Merge pull request #31 from aelefebv/docs

Docs
aelefebv · Oct 3, 2024 · 0f55336 · 0f55336
2 parents 6474d36 + 3731999
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diff --git a/.DS_Store b/.DS_Store
diff --git a/.gitignore b/.gitignore
@@ -68,9 +68,6 @@ instance/
 # Scrapy stuff:
 .scrapy
 
-# Sphinx documentation
-docs/_build/
-
 # PyBuilder
 target/
 

diff --git a/docs/.DS_Store b/docs/.DS_Store
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/main.doctree b/docs/_build/doctrees/main.doctree
diff --git a/docs/_build/doctrees/modules.doctree b/docs/_build/doctrees/modules.doctree
diff --git a/docs/_build/doctrees/nellie.doctree b/docs/_build/doctrees/nellie.doctree
diff --git a/docs/_build/doctrees/nellie.feature_extraction.doctree b/docs/_build/doctrees/nellie.feature_extraction.doctree
diff --git a/docs/_build/doctrees/nellie.im_info.doctree b/docs/_build/doctrees/nellie.im_info.doctree
diff --git a/docs/_build/doctrees/nellie.segmentation.doctree b/docs/_build/doctrees/nellie.segmentation.doctree
diff --git a/docs/_build/doctrees/nellie.tracking.doctree b/docs/_build/doctrees/nellie.tracking.doctree
diff --git a/docs/_build/doctrees/nellie.utils.doctree b/docs/_build/doctrees/nellie.utils.doctree
diff --git a/docs/_build/doctrees/nellie_napari.doctree b/docs/_build/doctrees/nellie_napari.doctree
diff --git a/docs/_build/doctrees/tests.doctree b/docs/_build/doctrees/tests.doctree
diff --git a/docs/_build/doctrees/tests.unit.doctree b/docs/_build/doctrees/tests.unit.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_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: 44e986329f1902031559e4ed323a7345
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html
@@ -0,0 +1,120 @@
+<!DOCTYPE html>
+
+<html 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 &#8212; Nellie 0.3.2 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="../_static/alabaster.css?v=12dfc556" />
+    <script src="../_static/documentation_options.js?v=71d9d8e6"></script>
+    <script src="../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" />
+
+  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+
+
+
+
+
+  </head><body>
+
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+
+
+          <div class="body" role="main">
+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="main.html">main</a></li>
+<li><a href="nellie/cli.html">nellie.cli</a></li>
+<li><a href="nellie/feature_extraction/hierarchical.html">nellie.feature_extraction.hierarchical</a></li>
+<li><a href="nellie/im_info/verifier.html">nellie.im_info.verifier</a></li>
+<li><a href="nellie/run.html">nellie.run</a></li>
+<li><a href="nellie/segmentation/filtering.html">nellie.segmentation.filtering</a></li>
+<li><a href="nellie/segmentation/labelling.html">nellie.segmentation.labelling</a></li>
+<li><a href="nellie/segmentation/mocap_marking.html">nellie.segmentation.mocap_marking</a></li>
+<li><a href="nellie/segmentation/networking.html">nellie.segmentation.networking</a></li>
+<li><a href="nellie/tracking/all_tracks_for_label.html">nellie.tracking.all_tracks_for_label</a></li>
+<li><a href="nellie/tracking/flow_interpolation.html">nellie.tracking.flow_interpolation</a></li>
+<li><a href="nellie/tracking/hu_tracking.html">nellie.tracking.hu_tracking</a></li>
+<li><a href="nellie/tracking/voxel_reassignment.html">nellie.tracking.voxel_reassignment</a></li>
+<li><a href="nellie/utils/general.html">nellie.utils.general</a></li>
+<li><a href="nellie/utils/gpu_functions.html">nellie.utils.gpu_functions</a></li>
+<li><a href="nellie_napari/nellie_analysis.html">nellie_napari.nellie_analysis</a></li>
+<li><a href="nellie_napari/nellie_fileselect.html">nellie_napari.nellie_fileselect</a></li>
+<li><a href="nellie_napari/nellie_home.html">nellie_napari.nellie_home</a></li>
+<li><a href="nellie_napari/nellie_loader.html">nellie_napari.nellie_loader</a></li>
+<li><a href="nellie_napari/nellie_processor.html">nellie_napari.nellie_processor</a></li>
+<li><a href="nellie_napari/nellie_settings.html">nellie_napari.nellie_settings</a></li>
+<li><a href="nellie_napari/nellie_visualizer.html">nellie_napari.nellie_visualizer</a></li>
+</ul>
+
+          </div>
+
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
+        <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">Nellie</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">nellie</a></li>
+</ul>
+
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="../index.html">Documentation overview</a><ul>
+  </ul></li>
+</ul>
+</div>
+<search id="searchbox" style="display: none" role="search">
+  <h3 id="searchlabel">Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="../search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</search>
+<script>document.getElementById('searchbox').style.display = "block"</script>
+
+
+
+
+
+
+
+
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="footer">
+      &#169;2024, Austin E. Y. T. Lefebvre.
+
+      |
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.0.2</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
+
+    </div>
+
+
+
+
+  </body>
+</html>
diff --git a/docs/_build/html/_modules/main.html b/docs/_build/html/_modules/main.html
@@ -0,0 +1,111 @@
+<!DOCTYPE html>
+
+<html lang="en" data-content_root="../">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>main &#8212; Nellie 0.3.2 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d1102ebc" />
+    <link rel="stylesheet" type="text/css" href="../_static/alabaster.css?v=12dfc556" />
+    <script src="../_static/documentation_options.js?v=71d9d8e6"></script>
+    <script src="../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" />
+
+  <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+
+
+
+
+
+  </head><body>
+
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+
+
+          <div class="body" role="main">
+
+  <h1>Source code for main</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span> <span class="nn">napari</span>
+<span class="kn">from</span> <span class="nn">nellie_napari</span> <span class="kn">import</span> <span class="n">NellieLoader</span>
+
+
+<div class="viewcode-block" id="main">
+<a class="viewcode-back" href="../main.html#main.main">[docs]</a>
+<span class="k">def</span> <span class="nf">main</span><span class="p">():</span>
+    <span class="n">viewer</span> <span class="o">=</span> <span class="n">napari</span><span class="o">.</span><span class="n">Viewer</span><span class="p">()</span>
+    <span class="n">napari</span><span class="o">.</span><span class="n">run</span><span class="p">()</span></div>
+
+
+
+<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
+    <span class="n">main</span><span class="p">()</span>
+
+</pre></div>
+
+          </div>
+
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
+        <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="../index.html">Nellie</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="../index.html">Documentation overview</a><ul>
+  <li><a href="index.html">Module code</a><ul>
+  </ul></li>
+  </ul></li>
+</ul>
+</div>
+<search id="searchbox" style="display: none" role="search">
+  <h3 id="searchlabel">Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="../search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</search>
+<script>document.getElementById('searchbox').style.display = "block"</script>
+
+
+
+
+
+
+
+
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="footer">
+      &#169;2024, Austin E. Y. T. Lefebvre.
+
+      |
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.0.2</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
+
+    </div>
+
+
+
+
+  </body>
+</html>