beta 3

fastlmm · Nov 6, 2023 · 6fc8ae5 · 6fc8ae5
1 parent 67972a4
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Showing 17 changed files with 74 additions and 28 deletions.
diff --git a/.gitignore b/.gitignore
@@ -148,4 +148,3 @@ old4cargo.lock
 old5Cargo.lock
 oldCargo.lock
 bed_reader/Untitled-1.ipynb
-bed_reader/_open_bed.py
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,7 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - (Python) Added new `read_sparse()` method for creating
   `sympy.sparse.csc_matrix` and `sympy.sparse.csr_matrix`. This
-  method can save memory when a *.bed file contains mostly 0's.
+  method can save memory when a *.bed file contains mostly zeros.
 
 - (Rust) Rust methods that returned `Result` now return
   `Result<_,Box<BedErrorPlus>>`. Before, they returned

diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -1,7 +1,7 @@
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [package]
-version = "1.0.0-beta.2"
+version = "1.0.0-beta.3"
 name = "bed-reader"
 description = "Read and write the PLINK BED format, simply and efficiently."
 repository = "https://github.com/fastlmm/bed-reader"

diff --git a/bed_reader/_open_bed.py b/bed_reader/_open_bed.py
@@ -1192,7 +1192,14 @@ def read_sparse(
     ) -> (Union[sparse.csc_matrix, sparse.csr_matrix]) if sparse is not None else None:
         """
         Read genotype information into a :mod:`scipy.sparse` matrix. Sparse matrices
-        may be useful when the data is mostly 0.
+        may be useful when the data is mostly zeros.
+
+        .. note::
+            This method requires :mod:`scipy`. Install `scipy` with:
+
+            .. code-block:: bash
+
+                pip install --upgrade bed-reader[sparse]
 
         Parameters
         ----------
@@ -1510,8 +1517,8 @@ def _read_csv(filepath, delimiter=None, dtype=None, usecols=None):
 
 
 if __name__ == "__main__":
-    logging.basicConfig(level=logging.INFO)
-
     import pytest
 
+    logging.basicConfig(level=logging.INFO)
+
     pytest.main(["--doctest-modules", __file__])
diff --git a/bed_reader/_sample_data.py b/bed_reader/_sample_data.py
@@ -44,6 +44,14 @@ def sample_file(filepath: Union[str, Path]) -> str:
         Local name of sample .bed file.
 
 
+    .. note::
+        This function requires the :mod:`pooch` package. Install `pooch` with:
+
+        .. code-block:: bash
+
+            pip install --upgrade bed-reader[samples]
+
+
     By default this function puts files under the user's cache directory.
     Override this by setting
     the `BED_READER_DATA_DIR` environment variable.

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: 93cd283100cdb6074a5966603b955a1a
+config: bd3c16945e06a1735271b50da76cccd3
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_modules/bed_reader/_open_bed.html b/docs/_modules/bed_reader/_open_bed.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>bed_reader._open_bed &mdash; Bed Reader 1.0.0-beta.1 documentation</title>
+  <title>bed_reader._open_bed &mdash; Bed Reader 1.0.0-beta.2 documentation</title>
       <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -30,7 +30,7 @@
             Bed Reader
           </a>
               <div class="version">
-                1.0.0-beta.1
+                1.0.0-beta.2
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
@@ -1261,7 +1261,14 @@ <h1>Source code for bed_reader._open_bed</h1><div class="highlight"><pre>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="p">(</span><span class="n">Union</span><span class="p">[</span><span class="n">sparse</span><span class="o">.</span><span class="n">csc_matrix</span><span class="p">,</span> <span class="n">sparse</span><span class="o">.</span><span class="n">csr_matrix</span><span class="p">])</span> <span class="k">if</span> <span class="n">sparse</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="k">else</span> <span class="kc">None</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Read genotype information into a :mod:`scipy.sparse` matrix. Sparse matrices</span>
-<span class="sd">        may be useful when the data is mostly 0.</span>
+<span class="sd">        may be useful when the data is mostly zeros.</span>
+
+<span class="sd">        .. note::</span>
+<span class="sd">            This method requires :mod:`scipy`. Install `scipy` with:</span>
+
+<span class="sd">            .. code-block:: bash</span>
+
+<span class="sd">                pip install --upgrade bed-reader[sparse]</span>
 
 <span class="sd">        Parameters</span>
 <span class="sd">        ----------</span>
@@ -1579,10 +1586,10 @@ <h1>Source code for bed_reader._open_bed</h1><div class="highlight"><pre>
 
 
 <span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
-    <span class="n">logging</span><span class="o">.</span><span class="n">basicConfig</span><span class="p">(</span><span class="n">level</span><span class="o">=</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
-
     <span class="kn">import</span> <span class="nn">pytest</span>
 
+    <span class="n">logging</span><span class="o">.</span><span class="n">basicConfig</span><span class="p">(</span><span class="n">level</span><span class="o">=</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
+
     <span class="n">pytest</span><span class="o">.</span><span class="n">main</span><span class="p">([</span><span class="s2">&quot;--doctest-modules&quot;</span><span class="p">,</span> <span class="vm">__file__</span><span class="p">])</span>
 </pre></div>
 

diff --git a/docs/_modules/bed_reader/_sample_data.html b/docs/_modules/bed_reader/_sample_data.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>bed_reader._sample_data &mdash; Bed Reader 1.0.0 documentation</title>
+  <title>bed_reader._sample_data &mdash; Bed Reader 1.0.0-beta.2 documentation</title>
       <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -30,7 +30,7 @@
             Bed Reader
           </a>
               <div class="version">
-                1.0.0
+                1.0.0-beta.2
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
@@ -113,6 +113,14 @@ <h1>Source code for bed_reader._sample_data</h1><div class="highlight"><pre>
 <span class="sd">        Local name of sample .bed file.</span>
 
 
+<span class="sd">    .. note::</span>
+<span class="sd">        This function requires the :mod:`pooch` package. Install `pooch` with:</span>
+
+<span class="sd">        .. code-block:: bash</span>
+
+<span class="sd">            pip install --upgrade bed-reader[samples]</span>
+
+
 <span class="sd">    By default this function puts files under the user&#39;s cache directory.</span>
 <span class="sd">    Override this by setting</span>
 <span class="sd">    the `BED_READER_DATA_DIR` environment variable.</span>

diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; Bed Reader 1.0.0-beta.2 documentation</title>
+  <title>Overview: module code &mdash; Bed Reader 1.0.0-beta.3 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -30,7 +30,7 @@
             Bed Reader
           </a>
               <div class="version">
-                1.0.0-beta.2
+                1.0.0-beta.3
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">

diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.0.0-beta.2',
+    VERSION: '1.0.0-beta.3',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Index &mdash; Bed Reader 1.0.0-beta.2 documentation</title>
+  <title>Index &mdash; Bed Reader 1.0.0-beta.3 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -30,7 +30,7 @@
             Bed Reader
           </a>
               <div class="version">
-                1.0.0-beta.2
+                1.0.0-beta.3
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">

diff --git a/docs/index.html b/docs/index.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>bed_reader Documentation &mdash; Bed Reader 1.0.0-beta.2 documentation</title>
+  <title>bed_reader Documentation &mdash; Bed Reader 1.0.0-beta.3 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -31,7 +31,7 @@
             Bed Reader
           </a>
               <div class="version">
-                1.0.0-beta.2
+                1.0.0-beta.3
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -844,7 +844,14 @@ <h3>open_bed<a class="headerlink" href="#open-bed" title="Permalink to this head
 <dt class="sig sig-object py" id="bed_reader.open_bed.read_sparse">
 <span class="sig-name descname"><span class="pre">read_sparse</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dtype</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#type" title="(in Python v3.12)"><span class="pre">type</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'float32'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">format</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'csc'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_threads</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.sparse.csc_matrix.html#scipy.sparse.csc_matrix" title="(in SciPy v1.11.3)"><span class="pre">csc_matrix</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.sparse.csr_matrix.html#scipy.sparse.csr_matrix" title="(in SciPy v1.11.3)"><span class="pre">csr_matrix</span></a></span></span><a class="reference internal" href="_modules/bed_reader/_open_bed.html#open_bed.read_sparse"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#bed_reader.open_bed.read_sparse" title="Permalink to this definition"></a></dt>
 <dd><p>Read genotype information into a <a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/sparse.html#module-scipy.sparse" title="(in SciPy v1.11.3)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scipy.sparse</span></code></a> matrix. Sparse matrices
-may be useful when the data is mostly 0.</p>
+may be useful when the data is mostly zeros.</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>This method requires <a class="reference external" href="https://docs.scipy.org/doc/scipy/index.html#module-scipy" title="(in SciPy v1.11.3)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scipy</span></code></a>. Install <cite>scipy</cite> with:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>--upgrade<span class="w"> </span>bed-reader<span class="o">[</span>sparse<span class="o">]</span>
+</pre></div>
+</div>
+</div>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
@@ -1166,6 +1173,13 @@ <h3>sample_file<a class="headerlink" href="#sample-file" title="Permalink to thi
 <dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)">str</a></p>
 </dd>
 </dl>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>This function requires the <code class="xref py py-mod docutils literal notranslate"><span class="pre">pooch</span></code> package. Install <cite>pooch</cite> with:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>--upgrade<span class="w"> </span>bed-reader<span class="o">[</span>samples<span class="o">]</span>
+</pre></div>
+</div>
+</div>
 <p>By default this function puts files under the user’s cache directory.
 Override this by setting
 the <cite>BED_READER_DATA_DIR</cite> environment variable.</p>

diff --git a/docs/objects.inv b/docs/objects.inv
@@ -1,6 +1,6 @@
 # Sphinx inventory version 2
 # Project: Bed Reader
-# Version: 1.0.0-beta.2
+# Version: 1.0.0-beta.3
 # The remainder of this file is compressed using zlib.
 xڥ��n�0����`R=RYκ,F�2b(,S'>Ӹ���м=�N4I�������}|;)��-T�(�n�j�]ŉ1�"&)�lk+����.R��������[�9p(n=�hֶ[D~ZN�M�(�,Sr9\�Z	e������O�֠Wp�.��J��T+�rT�u�kj�j��j�+��q�V�m��^��!��R����	��4+�Ysd��#c�hܵ?1r<��
 �i����xw}��\ʦ�O CKw���}��ѠC{���eTU㺊�Aѝ�Z�?^�v;���=":T���k	<^��%��I���D�<3��7Cg�)9L{ԸWx����r")���I��'�~@����"3^��D��{����?��I�;2��o����ᗏ��ٛ5�L��<�PYę�=�<I��ꐘ/���ɥQ�<�Ό�����x��ǐ��������fFL~X���'��0�g3�� ��d���0�4�a���*jp�����

diff --git a/docs/search.html b/docs/search.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Search &mdash; Bed Reader 1.0.0-beta.2 documentation</title>
+  <title>Search &mdash; Bed Reader 1.0.0-beta.3 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
 
@@ -33,7 +33,7 @@
             Bed Reader
           </a>
               <div class="version">
-                1.0.0-beta.2
+                1.0.0-beta.3
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="#" method="get">