htdocs update (master)

Author: DiamondLightSource-build-server

documentation/programs/dials_cosym.html

@@ -281,7 +281,7 @@ <h2>Example<a class="headerlink" href="#example" title="Link to this heading">¶
 <div class="header docutils container">
 <p><strong>Show/Hide Log</strong></p>
 </div>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>DIALS 3.dev.1271-gd77d5dad1
 The following parameters have been modified:
 
 input {

documentation/tutorials/mpro_x0692.html

@@ -79,7 +79,7 @@ <h3>Import<a class="headerlink" href="#import" title="Link to this heading">¶</
 </div>
 <p>The output just describes what the software understands of the images it was
 passed, in this case one sequence of data containing 400 images:</p>
-<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>DIALS 3.dev.1271-gd77d5dad1
 The following parameters have been modified:
 
 input {
@@ -128,7 +128,7 @@ <h3>Find Spots<a class="headerlink" href="#find-spots" title="Link to this headi
 <div class="header docutils container">
 <p><strong>Show/Hide Log</strong></p>
 </div>
-<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1271-gd77d5dad1
 <span class="linenos">  2</span>The following parameters have been modified:
 <span class="linenos">  3</span>
 <span class="linenos">  4</span>spotfinder {
@@ -637,7 +637,7 @@ <h3>Indexing<a class="headerlink" href="#indexing" title="Link to this heading">
 <div class="header docutils container">
 <p><strong>Show/Hide Log</strong></p>
 </div>
-<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1271-gd77d5dad1
 <span class="linenos">  2</span>The following parameters have been modified:
 <span class="linenos">  3</span>
 <span class="linenos">  4</span>input {
@@ -1365,7 +1365,7 @@ <h3>Bravais Lattice Refinement<a class="headerlink" href="#bravais-lattice-refin
 <div class="header docutils container">
 <p><strong>Show/Hide Log</strong></p>
 </div>
-<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos"> 1</span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos"> 1</span>DIALS 3.dev.1271-gd77d5dad1
 <span class="linenos"> 2</span>The following parameters have been modified:
 <span class="linenos"> 3</span>
 <span class="linenos"> 4</span>refinement {
@@ -1474,7 +1474,7 @@ <h3>Bravais Lattice Refinement<a class="headerlink" href="#bravais-lattice-refin
 <div class="header docutils container">
 <p><strong>Show/Hide Log</strong></p>
 </div>
-<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos"> 1</span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos"> 1</span>DIALS 3.dev.1271-gd77d5dad1
 <span class="linenos"> 2</span>The following parameters have been modified:
 <span class="linenos"> 3</span>
 <span class="linenos"> 4</span>refinement {
@@ -1599,7 +1599,7 @@ <h3>Integration<a class="headerlink" href="#integration" title="Link to this hea
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 </div>
-<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">   1</span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">   1</span>DIALS 3.dev.1271-gd77d5dad1
 <span class="linenos">   2</span>The following parameters have been modified:
 <span class="linenos">   3</span>integration {
 <span class="linenos">   4</span>  mp {
@@ -2149,12 +2149,12 @@ <h3>Integration<a class="headerlink" href="#integration" title="Link to this hea
 <span class="linenos"> 548</span>
 <span class="linenos"> 549</span>Timing information for reference profile formation
 <span class="linenos"> 550</span>+-------------------+---------------+
-<span class="linenos"> 551</span>| Read time         | 16.78 seconds |
-<span class="linenos"> 552</span>| Extract time      | 0.40 seconds  |
+<span class="linenos"> 551</span>| Read time         | 17.85 seconds |
+<span class="linenos"> 552</span>| Extract time      | 0.41 seconds  |
 <span class="linenos"> 553</span>| Pre-process time  | 0.02 seconds  |
-<span class="linenos"> 554</span>| Process time      | 9.23 seconds  |
+<span class="linenos"> 554</span>| Process time      | 9.28 seconds  |
 <span class="linenos"> 555</span>| Post-process time | 0.00 seconds  |
-<span class="linenos"> 556</span>| Total time        | 26.53 seconds |
+<span class="linenos"> 556</span>| Total time        | 27.67 seconds |
 <span class="linenos"> 557</span>+-------------------+---------------+
 <span class="linenos"> 558</span>
 <span class="linenos"> 559</span>================================================================================
@@ -2685,12 +2685,12 @@ <h3>Integration<a class="headerlink" href="#integration" title="Link to this hea
 <span class="linenos">1084</span>
 <span class="linenos">1085</span>Timing information for integration
 <span class="linenos">1086</span>+-------------------+----------------+
-<span class="linenos">1087</span>| Read time         | 18.80 seconds  |
-<span class="linenos">1088</span>| Extract time      | 6.46 seconds   |
+<span class="linenos">1087</span>| Read time         | 23.70 seconds  |
+<span class="linenos">1088</span>| Extract time      | 7.81 seconds   |
 <span class="linenos">1089</span>| Pre-process time  | 0.27 seconds   |
-<span class="linenos">1090</span>| Process time      | 136.88 seconds |
+<span class="linenos">1090</span>| Process time      | 141.35 seconds |
 <span class="linenos">1091</span>| Post-process time | 0.00 seconds   |
-<span class="linenos">1092</span>| Total time        | 163.42 seconds |
+<span class="linenos">1092</span>| Total time        | 174.24 seconds |
 <span class="linenos">1093</span>+-------------------+----------------+
 <span class="linenos">1094</span>
 <span class="linenos">1095</span>Removing 22844 unintegrated reflections of 199389 total
@@ -2742,7 +2742,7 @@ <h3>Symmetry analysis<a class="headerlink" href="#symmetry-analysis" title="Link
 <div class="header docutils container">
 <p><strong>Show/Hide Log</strong></p>
 </div>
-<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1271-gd77d5dad1
 <span class="linenos">  2</span>The following parameters have been modified:
 <span class="linenos">  3</span>
 <span class="linenos">  4</span>best_monoclinic_beta = False
@@ -2914,7 +2914,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
 <div class="header docutils container">
 <p><strong>Show/Hide Log</strong></p>
 </div>
-<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1271-gd77d5dad1
 <span class="linenos">  2</span>The following parameters have been modified:
 <span class="linenos">  3</span>input {
 <span class="linenos">  4</span>  experiments = symmetrized.expt
@@ -2983,7 +2983,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
 <span class="linenos"> 67</span>Components to be refined in this cycle for all datasets: scale, decay, absorption
 <span class="linenos"> 68</span>Performing a round of scaling with an LBFGS minimizer. 
 <span class="linenos"> 69</span>
-<span class="linenos"> 70</span>Time taken for refinement 7.65
+<span class="linenos"> 70</span>Time taken for refinement 7.74
 <span class="linenos"> 71</span>
 <span class="linenos"> 72</span>Refinement steps:
 <span class="linenos"> 73</span>+--------+--------+----------+
@@ -3125,7 +3125,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
 <span class="linenos">209</span>Components to be refined in this cycle for all datasets: scale, decay, absorption
 <span class="linenos">210</span>Performing a round of scaling with a Levenberg-Marquardt minimizer.
 <span class="linenos">211</span>
-<span class="linenos">212</span>Time taken for refinement 4.37
+<span class="linenos">212</span>Time taken for refinement 4.40
 <span class="linenos">213</span>
 <span class="linenos">214</span>Refinement steps:
 <span class="linenos">215</span>+--------+--------+----------+
@@ -3149,7 +3149,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
 <span class="linenos">233</span>Components to be refined in this cycle for all datasets: scale, decay, absorption
 <span class="linenos">234</span>Performing a round of scaling with a Levenberg-Marquardt minimizer.
 <span class="linenos">235</span>
-<span class="linenos">236</span>Time taken for refinement 0.90
+<span class="linenos">236</span>Time taken for refinement 0.91
 <span class="linenos">237</span>
 <span class="linenos">238</span>Refinement steps:
 <span class="linenos">239</span>+--------+--------+----------+
@@ -3199,7 +3199,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
 <span class="linenos">283</span>The reflection table variances have been adjusted to account for the
 <span class="linenos">284</span>uncertainty in the scaling model
 <span class="linenos">285</span>
-<span class="linenos">286</span>Total time taken: 21.0210s 
+<span class="linenos">286</span>Total time taken: 21.1864s 
 <span class="linenos">287</span>
 <span class="linenos">288</span>================================================================================
 <span class="linenos">289</span>

documentation/tutorials/processing_in_detail_betalactamase.html

@@ -85,7 +85,7 @@ <h3>Import<a class="headerlink" href="#import" title="Link to this heading">¶</
 </div>
 <p>The output just describes what the software understands of the images it was
 passed, in this case one sequence of data containing 720 images:</p>
-<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>DIALS 3.dev.1271-gd77d5dad1
 The following parameters have been modified:
 
 input {
@@ -134,7 +134,7 @@ <h3>Find Spots<a class="headerlink" href="#find-spots" title="Link to this headi
 <div class="header docutils container">
 <p><strong>Show/Hide Log</strong></p>
 </div>
-<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1271-gd77d5dad1
 <span class="linenos">  2</span>The following parameters have been modified:
 <span class="linenos">  3</span>
 <span class="linenos">  4</span>spotfinder {
@@ -965,7 +965,7 @@ <h3>Indexing<a class="headerlink" href="#indexing" title="Link to this heading">
 <div class="header docutils container">
 <p><strong>Show/Hide Log</strong></p>
 </div>
-<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1271-gd77d5dad1
 <span class="linenos">  2</span>The following parameters have been modified:
 <span class="linenos">  3</span>
 <span class="linenos">  4</span>input {
@@ -1693,7 +1693,7 @@ <h3>Bravais Lattice Refinement<a class="headerlink" href="#bravais-lattice-refin
 <div class="header docutils container">
 <p><strong>Show/Hide Log</strong></p>
 </div>
-<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1271-gd77d5dad1
 <span class="linenos">  2</span>The following parameters have been modified:
 <span class="linenos">  3</span>
 <span class="linenos">  4</span>input {
@@ -1869,7 +1869,7 @@ <h3>Integration<a class="headerlink" href="#integration" title="Link to this hea
 <div class="header docutils container">
 <p><strong>Show/Hide Log</strong></p>
 </div>
-<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">   1</span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">   1</span>DIALS 3.dev.1271-gd77d5dad1
 <span class="linenos">   2</span>The following parameters have been modified:
 <span class="linenos">   3</span>integration {
 <span class="linenos">   4</span>  mp {
@@ -2717,12 +2717,12 @@ <h3>Integration<a class="headerlink" href="#integration" title="Link to this hea
 <span class="linenos"> 846</span>
 <span class="linenos"> 847</span>Timing information for reference profile formation
 <span class="linenos"> 848</span>+-------------------+---------------+
-<span class="linenos"> 849</span>| Read time         | 63.72 seconds |
-<span class="linenos"> 850</span>| Extract time      | 0.64 seconds  |
+<span class="linenos"> 849</span>| Read time         | 64.71 seconds |
+<span class="linenos"> 850</span>| Extract time      | 0.52 seconds  |
 <span class="linenos"> 851</span>| Pre-process time  | 0.11 seconds  |
-<span class="linenos"> 852</span>| Process time      | 29.55 seconds |
+<span class="linenos"> 852</span>| Process time      | 29.58 seconds |
 <span class="linenos"> 853</span>| Post-process time | 0.00 seconds  |
-<span class="linenos"> 854</span>| Total time        | 94.12 seconds |
+<span class="linenos"> 854</span>| Total time        | 95.15 seconds |
 <span class="linenos"> 855</span>+-------------------+---------------+
 <span class="linenos"> 856</span>
 <span class="linenos"> 857</span>================================================================================
@@ -3573,12 +3573,12 @@ <h3>Integration<a class="headerlink" href="#integration" title="Link to this hea
 <span class="linenos">1702</span>
 <span class="linenos">1703</span>Timing information for integration
 <span class="linenos">1704</span>+-------------------+----------------+
-<span class="linenos">1705</span>| Read time         | 53.51 seconds  |
-<span class="linenos">1706</span>| Extract time      | 2.77 seconds   |
-<span class="linenos">1707</span>| Pre-process time  | 0.47 seconds   |
-<span class="linenos">1708</span>| Process time      | 146.43 seconds |
+<span class="linenos">1705</span>| Read time         | 58.85 seconds  |
+<span class="linenos">1706</span>| Extract time      | 2.83 seconds   |
+<span class="linenos">1707</span>| Pre-process time  | 0.46 seconds   |
+<span class="linenos">1708</span>| Process time      | 145.83 seconds |
 <span class="linenos">1709</span>| Post-process time | 0.00 seconds   |
-<span class="linenos">1710</span>| Total time        | 203.83 seconds |
+<span class="linenos">1710</span>| Total time        | 208.92 seconds |
 <span class="linenos">1711</span>+-------------------+----------------+
 <span class="linenos">1712</span>
 <span class="linenos">1713</span>Removing 41623 unintegrated reflections of 368701 total
@@ -3630,7 +3630,7 @@ <h3>Symmetry analysis<a class="headerlink" href="#symmetry-analysis" title="Link
 <div class="header docutils container">
 <p><strong>Show/Hide Log</strong></p>
 </div>
-<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1271-gd77d5dad1
 <span class="linenos">  2</span>The following parameters have been modified:
 <span class="linenos">  3</span>
 <span class="linenos">  4</span>input {
@@ -3802,7 +3802,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
 <div class="header docutils container">
 <p><strong>Show/Hide Log</strong></p>
 </div>
-<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1268-gfb0c04f54
+<div class="highlight-none notranslate"><div class="highlight"><pre><span></span><span class="linenos">  1</span>DIALS 3.dev.1271-gd77d5dad1
 <span class="linenos">  2</span>The following parameters have been modified:
 <span class="linenos">  3</span>input {
 <span class="linenos">  4</span>  experiments = symmetrized.expt
@@ -3871,7 +3871,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
 <span class="linenos"> 67</span>Components to be refined in this cycle for all datasets: scale, decay, absorption
 <span class="linenos"> 68</span>Performing a round of scaling with an LBFGS minimizer. 
 <span class="linenos"> 69</span>
-<span class="linenos"> 70</span>Time taken for refinement 3.60
+<span class="linenos"> 70</span>Time taken for refinement 3.56
 <span class="linenos"> 71</span>
 <span class="linenos"> 72</span>Refinement steps:
 <span class="linenos"> 73</span>+--------+--------+----------+
@@ -3929,7 +3929,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
 <span class="linenos">125</span>Components to be refined in this cycle for all datasets: scale, decay, absorption
 <span class="linenos">126</span>Performing a round of scaling with an LBFGS minimizer. 
 <span class="linenos">127</span>
-<span class="linenos">128</span>Time taken for refinement 1.01
+<span class="linenos">128</span>Time taken for refinement 1.02
 <span class="linenos">129</span>
 <span class="linenos">130</span>Refinement steps:
 <span class="linenos">131</span>+--------+--------+----------+
@@ -3981,7 +3981,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
 <span class="linenos">177</span>Components to be refined in this cycle for all datasets: scale, decay, absorption
 <span class="linenos">178</span>Performing a round of scaling with a Levenberg-Marquardt minimizer.
 <span class="linenos">179</span>
-<span class="linenos">180</span>Time taken for refinement 3.61
+<span class="linenos">180</span>Time taken for refinement 3.53
 <span class="linenos">181</span>
 <span class="linenos">182</span>Refinement steps:
 <span class="linenos">183</span>+--------+--------+----------+
@@ -4002,7 +4002,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
 <span class="linenos">198</span>Components to be refined in this cycle for all datasets: scale, decay, absorption
 <span class="linenos">199</span>Performing a round of scaling with a Levenberg-Marquardt minimizer.
 <span class="linenos">200</span>
-<span class="linenos">201</span>Time taken for refinement 1.14
+<span class="linenos">201</span>Time taken for refinement 1.11
 <span class="linenos">202</span>
 <span class="linenos">203</span>Refinement steps:
 <span class="linenos">204</span>+--------+--------+----------+
@@ -4052,7 +4052,7 @@ <h3>Scaling and Merging<a class="headerlink" href="#scaling-and-merging" title="
 <span class="linenos">248</span>The reflection table variances have been adjusted to account for the
 <span class="linenos">249</span>uncertainty in the scaling model
 <span class="linenos">250</span>
-<span class="linenos">251</span>Total time taken: 18.8791s 
+<span class="linenos">251</span>Total time taken: 18.6707s 
 <span class="linenos">252</span>
 <span class="linenos">253</span>================================================================================
 <span class="linenos">254</span>