deploy: 5e788f0

_modules/mltb2/data.html

@@ -84,10 +84,21 @@ <h1>Source code for mltb2.data</h1><div class="highlight"><pre>
 <span class="c1"># This software is distributed under the terms of the MIT license</span>
 <span class="c1"># which is available at https://opensource.org/licenses/MIT</span>
 
-<span class="sd">&quot;&quot;&quot;Data loading module.</span>
+<span class="sd">&quot;&quot;&quot;This module offers tools for loading data.</span>
 
-<span class="sd">Use pip to install the necessary dependencies for this module:</span>
-<span class="sd">``pip install mltb2[data]``</span>
+<span class="sd">The following tabular data sets from the biological and medical domain are supported:</span>
+
+<span class="sd">- colon: `&lt;http://genomics-pubs.princeton.edu/oncology/affydata/index.html&gt;`_</span>
+<span class="sd">- prostate: `&lt;https://web.stanford.edu/~hastie/CASI_files/DATA/prostate.html&gt;`_</span>
+<span class="sd">- leukemia_big: `&lt;https://web.stanford.edu/~hastie/CASI_files/DATA/leukemia.html&gt;`_</span>
+
+<span class="sd">After loading the data from the internet it is parsed, converted and</span>
+<span class="sd">cached in the mltb2 data directory.</span>
+<span class="sd">This data directory is determined by :func:`mltb2.files.get_and_create_mltb2_data_dir`.</span>
+
+<span class="sd">Hint:</span>
+<span class="sd">    Use pip to install the necessary dependencies for this module:</span>
+<span class="sd">    ``pip install mltb2[data]``</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">os</span>

_modules/mltb2/fasttext.html

@@ -82,11 +82,11 @@ <h1>Source code for mltb2.fasttext</h1><div class="highlight"><pre>
 <span class="c1"># This software is distributed under the terms of the MIT license</span>
 <span class="c1"># which is available at https://opensource.org/licenses/MIT</span>
 
-<span class="sd">&quot;&quot;&quot;fastText specific module.</span>
+<span class="sd">&quot;&quot;&quot;This module offers tools for `fastText &lt;https://fasttext.cc/docs/en/support.html&gt;`_.</span>
 
-<span class="sd">This module is based on `fastText &lt;https://fasttext.cc/docs/en/support.html&gt;`_.</span>
-<span class="sd">Use pip to install the necessary dependencies for this module:</span>
-<span class="sd">``pip install mltb2[fasttext]``</span>
+<span class="sd">Hint:</span>
+<span class="sd">    Use pip to install the necessary dependencies for this module:</span>
+<span class="sd">    ``pip install mltb2[fasttext]``</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">os</span>

_modules/mltb2/files.html

@@ -84,8 +84,11 @@ <h1>Source code for mltb2.files</h1><div class="highlight"><pre>
 
 <span class="sd">&quot;&quot;&quot;File utils module.</span>
 
-<span class="sd">Use pip to install the necessary dependencies for this module:</span>
-<span class="sd">``pip install mltb2[files]``</span>
+<span class="sd">This module provides utility functions for other modules.</span>
+
+<span class="sd">Hint:</span>
+<span class="sd">    Use pip to install the necessary dependencies for this module:</span>
+<span class="sd">    ``pip install mltb2[files]``</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 
@@ -98,11 +101,15 @@ <h1>Source code for mltb2.files</h1><div class="highlight"><pre>
 
 
 <div class="viewcode-block" id="get_and_create_mltb2_data_dir"><a class="viewcode-back" href="../../api-reference/files.html#mltb2.files.get_and_create_mltb2_data_dir">[docs]</a><span class="k">def</span> <span class="nf">get_and_create_mltb2_data_dir</span><span class="p">(</span><span class="n">mltb2_base_data_dir</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Return and create mltb data dir.</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Return and create a data dir for mltb2.</span>
+
+<span class="sd">    The exact directory is given by the ``mltb2_base_data_dir`` as the base folder</span>
+<span class="sd">    and then the folder ``mltb2`` is appended.</span>
 
 <span class="sd">    Args:</span>
 <span class="sd">        mltb2_base_data_dir: The base data directory. If ``None`` the default</span>
-<span class="sd">            user data directory is used.</span>
+<span class="sd">            user data directory is used. The default user data directory is</span>
+<span class="sd">            determined by :func:`platformdirs.user_data_dir`.</span>
 
 <span class="sd">    Returns:</span>
 <span class="sd">        The directory path.</span>

_modules/mltb2/md.html

@@ -85,8 +85,9 @@ <h1>Source code for mltb2.md</h1><div class="highlight"><pre>
 
 <span class="sd">&quot;&quot;&quot;Markdown specific module.</span>
 
-<span class="sd">Use pip to install the necessary dependencies for this module:</span>
-<span class="sd">``pip install mltb2[md]``</span>
+<span class="sd">Hint:</span>
+<span class="sd">    Use pip to install the necessary dependencies for this module:</span>
+<span class="sd">    ``pip install mltb2[md]``</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">re</span>

_modules/mltb2/openai.html

@@ -84,8 +84,9 @@ <h1>Source code for mltb2.openai</h1><div class="highlight"><pre>
 
 <span class="sd">&quot;&quot;&quot;OpenAI specific module.</span>
 
-<span class="sd">Use pip to install the necessary dependencies for this module:</span>
-<span class="sd">``pip install mltb2[openai]``</span>
+<span class="sd">Hint:</span>
+<span class="sd">    Use pip to install the necessary dependencies for this module:</span>
+<span class="sd">    ``pip install mltb2[openai]``</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 

_modules/mltb2/optuna.html

@@ -82,11 +82,11 @@ <h1>Source code for mltb2.optuna</h1><div class="highlight"><pre>
 <span class="c1"># This software is distributed under the terms of the MIT license</span>
 <span class="c1"># which is available at https://opensource.org/licenses/MIT</span>
 
-<span class="sd">&quot;&quot;&quot;Optuna specific module.</span>
+<span class="sd">&quot;&quot;&quot;This module offers tools for `Optuna &lt;https://optuna.readthedocs.io/en/stable/&gt;`_.</span>
 
-<span class="sd">This module is based on `Optuna &lt;https://optuna.readthedocs.io/en/stable/&gt;`_.</span>
-<span class="sd">Use pip to install the necessary dependencies for this module:</span>
-<span class="sd">``pip install mltb2[optuna]``</span>
+<span class="sd">Hint:</span>
+<span class="sd">    Use pip to install the necessary dependencies for this module:</span>
+<span class="sd">    ``pip install mltb2[optuna]``</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 

_modules/mltb2/plot.html

@@ -85,8 +85,10 @@ <h1>Source code for mltb2.plot</h1><div class="highlight"><pre>
 <span class="sd">&quot;&quot;&quot;Plot tools module.</span>
 
 <span class="sd">This module is based on `Matplotlib &lt;https://matplotlib.org/&gt;`_.</span>
-<span class="sd">Use pip to install the necessary dependencies for this module:</span>
-<span class="sd">``pip install mltb2[plot]``</span>
+
+<span class="sd">Hint:</span>
+<span class="sd">    Use pip to install the necessary dependencies for this module:</span>
+<span class="sd">    ``pip install mltb2[plot]``</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Optional</span>
@@ -111,7 +113,9 @@ <h1>Source code for mltb2.plot</h1><div class="highlight"><pre>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Create twin axes timeseries plot.</span>
 
 <span class="sd">    Plots two different timeseries curves in one diagram but two different y-axes.</span>
-<span class="sd">    This function does not call `matplotlib.pyplot.plot()`.</span>
+
+<span class="sd">    Hint:</span>
+<span class="sd">        This function does not use `matplotlib.pyplot.plot`.</span>
 
 <span class="sd">    Args:</span>
 <span class="sd">        values_1: (``array_like``) Values for the first timeseries curve.</span>
@@ -168,7 +172,8 @@ <h1>Source code for mltb2.plot</h1><div class="highlight"><pre>
 <span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Prints one or more boxplots in a single diagram.</span>
 
-<span class="sd">    This function does not call `matplotlib.pyplot.plot()`.</span>
+<span class="sd">    Hint:</span>
+<span class="sd">        This function does not use `matplotlib.pyplot.plot`.</span>
 
 <span class="sd">    Args:</span>
 <span class="sd">        values: Values for the boxplot(s).</span>
@@ -211,7 +216,8 @@ <h1>Source code for mltb2.plot</h1><div class="highlight"><pre>
 <span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Create boxplot form dictionary.</span>
 
-<span class="sd">    This function does not call `matplotlib.pyplot.plot()`.</span>
+<span class="sd">    Hint:</span>
+<span class="sd">        This function does not use `matplotlib.pyplot.plot`.</span>
 
 <span class="sd">    Args:</span>
 <span class="sd">        values_dict: Dictionary with values for the boxplot(s).</span>
@@ -232,7 +238,7 @@ <h1>Source code for mltb2.plot</h1><div class="highlight"><pre>
 
 
 <div class="viewcode-block" id="save_last_figure"><a class="viewcode-back" href="../../api-reference/plot.html#mltb2.plot.save_last_figure">[docs]</a><span class="k">def</span> <span class="nf">save_last_figure</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Saves the last plot.</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Saves the last plot made by Matplotlib.</span>
 
 <span class="sd">    For jupyter notebooks this has to be called in the same cell that created the plot.</span>
 <span class="sd">    &quot;&quot;&quot;</span>

_modules/mltb2/somajo.html

@@ -82,11 +82,11 @@ <h1>Source code for mltb2.somajo</h1><div class="highlight"><pre>
 <span class="c1"># This software is distributed under the terms of the MIT license</span>
 <span class="c1"># which is available at https://opensource.org/licenses/MIT</span>
 
-<span class="sd">&quot;&quot;&quot;SoMaJo specific module.</span>
+<span class="sd">&quot;&quot;&quot;This module offers `SoMaJo &lt;https://github.com/tsproisl/SoMaJo&gt;`_ specific tools.</span>
 
-<span class="sd">This module is based on `SoMaJo &lt;https://github.com/tsproisl/SoMaJo&gt;`_.</span>
-<span class="sd">Use pip to install the necessary dependencies for this module:</span>
-<span class="sd">``pip install mltb2[somajo]``</span>
+<span class="sd">Hint:</span>
+<span class="sd">    Use pip to install the necessary dependencies for this module:</span>
+<span class="sd">    ``pip install mltb2[somajo]``</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 

_modules/mltb2/somajo_transformers.html

@@ -83,13 +83,15 @@ <h1>Source code for mltb2.somajo_transformers</h1><div class="highlight"><pre>
 <span class="c1"># This software is distributed under the terms of the MIT license</span>
 <span class="c1"># which is available at https://opensource.org/licenses/MIT</span>
 
-<span class="sd">&quot;&quot;&quot;Hugging Face Transformers and SoMaJo specific module.</span>
+<span class="sd">&quot;&quot;&quot;This module offers Hugging Face Transformers and SoMaJo specific tools.</span>
 
 <span class="sd">This module is based on</span>
 <span class="sd">`Hugging Face Transformers &lt;https://huggingface.co/docs/transformers/index&gt;`_ and</span>
 <span class="sd">`SoMaJo &lt;https://github.com/tsproisl/SoMaJo&gt;`_.</span>
-<span class="sd">Use pip to install the necessary dependencies for this module:</span>
-<span class="sd">``pip install mltb2[somajo_transformers]``</span>
+
+<span class="sd">Hint:</span>
+<span class="sd">    Use pip to install the necessary dependencies for this module:</span>
+<span class="sd">    ``pip install mltb2[somajo_transformers]``</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 

_modules/mltb2/text.html

@@ -82,7 +82,14 @@ <h1>Source code for mltb2.text</h1><div class="highlight"><pre>
 <span class="c1"># This software is distributed under the terms of the MIT license</span>
 <span class="c1"># which is available at https://opensource.org/licenses/MIT</span>
 
-<span class="sd">&quot;&quot;&quot;Text specific module.&quot;&quot;&quot;</span>
+<span class="sd">&quot;&quot;&quot;This module offers text specific tools.</span>
+
+<span class="sd">It offers the following functionality:</span>
+
+<span class="sd">- detect or clean invisible characters</span>
+<span class="sd">- detect or replace special whitespaces</span>
+<span class="sd">- remove duplicate whitespaces</span>
+<span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">re</span>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Dict</span><span class="p">,</span> <span class="n">Final</span><span class="p">,</span> <span class="n">Pattern</span><span class="p">,</span> <span class="n">Tuple</span>

_modules/mltb2/transformers.html

@@ -82,12 +82,11 @@ <h1>Source code for mltb2.transformers</h1><div class="highlight"><pre>
 <span class="c1"># This software is distributed under the terms of the MIT license</span>
 <span class="c1"># which is available at https://opensource.org/licenses/MIT</span>
 
-<span class="sd">&quot;&quot;&quot;Hugging Face Transformers specific module.</span>
+<span class="sd">&quot;&quot;&quot;This module offers `Hugging Face Transformers &lt;https://huggingface.co/docs/transformers/index&gt;`_ specific tools.</span>
 
-<span class="sd">This module is based on</span>
-<span class="sd">`Hugging Face Transformers &lt;https://huggingface.co/docs/transformers/index&gt;`_.</span>
-<span class="sd">Use pip to install the necessary dependencies for this module:</span>
-<span class="sd">``pip install mltb2[transformers]``</span>
+<span class="sd">Hint:</span>
+<span class="sd">    Use pip to install the necessary dependencies for this module:</span>
+<span class="sd">    ``pip install mltb2[transformers]``</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">os</span>

api-reference/data.html

@@ -103,9 +103,21 @@
 
   <section id="module-mltb2.data">
 <span id="data"></span><span id="data-code-doc"></span><h1><a class="reference internal" href="#module-mltb2.data" title="mltb2.data"><code class="xref py py-mod docutils literal notranslate"><span class="pre">data</span></code></a><a class="headerlink" href="#module-mltb2.data" title="Permalink to this heading"></a></h1>
-<p>Data loading module.</p>
+<p>This module offers tools for loading data.</p>
+<p>The following tabular data sets from the biological and medical domain are supported:</p>
+<ul class="simple">
+<li><p>colon: <a class="reference external" href="http://genomics-pubs.princeton.edu/oncology/affydata/index.html">http://genomics-pubs.princeton.edu/oncology/affydata/index.html</a></p></li>
+<li><p>prostate: <a class="reference external" href="https://web.stanford.edu/~hastie/CASI_files/DATA/prostate.html">https://web.stanford.edu/~hastie/CASI_files/DATA/prostate.html</a></p></li>
+<li><p>leukemia_big: <a class="reference external" href="https://web.stanford.edu/~hastie/CASI_files/DATA/leukemia.html">https://web.stanford.edu/~hastie/CASI_files/DATA/leukemia.html</a></p></li>
+</ul>
+<p>After loading the data from the internet it is parsed, converted and
+cached in the mltb2 data directory.
+This data directory is determined by <a class="reference internal" href="files.html#mltb2.files.get_and_create_mltb2_data_dir" title="mltb2.files.get_and_create_mltb2_data_dir"><code class="xref py py-func docutils literal notranslate"><span class="pre">mltb2.files.get_and_create_mltb2_data_dir()</span></code></a>.</p>
+<div class="admonition hint">
+<p class="admonition-title">Hint</p>
 <p>Use pip to install the necessary dependencies for this module:
 <code class="docutils literal notranslate"><span class="pre">pip</span> <span class="pre">install</span> <span class="pre">mltb2[data]</span></code></p>
+</div>
 <dl class="py function">
 <dt class="sig sig-object py" id="mltb2.data._load_colon_data">
 <span class="sig-prename descclassname"><span class="pre">mltb2.data.</span></span><span class="sig-name descname"><span class="pre">_load_colon_data</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="reference internal" href="../_modules/mltb2/data.html#_load_colon_data"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mltb2.data._load_colon_data" title="Permalink to this definition"></a></dt>

api-reference/fasttext.html

@@ -103,10 +103,12 @@
 
   <section id="module-mltb2.fasttext">
 <span id="fasttext"></span><span id="fasttext-code-doc"></span><h1><a class="reference internal" href="#module-mltb2.fasttext" title="mltb2.fasttext"><code class="xref py py-mod docutils literal notranslate"><span class="pre">fasttext</span></code></a><a class="headerlink" href="#module-mltb2.fasttext" title="Permalink to this heading"></a></h1>
-<p>fastText specific module.</p>
-<p>This module is based on <a class="reference external" href="https://fasttext.cc/docs/en/support.html">fastText</a>.
-Use pip to install the necessary dependencies for this module:
+<p>This module offers tools for <a class="reference external" href="https://fasttext.cc/docs/en/support.html">fastText</a>.</p>
+<div class="admonition hint">
+<p class="admonition-title">Hint</p>
+<p>Use pip to install the necessary dependencies for this module:
 <code class="docutils literal notranslate"><span class="pre">pip</span> <span class="pre">install</span> <span class="pre">mltb2[fasttext]</span></code></p>
+</div>
 <dl class="py class">
 <dt class="sig sig-object py" id="mltb2.fasttext.FastTextLanguageIdentification">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">mltb2.fasttext.</span></span><span class="sig-name descname"><span class="pre">FastTextLanguageIdentification</span></span><a class="reference internal" href="../_modules/mltb2/fasttext.html#FastTextLanguageIdentification"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mltb2.fasttext.FastTextLanguageIdentification" title="Permalink to this definition"></a></dt>