Deployed 61d6dba to v10.0.X with MkDocs 1.6.0 and mike 2.1.1

v10.0.X/index.html

@@ -1798,21 +1798,16 @@ <h2 id="for-developers">For developers</h2>
 <p>We strongly encourage you to contribute any developments you make back to the main repository. 
 See <a href="https://github.com/cms-analysis/HiggsAnalysis-CombinedLimit/blob/main/contributing.md">contributing.md</a> for details about contributing. </p>
 <h2 id="combineharvestercombinetools">CombineHarvester/CombineTools</h2>
+<p>CombineHarvester/CombineTools is a package for the creation of datacards/workspaces used with <span style="font-variant:small-caps;">Combine v10</span> for a number of analyses in CMS. See the <a href="http://cms-analysis.github.io/CombineHarvester/"><code>CombineHarvester</code></a> documentation pages for more details on using this tool and additional features available in the full package.</p>
+<p>This package also comes with useful features for <span style="font-variant:small-caps;">Combine</span> such as the automated datacard validation (see <a href="docs/part3/validation">instructions</a>). The repository can be checked out and compiled using, </p>
+<pre><code class="language-sh">git clone https://github.com/cms-analysis/CombineHarvester.git CombineHarvester
+scram b
+</code></pre>
+<p>See the <a href="http://cms-analysis.github.io/CombineHarvester/"><code>CombineHarvester</code></a> documentation for full instructions and reccomended versions. </p>
 <div class="admonition info">
 <p class="admonition-title">Info</p>
-<p>Starting with <span style="font-variant:small-caps;">Combine v10</span>, CombineTool functionalities for job submition and parallelization (combineTool.py) as well as many plotting functions have been integrated into the <span style="font-variant:small-caps;">Combine</span> package.
-For these tasks you no longer have to follow the instructions below.</p>
+<p>Starting with <span style="font-variant:small-caps;">Combine v10</span>, specific ombineTool functionalities for job submition and parallelization (<code>combineTool.py</code>) as well as many plotting functions have been integrated into the <span style="font-variant:small-caps;">Combine</span> package. For these tasks you no longer have to follow the instructions above.</p>
 </div>
-<p>CombineTools is an additional packages with useful features for <span style="font-variant:small-caps;">Combine</span>, which is used for example for the automated datacard validation (see <a href="docs/part3/validation">instructions</a>).
-Since the repository contains a certain amount of analysis-specific code, the following scripts can be used to clone it with a sparse checkout for just the core <a href="https://github.com/cms-analysis/CombineHarvester/tree/main/CombineTools/"><code>CombineHarvester/CombineTools</code></a> subpackage, speeding up the checkout and compile times:</p>
-<p>git clone via ssh:</p>
-<pre><code class="language-sh">bash &lt;(curl -s https://raw.githubusercontent.com/cms-analysis/CombineHarvester/main/CombineTools/scripts/sparse-checkout-ssh.sh)
-</code></pre>
-<p>git clone via https:</p>
-<pre><code class="language-sh">bash &lt;(curl -s https://raw.githubusercontent.com/cms-analysis/CombineHarvester/main/CombineTools/scripts/sparse-checkout-https.sh)
-</code></pre>
-<p>make sure to run <code>scram</code>  to compile the <code>CombineTools</code> package.</p>
-<p>See the <a href="http://cms-analysis.github.io/CombineHarvester/"><code>CombineHarvester</code></a> documentation pages for more details on using this tool and additional features available in the full package.</p>
 <h2 id="citation">Citation</h2>
 <p>If you use <span style="font-variant:small-caps;">Combine</span>, please cite the following CMS publication <a href="https://arxiv.org/abs/2404.06614">here</a>. </p>
 <details>

v10.0.X/part3/commonstatsmethods/index.html

@@ -2534,7 +2534,7 @@ <h3 id="complex-models">Complex models</h3>
 <p class="admonition-title">Warning</p>
 <p>This option should not be used with <code>--expectedFromGrid</code> if you did not create the grid with the same option. The reason is that the value of the test-statistic that is used to calculate the limit will not be properly calcualted if <code>--noUpdateGrid</code> is included. In future versions of the tool, this option will be ignored if using <code>--expectedFromGrid</code>. </p>
 </div>
-<p>The splitting of the jobs can be left to the user's preference. However, users may wish to use the <strong>combineTool</strong> for automating this, as described in the section on <a href="http://cms-analysis.github.io/HiggsAnalysis-CombinedLimit/part3/runningthetool/#combinetool-for-job-submission">combineTool for job submission</a></p>
+<p>The splitting of the jobs can be left to the user's preference. However, users may wish to use <code>combineTool.py</code> for automating this, as described in the section on <a href="http://cms-analysis.github.io/HiggsAnalysis-CombinedLimit/part3/runningthetool/#combinetool-for-job-submission">combineTool for job submission</a></p>
 <h4 id="plotting">Plotting</h4>
 <p>A plot of the CL<sub>s</sub> (or <span class="arithmatex">\(p_{\mu}\)</span>) as a function of <strong>r</strong>, which is used to find the crossing, can be produced using the option <code>--plot=limit_scan.png</code>. This can be useful for judging if the chosen grid was sufficient for determining the upper limit.</p>
 <p>If we use our <a href="https://github.com/cms-analysis/HiggsAnalysis-CombinedLimit/blob/main/data/tutorials/counting/realistic-counting-experiment.txt">realistic-counting-experiment.txt</a> datacard and generate a grid of points <span class="arithmatex">\(r\varepsilon[1.4,2.2]\)</span> in steps of 0.1, with 5000 toys for each point, the plot of the observed CL<sub>s</sub> vs <strong>r</strong> should look like the following,</p>
@@ -2579,7 +2579,7 @@ <h3 id="observed-significance">Observed significance</h3>
 <h3 id="expected-significance-assuming-some-signal">Expected significance, assuming some signal</h3>
 <p>The <em>expected</em> significance, assuming a signal with <strong>r=X</strong> can be calculated, by including the option <code>--expectSignal X</code> when generating the distribution of the test statistic and using the option <code>--expectedFromGrid=0.5</code> when calculating the significance for the median. To get the ±1σ bands, use 0.16 and 0.84 instead of 0.5, and so on.</p>
 <p>The total number of background toys needs to be large enough to compute the value of the significance, but you need fewer signal toys (especially when you are only computing the median expected significance). For large significances, you can run most of the toys without the <code>--fullBToys</code> option, which will be about a factor 2 faster. Only a small part of the toys needs to be run with that option turned on.</p>
-<p>As with calculating limits with toys, these jobs can be submitted to the grid or batch systems with the help of the <code>combineTool</code>, as described in the section on <a href="http://cms-analysis.github.io/HiggsAnalysis-CombinedLimit/part3/runningthetool/#combinetool-for-job-submission">combineTool for job submission</a></p>
+<p>As with calculating limits with toys, these jobs can be submitted to the grid or batch systems with the help of the <code>combineTool.py</code> script, as described in the section on <a href="http://cms-analysis.github.io/HiggsAnalysis-CombinedLimit/part3/runningthetool/#combinetool-for-job-submission">combineTool for job submission</a></p>
 <h2 id="goodness-of-fit-tests">Goodness of fit tests</h2>
 <p>The <code>GoodnessOfFit</code> method can be used to evaluate how compatible the observed data are with the model PDF.</p>
 <p>This method implements several algorithms, and will compute a goodness of fit indicator for the chosen algorithm and the data. The procedure is therefore to first run on the real data</p>
@@ -2650,7 +2650,7 @@ <h3 id="masking-analysis-regions-in-the-saturated-model">Masking analysis region
 <p><img alt="" src="../images/gof_CRonly.png" /></p>
 </details>
 <h3 id="making-a-plot-of-the-gof-test-statistic-distribution">Making a plot of the GoF test statistic distribution</h3>
-<p>If you have also checked out the <a href="http://cms-analysis.github.io/HiggsAnalysis-CombinedLimit/#combine-tool">combineTool</a>, you can use this to run batch jobs or on the grid (see <a href="http://cms-analysis.github.io/HiggsAnalysis-CombinedLimit/part3/runningthetool/#combinetool-for-job-submission">here</a>) and produce a plot of the results. Once the jobs have completed, you can hadd them together and run (e.g for the saturated model),</p>
+<p>You can use the <code>combineTool.py</code> script to run batch jobs or on the grid (see <a href="http://cms-analysis.github.io/HiggsAnalysis-CombinedLimit/part3/runningthetool/#combinetool-for-job-submission">here</a>) and produce a plot of the results. Once the jobs have completed, you can hadd them together and run (e.g for the saturated model),</p>
 <pre><code class="language-sh">combineTool.py -M CollectGoodnessOfFit --input data_run.root toys_run.root -m 125.0 -o gof.json
 plotGof.py gof.json --statistic saturated --mass 125.0 -o gof_plot --title-right=&quot;my label&quot;
 </code></pre>

v10.0.X/part3/nonstandard/index.html

@@ -1892,7 +1892,7 @@ <h2 id="scaling-constraints">Scaling constraints</h2>
 <h2 id="nuisance-parameter-impacts">Nuisance parameter impacts</h2>
 <p>The impact of a nuisance parameter (NP) θ on a parameter of interest (POI) μ is defined as the shift Δμ that is induced as θ is fixed and brought to its +1σ or −1σ post-fit values, with all other parameters profiled as normal (see <a href="https://link.springer.com/article/10.1007/JHEP01(2015)069">JHEP 01 (2015) 069</a> for a description of this method).</p>
 <p>This is effectively a measure of the correlation between the NP and the POI, and is useful for determining which NPs have the largest effect on the POI uncertainty.</p>
-<p>It is possible to use the <code>MultiDimFit</code> method of <span style="font-variant:small-caps;">Combine</span> with the option <code>--algo impact -P parameter</code> to calculate the impact of a particular nuisance parameter on the parameter(s) of interest. We will use the <code>combineTool.py</code> script to automate the fits (see the <a href="http://cms-analysis.github.io/HiggsAnalysis-CombinedLimit/#combine-tool"><code>combineTool</code></a> section to check out the tool.</p>
+<p>It is possible to use the <code>MultiDimFit</code> method of <span style="font-variant:small-caps;">Combine</span> with the option <code>--algo impact -P parameter</code> to calculate the impact of a particular nuisance parameter on the parameter(s) of interest. We will use the <code>combineTool.py</code> script to automate the fits.</p>
 <p>We will use an example workspace from the <a href="https://github.com/cms-analysis/HiggsAnalysis-CombinedLimit/blob/main/data/tutorials/htt/125/htt_tt.txt"><span class="arithmatex">\(H\rightarrow\tau\tau\)</span> datacard</a>,</p>
 <pre><code>$ cp HiggsAnalysis/CombinedLimit/data/tutorials/htt/125/htt_tt.txt .
 $ text2workspace.py htt_tt.txt -m 125

v10.0.X/part3/runningthetool/index.html

@@ -1847,7 +1847,7 @@ <h3 id="loading-snapshots">Loading snapshots</h3>
 </li>
 </ul>
 <h2 id="combinetool-for-job-submission">combineTool for job submission</h2>
-<p>For longer tasks that cannot be run locally, several methods in <span style="font-variant:small-caps;">Combine</span> can be split to run on a <em>batch</em> system or on the <em>Grid</em>. The splitting and submission is handled using the <code>combineTool</code> (see <a href="http://cms-analysis.github.io/HiggsAnalysis-CombinedLimit/#combine-tool">this getting started</a> section to check out the tool)</p>
+<p>For longer tasks that cannot be run locally, several methods in <span style="font-variant:small-caps;">Combine</span> can be split to run on a <em>batch</em> system or on the <em>Grid</em>. The splitting and submission is handled using the <code>combineTool.py</code> script.</p>
 <h3 id="submission-to-condor">Submission to Condor</h3>
 <p>The syntax for running on condor with the tool is</p>
 <pre><code class="language-sh">combineTool.py -M ALGO [options] --job-mode condor --sub-opts='CLASSADS' --task-name NAME [--dry-run]

v10.0.X/part3/validation/index.html

@@ -1477,8 +1477,8 @@
 
 <h1 id="validating-datacards">Validating datacards</h1>
 <p>This section covers the main features of the datacard validation tool that helps you spot potential problems with your datacards at an early stage. The tool is implemented
-in the <a href="https://github.com/cms-analysis/CombineHarvester/blob/113x/CombineTools"><code>CombineHarvester/CombineTools</code></a> subpackage. See the <a href="http://cms-analysis.github.io/HiggsAnalysis-CombinedLimit/#combine-tool"><code>combineTool</code></a> 
-section of the documentation for checkout instructions.</p>
+in the <a href="https://github.com/cms-analysis/CombineHarvester/blob/113x/CombineTools"><code>CombineHarvester/CombineTools</code></a> subpackage. See the <a href="https://cms-analysis.github.io/HiggsAnalysis-CombinedLimit/latest/#combineharvestercombinetools"><code>combineTool</code></a> 
+section of the documentation for checkout instructions for the full tool, which is needed for this task.</p>
 <p>The datacard validation tool contains a number of checks. It is possible to call subsets of these checks when creating datacards within <code>CombineHarvester</code>. However, for now we will only
 describe the usage of the validation tool on already existing datacards. If you create your datacards with <code>CombineHarvester</code> and would like to include the checks at the datacard creation
 stage, please contact us via <a href="https://cms-talk.web.cern.ch/c/physics/cat/cat-stats/279">https://cms-talk.web.cern.ch/c/physics/cat/cat-stats/279</a>.</p>