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chapters/extras/delayedarrays.html

@@ -66,7 +66,7 @@
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@@ -310,19 +293,19 @@ <h2 class="anchored" data-anchor-id="quick-start">Quick start</h2>
 <span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>x <span class="op">=</span> numpy.random.rand(<span class="dv">100</span>, <span class="dv">20</span>)</span>
 <span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>x</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-display" data-execution_count="1">
-<pre><code>array([[0.68979015, 0.20248322, 0.01749666, ..., 0.03549872, 0.22937732,
-        0.54040654],
-       [0.87621931, 0.67145471, 0.25943006, ..., 0.68197162, 0.71375692,
-        0.91075305],
-       [0.62215974, 0.14743395, 0.51327641, ..., 0.89469923, 0.78999849,
-        0.11074316],
+<pre><code>array([[0.83036463, 0.77414806, 0.96626442, ..., 0.12923135, 0.31736425,
+        0.78857936],
+       [0.79265308, 0.07398222, 0.58714121, ..., 0.78003994, 0.34102163,
+        0.29819743],
+       [0.83420092, 0.62119145, 0.32038443, ..., 0.18527618, 0.92213425,
+        0.98321539],
        ...,
-       [0.45554749, 0.89359346, 0.919647  , ..., 0.34600461, 0.16655526,
-        0.66614957],
-       [0.67307148, 0.38802098, 0.29485673, ..., 0.57726099, 0.07828719,
-        0.86869147],
-       [0.57024268, 0.76646119, 0.02388173, ..., 0.10498704, 0.97908422,
-        0.62380837]])</code></pre>
+       [0.7741491 , 0.61407152, 0.64286211, ..., 0.60549491, 0.35160599,
+        0.27134048],
+       [0.16456797, 0.60802831, 0.11803797, ..., 0.48493342, 0.67072711,
+        0.38908978],
+       [0.90822706, 0.262654  , 0.89459738, ..., 0.0154734 , 0.76876495,
+        0.16738359]])</code></pre>
 </div>
 </div>
 <p>We can wrap this in a <code>DelayedArray</code> class:</p>
@@ -332,19 +315,19 @@ <h2 class="anchored" data-anchor-id="quick-start">Quick start</h2>
 <span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>d</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-display" data-execution_count="2">
 <pre><code>&lt;100 x 20&gt; DelayedArray object of type 'float64'
-[[0.68979015, 0.20248322, 0.01749666, ..., 0.03549872, 0.22937732,
-  0.54040654],
- [0.87621931, 0.67145471, 0.25943006, ..., 0.68197162, 0.71375692,
-  0.91075305],
- [0.62215974, 0.14743395, 0.51327641, ..., 0.89469923, 0.78999849,
-  0.11074316],
+[[0.83036463, 0.77414806, 0.96626442, ..., 0.12923135, 0.31736425,
+  0.78857936],
+ [0.79265308, 0.07398222, 0.58714121, ..., 0.78003994, 0.34102163,
+  0.29819743],
+ [0.83420092, 0.62119145, 0.32038443, ..., 0.18527618, 0.92213425,
+  0.98321539],
  ...,
- [0.45554749, 0.89359346, 0.919647  , ..., 0.34600461, 0.16655526,
-  0.66614957],
- [0.67307148, 0.38802098, 0.29485673, ..., 0.57726099, 0.07828719,
-  0.86869147],
- [0.57024268, 0.76646119, 0.02388173, ..., 0.10498704, 0.97908422,
-  0.62380837]]</code></pre>
+ [0.7741491 , 0.61407152, 0.64286211, ..., 0.60549491, 0.35160599,
+  0.27134048],
+ [0.16456797, 0.60802831, 0.11803797, ..., 0.48493342, 0.67072711,
+  0.38908978],
+ [0.90822706, 0.262654  , 0.89459738, ..., 0.0154734 , 0.76876495,
+  0.16738359]]</code></pre>
 </div>
 </div>
 <p>And then we can use it in a variety of operations. For example, in genomics, a typical quality control task is to slice the matrix to remove uninteresting features (rows) or samples (columns):</p>
@@ -370,14 +353,14 @@ <h2 class="anchored" data-anchor-id="quick-start">Quick start</h2>
 <span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a>transformed[<span class="dv">1</span>:<span class="dv">5</span>,:]</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-display" data-execution_count="5">
 <pre><code>&lt;4 x 7&gt; DelayedArray object of type 'float64'
-[[0.03245719, 0.0172179 , 0.01355181, ..., 0.02323966, 0.01334551,
-  0.00998164],
- [0.02174287, 0.0361274 , 0.03961761, ..., 0.03000277, 0.00403579,
-  0.00472687],
- [0.02650649, 0.01919338, 0.02456315, ..., 0.01862729, 0.00358018,
-  0.00198679],
- [0.01665111, 0.02102558, 0.02956681, ..., 0.01900289, 0.0264652 ,
-  0.01155552]]</code></pre>
+[[0.02304854, 0.01969416, 0.03174706, ..., 0.01874655, 0.01477573,
+  0.03300205],
+ [0.03228073, 0.01189148, 0.02882576, ..., 0.00384962, 0.02672003,
+  0.02503467],
+ [0.02085586, 0.01467898, 0.01461294, ..., 0.03113985, 0.02735327,
+  0.01582188],
+ [0.03059563, 0.02307142, 0.0294344 , ..., 0.02983387, 0.0218299 ,
+  0.03677819]]</code></pre>
 </div>
 </div>
 <p>Each operation just returns a <code>DelayedArray</code> with an increasing stack of delayed operations, without evaluating anything or making any copies. Check out the <a href="https://biocpy.github.io/DelayedArray/">documentation</a> for more information.</p>
@@ -453,19 +436,19 @@ <h2 class="anchored" data-anchor-id="interoperability-with-other-packages">Inter
 <div class="cell" data-execution_count="11">
 <div class="sourceCode cell-code" id="cb20"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb20-1"><a href="#cb20-1" aria-hidden="true" tabindex="-1"></a>d.seed</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-display" data-execution_count="11">
-<pre><code>array([[0.68979015, 0.20248322, 0.01749666, ..., 0.03549872, 0.22937732,
-        0.54040654],
-       [0.87621931, 0.67145471, 0.25943006, ..., 0.68197162, 0.71375692,
-        0.91075305],
-       [0.62215974, 0.14743395, 0.51327641, ..., 0.89469923, 0.78999849,
-        0.11074316],
+<pre><code>array([[0.83036463, 0.77414806, 0.96626442, ..., 0.12923135, 0.31736425,
+        0.78857936],
+       [0.79265308, 0.07398222, 0.58714121, ..., 0.78003994, 0.34102163,
+        0.29819743],
+       [0.83420092, 0.62119145, 0.32038443, ..., 0.18527618, 0.92213425,
+        0.98321539],
        ...,
-       [0.45554749, 0.89359346, 0.919647  , ..., 0.34600461, 0.16655526,
-        0.66614957],
-       [0.67307148, 0.38802098, 0.29485673, ..., 0.57726099, 0.07828719,
-        0.86869147],
-       [0.57024268, 0.76646119, 0.02388173, ..., 0.10498704, 0.97908422,
-        0.62380837]])</code></pre>
+       [0.7741491 , 0.61407152, 0.64286211, ..., 0.60549491, 0.35160599,
+        0.27134048],
+       [0.16456797, 0.60802831, 0.11803797, ..., 0.48493342, 0.67072711,
+        0.38908978],
+       [0.90822706, 0.262654  , 0.89459738, ..., 0.0154734 , 0.76876495,
+        0.16738359]])</code></pre>
 </div>
 </div>
 <p>Each layer has its own specific attributes that define the operation, e.g.,</p>

chapters/extras/index.html

@@ -32,7 +32,7 @@
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