docs for version 2.1.0

jbloomlab · Apr 11, 2024 · cef6124 · cef6124
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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: ad82fa3e508d3df5c0a2eafda2b8e0f7
+config: 4b60f1f4abdfdf01b83f38bc77a57247
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_images/curvefits_example_40_0.png b/_images/curvefits_example_40_0.png
diff --git a/_images/curvefits_example_42_0.png b/_images/curvefits_example_42_0.png
diff --git a/_images/curvefits_example_44_0.png b/_images/curvefits_example_44_0.png
diff --git a/_images/curvefits_example_46_0.png b/_images/curvefits_example_46_0.png
diff --git a/_images/curvefits_example_48_0.png b/_images/curvefits_example_48_0.png
diff --git a/_images/curvefits_example_50_0.png b/_images/curvefits_example_50_0.png
diff --git a/_images/curvefits_example_52_0.png b/_images/curvefits_example_52_0.png
diff --git a/_images/curvefits_example_54_0.png b/_images/curvefits_example_54_0.png
diff --git a/_images/curvefits_example_56_0.png b/_images/curvefits_example_56_0.png
diff --git a/_images/curvefits_example_58_0.png b/_images/curvefits_example_58_0.png
diff --git a/_images/curvefits_example_60_0.png b/_images/curvefits_example_60_0.png
diff --git a/_images/curvefits_example_64_0.png b/_images/curvefits_example_64_0.png
diff --git a/_images/curvefits_example_67_0.png b/_images/curvefits_example_67_0.png
diff --git a/_images/curvefits_example_69_0.png b/_images/curvefits_example_69_0.png
diff --git a/_images/hillcurve_example_24_0.png b/_images/hillcurve_example_24_0.png
diff --git a/_modules/index.html b/_modules/index.html
@@ -4,10 +4,10 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Overview: module code &#8212; neutcurve 2.0.0 documentation</title>
+    <title>Overview: module code &#8212; neutcurve 2.1.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=b76e3c8a" />
     <link rel="stylesheet" type="text/css" href="../_static/alabaster.css?v=c878986b" />
-    <script src="../_static/documentation_options.js?v=51b770b3"></script>
+    <script src="../_static/documentation_options.js?v=20623aea"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
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diff --git a/_modules/neutcurve/curvefits.html b/_modules/neutcurve/curvefits.html
@@ -4,10 +4,10 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>neutcurve.curvefits &#8212; neutcurve 2.0.0 documentation</title>
+    <title>neutcurve.curvefits &#8212; neutcurve 2.1.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=b76e3c8a" />
     <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=c878986b" />
-    <script src="../../_static/documentation_options.js?v=51b770b3"></script>
+    <script src="../../_static/documentation_options.js?v=20623aea"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
@@ -647,9 +647,16 @@ <h1>Source code for neutcurve.curvefits</h1><div class="highlight"><pre>
                 <span class="n">ic_cols</span> <span class="o">+=</span> <span class="p">[</span><span class="n">prefix</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">prefix</span><span class="si">}</span><span class="s2">_bound&quot;</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">prefix</span><span class="si">}</span><span class="s2">_str&quot;</span><span class="p">]</span>
             <span class="k">if</span> <span class="n">ic50_error</span> <span class="o">==</span> <span class="s2">&quot;fit_stdev&quot;</span><span class="p">:</span>
                 <span class="n">ic_cols</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="s2">&quot;ic50_error&quot;</span><span class="p">)</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">_fitparams</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">d</span><span class="p">)[</span>
-                <span class="p">[</span><span class="s2">&quot;serum&quot;</span><span class="p">,</span> <span class="s2">&quot;virus&quot;</span><span class="p">,</span> <span class="s2">&quot;replicate&quot;</span><span class="p">,</span> <span class="s2">&quot;nreplicates&quot;</span><span class="p">]</span> <span class="o">+</span> <span class="n">ic_cols</span> <span class="o">+</span> <span class="n">params</span>
-            <span class="p">]</span><span class="o">.</span><span class="n">assign</span><span class="p">(</span><span class="n">nreplicates</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="s2">&quot;nreplicates&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s2">&quot;Int64&quot;</span><span class="p">)))</span>
+            <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">d</span><span class="p">):</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_fitparams</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">d</span><span class="p">)[</span>
+                    <span class="p">[</span><span class="s2">&quot;serum&quot;</span><span class="p">,</span> <span class="s2">&quot;virus&quot;</span><span class="p">,</span> <span class="s2">&quot;replicate&quot;</span><span class="p">,</span> <span class="s2">&quot;nreplicates&quot;</span><span class="p">]</span> <span class="o">+</span> <span class="n">ic_cols</span> <span class="o">+</span> <span class="n">params</span>
+                <span class="p">]</span><span class="o">.</span><span class="n">assign</span><span class="p">(</span><span class="n">nreplicates</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="p">(</span><span class="n">x</span><span class="p">[</span><span class="s2">&quot;nreplicates&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="s2">&quot;Int64&quot;</span><span class="p">)))</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_fitparams</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+                    <span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;serum&quot;</span><span class="p">,</span> <span class="s2">&quot;virus&quot;</span><span class="p">,</span> <span class="s2">&quot;replicate&quot;</span><span class="p">,</span> <span class="s2">&quot;nreplicates&quot;</span><span class="p">]</span>
+                    <span class="o">+</span> <span class="n">ic_cols</span>
+                    <span class="o">+</span> <span class="n">params</span><span class="p">,</span>
+                <span class="p">)</span>
 
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_fitparams</span><span class="p">[</span><span class="n">key</span><span class="p">]</span></div>
 
@@ -1294,6 +1301,7 @@ <h1>Source code for neutcurve.curvefits</h1><div class="highlight"><pre>
         <span class="n">sharex</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
         <span class="n">sharey</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
         <span class="n">vlines</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+        <span class="n">draw_in_bounds</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
     <span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Plot arbitrary grid of curves.</span>
 
@@ -1369,6 +1377,8 @@ <h1>Source code for neutcurve.curvefits</h1><div class="highlight"><pre>
 <span class="sd">                Values are lists of dicts with a key &#39;x&#39; giving the x-location</span>
 <span class="sd">                of the vertical line, and optionally keys &#39;linewidth&#39;,</span>
 <span class="sd">                &#39;color&#39;, and &#39;linestyle&#39;.</span>
+<span class="sd">            `draw_in_bounds` (bool)</span>
+<span class="sd">                Same meaning as for meth:`neutcurve.hillcurve.HillCurve.plot`.</span>
 
 <span class="sd">        Returns:</span>
 <span class="sd">            The 2-tuple `(fig, axes)` of matplotlib figure and 2D axes array.</span>
@@ -1519,6 +1529,7 @@ <h1>Source code for neutcurve.curvefits</h1><div class="highlight"><pre>
                     <span class="n">xlabel</span><span class="o">=</span><span class="n">ixlabel</span><span class="p">,</span>
                     <span class="n">ylabel</span><span class="o">=</span><span class="n">iylabel</span><span class="p">,</span>
                     <span class="n">yticklocs</span><span class="o">=</span><span class="n">yticklocs</span><span class="p">,</span>
+                    <span class="n">draw_in_bounds</span><span class="o">=</span><span class="n">draw_in_bounds</span><span class="p">,</span>
                     <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span>
                 <span class="p">)</span>
                 <span class="n">label</span> <span class="o">=</span> <span class="n">curvedict</span><span class="p">[</span><span class="s2">&quot;label&quot;</span><span class="p">]</span>

diff --git a/_modules/neutcurve/hillcurve.html b/_modules/neutcurve/hillcurve.html
@@ -4,10 +4,10 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>neutcurve.hillcurve &#8212; neutcurve 2.0.0 documentation</title>
+    <title>neutcurve.hillcurve &#8212; neutcurve 2.1.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=b76e3c8a" />
     <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=c878986b" />
-    <script src="../../_static/documentation_options.js?v=51b770b3"></script>
+    <script src="../../_static/documentation_options.js?v=20623aea"></script>
     <script src="../../_static/doctools.js?v=888ff710"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
@@ -1270,6 +1270,7 @@ <h1>Source code for neutcurve.hillcurve</h1><div class="highlight"><pre>
         <span class="n">linewidth</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
         <span class="n">linestyle</span><span class="o">=</span><span class="s2">&quot;-&quot;</span><span class="p">,</span>
         <span class="n">yticklocs</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+        <span class="n">draw_in_bounds</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
     <span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Plot the neutralization curve.</span>
 
@@ -1296,12 +1297,16 @@ <h1>Source code for neutcurve.hillcurve</h1><div class="highlight"><pre>
 <span class="sd">                Line style.</span>
 <span class="sd">            `yticklocs` (`None` or list)</span>
 <span class="sd">                Exact locations to place yticks; `None` means auto-locate.</span>
+<span class="sd">            `draw_in_bounds` (bool)</span>
+<span class="sd">                By default, the plotted curve extends a bit outside the actual</span>
+<span class="sd">                data points on both sides. If this is set to `True`, then the</span>
+<span class="sd">                plotted curve stops at the bounds of the data points.</span>
 
 <span class="sd">        Returns:</span>
 <span class="sd">            The 2-tuple `(fig, ax)` giving the matplotlib figure and axis.</span>
 
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">dataframe</span><span class="p">(</span><span class="n">concentrations</span><span class="p">)</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">dataframe</span><span class="p">(</span><span class="n">concentrations</span><span class="p">,</span> <span class="n">extend</span><span class="o">=</span><span class="mi">0</span> <span class="k">if</span> <span class="n">draw_in_bounds</span> <span class="k">else</span> <span class="mf">0.1</span><span class="p">)</span>
 
         <span class="k">if</span> <span class="n">ax</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="n">fig</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">()</span>
@@ -1352,7 +1357,7 @@ <h1>Source code for neutcurve.hillcurve</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="HillCurve.dataframe">
 <a class="viewcode-back" href="../../neutcurve.hillcurve.html#neutcurve.hillcurve.HillCurve.dataframe">[docs]</a>
-    <span class="k">def</span> <span class="nf">dataframe</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">concentrations</span><span class="o">=</span><span class="s2">&quot;auto&quot;</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">dataframe</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">concentrations</span><span class="o">=</span><span class="s2">&quot;auto&quot;</span><span class="p">,</span> <span class="n">extend</span><span class="o">=</span><span class="mf">0.1</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Get data frame with curve data for plotting.</span>
 
 <span class="sd">        Useful if you want to get both the points and the fit</span>
@@ -1364,6 +1369,9 @@ <h1>Source code for neutcurve.hillcurve</h1><div class="highlight"><pre>
 <span class="sd">                If &#39;auto&#39; the automatically computed from data</span>
 <span class="sd">                range using :func:`concentrationRange`. If</span>
 <span class="sd">                &#39;measured&#39; then only include measured values.</span>
+<span class="sd">            `extend` (float)</span>
+<span class="sd">                The value passed to :func:`concentrationRange` if `concentrations`</span>
+<span class="sd">                is &#39;auto&#39;.</span>
 
 <span class="sd">        Returns:</span>
 <span class="sd">            A pandas DataFrame with the following columns:</span>
@@ -1376,7 +1384,7 @@ <h1>Source code for neutcurve.hillcurve</h1><div class="highlight"><pre>
 
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="n">concentrations</span> <span class="o">==</span> <span class="s2">&quot;auto&quot;</span><span class="p">:</span>
-            <span class="n">concentrations</span> <span class="o">=</span> <span class="n">concentrationRange</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">cs</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">cs</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
+            <span class="n">concentrations</span> <span class="o">=</span> <span class="n">concentrationRange</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">cs</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="bp">self</span><span class="o">.</span><span class="n">cs</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">extend</span><span class="o">=</span><span class="n">extend</span><span class="p">)</span>
         <span class="k">elif</span> <span class="n">concentrations</span> <span class="o">==</span> <span class="s2">&quot;measured&quot;</span><span class="p">:</span>
             <span class="n">concentrations</span> <span class="o">=</span> <span class="p">[]</span>
         <span class="n">concentrations</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">concatenate</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">cs</span><span class="p">,</span> <span class="n">concentrations</span><span class="p">])</span>

diff --git a/_static/documentation_options.js b/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '2.0.0',
+    VERSION: '2.1.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/acknowledgments.html b/acknowledgments.html
@@ -5,10 +5,10 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Acknowledgements &#8212; neutcurve 2.0.0 documentation</title>
+    <title>Acknowledgements &#8212; neutcurve 2.1.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b76e3c8a" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=c878986b" />
-    <script src="_static/documentation_options.js?v=51b770b3"></script>
+    <script src="_static/documentation_options.js?v=20623aea"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>

diff --git a/combine_curvefits.html b/combine_curvefits.html
@@ -5,11 +5,11 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Combining CurveFits objects &#8212; neutcurve 2.0.0 documentation</title>
+    <title>Combining CurveFits objects &#8212; neutcurve 2.1.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b76e3c8a" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=c878986b" />
     <link rel="stylesheet" type="text/css" href="_static/nbsphinx-code-cells.css?v=2aa19091" />
-    <script src="_static/documentation_options.js?v=51b770b3"></script>
+    <script src="_static/documentation_options.js?v=20623aea"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>

diff --git a/constrain_params_range.html b/constrain_params_range.html
@@ -5,11 +5,11 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Constrain fit parameters to a range of reasonable values &#8212; neutcurve 2.0.0 documentation</title>
+    <title>Constrain fit parameters to a range of reasonable values &#8212; neutcurve 2.1.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=b76e3c8a" />
     <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=c878986b" />
     <link rel="stylesheet" type="text/css" href="_static/nbsphinx-code-cells.css?v=2aa19091" />
-    <script src="_static/documentation_options.js?v=51b770b3"></script>
+    <script src="_static/documentation_options.js?v=20623aea"></script>
     <script src="_static/doctools.js?v=888ff710"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>