Deploying to gh-pages from @ 6f53d6f 🚀

coverage/coverage.xml

@@ -1,9 +1,9 @@
 <?xml version="1.0" ?>
-<coverage version="7.6.10" timestamp="1737472826804" lines-valid="2545" lines-covered="2007" line-rate="0.7886" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
+<coverage version="7.6.10" timestamp="1737472848303" lines-valid="2545" lines-covered="2007" line-rate="0.7886" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
 	<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.6.10 -->
 	<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
 	<sources>
-		<source>/home/gbayarri/actions-runner-bioexcel/_work/biobb_analysis/biobb_analysis</source>
+		<source>/home/user/actions-runner/_work/biobb_analysis/biobb_analysis</source>
 	</sources>
 	<packages>
 		<package name="biobb_analysis" line-rate="1" branch-rate="0" complexity="0">

coverage/z_153b2b1bc44effd1_common_py.html

@@ -499,17 +499,17 @@ <h2>
     <p class="pln"><span class="n"><a id="t417" href="#t417">417</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t418" href="#t418">418</a></span><span class="t">    <span class="key">if</span> <span class="nam">ref</span> <span class="op">==</span> <span class="str">'first'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t419" href="#t419">419</a></span><span class="t">        <span class="key">if</span> <span class="nam">output</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t420" href="#t420">420</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms first out '</span> <span class="op">+</span> <span class="nam">output_cpptraj_path</span> <span class="op">+</span> <span class="str">f' {flags_str}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t420" href="#t420">420</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms first out '</span> <span class="op">+</span> <span class="nam">output_cpptraj_path</span> <span class="op">+</span> <span class="fst">f'</span><span class="fst"> </span><span class="op">{</span><span class="nam">flags_str</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t421" href="#t421">421</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t422" href="#t422">422</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms first'</span> <span class="op">+</span> <span class="str">f' {flags_str}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t422" href="#t422">422</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms first'</span> <span class="op">+</span> <span class="fst">f'</span><span class="fst"> </span><span class="op">{</span><span class="nam">flags_str</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t423" href="#t423">423</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t424" href="#t424">424</a></span><span class="t">    <span class="key">if</span> <span class="nam">ref</span> <span class="op">==</span> <span class="str">'average'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t425" href="#t425">425</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'average crdset '</span> <span class="op">+</span> <span class="nam">get_default_value</span><span class="op">(</span><span class="str">'average'</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t426" href="#t426">426</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'run'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t427" href="#t427">427</a></span><span class="t">        <span class="key">if</span> <span class="nam">output</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t428" href="#t428">428</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms ref '</span> <span class="op">+</span> <span class="nam">get_default_value</span><span class="op">(</span><span class="str">'average'</span><span class="op">)</span> <span class="op">+</span> <span class="str">' '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="str">' out '</span> <span class="op">+</span> <span class="nam">output_cpptraj_path</span> <span class="op">+</span> <span class="str">f' {flags_str}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t428" href="#t428">428</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms ref '</span> <span class="op">+</span> <span class="nam">get_default_value</span><span class="op">(</span><span class="str">'average'</span><span class="op">)</span> <span class="op">+</span> <span class="str">' '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="str">' out '</span> <span class="op">+</span> <span class="nam">output_cpptraj_path</span> <span class="op">+</span> <span class="fst">f'</span><span class="fst"> </span><span class="op">{</span><span class="nam">flags_str</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t429" href="#t429">429</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t430" href="#t430">430</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms ref '</span> <span class="op">+</span> <span class="nam">get_default_value</span><span class="op">(</span><span class="str">'average'</span><span class="op">)</span> <span class="op">+</span> <span class="str">' '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="str">f' {flags_str}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t430" href="#t430">430</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms ref '</span> <span class="op">+</span> <span class="nam">get_default_value</span><span class="op">(</span><span class="str">'average'</span><span class="op">)</span> <span class="op">+</span> <span class="str">' '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="fst">f'</span><span class="fst"> </span><span class="op">{</span><span class="nam">flags_str</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t431" href="#t431">431</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t432" href="#t432">432</a></span><span class="t">    <span class="key">if</span> <span class="nam">ref</span> <span class="op">==</span> <span class="str">'experimental'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t433" href="#t433">433</a></span><span class="t">        <span class="key">if</span> <span class="key">not</span> <span class="nam">input_exp_path</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
@@ -520,9 +520,9 @@ <h2>
     <p class="run"><span class="n"><a id="t438" href="#t438">438</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'reference '</span> <span class="op">+</span> <span class="nam">input_exp_path</span> <span class="op">+</span> <span class="str">' '</span> <span class="op">+</span> <span class="nam">solute</span> <span class="op">+</span> <span class="str">' parm [exp]'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t439" href="#t439">439</a></span><span class="t">        <span class="nam">backbone</span><span class="op">,</span> <span class="nam">msg</span> <span class="op">=</span> <span class="nam">get_mask_atoms</span><span class="op">(</span><span class="str">'backbone'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t440" href="#t440">440</a></span><span class="t">        <span class="key">if</span> <span class="nam">output</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t441" href="#t441">441</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms reference '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="str">' out '</span> <span class="op">+</span> <span class="nam">output_cpptraj_path</span> <span class="op">+</span> <span class="str">f' {flags_str}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t441" href="#t441">441</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms reference '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="str">' out '</span> <span class="op">+</span> <span class="nam">output_cpptraj_path</span> <span class="op">+</span> <span class="fst">f'</span><span class="fst"> </span><span class="op">{</span><span class="nam">flags_str</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t442" href="#t442">442</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t443" href="#t443">443</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms reference '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="str">f' {flags_str}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t443" href="#t443">443</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'rms reference '</span> <span class="op">+</span> <span class="nam">mask</span> <span class="op">+</span> <span class="fst">f'</span><span class="fst"> </span><span class="op">{</span><span class="nam">flags_str</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t444" href="#t444">444</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t445" href="#t445">445</a></span><span class="t">    <span class="key">return</span> <span class="nam">instructions_list</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t446" href="#t446">446</a></span><span class="t">&nbsp;</span><span class="r"></span></p>

coverage/z_8185a593ca2a23a7_gmx_cluster_py.html

@@ -221,7 +221,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="com"># standard input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="str">f'{self.fit_selection} {self.output_selection}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="fst">f'</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">fit_selection</span><span class="op">}</span><span class="fst"> </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">output_selection</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">,</span> <span class="str">'cluster'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>

coverage/z_8185a593ca2a23a7_gmx_image_py.html

@@ -233,7 +233,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="com"># standard input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="str">f'{selections}'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'stdin_file_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_stdin_file</span><span class="op">(</span><span class="fst">f'</span><span class="op">{</span><span class="nam">selections</span><span class="op">}</span><span class="fst">'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">,</span> <span class="str">'trjconv'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>