HEP-PBSP · comane · Jul 2, 2023 · Jul 3, 2023 · Jul 3, 2023 · Jul 3, 2023
diff --git a/.gitignore b/.gitignore
@@ -60,7 +60,7 @@ cmake_install.cmake
 install_manifest.txt
 compile_commands.json
 CTestTestfile.cmake
-build
+#build
 
 ### JupyterNotebook ###
 .ipynb_checkpoints
@@ -305,7 +305,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
-build/
+#build/
 develop-eggs/
 dist/
 downloads/
@@ -355,7 +355,7 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/_build/
+#docs/_build/
 
 # PyBuilder
 target/

diff --git a/docs/.nojekyll b/docs/.nojekyll
diff --git a/docs/index.html b/docs/index.html
@@ -0,0 +1 @@
+<meta http-equiv="refresh" content="0; url=./sphinx/build/html/index.html" />
diff --git a/docs/sphinx/README.md b/docs/sphinx/README.md
@@ -0,0 +1,26 @@
+The following are needed for the documentation set-up:
+
+- conda install sphinx
+- conda install sphinxcontrib-bibtex
+- conda install sphinx-book-theme
+
+(See e.g. https://sphinx-themes.org/ for other choices of themes)
+
+
+From within the sphinx directory:
+
+- sphinx-build -b html source build
+- or 'make html'
+
+
+Then 'open build/html/index.html' will open the webpage.
+
+
+Important files:
+
+- sphinx/source/conf.py configures the set-up.  The project name, authors, version as well as extensions and project theme can all be changed here.
+- sphinx/source/index.rst is the 'front page', and table of contents etc are specified here
+- sphinx/source/simunet_analysis.rst contains some first basic examples of how we can generate documentation directly from the code docstrings.
+
+
+See also https://www.sphinx-doc.org/en/master/index.html for much more info on Sphinx
diff --git a/docs/sphinx/build/doctrees/bibliography.doctree b/docs/sphinx/build/doctrees/bibliography.doctree
diff --git a/docs/sphinx/build/doctrees/datasets.doctree b/docs/sphinx/build/doctrees/datasets.doctree
diff --git a/docs/sphinx/build/doctrees/environment.pickle b/docs/sphinx/build/doctrees/environment.pickle
diff --git a/docs/sphinx/build/doctrees/features.doctree b/docs/sphinx/build/doctrees/features.doctree
diff --git a/docs/sphinx/build/doctrees/index.doctree b/docs/sphinx/build/doctrees/index.doctree
diff --git a/docs/sphinx/build/doctrees/methodology.doctree b/docs/sphinx/build/doctrees/methodology.doctree
diff --git a/docs/sphinx/build/doctrees/results/drellyan.doctree b/docs/sphinx/build/doctrees/results/drellyan.doctree
diff --git a/docs/sphinx/build/doctrees/results/overview.doctree b/docs/sphinx/build/doctrees/results/overview.doctree
diff --git a/docs/sphinx/build/doctrees/results/top.doctree b/docs/sphinx/build/doctrees/results/top.doctree
diff --git a/docs/sphinx/build/doctrees/results/top_simultaneous.doctree b/docs/sphinx/build/doctrees/results/top_simultaneous.doctree
diff --git a/docs/sphinx/build/doctrees/results/top_sm.doctree b/docs/sphinx/build/doctrees/results/top_sm.doctree
diff --git a/docs/sphinx/build/doctrees/results/top_smeft.doctree b/docs/sphinx/build/doctrees/results/top_smeft.doctree
diff --git a/docs/sphinx/build/doctrees/simunet_analysis.doctree b/docs/sphinx/build/doctrees/simunet_analysis.doctree
diff --git a/docs/sphinx/build/doctrees/tutorials/Installation.doctree b/docs/sphinx/build/doctrees/tutorials/Installation.doctree
diff --git a/docs/sphinx/build/doctrees/tutorials/contaminated_fit.doctree b/docs/sphinx/build/doctrees/tutorials/contaminated_fit.doctree
diff --git a/docs/sphinx/build/doctrees/tutorials/simu_closure_test.doctree b/docs/sphinx/build/doctrees/tutorials/simu_closure_test.doctree
diff --git a/docs/sphinx/build/doctrees/tutorials/simu_fit.doctree b/docs/sphinx/build/doctrees/tutorials/simu_fit.doctree
diff --git a/docs/sphinx/build/doctrees/tutorials/tutorials_overview.doctree b/docs/sphinx/build/doctrees/tutorials/tutorials_overview.doctree
diff --git a/docs/sphinx/build/html/.buildinfo b/docs/sphinx/build/html/.buildinfo
@@ -0,0 +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: 81a4d505685fc20ab270645bf4144170
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/sphinx/build/html/_images/cont_effects.png b/docs/sphinx/build/html/_images/cont_effects.png
diff --git a/docs/sphinx/build/html/_images/ctg_plot.png b/docs/sphinx/build/html/_images/ctg_plot.png
diff --git a/docs/sphinx/build/html/_images/fitH_gg_lumi.png b/docs/sphinx/build/html/_images/fitH_gg_lumi.png
diff --git a/docs/sphinx/build/html/_images/fitH_gg_lumi_unc.png b/docs/sphinx/build/html/_images/fitH_gg_lumi_unc.png
diff --git a/docs/sphinx/build/html/_images/fitH_vs_notop_vs_40_g_172.png b/docs/sphinx/build/html/_images/fitH_vs_notop_vs_40_g_172.png
diff --git a/docs/sphinx/build/html/_images/fitH_vs_notop_vs_40_g_172_unc.png b/docs/sphinx/build/html/_images/fitH_vs_notop_vs_40_g_172_unc.png
diff --git a/docs/sphinx/build/html/_images/np_values.png b/docs/sphinx/build/html/_images/np_values.png
diff --git a/docs/sphinx/build/html/_images/pdf_eft_corr.png b/docs/sphinx/build/html/_images/pdf_eft_corr.png
diff --git a/docs/sphinx/build/html/_images/pdf_shift_lumis.png b/docs/sphinx/build/html/_images/pdf_shift_lumis.png
diff --git a/docs/sphinx/build/html/_images/plot_bsm_corr_linear.png b/docs/sphinx/build/html/_images/plot_bsm_corr_linear.png
diff --git a/docs/sphinx/build/html/_images/plot_bsm_corr_quad.png b/docs/sphinx/build/html/_images/plot_bsm_corr_quad.png
diff --git a/docs/sphinx/build/html/_images/plot_fisher_information_by_sector.png b/docs/sphinx/build/html/_images/plot_fisher_information_by_sector.png
diff --git a/docs/sphinx/build/html/_images/simunet-DY-WY.png b/docs/sphinx/build/html/_images/simunet-DY-WY.png
diff --git a/docs/sphinx/build/html/_images/simunet-DY-qq.png b/docs/sphinx/build/html/_images/simunet-DY-qq.png
diff --git a/docs/sphinx/build/html/_images/simunet_figure.png b/docs/sphinx/build/html/_images/simunet_figure.png
diff --git a/docs/sphinx/build/html/_images/sm_smeft_pdf.png b/docs/sphinx/build/html/_images/sm_smeft_pdf.png
diff --git a/docs/sphinx/build/html/_images/smeft-pdf-95cl-bounds.png b/docs/sphinx/build/html/_images/smeft-pdf-95cl-bounds.png
diff --git a/docs/sphinx/build/html/_images/smeft_lin_nlo_comparison.png b/docs/sphinx/build/html/_images/smeft_lin_nlo_comparison.png
diff --git a/docs/sphinx/build/html/_images/smeft_quad_nlo_comparison.png b/docs/sphinx/build/html/_images/smeft_quad_nlo_comparison.png
diff --git a/docs/sphinx/build/html/_images/wilsons_summary.png b/docs/sphinx/build/html/_images/wilsons_summary.png
diff --git a/docs/sphinx/build/html/_modules/index.html b/docs/sphinx/build/html/_modules/index.html
@@ -0,0 +1,332 @@
+
+
+<!DOCTYPE html>
+
+
+<html lang="en" >
+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Overview: module code &#8212; SIMUnet  documentation</title>
+
+
+
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
+    document.documentElement.dataset.theme = localStorage.getItem("theme") || "light";
+  </script>
+
+  <!-- Loaded before other Sphinx assets -->
+  <link href="../_static/styles/theme.css?digest=e353d410970836974a52" rel="stylesheet" />
+<link href="../_static/styles/bootstrap.css?digest=e353d410970836974a52" rel="stylesheet" />
+<link href="../_static/styles/pydata-sphinx-theme.css?digest=e353d410970836974a52" rel="stylesheet" />
+
+
+  <link href="../_static/vendor/fontawesome/6.1.2/css/all.min.css?digest=e353d410970836974a52" rel="stylesheet" />
+  <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.1.2/webfonts/fa-solid-900.woff2" />
+<link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.1.2/webfonts/fa-brands-400.woff2" />
+<link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.1.2/webfonts/fa-regular-400.woff2" />
+
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
+    <link rel="stylesheet" href="../_static/styles/sphinx-book-theme.css?digest=14f4ca6b54d191a8c7657f6c759bf11a5fb86285" type="text/css" />
+    <link rel="stylesheet" type="text/css" href="../_static/copybutton.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/custom.css" />
+
+  <!-- Pre-loaded scripts that we'll load fully later -->
+  <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=e353d410970836974a52" />
+<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=e353d410970836974a52" />
+
+    <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
+    <script src="../_static/jquery.js"></script>
+    <script src="../_static/underscore.js"></script>
+    <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
+    <script src="../_static/doctools.js"></script>
+    <script src="../_static/clipboard.min.js"></script>
+    <script src="../_static/copybutton.js"></script>
+    <script src="../_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
+    <script src="../_static/theme_logo_switcher.js"></script>
+    <script src="../_static/no_sidebar_overlap.js"></script>
+    <script>DOCUMENTATION_OPTIONS.pagename = '_modules/index';</script>
+    <link rel="shortcut icon" href="../_static/favicon.ico"/>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" />
+  <meta name="viewport" content="width=device-width, initial-scale=1"/>
+  <meta name="docsearch:language" content="en"/>
+  </head>
+
+
+  <body data-bs-spy="scroll" data-bs-target=".bd-toc-nav" data-offset="180" data-bs-root-margin="0px 0px -60%" data-default-mode="">
+
+
+
+  <a class="skip-link" href="#main-content">Skip to main content</a>
+
+  <input type="checkbox"
+          class="sidebar-toggle"
+          name="__primary"
+          id="__primary"/>
+  <label class="overlay overlay-primary" for="__primary"></label>
+
+  <input type="checkbox"
+          class="sidebar-toggle"
+          name="__secondary"
+          id="__secondary"/>
+  <label class="overlay overlay-secondary" for="__secondary"></label>
+
+  <div class="search-button__wrapper">
+    <div class="search-button__overlay"></div>
+    <div class="search-button__search-container">
+<form class="bd-search d-flex align-items-center"
+      action="../search.html"
+      method="get">
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+         class="form-control"
+         name="q"
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+         placeholder="Search..."
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+         spellcheck="false"/>
+  <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
+</form></div>
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+  <div class="sidebar-header-items sidebar-primary__section">
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+    <div class="sidebar-primary-items__start sidebar-primary__section">
+        <div class="sidebar-primary-item">
+
+
+<a class="navbar-brand logo" href="../index.html">
+
+
+
+
+
+
+
+
+
+    <img src="../_static/PBSP_white_line.png" class="logo__image only-light" alt="Logo image"/>
+    <script>document.write(`<img src="../_static/PBSP_white_line.png" class="logo__image only-dark" alt="Logo image"/>`);</script>
+
+
+</a></div>
+        <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
+    <div class="bd-toc-item navbar-nav active">
+        <ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="../methodology.html"><strong>Methodology</strong></a></li>
+<li class="toctree-l1"><a class="reference internal" href="../features.html"><strong>Features</strong></a></li>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../tutorials/tutorials_overview.html"><strong>Tutorials</strong></a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/Installation.html">SIMUnet installation guide</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/simu_fit.html">Simultaneous fits</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/contaminated_fit.html">Contaminated fits</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../tutorials/simu_closure_test.html">SIMUnet closure test</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../datasets.html"><strong>Dataset selection</strong></a></li>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../results/overview.html"><strong>Results</strong></a><input class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-2"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../results/drellyan.html">The Drell-Yan sector</a></li>
+<li class="toctree-l2 has-children"><a class="reference internal" href="../results/top.html">The Top Sector</a><input class="toctree-checkbox" id="toctree-checkbox-3" name="toctree-checkbox-3" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-3"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l3"><a class="reference internal" href="../results/top_sm.html">SM PDF fits</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../results/top_smeft.html">SMEFT-only fit</a></li>
+<li class="toctree-l3"><a class="reference internal" href="../results/top_simultaneous.html">Simultaneous SMEFT and PDF fits</a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../simunet_analysis.html"><strong>Functions documentation</strong></a></li>
+<li class="toctree-l1"><a class="reference internal" href="../bibliography.html"><strong>Bibliography</strong></a></li>
+</ul>
+
+    </div>
+</nav></div>
+    </div>
+
+
+  <div class="sidebar-primary-items__end sidebar-primary__section">
+  </div>
+
+  <div id="rtd-footer-container"></div>
+
+
+      </div>
+
+      <main id="main-content" class="bd-main">
+
+
+
+<div class="sbt-scroll-pixel-helper"></div>
+
+          <div class="bd-content">
+            <div class="bd-article-container">
+
+              <div class="bd-header-article">
+<div class="header-article-items header-article__inner">
+
+    <div class="header-article-items__start">
+
+        <div class="header-article-item"><label class="sidebar-toggle primary-toggle btn btn-sm" for="__primary" title="Toggle primary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
+  <span class="fa-solid fa-bars"></span>
+</label></div>
+
+    </div>
+
+
+    <div class="header-article-items__end">
+
+        <div class="header-article-item">
+
+<div class="article-header-buttons">
+
+
+
+<button onclick="toggleFullScreen()"
+  class="btn btn-sm btn-fullscreen-button"
+  title="Fullscreen mode"
+  data-bs-placement="bottom" data-bs-toggle="tooltip"
+>
+
+
+<span class="btn__icon-container">
+  <i class="fas fa-expand"></i>
+  </span>
+
+</button>
+
+
+<script>
+document.write(`
+  <button class="theme-switch-button btn btn-sm btn-outline-primary navbar-btn rounded-circle" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
+    <span class="theme-switch" data-mode="light"><i class="fa-solid fa-sun"></i></span>
+    <span class="theme-switch" data-mode="dark"><i class="fa-solid fa-moon"></i></span>
+    <span class="theme-switch" data-mode="auto"><i class="fa-solid fa-circle-half-stroke"></i></span>
+  </button>
+`);
+</script>
+
+<script>
+document.write(`
+  <button class="btn btn-sm navbar-btn search-button search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
+    <i class="fa-solid fa-magnifying-glass"></i>
+  </button>
+`);
+</script>
+
+</div></div>
+
+    </div>
+
+</div>
+</div>
+
+
+
+<div id="jb-print-docs-body" class="onlyprint">
+    <h1></h1>
+    <!-- Table of contents -->
+    <div id="print-main-content">
+        <div id="jb-print-toc">
+
+        </div>
+    </div>
+</div>
+
+
+
+<div id="searchbox"></div>
+                <article class="bd-article" role="main">
+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="validphys/simunet_analysis.html">validphys.simunet_analysis</a></li>
+</ul>
+
+                </article>
+
+
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+
+                <footer class="bd-footer-article">
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+<p class="component-author">
+By PBSP
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+      © Copyright 2023, PBSP.
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+
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