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Release 0.6.5 #176

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Jul 4, 2024
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Release 0.6.5 #176

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73979db
Prepare to release 0.6.5
raphaelvallat Jul 4, 2024
c1c73f0
Update docs
raphaelvallat Jul 4, 2024
17e0654
Update docs
raphaelvallat Jul 4, 2024
76b3077
Update typo statsitics
raphaelvallat Jul 4, 2024
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4 changes: 2 additions & 2 deletions .github/workflows/python_tests.yml
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Expand Up @@ -11,8 +11,8 @@ jobs:
strategy:
fail-fast: false
matrix:
platform: [ubuntu-latest, macos-latest, windows-latest]
python-version: ["3.8", "3.9", "3.10", "3.11"]
platform: [ubuntu-latest, windows-latest] # macos-latest
python-version: ["3.9", "3.10", "3.11"]

runs-on: ${{ matrix.platform }}

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2 changes: 2 additions & 0 deletions docs/api.rst
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Expand Up @@ -43,6 +43,8 @@ Hypnogram & sleep statistics
sleep_statistics
Hypnogram
simulate_hypnogram
EpochByEpochAgreement
SleepStatsAgreement

Spectral analyses
-----------------
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# 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: 489cdac284cc185cfdae105616c5af8a
config: f80ed99698c532d7a1c5d14ebdacc629
tags: 645f666f9bcd5a90fca523b33c5a78b7
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5 changes: 3 additions & 2 deletions docs/build/html/_modules/index.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &#8212; yasa 0.6.4 documentation</title>
<title>Overview: module code &#8212; yasa 0.6.5 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" />
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</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>0.6.4</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.6.5</b></span>
</div>

<div class="collapse navbar-collapse nav-collapse">
Expand Down Expand Up @@ -94,6 +94,7 @@

<h1>All modules for which code is available</h1>
<ul><li><a href="yasa/detection.html">yasa.detection</a></li>
<li><a href="yasa/evaluation.html">yasa.evaluation</a></li>
<li><a href="yasa/heart.html">yasa.heart</a></li>
<li><a href="yasa/hypno.html">yasa.hypno</a></li>
<li><a href="yasa/others.html">yasa.others</a></li>
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5 changes: 3 additions & 2 deletions docs/build/html/_modules/yasa/detection.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>yasa.detection &#8212; yasa 0.6.4 documentation</title>
<title>yasa.detection &#8212; yasa 0.6.5 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" />
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</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>0.6.4</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.6.5</b></span>
</div>

<div class="collapse navbar-collapse nav-collapse">
Expand Down Expand Up @@ -101,6 +101,7 @@ <h1>Source code for yasa.detection</h1><div class="highlight"><pre>
<span class="sd">- GitHub: https://github.com/raphaelvallat/yasa</span>
<span class="sd">- License: BSD 3-Clause License</span>
<span class="sd">&quot;&quot;&quot;</span>

<span class="kn">import</span> <span class="nn">mne</span>
<span class="kn">import</span> <span class="nn">logging</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
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1,626 changes: 1,626 additions & 0 deletions docs/build/html/_modules/yasa/evaluation.html
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5 changes: 3 additions & 2 deletions docs/build/html/_modules/yasa/heart.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>yasa.heart &#8212; yasa 0.6.4 documentation</title>
<title>yasa.heart &#8212; yasa 0.6.5 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" />
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</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>0.6.4</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.6.5</b></span>
</div>

<div class="collapse navbar-collapse nav-collapse">
Expand Down Expand Up @@ -99,6 +99,7 @@ <h1>Source code for yasa.heart</h1><div class="highlight"><pre>
<span class="sd">Author: Dr Raphael Vallat &lt;[email protected]&gt;, UC Berkeley.</span>
<span class="sd">Date: May 2022</span>
<span class="sd">&quot;&quot;&quot;</span>

<span class="kn">import</span> <span class="nn">logging</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
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45 changes: 42 additions & 3 deletions docs/build/html/_modules/yasa/hypno.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>yasa.hypno &#8212; yasa 0.6.4 documentation</title>
<title>yasa.hypno &#8212; yasa 0.6.5 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" />
Expand Down Expand Up @@ -43,7 +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>0.6.4</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.6.5</b></span>
</div>

<div class="collapse navbar-collapse nav-collapse">
Expand Down Expand Up @@ -96,6 +96,7 @@ <h1>Source code for yasa.hypno</h1><div class="highlight"><pre>
<span></span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd">Hypnogram-related functions and class.</span>
<span class="sd">&quot;&quot;&quot;</span>

<span class="kn">import</span> <span class="nn">mne</span>
<span class="kn">import</span> <span class="nn">logging</span>

Expand All @@ -105,6 +106,7 @@ <h1>Source code for yasa.hypno</h1><div class="highlight"><pre>
<span class="kn">from</span> <span class="nn">yasa.io</span> <span class="kn">import</span> <span class="n">set_log_level</span>
<span class="kn">from</span> <span class="nn">yasa.plotting</span> <span class="kn">import</span> <span class="n">plot_hypnogram</span>
<span class="kn">from</span> <span class="nn">yasa.sleepstats</span> <span class="kn">import</span> <span class="n">transition_matrix</span>
<span class="kn">from</span> <span class="nn">yasa.evaluation</span> <span class="kn">import</span> <span class="n">EpochByEpochAgreement</span>
<span class="kn">from</span> <span class="nn">pandas.api.types</span> <span class="kn">import</span> <span class="n">CategoricalDtype</span>

<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span>
Expand Down Expand Up @@ -575,7 +577,7 @@ <h1>Source code for yasa.hypno</h1><div class="highlight"><pre>
<span class="sd"> Name: Stage, dtype: int16</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="c1"># Return as int16 (-32768 to 32767) to reduce memory usage</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">hypno</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mapping</span><span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">int16</span><span class="p">)</span></div>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">hypno</span><span class="o">.</span><span class="n">cat</span><span class="o">.</span><span class="n">rename_categories</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mapping</span><span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">int16</span><span class="p">)</span></div>

<div class="viewcode-block" id="Hypnogram.consolidate_stages"><a class="viewcode-back" href="../../generated/yasa.Hypnogram.html#yasa.Hypnogram.consolidate_stages">[docs]</a> <span class="k">def</span> <span class="nf">consolidate_stages</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new_n_stages</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Reduce the number of stages in a hypnogram to match actigraphy or wearables.</span>
Expand Down Expand Up @@ -665,6 +667,43 @@ <h1>Source code for yasa.hypno</h1><div class="highlight"><pre>
<span class="n">scorer</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">scorer</span><span class="p">,</span>
<span class="p">)</span></div>

<div class="viewcode-block" id="Hypnogram.evaluate"><a class="viewcode-back" href="../../generated/yasa.Hypnogram.html#yasa.Hypnogram.evaluate">[docs]</a> <span class="k">def</span> <span class="nf">evaluate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">obs_hyp</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Evaluate agreement between two hypnograms of the same sleep session.</span>

<span class="sd"> For example, the reference hypnogram (i.e., ``self``) might be a manually-scored hypnogram</span>
<span class="sd"> and the reference hypnogram (i.e., ``ref_hyp``) might be a hypnogram from actigraphy, a</span>
<span class="sd"> wearable device, or an automated scorer (e.g., :py:meth:`yasa.SleepStaging.predict`).</span>

<span class="sd"> Parameters</span>
<span class="sd"> ----------</span>
<span class="sd"> self : :py:class:`yasa.Hypnogram`</span>
<span class="sd"> Reference or ground-truth hypnogram.</span>
<span class="sd"> obs_hyp : :py:class:`yasa.Hypnogram`</span>
<span class="sd"> The observed or to-be-evaluated hypnogram.</span>

<span class="sd"> Returns</span>
<span class="sd"> -------</span>
<span class="sd"> ebe : :py:class:`yasa.EpochByEpochAgreement`</span>
<span class="sd"> See :py:class:`~yasa.EpochByEpochAgreement` documentation for more detail.</span>

<span class="sd"> Examples</span>
<span class="sd"> --------</span>
<span class="sd"> &gt;&gt;&gt; from yasa import simulate_hypnogram</span>
<span class="sd"> &gt;&gt;&gt; hyp_a = simulate_hypnogram(tib=90, scorer=&quot;AASM&quot;, seed=8)</span>
<span class="sd"> &gt;&gt;&gt; hyp_b = hyp_a.simulate_similar(scorer=&quot;YASA&quot;, seed=9)</span>
<span class="sd"> &gt;&gt;&gt; ebe = hyp_a.evaluate(hyp_b)</span>
<span class="sd"> &gt;&gt;&gt; ebe.get_agreement().round(3)</span>
<span class="sd"> accuracy 0.550</span>
<span class="sd"> balanced_acc 0.355</span>
<span class="sd"> kappa 0.227</span>
<span class="sd"> mcc 0.231</span>
<span class="sd"> precision 0.515</span>
<span class="sd"> recall 0.550</span>
<span class="sd"> fbeta 0.524</span>
<span class="sd"> Name: agreement, dtype: float64</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">return</span> <span class="n">EpochByEpochAgreement</span><span class="p">([</span><span class="bp">self</span><span class="p">],</span> <span class="p">[</span><span class="n">obs_hyp</span><span class="p">])</span></div>

<div class="viewcode-block" id="Hypnogram.find_periods"><a class="viewcode-back" href="../../generated/yasa.Hypnogram.html#yasa.Hypnogram.find_periods">[docs]</a> <span class="k">def</span> <span class="nf">find_periods</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">threshold</span><span class="o">=</span><span class="s2">&quot;5min&quot;</span><span class="p">,</span> <span class="n">equal_length</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;Find sequences of consecutive values exceeding a certain duration in hypnogram.</span>

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5 changes: 3 additions & 2 deletions docs/build/html/_modules/yasa/others.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>yasa.others &#8212; yasa 0.6.4 documentation</title>
<title>yasa.others &#8212; yasa 0.6.5 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" />
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</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>0.6.4</b></span>
<span class="navbar-text navbar-version pull-left"><b>0.6.5</b></span>
</div>

<div class="collapse navbar-collapse nav-collapse">
Expand Down Expand Up @@ -96,6 +96,7 @@ <h1>Source code for yasa.others</h1><div class="highlight"><pre>
<span></span><span class="sd">&quot;&quot;&quot;</span>
<span class="sd">This file contains several helper functions to manipulate 1D and 2D EEG data.</span>
<span class="sd">&quot;&quot;&quot;</span>

<span class="kn">import</span> <span class="nn">logging</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">scipy.interpolate</span> <span class="kn">import</span> <span class="n">interp1d</span>
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