkout#1447</a></li>\r\n</ul>\r\n<h2>New Contributors</h2>\r\n<ul>\r\n<li><a href=\"https://github.com/takost\"><code>@​takost</code></a> made\r\ntheir first contribution in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1436\">actions/checkout#1436</a></li>\r\n<li><a\r\nhref=\"https://github.com/simonbaird\"><code>@​simonbaird</code></a> made\r\ntheir first contribution in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1067\">actions/checkout#1067</a></li>\r\n</ul>\r\n<p><strong>Full Changelog</strong>: <a\r\nhref=\"https://github.com/actions/checkout/compare/v3...v4.0.0\">https://github.com/actions/checkout/compare/v3...v4.0.0</a></p>\r\n<h2>v3.6.0</h2>\r\n<h2>What's Changed</h2>\r\n<ul>\r\n<li>Mark test scripts with Bash'isms to be run via Bash by <a\r\nhref=\"https://github.com/dscho\"><code>@​dscho</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1377\">actions/checkout#1377</a></li>\r\n<li>Add option to fetch tags even if fetch-depth &gt; 0 by <a\r\nhref=\"https://github.com/RobertWieczoreck\"><code>@​RobertWieczoreck</code></a>\r\nin <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/579\">actions/checkout#579</a></li>\r\n<li>Release 3.6.0 by <a\r\nhref=\"https://github.com/luketomlinson\"><code>@​luketomlinson</code></a>\r\nin <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1437\">actions/checkout#1437</a></li>\r\n</ul>\r\n<h2>New Contributors</h2>\r\n<ul>\r\n<li><a\r\nhref=\"https://github.com/RobertWieczoreck\"><code>@​RobertWieczoreck</code></a>\r\nmade their first contribution in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/579\">actions/checkout#579</a></li>\r\n<li><a\r\nhref=\"https://github.com/luketomlinson\"><code>@​luketomlinson</code></a>\r\nmade their first contribution in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1437\">actions/checkout#1437</a></li>\r\n</ul>\r\n<p><strong>Full Changelog</strong>: <a\r\nhref=\"https://github.com/actions/checkout/compare/v3.5.3...v3.6.0\">https://github.com/actions/checkout/compare/v3.5.3...v3.6.0</a></p>\r\n<h2>v3.5.3</h2>\r\n<h2>What's Changed</h2>\r\n<ul>\r\n<li>Fix: Checkout Issue in self hosted runner due to faulty submodule\r\ncheck-ins by <a\r\nhref=\"https://github.com/megamanics\"><code>@​megamanics</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1196\">actions/checkout#1196</a></li>\r\n<li>Fix typos found by codespell by <a\r\nhref=\"https://github.com/DimitriPapadopoulos\"><code>@​DimitriPapadopoulos</code></a>\r\nin <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1287\">actions/checkout#1287</a></li>\r\n<li>Add support for sparse checkouts by <a\r\nhref=\"https://github.com/dscho\"><code>@​dscho</code></a> and <a\r\nhref=\"https://github.com/dfdez\"><code>@​dfdez</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1369\">actions/checkout#1369</a></li>\r\n<li>Release v3.5.3 by <a\r\nhref=\"https://github.com/TingluoHuang\"><code>@​TingluoHuang</code></a>\r\nin <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1376\">actions/checkout#1376</a></li>\r\n</ul>\r\n<h2>New Contributors</h2>\r\n<ul>\r\n<li><a\r\nhref=\"https://github.com/megamanics\"><code>@​megamanics</code></a> made\r\ntheir first contribution in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1196\">actions/checkout#1196</a></li>\r\n<li><a\r\nhref=\"https://github.com/DimitriPapadopoulos\"><code>@​DimitriPapadopoulos</code></a>\r\nmade their first contribution in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1287\">actions/checkout#1287</a></li>\r\n<li><a href=\"https://github.com/dfdez\"><code>@​dfdez</code></a> made\r\ntheir first contribution in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1369\">actions/checkout#1369</a></li>\r\n</ul>\r\n<p><strong>Full Changelog</strong>: <a\r\nhref=\"https://github.com/actions/checkout/compare/v3...v3.5.3\">https://github.com/actions/checkout/compare/v3...v3.5.3</a></p>\r\n<h2>v3.5.2</h2>\r\n<h2>What's Changed</h2>\r\n<ul>\r\n<li>Fix: Use correct API url / endpoint in GHES by <a\r\nhref=\"https://github.com/fhammerl\"><code>@​fhammerl</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1289\">actions/checkout#1289</a>\r\nbased on <a\r\nhref=\"https://redirect.github.com/actions/checkout/issues/1286\">#1286</a>\r\nby <a href=\"https://github.com/1newsr\"><code>@​1newsr</code></a></li>\r\n</ul>\r\n<p><strong>Full Changelog</strong>: <a\r\nhref=\"https://github.com/actions/checkout/compare/v3.5.1...v3.5.2\">https://github.com/actions/checkout/compare/v3.5.1...v3.5.2</a></p>\r\n<h2>v3.5.1</h2>\r\n<h2>What's Changed</h2>\r\n<ul>\r\n<li>Improve checkout performance on Windows runners by upgrading\r\n<code>@​actions/github</code> dependency by <a\r\nhref=\"https://github.com/BrettDong\"><code>@​BrettDong</code></a> in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1246\">actions/checkout#1246</a></li>\r\n</ul>\r\n<h2>New Contributors</h2>\r\n<ul>\r\n<li><a href=\"https://github.com/BrettDong\"><code>@​BrettDong</code></a>\r\nmade their first contribution in <a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1246\">actions/checkout#1246</a></li>\r\n</ul>\r\n<!-- raw HTML omitted -->\r\n</blockquote>\r\n<p>... (truncated)</p>\r\n</details>\r\n<details>\r\n<summary>Changelog</summary>\r\n<p><em>Sourced from <a\r\nhref=\"https://github.com/actions/checkout/blob/main/CHANGELOG.md\">actions/checkout's\r\nchangelog</a>.</em></p>\r\n<blockquote>\r\n<h1>Changelog</h1>\r\n<h2>v4.0.0</h2>\r\n<ul>\r\n<li><a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1067\">Support\r\nfetching without the --progress option</a></li>\r\n<li><a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1436\">Update to\r\nnode20</a></li>\r\n</ul>\r\n<h2>v3.6.0</h2>\r\n<ul>\r\n<li><a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1377\">Fix: Mark\r\ntest scripts with Bash'isms to be run via Bash</a></li>\r\n<li><a href=\"https://redirect.github.com/actions/checkout/pull/579\">Add\r\noption to fetch tags even if fetch-depth &gt; 0</a></li>\r\n</ul>\r\n<h2>v3.5.3</h2>\r\n<ul>\r\n<li><a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1196\">Fix:\r\nCheckout fail in self-hosted runners when faulty submodule are\r\nchecked-in</a></li>\r\n<li><a href=\"https://redirect.github.com/actions/checkout/pull/1287\">Fix\r\ntypos found by codespell</a></li>\r\n<li><a href=\"https://redirect.github.com/actions/checkout/pull/1369\">Add\r\nsupport for sparse checkouts</a></li>\r\n</ul>\r\n<h2>v3.5.2</h2>\r\n<ul>\r\n<li><a href=\"https://redirect.github.com/actions/checkout/pull/1289\">Fix\r\napi endpoint for GHES</a></li>\r\n</ul>\r\n<h2>v3.5.1</h2>\r\n<ul>\r\n<li><a href=\"https://redirect.github.com/actions/checkout/pull/1246\">Fix\r\nslow checkout on Windows</a></li>\r\n</ul>\r\n<h2>v3.5.0</h2>\r\n<ul>\r\n<li><a href=\"https://redirect.github.com/actions/checkout/pull/1237\">Add\r\nnew public key for known_hosts</a></li>\r\n</ul>\r\n<h2>v3.4.0</h2>\r\n<ul>\r\n<li><a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1209\">Upgrade\r\ncodeql actions to v2</a></li>\r\n<li><a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1210\">Upgrade\r\ndependencies</a></li>\r\n<li><a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1225\">Upgrade\r\n<code>@​actions/io</code></a></li>\r\n</ul>\r\n<h2>v3.3.0</h2>\r\n<ul>\r\n<li><a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1045\">Implement\r\nbranch list using callbacks from exec function</a></li>\r\n<li><a href=\"https://redirect.github.com/actions/checkout/pull/1050\">Add\r\nin explicit reference to private checkout options</a></li>\r\n<li>[Fix comment typos (that got added in <a\r\nhref=\"https://redirect.github.com/actions/checkout/issues/770\">#770</a>)](<a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1057\">actions/checkout#1057</a>)</li>\r\n</ul>\r\n<h2>v3.2.0</h2>\r\n<ul>\r\n<li><a href=\"https://redirect.github.com/actions/checkout/pull/942\">Add\r\nGitHub Action to perform release</a></li>\r\n<li><a href=\"https://redirect.github.com/actions/checkout/pull/967\">Fix\r\nstatus badge</a></li>\r\n<li><a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1002\">Replace\r\ndatadog/squid with ubuntu/squid Docker image</a></li>\r\n<li><a href=\"https://redirect.github.com/actions/checkout/pull/964\">Wrap\r\npipeline commands for submoduleForeach in quotes</a></li>\r\n<li><a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1029\">Update\r\n<code>@​actions/io</code> to 1.1.2</a></li>\r\n<li><a\r\nhref=\"https://redirect.github.com/actions/checkout/pull/1039\">Upgrading\r\nversion to 3.2.0</a></li>\r\n</ul>\r\n<h2>v3.1.0</h2>\r\n<ul>\r\n<li><a href=\"https://redirect.github.com/actions/checkout/pull/939\">Use\r\n<code>@​actions/core</code> <code>saveState</code> and\r\n<code>getState</code></a></li>\r\n<li><a href=\"https://redirect.github.com/actions/checkout/pull/922\">Add\r\n<code>github-server-url</code> input</a></li>\r\n</ul>\r\n<h2>v3.0.2</h2>\r\n<ul>\r\n<li><a href=\"https://redirect.github.com/actions/checkout/pull/770\">Add\r\ninput <code>set-safe-directory</code></a></li>\r\n</ul>\r\n<h2>v3.0.1</h2>\r\n<!-- raw HTML omitted -->\r\n</blockquote>\r\n<p>... (truncated)</p>\r\n</details>\r\n<details>\r\n<summary>Commits</summary>\r\n<ul>\r\n<li><a\r\nhref=\"https://github.com/actions/checkout/commit/3df4ab11eba7bda6032a0b82a6bb43b11571feac\"><code>3df4ab1</code></a>\r\nRelease 4.0.0 (<a\r\nhref=\"https://redirect.github.com/actions/checkout/issues/1447\">#1447</a>)</li>\r\n<li><a\r\nhref=\"https://github.com/actions/checkout/commit/8b5e8b768746b50394015010d25e690bfab9dfbc\"><code>8b5e8b7</code></a>\r\nSupport fetching without the --progress option (<a\r\nhref=\"https://redirect.github.com/actions/checkout/issues/1067\">#1067</a>)</li>\r\n<li><a\r\nhref=\"https://github.com/actions/checkout/commit/97a652b80035363df47baee5031ec8670b8878ac\"><code>97a652b</code></a>\r\nUpdate default runtime to node20 (<a\r\nhref=\"https://redirect.github.com/actions/checkout/issues/1436\">#1436</a>)</li>\r\n<li>See full diff in <a\r\nhref=\"https://github.com/actions/checkout/compare/v3...v4\">compare\r\nview</a></li>\r\n</ul>\r\n</details>\r\n<br />\r\n\r\n\r\n[![Dependabot compatibility\r\nscore](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/checkout&package-manager=github_actions&previous-version=3&new-version=4)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)\r\n\r\nDependabot will resolve any conflicts with this PR as long as you don't\r\nalter it yourself. You can also trigger a rebase manually by commenting\r\n`@dependabot rebase`.\r\n\r\n[//]: # (dependabot-automerge-start)\r\n[//]: # (dependabot-automerge-end)\r\n\r\n---\r\n\r\n<details>\r\n<summary>Dependabot commands and options</summary>\r\n<br />\r\n\r\nYou can trigger Dependabot actions by commenting on this PR:\r\n- `@dependabot rebase` will rebase this PR\r\n- `@dependabot recreate` will recreate this PR, overwriting any edits\r\nthat have been made to it\r\n- `@dependabot merge` will merge this PR after your CI passes on it\r\n- `@dependabot squash and merge` will squash and merge this PR after\r\nyour CI passes on it\r\n- `@dependabot cancel merge` will cancel a previously requested merge\r\nand block automerging\r\n- `@dependabot reopen` will reopen this PR if it is closed\r\n- `@dependabot close` will close this PR and stop Dependabot recreating\r\nit. You can achieve the same result by closing it manually\r\n- `@dependabot show <dependency name> ignore conditions` will show all\r\nof the ignore conditions of the specified dependency\r\n- `@dependabot ignore this major version` will close this PR and stop\r\nDependabot creating any more for this major version (unless you reopen\r\nthe PR or upgrade to it yourself)\r\n- `@dependabot ignore this minor version` will close this PR and stop\r\nDependabot creating any more for this minor version (unless you reopen\r\nthe PR or upgrade to it yourself)\r\n- `@dependabot ignore this dependency` will close this PR and stop\r\nDependabot creating any more for this dependency (unless you reopen the\r\nPR or upgrade to it yourself)\r\n\r\n\r\n</details>\r\n\r\nSigned-off-by: dependabot[bot] <support@github.com>\r\nCo-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>","shortMessageHtmlLink":"Bump actions/checkout from 3 to 4 (<a class=\"issue-link js-issue-link\" 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[Commits](https://github.com/actions/checkout/compare/v3...v4)\n\n---\nupdated-dependencies:\n- dependency-name: actions/checkout\n  dependency-type: direct:production\n  update-type: version-update:semver-major\n...\n\nSigned-off-by: dependabot[bot] <support@github.com>","shortMessageHtmlLink":"Bump actions/checkout from 3 to 4"}},{"before":"0ef80e19c411e5eb2f88144d4873cb244fc58466","after":null,"ref":"refs/heads/lirber/fix_readthedocs","pushedAt":"2023-11-25T13:31:09.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"luizirber","name":"Luiz Irber","path":"/luizirber","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6642?s=80&v=4"}},{"before":"8f5536f0f4fc86c9e4ff1e844dafb7f1b62a1c0e","after":"efaef6aae922018ce71546c19fcbe47b1af77d2e","ref":"refs/heads/latest","pushedAt":"2023-11-25T13:31:08.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"luizirber","name":"Luiz 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dependency-type: direct:production\n  update-type: version-update:semver-major\n...\n\nSigned-off-by: dependabot[bot] <support@github.com>","shortMessageHtmlLink":"Bump actions/checkout from 3 to 4"}},{"before":"f3d75cb8a3b823edaa52255bfef914d4da7bb706","after":null,"ref":"refs/heads/actions_monthly","pushedAt":"2023-09-15T15:18:55.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"ctb","name":"C. 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