Update docs #5

draeger-lab · Apr 25, 2024 · 1e2b8c6 · 1e2b8c6
1 parent 52ba1cd
commit 1e2b8c6
Show file tree

Hide file tree

Showing 132 changed files with 11,478 additions and 2,942 deletions.
diff --git a/dev/CB_test_modules.ipynb b/dev/CB_test_modules.ipynb
@@ -1436,7 +1436,7 @@
    "source": [
     "# refinement - annotation\n",
     "#\n",
-    "# - problems with SBIannotator\n",
+    "# - problems with SBOannotator\n",
     "\n",
     "from specimen.core.refinement import annotation\n",
     "\n",
@@ -2666,46 +2666,6 @@
     "### Test Area 51"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "PosixPath('test/a/bit_12')"
-      ]
-     },
-     "execution_count": 2,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "from pathlib import Path\n",
-    "\n",
-    "Path('test','a','bit'+'_12')"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "4\n"
-     ]
-    }
-   ],
-   "source": [
-    "if not None:\n",
-    "    print(4)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/dev/docstring-format.mustache b/dev/docstring-format.mustache
@@ -6,10 +6,12 @@
 
 Args:
 {{#args}}
-    - {{var}} ({{typePlaceholder}}): {{descriptionPlaceholder}}
+    - {{var}} ({{typePlaceholder}}): 
+        {{descriptionPlaceholder}}
 {{/args}}
 {{#kwargs}}
-    - {{var}} ({{typePlaceholder}}, optional): {{descriptionPlaceholder}}. Defaults to {{&default}}.
+    - {{var}} ({{typePlaceholder}}, optional): 
+        {{descriptionPlaceholder}}. Defaults to {{&default}}.
 {{/kwargs}}
 {{/parametersExist}}
 {{#exceptionsExist}}
@@ -23,7 +25,8 @@ Raises:
 
 Returns:
 {{#returns}}
-    {{typePlaceholder}}: {{descriptionPlaceholder}}
+    {{typePlaceholder}}: 
+        {{descriptionPlaceholder}}
 {{/returns}}
 {{/returnsExist}}
 {{#yieldsExist}}

diff --git a/docs/build/doctrees/about-pipeline.doctree b/docs/build/doctrees/about-pipeline.doctree
diff --git a/docs/build/doctrees/dev-notes.doctree b/docs/build/doctrees/dev-notes.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/help.doctree b/docs/build/doctrees/help.doctree
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/doctrees/installation.doctree b/docs/build/doctrees/installation.doctree
diff --git a/docs/build/doctrees/modules/classes.doctree b/docs/build/doctrees/modules/classes.doctree
diff --git a/docs/build/doctrees/modules/cmd.doctree b/docs/build/doctrees/modules/cmd.doctree
diff --git a/docs/build/doctrees/modules/core.doctree b/docs/build/doctrees/modules/core.doctree
diff --git a/docs/build/doctrees/modules/util.doctree b/docs/build/doctrees/modules/util.doctree
diff --git a/docs/build/doctrees/modules/workflow.doctree b/docs/build/doctrees/modules/workflow.doctree
diff --git a/docs/build/doctrees/run-pipeline.doctree b/docs/build/doctrees/run-pipeline.doctree
diff --git a/docs/build/doctrees/specimen.classes.doctree b/docs/build/doctrees/specimen.classes.doctree
diff --git a/docs/build/doctrees/specimen.core.doctree b/docs/build/doctrees/specimen.core.doctree
diff --git a/docs/build/doctrees/specimen.core.refinement.doctree b/docs/build/doctrees/specimen.core.refinement.doctree
diff --git a/docs/build/doctrees/specimen.doctree b/docs/build/doctrees/specimen.doctree
diff --git a/docs/build/doctrees/specimen.util.doctree b/docs/build/doctrees/specimen.util.doctree
diff --git a/docs/build/doctrees/step-desc/analysis.doctree b/docs/build/doctrees/step-desc/analysis.doctree
diff --git a/docs/build/doctrees/step-desc/bidirect_blast.doctree b/docs/build/doctrees/step-desc/bidirect_blast.doctree
diff --git a/docs/build/doctrees/step-desc/gen_draft.doctree b/docs/build/doctrees/step-desc/gen_draft.doctree
diff --git a/docs/build/doctrees/step-desc/refine-parts/annot.doctree b/docs/build/doctrees/step-desc/refine-parts/annot.doctree
diff --git a/docs/build/doctrees/step-desc/refine-parts/cleanup.doctree b/docs/build/doctrees/step-desc/refine-parts/cleanup.doctree
diff --git a/docs/build/doctrees/step-desc/refine-parts/extension.doctree b/docs/build/doctrees/step-desc/refine-parts/extension.doctree
diff --git a/docs/build/doctrees/step-desc/refine-parts/smooth.doctree b/docs/build/doctrees/step-desc/refine-parts/smooth.doctree
diff --git a/docs/build/doctrees/step-desc/refinement.doctree b/docs/build/doctrees/step-desc/refinement.doctree
diff --git a/docs/build/doctrees/step-desc/validation.doctree b/docs/build/doctrees/step-desc/validation.doctree
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
@@ -0,0 +1,126 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Overview: module code &mdash; SPECIMEN 1.0.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=559046d4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+      <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom_theme.css?v=ef5873f9" />
+
+
+    <link rel="shortcut icon" href="../_static/LogoSPECIMEN.png"/>
+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=8d563738"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
+        <script src="../_static/copybutton.js?v=7859de39"></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>
+    <script src="../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+
+
+          <a href="../index.html">
+
+              <img src="../_static/LogoSPECIMEN.png" class="logo" alt="Logo"/>
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../about-pipeline.html">About SPECIMEN</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../run-pipeline.html">Run the Pipeline</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../specimen.html">Contents of SPECIMEN</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../help.html">Help &amp; FAQ</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../dev-notes.html">Notes for Developers</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../index.html">SPECIMEN</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Overview: module code</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="specimen/classes/reports.html">specimen.classes.reports</a></li>
+<li><a href="specimen/core/analysis.html">specimen.core.analysis</a></li>
+<li><a href="specimen/core/bidirectional_blast.html">specimen.core.bidirectional_blast</a></li>
+<li><a href="specimen/core/generate_draft_model.html">specimen.core.generate_draft_model</a></li>
+<li><a href="specimen/core/refinement/annotation.html">specimen.core.refinement.annotation</a></li>
+<li><a href="specimen/core/refinement/cleanup.html">specimen.core.refinement.cleanup</a></li>
+<li><a href="specimen/core/refinement/extension.html">specimen.core.refinement.extension</a></li>
+<li><a href="specimen/core/refinement/smoothing.html">specimen.core.refinement.smoothing</a></li>
+<li><a href="specimen/core/validation.html">specimen.core.validation</a></li>
+<li><a href="specimen/util/set_up.html">specimen.util.set_up</a></li>
+<li><a href="specimen/util/util.html">specimen.util.util</a></li>
+<li><a href="specimen/workflow.html">specimen.workflow</a></li>
+</ul>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2024, Carolin Brune.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+
+</footer>
+        </div>
+      </div>
+    </section>
+  </div>
+  <script>
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
+</html>