changed python wrapper file name

mikekatz04 · Jan 25, 2024 · 8bf2413 · 8bf2413
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diff --git a/README.md b/README.md
@@ -137,7 +137,7 @@ Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduc
 
 We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/mikekatz04/BBHx/tags).
 
-Current Version: 1.0.5
+Current Version: 1.0.6
 
 ## Authors
 

diff --git a/bbhx/response/fastfdresponse.py b/bbhx/response/fastfdresponse.py
@@ -20,13 +20,13 @@
 
 try:
     import cupy as xp
-    from pyResponse import LISA_response_wrap as LISA_response_wrap_gpu
+    from pyFDResponse import LISA_response_wrap as LISA_response_wrap_gpu
 
 except (ImportError, ModuleNotFoundError) as e:
     print("No CuPy or GPU response available.")
     import numpy as xp
 
-from pyResponse_cpu import LISA_response_wrap as LISA_response_wrap_cpu
+from pyFDResponse_cpu import LISA_response_wrap as LISA_response_wrap_cpu
 from bbhx.utils.constants import *
 
 
@@ -69,7 +69,6 @@ class LISATDIResponse:
     """
 
     def __init__(self, TDItag="AET", order_fresnel_stencil=0, use_gpu=False):
-
         # gpu setup
         if use_gpu:
             self.response_gen = LISA_response_wrap_gpu
@@ -106,7 +105,7 @@ def citation(self):
 
     def _sanity_check_modes(self, ells, mms):
         """Make sure modes are allowed"""
-        for (ell, mm) in zip(ells, mms):
+        for ell, mm in zip(ells, mms):
             if (ell, mm) not in self.allowable_modes:
                 raise ValueError(
                     "Requested mode [(l,m) = ({},{})] is not available. Allowable modes include {}".format(

diff --git a/docs/doctrees/README.doctree b/docs/doctrees/README.doctree
diff --git a/docs/doctrees/bbhx_tutorial.doctree b/docs/doctrees/bbhx_tutorial.doctree
diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/index.doctree b/docs/doctrees/index.doctree
diff --git a/docs/doctrees/user/constants.doctree b/docs/doctrees/user/constants.doctree
diff --git a/docs/doctrees/user/like.doctree b/docs/doctrees/user/like.doctree
diff --git a/docs/doctrees/user/main.doctree b/docs/doctrees/user/main.doctree
diff --git a/docs/doctrees/user/response.doctree b/docs/doctrees/user/response.doctree
diff --git a/docs/doctrees/user/utils.doctree b/docs/doctrees/user/utils.doctree
diff --git a/docs/doctrees/user/waveforms.doctree b/docs/doctrees/user/waveforms.doctree
diff --git a/docs/html/README.html b/docs/html/README.html
@@ -1,21 +1,23 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>GPU-Accelerated Black Hole Binary Waveforms (bbhx) &mdash; bbhx  documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script src="_static/jquery.js"></script>
-        <script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
-        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
-        <script src="_static/doctools.js"></script>
-        <script src="_static/sphinx_highlight.js"></script>
+        <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=5929fcd5"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></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" />
@@ -85,9 +87,9 @@
            <div itemprop="articleBody">
 
   <section id="gpu-accelerated-black-hole-binary-waveforms-bbhx">
-<h1>GPU-Accelerated Black Hole Binary Waveforms (<code class="docutils literal notranslate"><span class="pre">bbhx</span></code>)<a class="headerlink" href="#gpu-accelerated-black-hole-binary-waveforms-bbhx" title="Permalink to this heading"></a></h1>
+<h1>GPU-Accelerated Black Hole Binary Waveforms (<code class="docutils literal notranslate"><span class="pre">bbhx</span></code>)<a class="headerlink" href="#gpu-accelerated-black-hole-binary-waveforms-bbhx" title="Link to this heading"></a></h1>
 <section id="designed-for-lisa-data-analysis-of-massive-black-hole-binaries">
-<h2>Designed for LISA data analysis of Massive Black Hole Binaries.<a class="headerlink" href="#designed-for-lisa-data-analysis-of-massive-black-hole-binaries" title="Permalink to this heading"></a></h2>
+<h2>Designed for LISA data analysis of Massive Black Hole Binaries.<a class="headerlink" href="#designed-for-lisa-data-analysis-of-massive-black-hole-binaries" title="Link to this heading"></a></h2>
 <p>This package implements GPU/CPU agnostic Massive Black Hole Binary
 waveforms and likelihood computations from
 <a class="reference external" href="https://arxiv.org/abs/2005.01827">arXiv:2005.01827</a> and
@@ -108,7 +110,7 @@ <h2>Designed for LISA data analysis of Massive Black Hole Binaries.<a class="hea
 See the <code class="docutils literal notranslate"><span class="pre">citation</span></code> attribute for each class or docstring for functions
 for more information.</p>
 <section id="getting-started">
-<h3>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this heading"></a></h3>
+<h3>Getting Started<a class="headerlink" href="#getting-started" title="Link to this heading"></a></h3>
 <p>Below is a quick set of instructions to get you started with <code class="docutils literal notranslate"><span class="pre">bbhx</span></code>.</p>
 <ol class="arabic simple" start="0">
 <li><p><a class="reference external" href="https://docs.anaconda.com/anaconda/install/">Install Anaconda</a> if
@@ -149,7 +151,7 @@ <h3>Getting Started<a class="headerlink" href="#getting-started" title="Permalin
 </section>
 </section>
 <section id="prerequisites">
-<h2>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to this heading"></a></h2>
+<h2>Prerequisites<a class="headerlink" href="#prerequisites" title="Link to this heading"></a></h2>
 <p>To install this software for CPU usage, you need <a class="reference external" href="https://www.gnu.org/software/gsl/">gsl
 &gt;2.0</a> , <a class="reference external" href="https://www.netlib.org/lapack/lug/node14.html">lapack
 (3.6.1)</a>, Python &gt;3.4,
@@ -171,7 +173,7 @@ <h2>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to
 it as the <code class="docutils literal notranslate"><span class="pre">CUDAHOME</span></code> environment variable.</p>
 </section>
 <section id="installing">
-<h2>Installing<a class="headerlink" href="#installing" title="Permalink to this heading"></a></h2>
+<h2>Installing<a class="headerlink" href="#installing" title="Link to this heading"></a></h2>
 <ol class="arabic simple" start="0">
 <li><p><a class="reference external" href="https://docs.anaconda.com/anaconda/install/">Install Anaconda</a> if
 you do not have it.</p></li>
@@ -241,44 +243,44 @@ <h2>Installing<a class="headerlink" href="#installing" title="Permalink to this
 </pre></div>
 </div>
 <section id="running-the-tests">
-<h3>Running the Tests<a class="headerlink" href="#running-the-tests" title="Permalink to this heading"></a></h3>
+<h3>Running the Tests<a class="headerlink" href="#running-the-tests" title="Link to this heading"></a></h3>
 <p>In the main directory of the package run in the terminal:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="o">-</span><span class="n">m</span> <span class="n">unittest</span> <span class="n">discover</span>
 </pre></div>
 </div>
 </section>
 <section id="contributing">
-<h3>Contributing<a class="headerlink" href="#contributing" title="Permalink to this heading"></a></h3>
+<h3>Contributing<a class="headerlink" href="#contributing" title="Link to this heading"></a></h3>
 <p>Please read <a class="reference external" href="CONTRIBUTING.md">CONTRIBUTING.md</a> for details on our
 code of conduct, and the process for submitting pull requests to us.</p>
 </section>
 <section id="versioning">
-<h3>Versioning<a class="headerlink" href="#versioning" title="Permalink to this heading"></a></h3>
+<h3>Versioning<a class="headerlink" href="#versioning" title="Link to this heading"></a></h3>
 <p>We use <a class="reference external" href="http://semver.org/">SemVer</a> for versioning. For the versions
 available, see the <a class="reference external" href="https://github.com/mikekatz04/BBHx/tags">tags on this
 repository</a>.</p>
-<p>Current Version: 1.0.5</p>
+<p>Current Version: 1.0.6</p>
 </section>
 <section id="authors">
-<h3>Authors<a class="headerlink" href="#authors" title="Permalink to this heading"></a></h3>
+<h3>Authors<a class="headerlink" href="#authors" title="Link to this heading"></a></h3>
 <ul class="simple">
 <li><p><strong>Michael Katz</strong></p></li>
 </ul>
 </section>
 </section>
 <section id="contibutors">
-<h2>Contibutors<a class="headerlink" href="#contibutors" title="Permalink to this heading"></a></h2>
+<h2>Contibutors<a class="headerlink" href="#contibutors" title="Link to this heading"></a></h2>
 <ul class="simple">
 <li><p>Sylvain Marsat</p></li>
 <li><p>John Baker</p></li>
 </ul>
 <section id="license">
-<h3>License<a class="headerlink" href="#license" title="Permalink to this heading"></a></h3>
+<h3>License<a class="headerlink" href="#license" title="Link to this heading"></a></h3>
 <p>This project is licensed under the GNU License - see the
 <a class="reference external" href="LICENSE.md">LICENSE.md</a> file for details.</p>
 </section>
 <section id="acknowledgments">
-<h3>Acknowledgments<a class="headerlink" href="#acknowledgments" title="Permalink to this heading"></a></h3>
+<h3>Acknowledgments<a class="headerlink" href="#acknowledgments" title="Link to this heading"></a></h3>
 <ul class="simple">
 <li><p>This research was also supported in part through the computational
 resources and staff contributions provided for the Quest/Grail high

diff --git a/docs/html/_sources/README.rst.txt b/docs/html/_sources/README.rst.txt
@@ -191,7 +191,7 @@ We use `SemVer <http://semver.org/>`__ for versioning. For the versions
 available, see the `tags on this
 repository <https://github.com/mikekatz04/BBHx/tags>`__.
 
-Current Version: 1.0.5
+Current Version: 1.0.6
 
 Authors
 -------

diff --git a/docs/html/_static/basic.css b/docs/html/_static/basic.css
@@ -237,6 +237,10 @@ a.headerlink {
     visibility: hidden;
 }
 
+a:visited {
+    color: #551A8B;
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -670,6 +674,16 @@ dd {
     margin-left: 30px;
 }
 
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -738,6 +752,14 @@ abbr, acronym {
     cursor: help;
 }
 
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
 /* -- code displays --------------------------------------------------------- */
 
 pre {

diff --git a/docs/html/_static/css/theme.css b/docs/html/_static/css/theme.css
diff --git a/docs/html/_static/documentation_options.js b/docs/html/_static/documentation_options.js
@@ -1,5 +1,4 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+const DOCUMENTATION_OPTIONS = {
     VERSION: '',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,

diff --git a/docs/html/_static/nbsphinx-code-cells.css b/docs/html/_static/nbsphinx-code-cells.css
@@ -62,12 +62,16 @@ div.nblast.container {
 }
 
 /* input prompt */
-div.nbinput.container div.prompt pre {
+div.nbinput.container div.prompt pre,
+/* for sphinx_immaterial theme: */
+div.nbinput.container div.prompt pre > code {
     color: #307FC1;
 }
 
 /* output prompt */
-div.nboutput.container div.prompt pre {
+div.nboutput.container div.prompt pre,
+/* for sphinx_immaterial theme: */
+div.nboutput.container div.prompt pre > code {
     color: #BF5B3D;
 }
 
@@ -204,8 +208,10 @@ div.nboutput.container div.output_area > div[class^='highlight']{
     overflow-y: hidden;
 }
 
-/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
-.prompt .copybtn {
+/* hide copy button on prompts for 'sphinx_copybutton' extension ... */
+.prompt .copybtn,
+/* ... and 'sphinx_immaterial' theme */
+.prompt .md-clipboard.md-icon {
     display: none;
 }
 

diff --git a/docs/html/_static/pygments.css b/docs/html/_static/pygments.css
@@ -17,6 +17,7 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
 .highlight .cs { color: #3D7B7B; font-style: italic } /* Comment.Special */
 .highlight .gd { color: #A00000 } /* Generic.Deleted */
 .highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .ges { font-weight: bold; font-style: italic } /* Generic.EmphStrong */
 .highlight .gr { color: #E40000 } /* Generic.Error */
 .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
 .highlight .gi { color: #008400 } /* Generic.Inserted */

diff --git a/docs/html/_static/searchtools.js b/docs/html/_static/searchtools.js
@@ -57,12 +57,12 @@ const _removeChildren = (element) => {
 const _escapeRegExp = (string) =>
   string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
 
-const _displayItem = (item, searchTerms) => {
+const _displayItem = (item, searchTerms, highlightTerms) => {
   const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
-  const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
   const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
   const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
 
   const [docName, title, anchor, descr, score, _filename] = item;
 
@@ -75,20 +75,24 @@ const _displayItem = (item, searchTerms) => {
     if (dirname.match(/\/index\/$/))
       dirname = dirname.substring(0, dirname.length - 6);
     else if (dirname === "index/") dirname = "";
-    requestUrl = docUrlRoot + dirname;
+    requestUrl = contentRoot + dirname;
     linkUrl = requestUrl;
   } else {
     // normal html builders
-    requestUrl = docUrlRoot + docName + docFileSuffix;
+    requestUrl = contentRoot + docName + docFileSuffix;
     linkUrl = docName + docLinkSuffix;
   }
   let linkEl = listItem.appendChild(document.createElement("a"));
   linkEl.href = linkUrl + anchor;
   linkEl.dataset.score = score;
   linkEl.innerHTML = title;
-  if (descr)
+  if (descr) {
     listItem.appendChild(document.createElement("span")).innerHTML =
       " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
   else if (showSearchSummary)
     fetch(requestUrl)
       .then((responseData) => responseData.text())
@@ -97,6 +101,9 @@ const _displayItem = (item, searchTerms) => {
           listItem.appendChild(
             Search.makeSearchSummary(data, searchTerms)
           );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
       });
   Search.output.appendChild(listItem);
 };
@@ -115,14 +122,15 @@ const _finishSearch = (resultCount) => {
 const _displayNextItem = (
   results,
   resultCount,
-  searchTerms
+  searchTerms,
+  highlightTerms,
 ) => {
   // results left, load the summary and display it
   // this is intended to be dynamic (don't sub resultsCount)
   if (results.length) {
-    _displayItem(results.pop(), searchTerms);
+    _displayItem(results.pop(), searchTerms, highlightTerms);
     setTimeout(
-      () => _displayNextItem(results, resultCount, searchTerms),
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
       5
     );
   }
@@ -360,7 +368,7 @@ const Search = {
     // console.info("search results:", Search.lastresults);
 
     // print the results
-    _displayNextItem(results, results.length, searchTerms);
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
   },
 
   /**

diff --git a/docs/html/_static/sphinx_highlight.js b/docs/html/_static/sphinx_highlight.js
@@ -29,14 +29,19 @@ const _highlight = (node, addItems, text, className) => {
       }
 
       span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
       parent.insertBefore(
         span,
         parent.insertBefore(
-          document.createTextNode(val.substr(pos + text.length)),
+          rest,
           node.nextSibling
         )
       );
       node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
 
       if (isInSVG) {
         const rect = document.createElementNS(
@@ -140,5 +145,10 @@ const SphinxHighlight = {
   },
 };
 
-_ready(SphinxHighlight.highlightSearchWords);
-_ready(SphinxHighlight.initEscapeListener);
+_ready(() => {
+  /* Do not call highlightSearchWords() when we are on the search page.
+   * It will highlight words from the *previous* search query.
+   */
+  if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
+  SphinxHighlight.initEscapeListener();
+});