updated docs

Jashcraf · Jan 23, 2023 · f69b08e · f69b08e
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diff --git a/.DS_Store b/.DS_Store
diff --git a/Makefile b/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     = source
+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/.DS_Store b/docs/.DS_Store
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/poke.doctree b/docs/_build/doctrees/poke.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -1,4 +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: 93b4632ae0e74d8fb5ec7a1ad140fd42
+config: e125f76c7c068ffac4c6e3b0c5996f3c
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt
@@ -11,6 +11,7 @@ Welcome to poke's documentation!
    :caption: Contents:
 
    modules
+   notebooks/jonespupils
 
 Indices and tables
 ==================

diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html
@@ -66,8 +66,205 @@
 <h1 id="index">Index</h1>
 
 <div class="genindex-jumpbox">
+ <a href="#A"><strong>A</strong></a>
+ | <a href="#C"><strong>C</strong></a>
+ | <a href="#F"><strong>F</strong></a>
+ | <a href="#G"><strong>G</strong></a>
+ | <a href="#J"><strong>J</strong></a>
+ | <a href="#M"><strong>M</strong></a>
+ | <a href="#P"><strong>P</strong></a>
+ | <a href="#R"><strong>R</strong></a>
+ | <a href="#T"><strong>T</strong></a>
+ | <a href="#V"><strong>V</strong></a>
+ | <a href="#W"><strong>W</strong></a>
 
 </div>
+<h2 id="A">A</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="poke.html#poke.plotting.AmplitudeResponseMatrix">AmplitudeResponseMatrix() (in module poke.plotting)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="poke.html#poke.plotting.AOIPlot">AOIPlot() (in module poke.plotting)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="poke.html#poke.thinfilms.ComputeThinFilmCoeffsCLY">ComputeThinFilmCoeffsCLY() (in module poke.thinfilms)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="poke.html#poke.polarization.ConstructOrthogonalTransferMatrices">ConstructOrthogonalTransferMatrices() (in module poke.polarization)</a>
+</li>
+      <li><a href="poke.html#poke.polarization.ConstructPRTMatrix">ConstructPRTMatrix() (in module poke.polarization)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="F">F</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="poke.html#poke.polarization.FresnelCoefficients">FresnelCoefficients() (in module poke.polarization)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="G">G</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="poke.html#poke.polarization.GlobalToLocalCoordinates">GlobalToLocalCoordinates() (in module poke.polarization)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="J">J</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="poke.html#poke.plotting.JonesPupil">JonesPupil() (in module poke.plotting)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="poke.html#poke.polarization.JonesToMueller">JonesToMueller() (in module poke.polarization)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="M">M</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="poke.html#poke.poke_math.MatmulList">MatmulList() (in module poke.poke_math)</a>
+</li>
+      <li>
+    module
+
+      <ul>
+        <li><a href="poke.html#module-poke">poke</a>
+</li>
+        <li><a href="poke.html#module-poke.plotting">poke.plotting</a>
+</li>
+        <li><a href="poke.html#module-poke.poke_math">poke.poke_math</a>
+</li>
+        <li><a href="poke.html#module-poke.polarization">poke.polarization</a>
+</li>
+        <li><a href="poke.html#module-poke.test_poke_math">poke.test_poke_math</a>
+</li>
+        <li><a href="poke.html#module-poke.thinfilms">poke.thinfilms</a>
+</li>
+        <li><a href="poke.html#module-poke.writing">poke.writing</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="poke.html#poke.plotting.MuellerPupil">MuellerPupil() (in module poke.plotting)</a>
+</li>
+      <li><a href="poke.html#poke.polarization.MuellerToJones">MuellerToJones() (in module poke.polarization)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="P">P</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="poke.html#poke.poke_math.PauliSpinMatrix">PauliSpinMatrix() (in module poke.poke_math)</a>
+</li>
+      <li><a href="poke.html#poke.plotting.PlotJonesPupil">PlotJonesPupil() (in module poke.plotting)</a>
+</li>
+      <li><a href="poke.html#poke.plotting.PlotRayset">PlotRayset() (in module poke.plotting)</a>
+</li>
+      <li><a href="poke.html#poke.plotting.PointSpreadMatrix">PointSpreadMatrix() (in module poke.plotting)</a>
+</li>
+      <li>
+    poke
+
+      <ul>
+        <li><a href="poke.html#module-poke">module</a>
+</li>
+      </ul></li>
+      <li>
+    poke.plotting
+
+      <ul>
+        <li><a href="poke.html#module-poke.plotting">module</a>
+</li>
+      </ul></li>
+      <li>
+    poke.poke_math
+
+      <ul>
+        <li><a href="poke.html#module-poke.poke_math">module</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li>
+    poke.polarization
+
+      <ul>
+        <li><a href="poke.html#module-poke.polarization">module</a>
+</li>
+      </ul></li>
+      <li>
+    poke.test_poke_math
+
+      <ul>
+        <li><a href="poke.html#module-poke.test_poke_math">module</a>
+</li>
+      </ul></li>
+      <li>
+    poke.thinfilms
+
+      <ul>
+        <li><a href="poke.html#module-poke.thinfilms">module</a>
+</li>
+      </ul></li>
+      <li>
+    poke.writing
+
+      <ul>
+        <li><a href="poke.html#module-poke.writing">module</a>
+</li>
+      </ul></li>
+      <li><a href="poke.html#poke.plotting.PRTPlot">PRTPlot() (in module poke.plotting)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="R">R</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="poke.html#poke.poke_math.rotation3D">rotation3D() (in module poke.poke_math)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="T">T</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="poke.html#poke.test_poke_math.test_rotation3D">test_rotation3D() (in module poke.test_poke_math)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="V">V</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="poke.html#poke.poke_math.vectorAngle">vectorAngle() (in module poke.poke_math)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="W">W</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="poke.html#poke.writing.WriteMatrixToFITS">WriteMatrixToFITS() (in module poke.writing)</a>
+</li>
+  </ul></td>
+</tr></table>
+
 
 
            </div>

diff --git a/docs/_build/html/modules.html b/docs/_build/html/modules.html
@@ -76,15 +76,15 @@ <h1>poke<a class="headerlink" href="#poke" title="Permalink to this headline">
 <li class="toctree-l1"><a class="reference internal" href="poke.html">poke package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="poke.html#submodules">Submodules</a></li>
 <li class="toctree-l2"><a class="reference internal" href="poke.html#poke-gbd-module">poke.gbd module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="poke.html#poke-plotting-module">poke.plotting module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="poke.html#module-poke.plotting">poke.plotting module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="poke.html#poke-poke-core-module">poke.poke_core module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="poke.html#poke-poke-math-module">poke.poke_math module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="poke.html#poke-polarization-module">poke.polarization module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="poke.html#module-poke.poke_math">poke.poke_math module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="poke.html#module-poke.polarization">poke.polarization module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="poke.html#poke-raytrace-module">poke.raytrace module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="poke.html#poke-test-poke-math-module">poke.test_poke_math module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="poke.html#poke-thinfilms-module">poke.thinfilms module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="poke.html#poke-writing-module">poke.writing module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="poke.html#module-contents">Module contents</a></li>
+<li class="toctree-l2"><a class="reference internal" href="poke.html#module-poke.test_poke_math">poke.test_poke_math module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="poke.html#module-poke.thinfilms">poke.thinfilms module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="poke.html#module-poke.writing">poke.writing module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="poke.html#module-poke">Module contents</a></li>
 </ul>
 </li>
 </ul>

diff --git a/docs/_build/html/objects.inv b/docs/_build/html/objects.inv