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castellinilinguini committed Jul 16, 2023
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157 changes: 83 additions & 74 deletions MarkdownLinks/changelog.html
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<li class="toctree-l3"><a class="reference internal" href="#fixed">Fixed</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#unreleased">[Unreleased]</a></li>
<li class="toctree-l2"><a class="reference internal" href="#id1">[0.4.0]</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id2">Added</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id3">Changed</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id4">Fixed</a></li>
<li class="toctree-l2"><a class="reference internal" href="#unreleased">[Unreleased]</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id1">Changed</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#id5">[0.3.1] - 2023-05-02</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id6">Fixed</a></li>
<li class="toctree-l2"><a class="reference internal" href="#id2">[0.4.0]</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id3">Added</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id4">Changed</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id5">Fixed</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#id7">[0.3.0] - 2023-04-27</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id8">Added</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id9">Fixed</a></li>
<li class="toctree-l2"><a class="reference internal" href="#id6">[0.3.1] - 2023-05-02</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id7">Fixed</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#id10">[0.2.1] - 2023-04-21</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id11">Fixed</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id12">Added</a></li>
<li class="toctree-l2"><a class="reference internal" href="#id8">[0.3.0] - 2023-04-27</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id9">Added</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id10">Fixed</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#id13">[0.2.0] - 2023-04-20</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id14">Changed</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id15">Fixed</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id16">Added</a></li>
<li class="toctree-l2"><a class="reference internal" href="#id11">[0.2.1] - 2023-04-21</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id12">Fixed</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id13">Added</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#id17">[0.1.5] - 2023-04-06</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id18">Changed</a></li>
<li class="toctree-l2"><a class="reference internal" href="#id14">[0.2.0] - 2023-04-20</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id15">Changed</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id16">Fixed</a></li>
<li class="toctree-l3"><a class="reference internal" href="#id17">Added</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#id19">[0.1.4] - 2023-04-06</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id20">Changed</a></li>
<li class="toctree-l2"><a class="reference internal" href="#id18">[0.1.5] - 2023-04-06</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id19">Changed</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#id21">[0.1.3] - 2023-04-05</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id22">Changed</a></li>
<li class="toctree-l2"><a class="reference internal" href="#id20">[0.1.4] - 2023-04-06</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id21">Changed</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#id23">[0.1.2] - 2023-04-05</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id24">Fixed</a></li>
<li class="toctree-l2"><a class="reference internal" href="#id22">[0.1.3] - 2023-04-05</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id23">Changed</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#id25">[0.1.1] - 2023-04-05</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id26">Fixed</a></li>
<li class="toctree-l2"><a class="reference internal" href="#id24">[0.1.2] - 2023-04-05</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id25">Fixed</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#id27">[0.1.0] - 2023-04-05</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id28">Added</a></li>
<li class="toctree-l2"><a class="reference internal" href="#id26">[0.1.1] - 2023-04-05</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id27">Fixed</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#id28">[0.1.0] - 2023-04-05</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#id29">Added</a></li>
</ul>
</li>
</ul>
Expand Down Expand Up @@ -169,150 +172,156 @@ <h3>Fixed<a class="headerlink" href="#fixed" title="Permalink to this heading">
</section>
<section id="unreleased">
<h2>[Unreleased]<a class="headerlink" href="#unreleased" title="Permalink to this heading"></a></h2>
</section>
<section id="id1">
<h2>[0.4.0]<a class="headerlink" href="#id1" title="Permalink to this heading"></a></h2>
<h3>Changed<a class="headerlink" href="#id1" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>Added linear interpolation in heat model evaluation</p></li>
</ul>
</section>
</section>
<section id="id2">
<h3>Added<a class="headerlink" href="#id2" title="Permalink to this heading"></a></h3>
<h2>[0.4.0]<a class="headerlink" href="#id2" title="Permalink to this heading"></a></h2>
<section id="id3">
<h3>Added<a class="headerlink" href="#id3" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>Added a new example model, a 2d heat conduction equation</p></li>
<li><p>Added a function to model to specify more complex parameter domains</p></li>
</ul>
</section>
<section id="id3">
<h3>Changed<a class="headerlink" href="#id3" title="Permalink to this heading"></a></h3>
<section id="id4">
<h3>Changed<a class="headerlink" href="#id4" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>Removed old functions from corona model</p></li>
<li><p>Temporarily removed stock and sbml models from test examples</p></li>
</ul>
</section>
<section id="id4">
<h3>Fixed<a class="headerlink" href="#id4" title="Permalink to this heading"></a></h3>
<section id="id5">
<h3>Fixed<a class="headerlink" href="#id5" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>Updated tutorial to be consistent with current state of the project</p></li>
<li><p>Fixed bug in dense grid generation causing parameter limits to be applied inconsistently when using slices</p></li>
</ul>
</section>
</section>
<section id="id5">
<h2>[0.3.1] - 2023-05-02<a class="headerlink" href="#id5" title="Permalink to this heading"></a></h2>
<section id="id6">
<h3>Fixed<a class="headerlink" href="#id6" title="Permalink to this heading"></a></h3>
<h2>[0.3.1] - 2023-05-02<a class="headerlink" href="#id6" title="Permalink to this heading"></a></h2>
<section id="id7">
<h3>Fixed<a class="headerlink" href="#id7" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>Bug in result manager causing burn-in and thinning to be performed on the wrong samples.</p></li>
<li><p>Bug in result manager that caused density evals to be saved as data samples for non-full slices.</p></li>
</ul>
</section>
</section>
<section id="id7">
<h2>[0.3.0] - 2023-04-27<a class="headerlink" href="#id7" title="Permalink to this heading"></a></h2>
<section id="id8">
<h3>Added<a class="headerlink" href="#id8" title="Permalink to this heading"></a></h3>
<h2>[0.3.0] - 2023-04-27<a class="headerlink" href="#id8" title="Permalink to this heading"></a></h2>
<section id="id9">
<h3>Added<a class="headerlink" href="#id9" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>Added data normalization to improve numerics and performance in the inference method.</p></li>
<li><p>Added possiblity to use no PCA transformation or completely custom transformation for inference.</p></li>
<li><p>More tests to validate EPI</p></li>
</ul>
</section>
<section id="id9">
<h3>Fixed<a class="headerlink" href="#id9" title="Permalink to this heading"></a></h3>
<section id="id10">
<h3>Fixed<a class="headerlink" href="#id10" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>Fixed grid results beeing unusable due to numerical issues</p></li>
<li><p>Fixed sbml models ignoring parameter_names argument</p></li>
</ul>
</section>
</section>
<section id="id10">
<h2>[0.2.1] - 2023-04-21<a class="headerlink" href="#id10" title="Permalink to this heading"></a></h2>
<section id="id11">
<h3>Fixed<a class="headerlink" href="#id11" title="Permalink to this heading"></a></h3>
<h2>[0.2.1] - 2023-04-21<a class="headerlink" href="#id11" title="Permalink to this heading"></a></h2>
<section id="id12">
<h3>Fixed<a class="headerlink" href="#id12" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>Fix sparse grid returning meaningless data</p></li>
<li><p>Fix menten data shape</p></li>
<li><p>Fix SBMLModel data_dim: Return states count instead of observables count</p></li>
</ul>
</section>
<section id="id12">
<h3>Added<a class="headerlink" href="#id12" title="Permalink to this heading"></a></h3>
<section id="id13">
<h3>Added<a class="headerlink" href="#id13" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>Validating the shapes of the inference results</p></li>
</ul>
</section>
</section>
<section id="id13">
<h2>[0.2.0] - 2023-04-20<a class="headerlink" href="#id13" title="Permalink to this heading"></a></h2>
<section id="id14">
<h3>Changed<a class="headerlink" href="#id14" title="Permalink to this heading"></a></h3>
<h2>[0.2.0] - 2023-04-20<a class="headerlink" href="#id14" title="Permalink to this heading"></a></h2>
<section id="id15">
<h3>Changed<a class="headerlink" href="#id15" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>Now using default emcee move policy during MCMC sampling to improve convergence speed</p></li>
<li><p>Changed argument calc_walker_acceptance_bool to get_walker_acceptance</p></li>
<li><p>Changed meaning of argument num_burn_in_samples to refer to the number of samples burned per chain, not in total</p></li>
</ul>
</section>
<section id="id15">
<h3>Fixed<a class="headerlink" href="#id15" title="Permalink to this heading"></a></h3>
<section id="id16">
<h3>Fixed<a class="headerlink" href="#id16" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>Fixed SwigPyObject pickling</p></li>
<li><p>Fixed dead lock for larger data sets and models</p></li>
</ul>
</section>
<section id="id16">
<h3>Added<a class="headerlink" href="#id16" title="Permalink to this heading"></a></h3>
<section id="id17">
<h3>Added<a class="headerlink" href="#id17" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>ResultManager is saving meta data for inference</p></li>
<li><p>ResultManager uses saved meta data to load inference results</p></li>
</ul>
</section>
</section>
<section id="id17">
<h2>[0.1.5] - 2023-04-06<a class="headerlink" href="#id17" title="Permalink to this heading"></a></h2>
<section id="id18">
<h3>Changed<a class="headerlink" href="#id18" title="Permalink to this heading"></a></h3>
<h2>[0.1.5] - 2023-04-06<a class="headerlink" href="#id18" title="Permalink to this heading"></a></h2>
<section id="id19">
<h3>Changed<a class="headerlink" href="#id19" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>Renamed epipy to eulerpi</p></li>
</ul>
</section>
</section>
<section id="id19">
<h2>[0.1.4] - 2023-04-06<a class="headerlink" href="#id19" title="Permalink to this heading"></a></h2>
<section id="id20">
<h3>Changed<a class="headerlink" href="#id20" title="Permalink to this heading"></a></h3>
<h2>[0.1.4] - 2023-04-06<a class="headerlink" href="#id20" title="Permalink to this heading"></a></h2>
<section id="id21">
<h3>Changed<a class="headerlink" href="#id21" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>Updated installation instructions</p></li>
</ul>
</section>
</section>
<section id="id21">
<h2>[0.1.3] - 2023-04-05<a class="headerlink" href="#id21" title="Permalink to this heading"></a></h2>
<section id="id22">
<h3>Changed<a class="headerlink" href="#id22" title="Permalink to this heading"></a></h3>
<h2>[0.1.3] - 2023-04-05<a class="headerlink" href="#id22" title="Permalink to this heading"></a></h2>
<section id="id23">
<h3>Changed<a class="headerlink" href="#id23" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>Updated dependencies</p></li>
</ul>
</section>
</section>
<section id="id23">
<h2>[0.1.2] - 2023-04-05<a class="headerlink" href="#id23" title="Permalink to this heading"></a></h2>
<section id="id24">
<h3>Fixed<a class="headerlink" href="#id24" title="Permalink to this heading"></a></h3>
<h2>[0.1.2] - 2023-04-05<a class="headerlink" href="#id24" title="Permalink to this heading"></a></h2>
<section id="id25">
<h3>Fixed<a class="headerlink" href="#id25" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>removed <code class="docutils literal notranslate"><span class="pre">__pycache__</span></code>, <code class="docutils literal notranslate"><span class="pre">build</span></code> and <code class="docutils literal notranslate"><span class="pre">.so</span></code> from pypi</p></li>
</ul>
</section>
</section>
<section id="id25">
<h2>[0.1.1] - 2023-04-05<a class="headerlink" href="#id25" title="Permalink to this heading"></a></h2>
<section id="id26">
<h3>Fixed<a class="headerlink" href="#id26" title="Permalink to this heading"></a></h3>
<h2>[0.1.1] - 2023-04-05<a class="headerlink" href="#id26" title="Permalink to this heading"></a></h2>
<section id="id27">
<h3>Fixed<a class="headerlink" href="#id27" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>fixed epi logo not showing on pypi</p></li>
</ul>
</section>
</section>
<section id="id27">
<h2>[0.1.0] - 2023-04-05<a class="headerlink" href="#id27" title="Permalink to this heading"></a></h2>
<section id="id28">
<h3>Added<a class="headerlink" href="#id28" title="Permalink to this heading"></a></h3>
<h2>[0.1.0] - 2023-04-05<a class="headerlink" href="#id28" title="Permalink to this heading"></a></h2>
<section id="id29">
<h3>Added<a class="headerlink" href="#id29" title="Permalink to this heading"></a></h3>
<ul class="simple">
<li><p>Initial release</p></li>
</ul>
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Expand Up @@ -216,17 +216,17 @@ <h2>How to start<a class="headerlink" href="#how-to-start" title="Permalink to t
<li class="toctree-l1"><a class="reference internal" href="MarkdownLinks/changelog.html">Changelog</a><ul>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#template">[Template]</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#unreleased">[Unreleased]</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id1">[0.4.0]</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id5">[0.3.1] - 2023-05-02</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id7">[0.3.0] - 2023-04-27</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id10">[0.2.1] - 2023-04-21</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id13">[0.2.0] - 2023-04-20</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id17">[0.1.5] - 2023-04-06</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id19">[0.1.4] - 2023-04-06</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id21">[0.1.3] - 2023-04-05</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id23">[0.1.2] - 2023-04-05</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id25">[0.1.1] - 2023-04-05</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id27">[0.1.0] - 2023-04-05</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id2">[0.4.0]</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id6">[0.3.1] - 2023-05-02</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id8">[0.3.0] - 2023-04-27</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id11">[0.2.1] - 2023-04-21</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id14">[0.2.0] - 2023-04-20</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id18">[0.1.5] - 2023-04-06</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id20">[0.1.4] - 2023-04-06</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id22">[0.1.3] - 2023-04-05</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id24">[0.1.2] - 2023-04-05</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id26">[0.1.1] - 2023-04-05</a></li>
<li class="toctree-l2"><a class="reference internal" href="MarkdownLinks/changelog.html#id28">[0.1.0] - 2023-04-05</a></li>
</ul>
</li>
</ul>
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