Merge pull request #1236 from cbworden/update_docs

Update docs
usgs · Sep 23, 2022 · a12d0dc · a12d0dc
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diff --git a/doc_source/manual4_0/sg_contributing.rst b/doc_source/manual4_0/sg_contributing.rst
@@ -439,14 +439,22 @@ The install script depends on the following files:
     the running of tests following the install users can run `bash install.sh -t`, otherwise they
     can manually run `py.test --cov=.` after the install is complete.
 
-  - "Development" Users who are contributing to ShakeMap development and need to update the ShakeMap 
-    code and the Python dependencies. `bash install.sh -u` will update dependencies, run tests, and 
-    generate a new deployment_<platform>.txt file if the tests are successful. If a developer wants to 
-    update the environment but NOT run tests and NOT generate a new deployment_<platform>.txt file, they
-    can run `bash install.sh -un`. Developers who want to update the Python version from the current
+  - "Development" Users who are making routine contributions to the ShakeMap software
+    and who do not anticipate adding new dependencies or otherwise changing existing
+    dependencies. These users may install much as the "Deployment users, above, with
+    the simple `bash install.sh`. The development workflow may then proceed as described
+    elsewhere in this document.
+
+  - "Configuration" Users who are contributing to ShakeMap development and need to update
+    the ShakeMap code and the Python dependencies. `bash install.sh -u` will update
+    dependencies, run tests, and generate a new deployment_<platform>.txt file if the
+    tests are successful. If a developer wants to update the environment but NOT run
+    tests and NOT generate a new deployment_<platform>.txt file, they can run
+    `bash install.sh -un`. Developers who want to update the Python version from the current
     default and the dependencies (many Python packages have version-specific builds) can run
     `bash install.sh -u -p 3.X`. Unless the "-n" option is added, tests will be run and a new 
-    deployment_<platform>.txt file will be created.
+    deployment_<platform>.txt file will be created. Note that this is a fairly major 
+    step and should be taken only in consultation with the ShakeMap development team.
 
 Core Modules
 =============

diff --git a/doc_source/shakelib/shakelib.distance.rst b/doc_source/shakelib/shakelib.distance.rst
diff --git a/doc_source/shakelib/shakelib.rst b/doc_source/shakelib/shakelib.rst
@@ -11,15 +11,13 @@ shakelib
    shakelib.gmice
    shakelib.gmpe
    shakelib.plotting
-   shakelib.rupture
    shakelib.utils
 
 Submodules
 
 .. toctree::
    :maxdepth: 12
 
-   shakelib.distance
    shakelib.multigmpe
    shakelib.sites
    shakelib.station

diff --git a/doc_source/shakelib/shakelib.rupture.base.rst b/doc_source/shakelib/shakelib.rupture.base.rst
diff --git a/doc_source/shakelib/shakelib.rupture.constants.rst b/doc_source/shakelib/shakelib.rupture.constants.rst
diff --git a/doc_source/shakelib/shakelib.rupture.edge_rupture.rst b/doc_source/shakelib/shakelib.rupture.edge_rupture.rst
diff --git a/doc_source/shakelib/shakelib.rupture.factory.rst b/doc_source/shakelib/shakelib.rupture.factory.rst
diff --git a/doc_source/shakelib/shakelib.rupture.origin.rst b/doc_source/shakelib/shakelib.rupture.origin.rst
diff --git a/doc_source/shakelib/shakelib.rupture.point_rupture.rst b/doc_source/shakelib/shakelib.rupture.point_rupture.rst
diff --git a/doc_source/shakelib/shakelib.rupture.quad_rupture.rst b/doc_source/shakelib/shakelib.rupture.quad_rupture.rst
diff --git a/doc_source/shakelib/shakelib.rupture.rst b/doc_source/shakelib/shakelib.rupture.rst
diff --git a/doc_source/shakelib/shakelib.rupture.utils.rst b/doc_source/shakelib/shakelib.rupture.utils.rst
diff --git a/docs/.buildinfo b/docs/.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: daa1315a262695cbd433fedb28627b0d
+config: f4d02ea22168e687dd158080fd595211
 tags: 645f666f9bcd5a90fca523b33c5a78b7
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diff --git a/docs/.doctrees/apidoc/shakemap.coremods.augment.doctree b/docs/.doctrees/apidoc/shakemap.coremods.augment.doctree
diff --git a/docs/.doctrees/apidoc/shakemap.coremods.base.doctree b/docs/.doctrees/apidoc/shakemap.coremods.base.doctree
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diff --git a/docs/.doctrees/apidoc/shakemap.coremods.coverage.doctree b/docs/.doctrees/apidoc/shakemap.coremods.coverage.doctree
diff --git a/docs/.doctrees/apidoc/shakemap.coremods.doctree b/docs/.doctrees/apidoc/shakemap.coremods.doctree
diff --git a/docs/.doctrees/apidoc/shakemap.coremods.dyfi.doctree b/docs/.doctrees/apidoc/shakemap.coremods.dyfi.doctree
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diff --git a/docs/.doctrees/shakelib/shakelib.gmice.fm11.doctree b/docs/.doctrees/shakelib/shakelib.gmice.fm11.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.gmice.gmice.doctree b/docs/.doctrees/shakelib/shakelib.gmice.gmice.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.gmice.wald99.doctree b/docs/.doctrees/shakelib/shakelib.gmice.wald99.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.gmice.wgrw12.doctree b/docs/.doctrees/shakelib/shakelib.gmice.wgrw12.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.gmpe.doctree b/docs/.doctrees/shakelib/shakelib.gmpe.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.gmpe.nga_east.doctree b/docs/.doctrees/shakelib/shakelib.gmpe.nga_east.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.gmpe.nullgmpe.doctree b/docs/.doctrees/shakelib/shakelib.gmpe.nullgmpe.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.multigmpe.doctree b/docs/.doctrees/shakelib/shakelib.multigmpe.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.plotting.contour.doctree b/docs/.doctrees/shakelib/shakelib.plotting.contour.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.plotting.doctree b/docs/.doctrees/shakelib/shakelib.plotting.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.plotting.plotrupture.doctree b/docs/.doctrees/shakelib/shakelib.plotting.plotrupture.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.sites.doctree b/docs/.doctrees/shakelib/shakelib.sites.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.station.doctree b/docs/.doctrees/shakelib/shakelib.station.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.utils.containers.doctree b/docs/.doctrees/shakelib/shakelib.utils.containers.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.utils.doctree b/docs/.doctrees/shakelib/shakelib.utils.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.utils.exception.doctree b/docs/.doctrees/shakelib/shakelib.utils.exception.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.utils.imt_string.doctree b/docs/.doctrees/shakelib/shakelib.utils.imt_string.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.utils.utils.doctree b/docs/.doctrees/shakelib/shakelib.utils.utils.doctree
diff --git a/docs/.doctrees/shakelib/shakelib.virtualipe.doctree b/docs/.doctrees/shakelib/shakelib.virtualipe.doctree
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -1,7 +1,7 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
@@ -12,6 +12,7 @@
     <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>
     <link rel="shortcut icon" href="../_static/northridge_points.ico"/>
     <link rel="index" title="Index" href="../genindex.html" />
@@ -43,7 +44,6 @@ <h1>All modules for which code is available</h1>
 <li><a href="shakelib/correlation/loth_baker_2013.html">shakelib.correlation.loth_baker_2013</a></li>
 <li><a href="shakelib/directivity/bayless2013.html">shakelib.directivity.bayless2013</a></li>
 <li><a href="shakelib/directivity/rowshandel2013.html">shakelib.directivity.rowshandel2013</a></li>
-<li><a href="shakelib/distance.html">shakelib.distance</a></li>
 <li><a href="shakelib/gmice/ak07.html">shakelib.gmice.ak07</a></li>
 <li><a href="shakelib/gmice/fm11.html">shakelib.gmice.fm11</a></li>
 <li><a href="shakelib/gmice/gmice.html">shakelib.gmice.gmice</a></li>
@@ -54,13 +54,6 @@ <h1>All modules for which code is available</h1>
 <li><a href="shakelib/multigmpe.html">shakelib.multigmpe</a></li>
 <li><a href="shakelib/plotting/contour.html">shakelib.plotting.contour</a></li>
 <li><a href="shakelib/plotting/plotrupture.html">shakelib.plotting.plotrupture</a></li>
-<li><a href="shakelib/rupture/base.html">shakelib.rupture.base</a></li>
-<li><a href="shakelib/rupture/edge_rupture.html">shakelib.rupture.edge_rupture</a></li>
-<li><a href="shakelib/rupture/factory.html">shakelib.rupture.factory</a></li>
-<li><a href="shakelib/rupture/origin.html">shakelib.rupture.origin</a></li>
-<li><a href="shakelib/rupture/point_rupture.html">shakelib.rupture.point_rupture</a></li>
-<li><a href="shakelib/rupture/quad_rupture.html">shakelib.rupture.quad_rupture</a></li>
-<li><a href="shakelib/rupture/utils.html">shakelib.rupture.utils</a></li>
 <li><a href="shakelib/sites.html">shakelib.sites</a></li>
 <li><a href="shakelib/station.html">shakelib.station</a></li>
 <li><a href="shakelib/utils/containers.html">shakelib.utils.containers</a></li>
@@ -137,9 +130,9 @@ <h1 class="logo logo-name">ShakeMap Documentation</h1>
 
 <h3>Navigation</h3>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../manual4_0/index.html">ShakeMap 4.0 Manual</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../programs/programs.html">ShakeMap 4.0 Command Line Interface</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../apidoc/shakemap.html">ShakeMap 4.0 API</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../manual4_0/index.html">ShakeMap 4.1 Manual</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../programs/programs.html">ShakeMap 4.1 Command Line Interface</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../apidoc/shakemap.html">ShakeMap 4.1 API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../manual3_5/index.html">ShakeMap 3.5 Manual (Deprecated)</a></li>
 </ul>
 
@@ -153,7 +146,7 @@ <h3 id="searchlabel">Quick search</h3>
     </form>
     </div>
 </div>
-<script>$('#searchbox').show(0);</script>
+<script>document.getElementById('searchbox').style.display = "block"</script>
         </div>
       </div>
       <div class="clearer"></div>

diff --git a/docs/_modules/shakelib/conversions/imc/boore_kishida_2017.html b/docs/_modules/shakelib/conversions/imc/boore_kishida_2017.html
@@ -1,7 +1,7 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
@@ -12,7 +12,9 @@
     <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>
+    <link rel="shortcut icon" href="../../../../_static/northridge_points.ico"/>
     <link rel="index" title="Index" href="../../../../genindex.html" />
     <link rel="search" title="Search" href="../../../../search.html" />
 
@@ -38,7 +40,11 @@ <h1>Source code for shakelib.conversions.imc.boore_kishida_2017</h1><div class="
 <span class="kn">import</span> <span class="nn">glob</span>
 <span class="kn">import</span> <span class="nn">logging</span>
 <span class="kn">import</span> <span class="nn">os.path</span>
-<span class="kn">import</span> <span class="nn">importlib.resources</span> <span class="k">as</span> <span class="nn">importlib_resources</span>
+
+<span class="c1"># This is what we want for the future (Python 2.9 an beyond):</span>
+<span class="c1"># import importlib.resources as importlib_resources</span>
+<span class="c1"># but right now we have to support Py 3.8, so we have this:</span>
+<span class="kn">import</span> <span class="nn">pkg_resources</span>
 
 <span class="c1"># Third party imports</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
@@ -307,7 +313,10 @@ <h1>Source code for shakelib.conversions.imc.boore_kishida_2017</h1><div class="
 <span class="sd">            string &#39;Null&#39;, then imc_in and imc_out evaluated to be the</span>
 <span class="sd">            same.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">datadir</span> <span class="o">=</span> <span class="n">importlib_resources</span><span class="o">.</span><span class="n">files</span><span class="p">(</span><span class="s2">&quot;shakelib.conversions.imc&quot;</span><span class="p">)</span> <span class="o">/</span> <span class="s2">&quot;data&quot;</span>
+        <span class="c1"># This is what we want for the future (Python 2.9 an beyond):</span>
+        <span class="c1"># datadir = importlib_resources.files(&quot;shakelib.conversions.imc&quot;) / &quot;data&quot;</span>
+        <span class="c1"># but right now we have to support Py 3.8, so we have this:</span>
+        <span class="n">datadir</span> <span class="o">=</span> <span class="n">pkg_resources</span><span class="o">.</span><span class="n">resource_filename</span><span class="p">(</span><span class="s2">&quot;shakelib.conversions.imc&quot;</span><span class="p">,</span> <span class="s2">&quot;data&quot;</span><span class="p">)</span>
         <span class="n">conv_files</span> <span class="o">=</span> <span class="n">glob</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">datadir</span><span class="p">,</span> <span class="s2">&quot;*.csv&quot;</span><span class="p">))</span>
         <span class="n">stub1</span> <span class="o">=</span> <span class="n">BooreKishida2017</span><span class="o">.</span><span class="n">_imcToFilestr</span><span class="p">(</span><span class="n">imc_in</span><span class="p">)</span>
         <span class="n">stub2</span> <span class="o">=</span> <span class="n">BooreKishida2017</span><span class="o">.</span><span class="n">_imcToFilestr</span><span class="p">(</span><span class="n">imc_out</span><span class="p">)</span>
@@ -410,9 +419,9 @@ <h1 class="logo logo-name">ShakeMap Documentation</h1>
 
 <h3>Navigation</h3>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../../../../manual4_0/index.html">ShakeMap 4.0 Manual</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../../programs/programs.html">ShakeMap 4.0 Command Line Interface</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../../apidoc/shakemap.html">ShakeMap 4.0 API</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../../manual4_0/index.html">ShakeMap 4.1 Manual</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../../programs/programs.html">ShakeMap 4.1 Command Line Interface</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../../apidoc/shakemap.html">ShakeMap 4.1 API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../../manual3_5/index.html">ShakeMap 3.5 Manual (Deprecated)</a></li>
 </ul>
 
@@ -426,7 +435,7 @@ <h3 id="searchlabel">Quick search</h3>
     </form>
     </div>
 </div>
-<script>$('#searchbox').show(0);</script>
+<script>document.getElementById('searchbox').style.display = "block"</script>
         </div>
       </div>
       <div class="clearer"></div>

diff --git a/docs/_modules/shakelib/conversions/imt/abrahamson_bhasin_2020.html b/docs/_modules/shakelib/conversions/imt/abrahamson_bhasin_2020.html
@@ -1,7 +1,7 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
@@ -12,7 +12,9 @@
     <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>
+    <link rel="shortcut icon" href="../../../../_static/northridge_points.ico"/>
     <link rel="index" title="Index" href="../../../../genindex.html" />
     <link rel="search" title="Search" href="../../../../search.html" />
 
@@ -277,9 +279,9 @@ <h1 class="logo logo-name">ShakeMap Documentation</h1>
 
 <h3>Navigation</h3>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../../../../manual4_0/index.html">ShakeMap 4.0 Manual</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../../programs/programs.html">ShakeMap 4.0 Command Line Interface</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../../apidoc/shakemap.html">ShakeMap 4.0 API</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../../manual4_0/index.html">ShakeMap 4.1 Manual</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../../programs/programs.html">ShakeMap 4.1 Command Line Interface</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../../apidoc/shakemap.html">ShakeMap 4.1 API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../../manual3_5/index.html">ShakeMap 3.5 Manual (Deprecated)</a></li>
 </ul>
 
@@ -293,7 +295,7 @@ <h3 id="searchlabel">Quick search</h3>
     </form>
     </div>
 </div>
-<script>$('#searchbox').show(0);</script>
+<script>document.getElementById('searchbox').style.display = "block"</script>
         </div>
       </div>
       <div class="clearer"></div>

diff --git a/docs/_modules/shakelib/directivity/bayless2013.html b/docs/_modules/shakelib/directivity/bayless2013.html
@@ -1,7 +1,7 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
@@ -12,7 +12,9 @@
     <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>
+    <link rel="shortcut icon" href="../../../_static/northridge_points.ico"/>
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" />
 
@@ -36,8 +38,8 @@ <h1>Source code for shakelib.directivity.bayless2013</h1><div class="highlight">
 <span class="kn">import</span> <span class="nn">openquake.hazardlib.geo</span> <span class="k">as</span> <span class="nn">geo</span>
 <span class="kn">import</span> <span class="nn">copy</span>
 
-<span class="kn">from</span> <span class="nn">shakelib.distance</span> <span class="kn">import</span> <span class="n">get_distance</span>
-<span class="kn">from</span> <span class="nn">shakelib.rupture.utils</span> <span class="kn">import</span> <span class="n">_distance_sq_to_segment</span>
+<span class="kn">from</span> <span class="nn">impactutils.rupture.distance</span> <span class="kn">import</span> <span class="n">get_distance</span>
+<span class="kn">from</span> <span class="nn">impactutils.rupture.utils</span> <span class="kn">import</span> <span class="n">_distance_sq_to_segment</span>
 <span class="kn">import</span> <span class="nn">impactutils.vectorutils.ecef</span> <span class="k">as</span> <span class="nn">ecef</span>
 <span class="kn">from</span> <span class="nn">impactutils.vectorutils.vector</span> <span class="kn">import</span> <span class="n">Vector</span>
 
@@ -520,9 +522,9 @@ <h1 class="logo logo-name">ShakeMap Documentation</h1>
 
 <h3>Navigation</h3>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../../../manual4_0/index.html">ShakeMap 4.0 Manual</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../programs/programs.html">ShakeMap 4.0 Command Line Interface</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../apidoc/shakemap.html">ShakeMap 4.0 API</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../manual4_0/index.html">ShakeMap 4.1 Manual</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../programs/programs.html">ShakeMap 4.1 Command Line Interface</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../apidoc/shakemap.html">ShakeMap 4.1 API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../manual3_5/index.html">ShakeMap 3.5 Manual (Deprecated)</a></li>
 </ul>
 
@@ -536,7 +538,7 @@ <h3 id="searchlabel">Quick search</h3>
     </form>
     </div>
 </div>
-<script>$('#searchbox').show(0);</script>
+<script>document.getElementById('searchbox').style.display = "block"</script>
         </div>
       </div>
       <div class="clearer"></div>