Bump version to 0.19.1; rebuild docs

docs/_sources/api/seismicrna.align.rst.txt

@@ -42,7 +42,7 @@ Submodules
    :show-inheritance:
 
 
-.. automodule:: seismicrna.align.sim
+.. automodule:: seismicrna.align.split
    :members:
    :undoc-members:
    :show-inheritance:

docs/api/seismicrna.align.tests.html

@@ -152,75 +152,6 @@
 
 </dd></dl>
 
-<dl class="py class" id="module-seismicrna.align.tests.sim_test">
-<dt class="sig sig-object py" id="seismicrna.align.tests.sim_test.TestAsSam">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">seismicrna.align.tests.sim_test.</span></span><span class="sig-name descname"><span class="pre">TestAsSam</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">methodName</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'runTest'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.sim_test.TestAsSam" title="Link to this definition"></a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">TestCase</span></code></p>
-<p>Test function <cite>as_sam</cite>.</p>
-<dl class="py method">
-<dt class="sig sig-object py" id="seismicrna.align.tests.sim_test.TestAsSam.test_line_in_sam_format">
-<span class="sig-name descname"><span class="pre">test_line_in_sam_format</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.sim_test.TestAsSam.test_line_in_sam_format" title="Link to this definition"></a></dt>
-<dd></dd></dl>
-
-</dd></dl>
-
-<dl class="py class">
-<dt class="sig sig-object py" id="seismicrna.align.tests.sim_test.TestFindBlankRange">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">seismicrna.align.tests.sim_test.</span></span><span class="sig-name descname"><span class="pre">TestFindBlankRange</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">methodName</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'runTest'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.sim_test.TestFindBlankRange" title="Link to this definition"></a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">TestCase</span></code></p>
-<p>Test function <cite>_find_blank_range</cite>.</p>
-<dl class="py method">
-<dt class="sig sig-object py" id="seismicrna.align.tests.sim_test.TestFindBlankRange.test_side3_equal_length">
-<span class="sig-name descname"><span class="pre">test_side3_equal_length</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.sim_test.TestFindBlankRange.test_side3_equal_length" title="Link to this definition"></a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="seismicrna.align.tests.sim_test.TestFindBlankRange.test_side3_neg_length">
-<span class="sig-name descname"><span class="pre">test_side3_neg_length</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.sim_test.TestFindBlankRange.test_side3_neg_length" title="Link to this definition"></a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="seismicrna.align.tests.sim_test.TestFindBlankRange.test_side3_over_length">
-<span class="sig-name descname"><span class="pre">test_side3_over_length</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.sim_test.TestFindBlankRange.test_side3_over_length" title="Link to this definition"></a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="seismicrna.align.tests.sim_test.TestFindBlankRange.test_side3_under_length">
-<span class="sig-name descname"><span class="pre">test_side3_under_length</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.sim_test.TestFindBlankRange.test_side3_under_length" title="Link to this definition"></a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="seismicrna.align.tests.sim_test.TestFindBlankRange.test_side3_zero_length">
-<span class="sig-name descname"><span class="pre">test_side3_zero_length</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.sim_test.TestFindBlankRange.test_side3_zero_length" title="Link to this definition"></a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="seismicrna.align.tests.sim_test.TestFindBlankRange.test_side5_equal_length">
-<span class="sig-name descname"><span class="pre">test_side5_equal_length</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.sim_test.TestFindBlankRange.test_side5_equal_length" title="Link to this definition"></a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="seismicrna.align.tests.sim_test.TestFindBlankRange.test_side5_neg_length">
-<span class="sig-name descname"><span class="pre">test_side5_neg_length</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.sim_test.TestFindBlankRange.test_side5_neg_length" title="Link to this definition"></a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="seismicrna.align.tests.sim_test.TestFindBlankRange.test_side5_over_length">
-<span class="sig-name descname"><span class="pre">test_side5_over_length</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.sim_test.TestFindBlankRange.test_side5_over_length" title="Link to this definition"></a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="seismicrna.align.tests.sim_test.TestFindBlankRange.test_side5_under_length">
-<span class="sig-name descname"><span class="pre">test_side5_under_length</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.sim_test.TestFindBlankRange.test_side5_under_length" title="Link to this definition"></a></dt>
-<dd></dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="seismicrna.align.tests.sim_test.TestFindBlankRange.test_side5_zero_length">
-<span class="sig-name descname"><span class="pre">test_side5_zero_length</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.sim_test.TestFindBlankRange.test_side5_zero_length" title="Link to this definition"></a></dt>
-<dd></dd></dl>
-
-</dd></dl>
-
 <p id="module-seismicrna.align.tests.xamgen_test">Tests for Alignment XAM Generation Module</p>
 <hr class="docutils" />
 <dl class="py class">

docs/api/seismicrna.core.html

@@ -3361,25 +3361,25 @@ <h3>Purpose<a class="headerlink" href="#purpose" title="Link to this heading">
 <p id="module-seismicrna.core.version">Version information for SEISMIC-RNA</p>
 <dl class="py function">
 <dt class="sig sig-object py" id="seismicrna.core.version.format_version">
-<span class="sig-prename descclassname"><span class="pre">seismicrna.core.version.</span></span><span class="sig-name descname"><span class="pre">format_version</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">major</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><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minor</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><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">19</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">patch</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><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prtag</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><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.version.format_version" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">seismicrna.core.version.</span></span><span class="sig-name descname"><span class="pre">format_version</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">major</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><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minor</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><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">19</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">patch</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><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prtag</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><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.version.format_version" title="Link to this definition"></a></dt>
 <dd></dd></dl>
 
 <dl class="py function">
 <dt class="sig sig-object py" id="seismicrna.core.version.parse_version">
-<span class="sig-prename descclassname"><span class="pre">seismicrna.core.version.</span></span><span class="sig-name descname"><span class="pre">parse_version</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">version</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><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'0.19.0'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.version.parse_version" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">seismicrna.core.version.</span></span><span class="sig-name descname"><span class="pre">parse_version</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">version</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><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'0.19.1'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.version.parse_version" title="Link to this definition"></a></dt>
 <dd><p>Major and minor versions, patch, and pre-release tag.</p>
 </dd></dl>
 
 <dl class="py function" id="module-seismicrna.core.write">
 <dt class="sig sig-object py" id="seismicrna.core.write.need_write">
-<span class="sig-prename descclassname"><span class="pre">seismicrna.core.write.</span></span><span class="sig-name descname"><span class="pre">need_write</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file</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/pathlib.html#pathlib.Path" title="(in Python v3.12)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">force</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#bool" title="(in Python v3.12)"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">warn</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#bool" title="(in Python v3.12)"><span class="pre">bool</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">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.write.need_write" title="Link to this definition"></a></dt>
-<dd><p>Determine whether a file must be written.</p>
+<span class="sig-prename descclassname"><span class="pre">seismicrna.core.write.</span></span><span class="sig-name descname"><span class="pre">need_write</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">query</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/pathlib.html#pathlib.Path" title="(in Python v3.12)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">force</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#bool" title="(in Python v3.12)"><span class="pre">bool</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">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">warn</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#bool" title="(in Python v3.12)"><span class="pre">bool</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">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.write.need_write" title="Link to this definition"></a></dt>
+<dd><p>Determine whether a file/directory must be written.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>file</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">Path</span></code>) – File for which to check the need for writing.</p></li>
-<li><p><strong>force</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False</span></code>) – Force the file to be written, even if it already exists.</p></li>
-<li><p><strong>warn</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span> <span class="pre">=</span> <span class="pre">True</span></code>) – If the file does not need to be written, then log a warning.</p></li>
+<li><p><strong>query</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">Path</span></code>) – File or directory for which to check the need for writing.</p></li>
+<li><p><strong>force</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span> <span class="pre">=</span> <span class="pre">False</span></code>) – Force the query to be written, even if it already exists.</p></li>
+<li><p><strong>warn</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span> <span class="pre">=</span> <span class="pre">True</span></code>) – If the query does not need to be written, then log a warning.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>