Release 0.6.4 (#153)

* Update version * Update changelog and API * Disable FutureWarning * Remove warnings import * black * Upgrade requirements * Add back Hypnogram and simulate_hypnogram * Update changelog * Update doc * Add former * Update docs * Remove outdated * remove outdated in init * update doc * Add push_pypi.md * Update pytest version * Remove Python 3.7 tests * Update setup.py * Update doc * Disable test random array
raphaelvallat · Jan 13, 2024 · 6b37c63 · 6b37c63
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diff --git a/.github/workflows/python_tests.yml b/.github/workflows/python_tests.yml
@@ -11,8 +11,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        platform: [ubuntu-latest, windows-latest]  # macos-latest,
-        python-version: [3.7, 3.8, 3.9]
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     runs-on: ${{ matrix.platform }}
 
@@ -39,7 +39,7 @@ jobs:
         pytest --cov --cov-report=xml --cov-config=setup.cfg --verbose
 
     - name: Upload coverage report
-      if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == 3.8 }}
+      if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == 3.9 }}
       uses: codecov/codecov-action@v1
       with:
         token: a58a0c62-fb11-4429-977b-65bec01ecb44

diff --git a/README.rst b/README.rst
@@ -119,7 +119,7 @@ Below some plots demonstrating the functionalities of YASA. To reproduce these,
 Development
 ~~~~~~~~~~~
 
-YASA was created and is maintained by `Raphael Vallat <https://raphaelvallat.com>`_, a postdoctoral researcher in `Matthew Walker's lab <https://www.humansleepscience.com/>`_ at UC Berkeley. Contributions are more than welcome so feel free to contact me, open an issue or submit a pull request!
+YASA was created and is maintained by `Raphael Vallat <https://raphaelvallat.com>`_, a former postdoctoral researcher in `Matthew Walker's lab <https://www.humansleepscience.com/>`_ at UC Berkeley. Contributions are more than welcome so feel free to contact me, open an issue or submit a pull request!
 
 To see the code or report a bug, please visit the `GitHub repository <https://github.com/raphaelvallat/yasa>`_.
 

diff --git a/docs/api.rst b/docs/api.rst
@@ -31,7 +31,6 @@ Hypnogram & sleep statistics
 .. autosummary::
    :toctree: generated/
 
-    Hypnogram
     hypno_upsample_to_data
     hypno_upsample_to_sf
     hypno_str_to_int
@@ -42,7 +41,8 @@ Hypnogram & sleep statistics
     plot_spectrogram
     transition_matrix
     sleep_statistics
-    simulate_hypno
+    Hypnogram
+    simulate_hypnogram
 
 Spectral analyses
 -----------------

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: 53802cc2376a375a855b3c0f38207c28
+config: 489cdac284cc185cfdae105616c5af8a
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_images/yasa-Hypnogram-1.png b/docs/build/html/_images/yasa-Hypnogram-1.png
diff --git a/docs/build/html/_images/yasa-plot_hypnogram-1.png b/docs/build/html/_images/yasa-plot_hypnogram-1.png
diff --git a/docs/build/html/_images/yasa-plot_hypnogram-2.png b/docs/build/html/_images/yasa-plot_hypnogram-2.png
diff --git a/docs/build/html/_images/yasa-plot_hypnogram-3.png b/docs/build/html/_images/yasa-plot_hypnogram-3.png
diff --git a/docs/build/html/_images/yasa-plot_spectrogram-1.png b/docs/build/html/_images/yasa-plot_spectrogram-1.png
diff --git a/docs/build/html/_images/yasa-plot_spectrogram-2.png b/docs/build/html/_images/yasa-plot_spectrogram-2.png
diff --git a/docs/build/html/_images/yasa-simulate_hypno-1.png b/docs/build/html/_images/yasa-simulate_hypno-1.png
diff --git a/docs/build/html/_images/yasa-simulate_hypnogram-1.png b/docs/build/html/_images/yasa-simulate_hypnogram-1.png
diff --git a/docs/build/html/_images/yasa-topoplot-1.png b/docs/build/html/_images/yasa-topoplot-1.png
diff --git a/docs/build/html/_images/yasa-topoplot-2.png b/docs/build/html/_images/yasa-topoplot-2.png
diff --git a/docs/build/html/_images/yasa-transition_matrix-1.png b/docs/build/html/_images/yasa-transition_matrix-1.png
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
@@ -1,35 +1,34 @@
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
     <meta charset="utf-8" />
-    <title>Overview: module code &#8212; yasa 0.6.3 documentation</title>
-    <link rel="stylesheet" href="../_static/bootstrap-sphinx.css" type="text/css" />
-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Overview: module code &#8212; yasa 0.6.4 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/bootstrap-sphinx.css" />
     <link rel="stylesheet" type="text/css" href="../_static/plot_directive.css" />
     <link rel="stylesheet" type="text/css" href="../_static/copybutton.css" />
     <link rel="stylesheet" type="text/css" href="../_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
     <link rel="stylesheet" type="text/css" href="../_static/panels-bootstrap.5fd3999ee7762ccc51105388f4a9d115.css" />
     <link rel="stylesheet" type="text/css" href="../_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    <script id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
+    <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/doctools.js"></script>
-    <script src="../_static/language_data.js"></script>
     <script src="../_static/clipboard.min.js"></script>
     <script src="../_static/copybutton.js"></script>
-    <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
 <meta charset='utf-8'>
 <meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
 <meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
 <meta name="apple-mobile-web-app-capable" content="yes">
-<script type="text/javascript" src="../_static/js/jquery-1.12.4.min.js "></script>
-<script type="text/javascript" src="../_static/js/jquery-fix.js "></script>
-<script type="text/javascript" src="../_static/bootstrap-3.4.1/js/bootstrap.min.js "></script>
-<script type="text/javascript" src="../_static/bootstrap-sphinx.js "></script>
+<script type="text/javascript" src="../_static/js/jquery-1.12.4.min.js"></script>
+<script type="text/javascript" src="../_static/js/jquery-fix.js"></script>
+<script type="text/javascript" src="../_static/bootstrap-3.4.1/js/bootstrap.min.js"></script>
+<script type="text/javascript" src="../_static/bootstrap-sphinx.js"></script>
 
   </head><body>
 
@@ -44,7 +43,7 @@
         </button>
         <a class="navbar-brand" href="../index.html"><span><img src="../_static/yasa_128x128.png"></span>
           yasa</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.6.3</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>0.6.4</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">
@@ -118,8 +117,8 @@ <h1>All modules for which code is available</h1>
 
     </p>
     <p>
-        &copy; Copyright 2018-2022, Dr. Raphael Vallat, Center for Human Sleep Science, UC Berkeley.<br/>
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.0.0.<br/>
+        &copy; Copyright 2018-2024, Dr. Raphael Vallat, Center for Human Sleep Science, UC Berkeley.<br/>
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.4.0.<br/>
     </p>
   </div>
 </footer>

diff --git a/docs/build/html/_modules/yasa/detection.html b/docs/build/html/_modules/yasa/detection.html
@@ -1,35 +1,34 @@
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
     <meta charset="utf-8" />
-    <title>yasa.detection &#8212; yasa 0.6.3 documentation</title>
-    <link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
-    <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>yasa.detection &#8212; yasa 0.6.4 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/bootstrap-sphinx.css" />
     <link rel="stylesheet" type="text/css" href="../../_static/plot_directive.css" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css" />
     <link rel="stylesheet" type="text/css" href="../../_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
     <link rel="stylesheet" type="text/css" href="../../_static/panels-bootstrap.5fd3999ee7762ccc51105388f4a9d115.css" />
     <link rel="stylesheet" type="text/css" href="../../_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    <script id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
+    <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/doctools.js"></script>
-    <script src="../../_static/language_data.js"></script>
     <script src="../../_static/clipboard.min.js"></script>
     <script src="../../_static/copybutton.js"></script>
-    <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="shortcut icon" href="../../_static/favicon.ico"/>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 <meta charset='utf-8'>
 <meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
 <meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
 <meta name="apple-mobile-web-app-capable" content="yes">
-<script type="text/javascript" src="../../_static/js/jquery-1.12.4.min.js "></script>
-<script type="text/javascript" src="../../_static/js/jquery-fix.js "></script>
-<script type="text/javascript" src="../../_static/bootstrap-3.4.1/js/bootstrap.min.js "></script>
-<script type="text/javascript" src="../../_static/bootstrap-sphinx.js "></script>
+<script type="text/javascript" src="../../_static/js/jquery-1.12.4.min.js"></script>
+<script type="text/javascript" src="../../_static/js/jquery-fix.js"></script>
+<script type="text/javascript" src="../../_static/bootstrap-3.4.1/js/bootstrap.min.js"></script>
+<script type="text/javascript" src="../../_static/bootstrap-sphinx.js"></script>
 
   </head><body>
 
@@ -44,7 +43,7 @@
         </button>
         <a class="navbar-brand" href="../../index.html"><span><img src="../../_static/yasa_128x128.png"></span>
           yasa</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.6.3</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>0.6.4</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">
@@ -919,7 +918,6 @@ <h1>Source code for yasa.detection</h1><div class="highlight"><pre>
     <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">()</span>
 
     <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">n_chan</span><span class="p">):</span>
-
         <span class="c1"># ####################################################################</span>
         <span class="c1"># START SINGLE CHANNEL DETECTION</span>
         <span class="c1"># ####################################################################</span>
@@ -2426,6 +2424,7 @@ <h1>Source code for yasa.detection</h1><div class="highlight"><pre>
     <span class="n">include</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span>
     <span class="n">amplitude</span><span class="o">=</span><span class="p">(</span><span class="mi">50</span><span class="p">,</span> <span class="mi">325</span><span class="p">),</span>
     <span class="n">duration</span><span class="o">=</span><span class="p">(</span><span class="mf">0.3</span><span class="p">,</span> <span class="mf">1.2</span><span class="p">),</span>
+    <span class="n">relative_prominence</span><span class="o">=</span><span class="mf">0.8</span><span class="p">,</span>
     <span class="n">freq_rem</span><span class="o">=</span><span class="p">(</span><span class="mf">0.5</span><span class="p">,</span> <span class="mi">5</span><span class="p">),</span>
     <span class="n">remove_outliers</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
     <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
@@ -2483,6 +2482,9 @@ <h1>Source code for yasa.detection</h1><div class="highlight"><pre>
 <span class="sd">    duration : tuple or list</span>
 <span class="sd">        The minimum and maximum duration of the REMs.</span>
 <span class="sd">        Default is 0.3 to 1.2 seconds.</span>
+<span class="sd">    relative_prominence : float</span>
+<span class="sd">        Relative prominence used to detect the peaks. The actual prominence is computed</span>
+<span class="sd">        by multiplying relative prominence by the minimal amplitude. Default is 0.8.</span>
 <span class="sd">    freq_rem : tuple or list</span>
 <span class="sd">        Frequency range of REMs. Default is 0.5 to 5 Hz.</span>
 <span class="sd">    remove_outliers : boolean</span>
@@ -2589,7 +2591,7 @@ <h1>Source code for yasa.detection</h1><div class="highlight"><pre>
         <span class="n">negp</span><span class="p">,</span>
         <span class="n">height</span><span class="o">=</span><span class="p">(</span><span class="n">hmin</span><span class="p">,</span> <span class="n">hmax</span><span class="p">),</span>
         <span class="n">distance</span><span class="o">=</span><span class="p">(</span><span class="n">duration</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">*</span> <span class="n">sf</span><span class="p">),</span>
-        <span class="n">prominence</span><span class="o">=</span><span class="p">(</span><span class="mf">0.8</span> <span class="o">*</span> <span class="n">hmin</span><span class="p">),</span>
+        <span class="n">prominence</span><span class="o">=</span><span class="p">(</span><span class="n">relative_prominence</span> <span class="o">*</span> <span class="n">hmin</span><span class="p">),</span>
         <span class="n">wlen</span><span class="o">=</span><span class="p">(</span><span class="n">duration</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*</span> <span class="n">sf</span><span class="p">),</span>
     <span class="p">)</span>
 
@@ -3458,8 +3460,8 @@ <h1>Source code for yasa.detection</h1><div class="highlight"><pre>
 
     </p>
     <p>
-        &copy; Copyright 2018-2022, Dr. Raphael Vallat, Center for Human Sleep Science, UC Berkeley.<br/>
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.0.0.<br/>
+        &copy; Copyright 2018-2024, Dr. Raphael Vallat, Center for Human Sleep Science, UC Berkeley.<br/>
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.4.0.<br/>
     </p>
   </div>
 </footer>

diff --git a/docs/build/html/_modules/yasa/heart.html b/docs/build/html/_modules/yasa/heart.html
@@ -1,35 +1,34 @@
 <!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
     <meta charset="utf-8" />
-    <title>yasa.heart &#8212; yasa 0.6.3 documentation</title>
-    <link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
-    <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>yasa.heart &#8212; yasa 0.6.4 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/bootstrap-sphinx.css" />
     <link rel="stylesheet" type="text/css" href="../../_static/plot_directive.css" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css" />
     <link rel="stylesheet" type="text/css" href="../../_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
     <link rel="stylesheet" type="text/css" href="../../_static/panels-bootstrap.5fd3999ee7762ccc51105388f4a9d115.css" />
     <link rel="stylesheet" type="text/css" href="../../_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    <script id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
+    <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/doctools.js"></script>
-    <script src="../../_static/language_data.js"></script>
     <script src="../../_static/clipboard.min.js"></script>
     <script src="../../_static/copybutton.js"></script>
-    <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="shortcut icon" href="../../_static/favicon.ico"/>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 <meta charset='utf-8'>
 <meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
 <meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
 <meta name="apple-mobile-web-app-capable" content="yes">
-<script type="text/javascript" src="../../_static/js/jquery-1.12.4.min.js "></script>
-<script type="text/javascript" src="../../_static/js/jquery-fix.js "></script>
-<script type="text/javascript" src="../../_static/bootstrap-3.4.1/js/bootstrap.min.js "></script>
-<script type="text/javascript" src="../../_static/bootstrap-sphinx.js "></script>
+<script type="text/javascript" src="../../_static/js/jquery-1.12.4.min.js"></script>
+<script type="text/javascript" src="../../_static/js/jquery-fix.js"></script>
+<script type="text/javascript" src="../../_static/bootstrap-3.4.1/js/bootstrap.min.js"></script>
+<script type="text/javascript" src="../../_static/bootstrap-sphinx.js"></script>
 
   </head><body>
 
@@ -44,7 +43,7 @@
         </button>
         <a class="navbar-brand" href="../../index.html"><span><img src="../../_static/yasa_128x128.png"></span>
           yasa</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.6.3</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>0.6.4</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">
@@ -304,8 +303,8 @@ <h1>Source code for yasa.heart</h1><div class="highlight"><pre>
 
     </p>
     <p>
-        &copy; Copyright 2018-2022, Dr. Raphael Vallat, Center for Human Sleep Science, UC Berkeley.<br/>
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.0.0.<br/>
+        &copy; Copyright 2018-2024, Dr. Raphael Vallat, Center for Human Sleep Science, UC Berkeley.<br/>
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 4.4.0.<br/>
     </p>
   </div>
 </footer>