tag:github.com,2008:https://github.com/iqtree/piqtree/releases 2025-05-09T07:50:00Z tag:github.com,2008:Repository/784030586/v0.5.0 2025-05-09T08:13:39Z <h2>Contributors</h2> <ul> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> added <code>nj_tree</code> as a hook for <code>cogent3.Alignment.quick_tree</code>.</li> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/YapengLang/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/YapengLang">@YapengLang</a> handled negative branch lengths from the rapidNJ tree.</li> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a>, <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/thomaskf/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/thomaskf">@thomaskf</a> general maintanence on the piqtree/IQ-TREE sides including work on windows behind the scenes.</li> </ul> <h2>ENH</h2> <ul> <li>Add support for Python 3.13, remove support for 3.10</li> <li>IQ-TREE's rapidNJ implementation can be used as a hook for <code>quick_tree</code> on <code>cogent3</code> alignment objects. Try <code>Alignment.quick_tree(use_hook="piqtree")</code>.</li> <li><code>nj_tree</code> now by default does not allow negative branch lengths. Set <code>allow_negative=True</code> if this behaviour is desired.</li> <li>Allow <code>str</code> to be used for <code>model</code> in <code>build_tree</code> and <code>fit_tree</code>. The value is automatically coerced into the <code>Model</code> class.</li> </ul> <h2>API</h2> <ul> <li>Simplify API for <code>piqtree_phylo</code> and <code>piqtree_fit</code> apps. Both now take a single parameter for the model, matching the parameter for <code>model</code> in <code>build_tree</code> and <code>fit_tree</code>.</li> </ul> <h2>What's Changed</h2> <ul> <li>Bump ruff from 0.8.2 to 0.8.3 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2741284906" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/140" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/140/hovercard" href="https://github.com/iqtree/piqtree/pull/140">#140</a></li> <li>Bump mypy from 1.13.0 to 1.14.1 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2769845670" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/149" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/149/hovercard" href="https://github.com/iqtree/piqtree/pull/149">#149</a></li> <li>Bump ruff from 0.8.3 to 0.9.1 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2782995372" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/150" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/150/hovercard" href="https://github.com/iqtree/piqtree/pull/150">#150</a></li> <li>DOC: add documentation for developers by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2786275443" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/151" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/151/hovercard" href="https://github.com/iqtree/piqtree/pull/151">#151</a></li> <li>ENH: RtD Error Handling + Backup Token Name by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2791614342" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/152" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/152/hovercard" href="https://github.com/iqtree/piqtree/pull/152">#152</a></li> <li>ENH: use get for when status isn't in GitHub API return by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2791638193" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/153" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/153/hovercard" href="https://github.com/iqtree/piqtree/pull/153">#153</a></li> <li>DOC: add contributing guide to README by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2791656057" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/154" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/154/hovercard" href="https://github.com/iqtree/piqtree/pull/154">#154</a></li> <li>ENH: Create CODE_OF_CONDUCT.md by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2791669546" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/155" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/155/hovercard" href="https://github.com/iqtree/piqtree/pull/155">#155</a></li> <li>Bump ruff from 0.9.1 to 0.9.2 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2798132874" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/156" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/156/hovercard" href="https://github.com/iqtree/piqtree/pull/156">#156</a></li> <li>Bump ruff from 0.9.2 to 0.9.3 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2812053696" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/157" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/157/hovercard" href="https://github.com/iqtree/piqtree/pull/157">#157</a></li> <li>Bump ruff from 0.9.3 to 0.9.4 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2826399522" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/158" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/158/hovercard" href="https://github.com/iqtree/piqtree/pull/158">#158</a></li> <li>Bump ruff from 0.9.4 to 0.9.7 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2873815522" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/162" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/162/hovercard" href="https://github.com/iqtree/piqtree/pull/162">#162</a></li> <li>Bump mypy from 1.14.1 to 1.15.0 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2841293661" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/159" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/159/hovercard" href="https://github.com/iqtree/piqtree/pull/159">#159</a></li> <li>Bump pypa/cibuildwheel from 2.22.0 to 2.23.0 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2890138809" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/164" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/164/hovercard" href="https://github.com/iqtree/piqtree/pull/164">#164</a></li> <li>Bump ruff from 0.9.7 to 0.9.10 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2906029619" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/166" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/166/hovercard" href="https://github.com/iqtree/piqtree/pull/166">#166</a></li> <li>Bump iqtree2 from <code>ccf68f4</code> to <code>39c2ea4</code> by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2912181510" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/167" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/167/hovercard" href="https://github.com/iqtree/piqtree/pull/167">#167</a></li> <li>Bump iqtree2 from <code>39c2ea4</code> to <code>92725d3</code> by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2918668493" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/169" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/169/hovercard" href="https://github.com/iqtree/piqtree/pull/169">#169</a></li> <li>ENH: add piqtree_nj as a cogent3 quick_tree hook by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2923577131" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/170" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/170/hovercard" href="https://github.com/iqtree/piqtree/pull/170">#170</a></li> <li>Bump ruff from 0.9.10 to 0.11.0 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2923694554" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/172" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/172/hovercard" href="https://github.com/iqtree/piqtree/pull/172">#172</a></li> <li>Bump iqtree2 from <code>92725d3</code> to <code>4da7093</code> by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2923707513" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/174" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/174/hovercard" href="https://github.com/iqtree/piqtree/pull/174">#174</a></li> <li>Bump iqtree2 from <code>4da7093</code> to <code>1320c4c</code> by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2923811510" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/175" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/175/hovercard" href="https://github.com/iqtree/piqtree/pull/175">#175</a></li> <li>MAINT: Add support for Python 3.13, drop for 3.10 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2934637231" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/180" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/180/hovercard" href="https://github.com/iqtree/piqtree/pull/180">#180</a></li> <li>Bump pypa/cibuildwheel from 2.23.0 to 2.23.1 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2923694771" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/173" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/173/hovercard" href="https://github.com/iqtree/piqtree/pull/173">#173</a></li> <li>ENH: provide piqtree_nj and nj_tree option for positive branch lengths by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/YapengLang/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/YapengLang">@YapengLang</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2899985511" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/165" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/165/hovercard" href="https://github.com/iqtree/piqtree/pull/165">#165</a></li> <li>DEV: Update minimum <code>cogent3</code> version by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2940183676" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/186" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/186/hovercard" href="https://github.com/iqtree/piqtree/pull/186">#186</a></li> <li>Bump ruff from 0.11.0 to 0.11.5 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2991881138" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/193" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/193/hovercard" href="https://github.com/iqtree/piqtree/pull/193">#193</a></li> <li>Bump pypa/cibuildwheel from 2.23.1 to 2.23.2 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2959433694" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/191" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/191/hovercard" href="https://github.com/iqtree/piqtree/pull/191">#191</a></li> <li>Bump ruff from 0.11.5 to 0.11.8 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="3038571650" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/199" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/199/hovercard" href="https://github.com/iqtree/piqtree/pull/199">#199</a></li> <li>Bump pypa/cibuildwheel from 2.23.2 to 2.23.3 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="3023678828" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/196" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/196/hovercard" href="https://github.com/iqtree/piqtree/pull/196">#196</a></li> <li>MAINT/API: Fix Table references in latest version of <code>cogent3</code>, simplify API of model for build and fit tree apps by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="3051071610" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/201" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/201/hovercard" href="https://github.com/iqtree/piqtree/pull/201">#201</a></li> <li>REL: Prepare for 0.5.0 release by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="3051180873" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/202" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/202/hovercard" href="https://github.com/iqtree/piqtree/pull/202">#202</a></li> <li>DEV: update trove classifiers for supported python versions by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="3051220671" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/203" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/203/hovercard" href="https://github.com/iqtree/piqtree/pull/203">#203</a></li> <li>DEV: add minimum cmake version by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="3051316796" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/204" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/204/hovercard" href="https://github.com/iqtree/piqtree/pull/204">#204</a></li> </ul> <p><strong>Full Changelog</strong>: <a class="commit-link" href="https://github.com/iqtree/piqtree/compare/v0.4.0...v0.5.0"><tt>v0.4.0...v0.5.0</tt></a></p> rmcar17 tag:github.com,2008:Repository/784030586/v0.4.0 2024-12-13T06:42:10Z <h1>Changes in release "0.4.0"</h1> <h2>Contributors</h2> <ul> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> integrated new functions from IQ-TREE in Python, added multithreading support, and wrote the API refererence and quickstart.</li> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/thomaskf/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/thomaskf">@thomaskf</a> exposed all new functions from IQ-TREE to be available from Python, and worked on multithreading support.</li> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> worked on setting up and writing the documentation and associated devtools, ModelFinder, and integration with <code>cogent3</code> apps.</li> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/YapengLang/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/YapengLang">@YapengLang</a> worked on bootstrapping support and extracting model parameters</li> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/KatherineCaley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/KatherineCaley">@KatherineCaley</a> worked on processing the ModelFinder results.</li> </ul> <h2>ENH</h2> <ul> <li>piqtree2 renamed piqtree to support future major releases of IQ-TREE.</li> <li>piqtree now supports multithreading!</li> <li>New function <code>nj_tree</code> constructs a rapid neighbour-joining tree from a pairwise distance matrix.</li> <li>New function <code>model_finder</code> finds the best model for a given alignment.</li> <li>New function <code>jc_distances</code> constructs a pairwise JC distance matrix from an alignment.</li> <li>New function <code>make_model</code> allows converting an IQ-TREE string representation of a model to a <code>Model</code> class.</li> <li>API for <code>random_trees</code> has changed - new order (<code>num_trees</code>, <code>num_taxa</code>, <code>tree_mode</code>, then <code>rand_seed</code>).</li> <li>API for <code>robinson_foulds</code> has changed - now accepts a Sequence of trees.</li> <li>Model parameters are now extracted from IQ-TREE where for now possible.</li> <li><code>build_tree</code> now supports ultrafast bootstrapping.</li> <li><code>Model</code> creation is now more robust.</li> <li>Use <code>piqtree.__iqtree_version__</code> to see what version of piqtree is being used.</li> <li>See what can now be done in our <a href="https://piqtree.readthedocs.io" rel="nofollow">new documentation</a>!</li> </ul> <h2>DOC</h2> <ul> <li><a href="https://piqtree.readthedocs.io" rel="nofollow">Documentation</a> is now on readthedocs!</li> </ul> <h2>What's Changed</h2> <ul> <li>DEV: remove ssh mounts (use ssh-agent instead) by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2521413924" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/64" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/64/hovercard" href="https://github.com/iqtree/piqtree/pull/64">#64</a></li> <li>Bump iqtree2 from <code>9ee7f6c</code> to <code>cf47d36</code> by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2509488872" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/63" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/63/hovercard" href="https://github.com/iqtree/piqtree/pull/63">#63</a></li> <li>DEV: remove ssh mount (use ssh-agent instead) by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2521481943" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/65" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/65/hovercard" href="https://github.com/iqtree/piqtree/pull/65">#65</a></li> <li>Bump iqtree2 from <code>cf47d36</code> to <code>07aa4b3</code> by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2535258105" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/70" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/70/hovercard" href="https://github.com/iqtree/piqtree/pull/70">#70</a></li> <li>ENH: attached rate and motif parameters to cogent3 tree object by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/YapengLang/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/YapengLang">@YapengLang</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2482644246" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/49" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/49/hovercard" href="https://github.com/iqtree/piqtree/pull/49">#49</a></li> <li>Bump pypa/cibuildwheel from 2.20.0 to 2.21.1 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2541532142" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/71" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/71/hovercard" href="https://github.com/iqtree/piqtree/pull/71">#71</a></li> <li>Bump iqtree2 from <code>07aa4b3</code> to <code>70152d2</code> by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2555524250" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/74" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/74/hovercard" href="https://github.com/iqtree/piqtree/pull/74">#74</a></li> <li>ENH: add support for nj tree, jc distances, and raw results of model finder by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2574784215" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/79" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/79/hovercard" href="https://github.com/iqtree/piqtree/pull/79">#79</a></li> <li>Bump pypa/cibuildwheel from 2.21.1 to 2.21.3 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2584695851" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/80" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/80/hovercard" href="https://github.com/iqtree/piqtree/pull/80">#80</a></li> <li>TST: added tests for branch lengths by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/YapengLang/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/YapengLang">@YapengLang</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2593362764" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/82" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/82/hovercard" href="https://github.com/iqtree/piqtree/pull/82">#82</a></li> <li>Bump iqtree2 from <code>70152d2</code> to <code>f04b6f2</code> by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2587629733" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/81" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/81/hovercard" href="https://github.com/iqtree/piqtree/pull/81">#81</a></li> <li>ENH: parse parameters in Lie Markov model and rate model by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/YapengLang/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/YapengLang">@YapengLang</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2596417685" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/88" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/88/hovercard" href="https://github.com/iqtree/piqtree/pull/88">#88</a></li> <li>DEV: Drop support for Python 3.9 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2593730806" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/86" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/86/hovercard" href="https://github.com/iqtree/piqtree/pull/86">#86</a></li> <li>MAINT: ensure unix line endings (artefact from initial windows development) by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2600994783" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/89" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/89/hovercard" href="https://github.com/iqtree/piqtree/pull/89">#89</a></li> <li>ENH: modifications in prep for the documentation by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2593611802" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/85" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/85/hovercard" href="https://github.com/iqtree/piqtree/pull/85">#85</a></li> <li>ENH: add bootstrapping parameter in build_tree, and update _process_tree_yaml to handle inconsistent newick by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/YapengLang/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/YapengLang">@YapengLang</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2632037719" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/91" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/91/hovercard" href="https://github.com/iqtree/piqtree/pull/91">#91</a></li> <li>ENH: Add JC Distance App by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2660627511" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/92" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/92/hovercard" href="https://github.com/iqtree/piqtree/pull/92">#92</a></li> <li>ENH: Model can be imported from top level by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2660664439" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/93" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/93/hovercard" href="https://github.com/iqtree/piqtree/pull/93">#93</a></li> <li>DOC: Use new Model API in README by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2660671557" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/94" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/94/hovercard" href="https://github.com/iqtree/piqtree/pull/94">#94</a></li> <li>DEV: Add Type Checking With mypy by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2660955223" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/95" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/95/hovercard" href="https://github.com/iqtree/piqtree/pull/95">#95</a></li> <li>MAINT: fix piqtree_fit app help by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2670348356" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/100" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/100/hovercard" href="https://github.com/iqtree/piqtree/pull/100">#100</a></li> <li>Misc changes by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2670454529" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/101" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/101/hovercard" href="https://github.com/iqtree/piqtree/pull/101">#101</a></li> <li>API and DOC by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2673768830" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/103" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/103/hovercard" href="https://github.com/iqtree/piqtree/pull/103">#103</a></li> <li>DEV: add ruff linting to CI by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2674214528" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/104" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/104/hovercard" href="https://github.com/iqtree/piqtree/pull/104">#104</a></li> <li>Prepping for rtd by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2682067364" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/105" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/105/hovercard" href="https://github.com/iqtree/piqtree/pull/105">#105</a></li> <li>Support serialisation of ModelFinderResult by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2682255321" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/106" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/106/hovercard" href="https://github.com/iqtree/piqtree/pull/106">#106</a></li> <li>DEV: git submodule update by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2684422272" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/107" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/107/hovercard" href="https://github.com/iqtree/piqtree/pull/107">#107</a></li> <li>DEV: bump version to trigger doc build by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2688457046" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/108" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/108/hovercard" href="https://github.com/iqtree/piqtree/pull/108">#108</a></li> <li>Bump pypa/cibuildwheel from 2.21.3 to 2.22.0 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2689041832" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/109" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/109/hovercard" href="https://github.com/iqtree/piqtree/pull/109">#109</a></li> <li>MAINT: Fix linting, pin ruff by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2689263509" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/110" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/110/hovercard" href="https://github.com/iqtree/piqtree/pull/110">#110</a></li> <li>DEV: added scripts for building and uploading docs by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2697423691" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/111" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/111/hovercard" href="https://github.com/iqtree/piqtree/pull/111">#111</a></li> <li>DEV: Simplify Workflows by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2700858681" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/112" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/112/hovercard" href="https://github.com/iqtree/piqtree/pull/112">#112</a></li> <li>Bump iqtree2 from <code>f04b6f2</code> to <code>18fa5a3</code> by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2700899856" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/113" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/113/hovercard" href="https://github.com/iqtree/piqtree/pull/113">#113</a></li> <li>Bump iqtree2 from <code>18fa5a3</code> to <code>ea7a080</code> by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2703938111" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/114" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/114/hovercard" href="https://github.com/iqtree/piqtree/pull/114">#114</a></li> <li>DOC: infrastructure by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2704041598" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/115" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/115/hovercard" href="https://github.com/iqtree/piqtree/pull/115">#115</a></li> <li>DOC: case matters by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2710126890" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/117" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/117/hovercard" href="https://github.com/iqtree/piqtree/pull/117">#117</a></li> <li>DOC: fixes to docs by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2710217506" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/118" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/118/hovercard" href="https://github.com/iqtree/piqtree/pull/118">#118</a></li> <li>DEV: added link to documentation to pyproject.toml by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2710239664" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/119" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/119/hovercard" href="https://github.com/iqtree/piqtree/pull/119">#119</a></li> <li>Bump iqtree2 from <code>ea7a080</code> to <code>da38244</code> by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2710358465" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/120" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/120/hovercard" href="https://github.com/iqtree/piqtree/pull/120">#120</a></li> <li>Bump ruff from 0.8.0 to 0.8.1 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2710414151" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/122" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/122/hovercard" href="https://github.com/iqtree/piqtree/pull/122">#122</a></li> <li>DOC: point README to documentation website by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2710404993" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/121" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/121/hovercard" href="https://github.com/iqtree/piqtree/pull/121">#121</a></li> <li>Bump iqtree2 from <code>da38244</code> to <code>839f3f1</code> by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2716495638" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/123" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/123/hovercard" href="https://github.com/iqtree/piqtree/pull/123">#123</a></li> <li>DEV: Support building all mac/linux wheels by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2716639183" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/124" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/124/hovercard" href="https://github.com/iqtree/piqtree/pull/124">#124</a></li> <li>ENH: refactor ModelFinderResult to use new ModelResultValue class, fixes <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2670742778" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/102" data-hovercard-type="issue" data-hovercard-url="/iqtree/piqtree/issues/102/hovercard" href="https://github.com/iqtree/piqtree/issues/102">#102</a> by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/KatherineCaley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/KatherineCaley">@KatherineCaley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2725823733" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/125" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/125/hovercard" href="https://github.com/iqtree/piqtree/pull/125">#125</a></li> <li>Bump ruff from 0.8.1 to 0.8.2 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2725984341" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/126" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/126/hovercard" href="https://github.com/iqtree/piqtree/pull/126">#126</a></li> <li>Bump iqtree2 from <code>839f3f1</code> to <code>ccf68f4</code> by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2734333130" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/127" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/127/hovercard" href="https://github.com/iqtree/piqtree/pull/127">#127</a></li> <li>ENH: export iqtree version to piqtree2 module by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2734403333" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/128" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/128/hovercard" href="https://github.com/iqtree/piqtree/pull/128">#128</a></li> <li>DEV: fix typo in linting ci job by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2734407070" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/129" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/129/hovercard" href="https://github.com/iqtree/piqtree/pull/129">#129</a></li> <li>DOC: add quickstart and API reference by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2734683236" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/130" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/130/hovercard" href="https://github.com/iqtree/piqtree/pull/130">#130</a></li> <li>DEV: make dockerfile setup dev environment by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2734779936" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/131" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/131/hovercard" href="https://github.com/iqtree/piqtree/pull/131">#131</a></li> <li>DEV: push to iqtree ghcr by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2734813266" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/132" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/132/hovercard" href="https://github.com/iqtree/piqtree/pull/132">#132</a></li> <li>DEV: fix build for dockerfile by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2734833467" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/133" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/133/hovercard" href="https://github.com/iqtree/piqtree/pull/133">#133</a></li> <li>DEV: revert docker editting by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2734871671" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/134" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/134/hovercard" href="https://github.com/iqtree/piqtree/pull/134">#134</a></li> <li>MAINT: rename piqtree2 to piqtree by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2737106029" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/135" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/135/hovercard" href="https://github.com/iqtree/piqtree/pull/135">#135</a></li> <li>DEV: store devcontainer in iqtree org, include btop and rename env to piq-dev by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2737148575" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/136" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/136/hovercard" href="https://github.com/iqtree/piqtree/pull/136">#136</a></li> <li>ENH: add <code>make_model</code> by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2737367411" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/137" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/137/hovercard" href="https://github.com/iqtree/piqtree/pull/137">#137</a></li> <li>DOC: Add documentation for model_finder by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2737433359" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/138" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/138/hovercard" href="https://github.com/iqtree/piqtree/pull/138">#138</a></li> <li>REL: release 0.4.0 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2737479380" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/139" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/139/hovercard" href="https://github.com/iqtree/piqtree/pull/139">#139</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/YapengLang/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/YapengLang">@YapengLang</a> made their first contribution in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2482644246" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/49" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/49/hovercard" href="https://github.com/iqtree/piqtree/pull/49">#49</a></li> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/KatherineCaley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/KatherineCaley">@KatherineCaley</a> made their first contribution in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2725823733" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/125" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/125/hovercard" href="https://github.com/iqtree/piqtree/pull/125">#125</a></li> </ul> <p><strong>Full Changelog</strong>: <a class="commit-link" href="https://github.com/iqtree/piqtree/compare/v0.3.1...v0.4.0"><tt>v0.3.1...v0.4.0</tt></a></p> rmcar17 tag:github.com,2008:Repository/784030586/v0.3.1 2024-08-29T09:15:46Z <h1>Changes in release "0.3.1"</h1> <h2>ENH</h2> <ul> <li>Add support for Lie Markov Models.</li> <li>Base frequencies default to None (specified by model).</li> </ul> <h2>BUG</h2> <ul> <li><code>piqtree2</code> apps are now pickleable (they can now be run with <code>parallel=True</code> in the cogent3 app infrastructure)</li> </ul> rmcar17 tag:github.com,2008:Repository/784030586/v0.3.0 2024-08-15T06:10:44Z <h2>Contributors</h2> <ul> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> Added new classes to enhance model specification when calling <code>build_tree</code> and <code>fit_tree</code>.</li> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/thomaskf/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/thomaskf">@thomaskf</a> fixed a bug in IQ-TREE resulting in segmentation faults on some invalid arguments.</li> </ul> <h2>ENH</h2> <ul> <li><code>build_tree</code> and <code>fit_tree</code> now allow specifying base frequencies, invariable sites and rate heterogeneity options.</li> </ul> <h2>BUG</h2> <ul> <li>Fixed a segmentation fault on repetitive calls to IQ-TREE with particular arguments.</li> </ul> <h2>What's Changed</h2> <ul> <li>Bump iqtree2 from <code>b73ea6c</code> to <code>5725858</code> by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2460049813" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/38" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/38/hovercard" href="https://github.com/iqtree/piqtree/pull/38">#38</a></li> <li>ENH: add freq rate type including rate het by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/rmcar17/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/rmcar17">@rmcar17</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2462199657" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/39" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/39/hovercard" href="https://github.com/iqtree/piqtree/pull/39">#39</a></li> </ul> <p><strong>Full Changelog</strong>: <a class="commit-link" href="https://github.com/iqtree/piqtree/compare/0.2.0...v0.3.0"><tt>0.2.0...v0.3.0</tt></a></p> rmcar17 tag:github.com,2008:Repository/784030586/0.2.0 2024-08-06T08:42:26Z <h2>Contributors</h2> <ul> <li> <p>Richard Morris</p> </li> <li> <p>Robert McArthur</p> </li> </ul> <h2>ENH</h2> <ul> <li><code>build_tree</code> and <code>fit_tree</code> now use enums for the substitution model.</li> </ul> <h2>BUG</h2> <ul> <li>Fixed an issue where calling <code>build_tree</code> or <code>fit_tree</code> twice, then another function with invalid input resulted in a segmentation fault.</li> </ul> <h2>DOC</h2> <ul> <li>Implement scriv as a tool to manage collection of changes, and automated collation into the changelog</li> </ul> rmcar17 tag:github.com,2008:Repository/784030586/v0.2.0 2024-08-06T08:15:10Z <p>DEV: remove universal wheels</p> rmcar17 tag:github.com,2008:Repository/784030586/v0.1.0 2024-07-05T23:55:43Z <h2>The first official release of piqtree2!</h2> <p>piqtree2 allows you to use IQ-TREE for phylogenetic analysis directly from python.</p> <p>Currently, we support phylogenetic reconstruction, fitting branch lengths to a fixed topology, generating random tress, and pairwise RF distance of trees.</p> <p>piqtree2 is still in early pre-alpha development, please raise an <a href="https://github.com/iqtree/piqtree2/issues">issue</a> if you encounter any problems or have any feature requests.</p> <h2>What's Changed</h2> <ul> <li>Build container workflow by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/khiron/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/khiron">@khiron</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2365195153" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/8" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/8/hovercard" href="https://github.com/iqtree/piqtree/pull/8">#8</a></li> <li>disable container build for now by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/khiron/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/khiron">@khiron</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2365887304" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/9" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/9/hovercard" href="https://github.com/iqtree/piqtree/pull/9">#9</a></li> <li>Python API for piqtree2 by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/khiron/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/khiron">@khiron</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2368947051" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/10" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/10/hovercard" href="https://github.com/iqtree/piqtree/pull/10">#10</a></li> <li>ENH: define cogent3 apps and add test stub by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2385112260" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/15" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/15/hovercard" href="https://github.com/iqtree/piqtree/pull/15">#15</a></li> <li>ENH: added available_models() convenience function by <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2389898705" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/18" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/18/hovercard" href="https://github.com/iqtree/piqtree/pull/18">#18</a></li> <li>Bump actions/checkout from 2 to 4 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2391726045" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/20" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/20/hovercard" href="https://github.com/iqtree/piqtree/pull/20">#20</a></li> <li>Bump pypa/cibuildwheel from 2.19.1 to 2.19.2 by <a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2391726006" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/19" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/19/hovercard" href="https://github.com/iqtree/piqtree/pull/19">#19</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/khiron/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/khiron">@khiron</a> made their first contribution in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2365195153" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/8" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/8/hovercard" href="https://github.com/iqtree/piqtree/pull/8">#8</a></li> <li><a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/users/GavinHuttley/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/GavinHuttley">@GavinHuttley</a> made their first contribution in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2385112260" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/15" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/15/hovercard" href="https://github.com/iqtree/piqtree/pull/15">#15</a></li> <li><a class="user-mention notranslate" data-hovercard-type="organization" data-hovercard-url="/orgs/dependabot/hovercard" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="https://github.com/dependabot">@dependabot</a> made their first contribution in <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="2391726045" data-permission-text="Title is private" data-url="https://github.com/iqtree/piqtree/issues/20" data-hovercard-type="pull_request" data-hovercard-url="/iqtree/piqtree/pull/20/hovercard" href="https://github.com/iqtree/piqtree/pull/20">#20</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/iqtree/piqtree2/commits/v0.1.0">https://github.com/iqtree/piqtree2/commits/v0.1.0</a></p> rmcar17