deploy: 6b38d0d

_sources/plugins/tutorials/add-pipeline.md

@@ -145,19 +145,21 @@ Here's the final Pipeline registration code that I ended up with in my `plugin_s
 ```python
 plugin.pipelines.register_function(
     function=align_and_summarize,
-    inputs=_align_and_summarize_inputs,
-    parameters=_align_and_summarize_parameters,
+    inputs=_nw_align_inputs,
+    parameters=_nw_align_parameters,
     outputs=_align_and_summarize_outputs,
-    input_descriptions=_align_and_summarize_input_descriptions,
-    parameter_descriptions=_align_and_summarize_parameter_descriptions,
+    input_descriptions=_nw_align_input_descriptions,
+    parameter_descriptions=_nw_align_parameter_descriptions,
     output_descriptions=_align_and_summarize_output_descriptions,
     name="Pairwise global alignment and summarization.",
     description=("Perform global pairwise sequence alignment using a slow "
                  "Needleman-Wunsch (NW) implementation, and generate a "
                  "visual summary of the alignment."),
-    citations=_align_and_summarize_output_citations,
-    examples={'Align two sequences and summarize the alignment.':
-              align_and_summarize_example_1}
+    # Only citations new to this Pipeline need to be defined. Citations for
+    # the Actions called from the Pipeline are automatically included.
+    citations=[],
+    examples={}
+)
 ```
 
 As a **required exercise** after adding this code to your `plugin_setup.py` file, define the variables used in this code block in such a way that it avoids the DRY violation mentioned above.

plugins/tutorials/add-pipeline.html

@@ -567,19 +567,21 @@ <h2>Register the Pipeline<a class="headerlink" href="#register-the-pipeline" tit
 <p>Here’s the final Pipeline registration code that I ended up with in my <code class="docutils literal notranslate"><span class="pre">plugin_setup.py</span></code> file, after defining some new variables in that file:</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">plugin</span><span class="o">.</span><span class="n">pipelines</span><span class="o">.</span><span class="n">register_function</span><span class="p">(</span>
     <span class="n">function</span><span class="o">=</span><span class="n">align_and_summarize</span><span class="p">,</span>
-    <span class="n">inputs</span><span class="o">=</span><span class="n">_align_and_summarize_inputs</span><span class="p">,</span>
-    <span class="n">parameters</span><span class="o">=</span><span class="n">_align_and_summarize_parameters</span><span class="p">,</span>
+    <span class="n">inputs</span><span class="o">=</span><span class="n">_nw_align_inputs</span><span class="p">,</span>
+    <span class="n">parameters</span><span class="o">=</span><span class="n">_nw_align_parameters</span><span class="p">,</span>
     <span class="n">outputs</span><span class="o">=</span><span class="n">_align_and_summarize_outputs</span><span class="p">,</span>
-    <span class="n">input_descriptions</span><span class="o">=</span><span class="n">_align_and_summarize_input_descriptions</span><span class="p">,</span>
-    <span class="n">parameter_descriptions</span><span class="o">=</span><span class="n">_align_and_summarize_parameter_descriptions</span><span class="p">,</span>
+    <span class="n">input_descriptions</span><span class="o">=</span><span class="n">_nw_align_input_descriptions</span><span class="p">,</span>
+    <span class="n">parameter_descriptions</span><span class="o">=</span><span class="n">_nw_align_parameter_descriptions</span><span class="p">,</span>
     <span class="n">output_descriptions</span><span class="o">=</span><span class="n">_align_and_summarize_output_descriptions</span><span class="p">,</span>
     <span class="n">name</span><span class="o">=</span><span class="s2">&quot;Pairwise global alignment and summarization.&quot;</span><span class="p">,</span>
     <span class="n">description</span><span class="o">=</span><span class="p">(</span><span class="s2">&quot;Perform global pairwise sequence alignment using a slow &quot;</span>
                  <span class="s2">&quot;Needleman-Wunsch (NW) implementation, and generate a &quot;</span>
                  <span class="s2">&quot;visual summary of the alignment.&quot;</span><span class="p">),</span>
-    <span class="n">citations</span><span class="o">=</span><span class="n">_align_and_summarize_output_citations</span><span class="p">,</span>
-    <span class="n">examples</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;Align two sequences and summarize the alignment.&#39;</span><span class="p">:</span>
-              <span class="n">align_and_summarize_example_1</span><span class="p">}</span>
+    <span class="c1"># Only citations new to this Pipeline need to be defined. Citations for</span>
+    <span class="c1"># the Actions called from the Pipeline are automatically included.</span>
+    <span class="n">citations</span><span class="o">=</span><span class="p">[],</span>
+    <span class="n">examples</span><span class="o">=</span><span class="p">{}</span>
+<span class="p">)</span>
 </pre></div>
 </div>
 <p>As a <strong>required exercise</strong> after adding this code to your <code class="docutils literal notranslate"><span class="pre">plugin_setup.py</span></code> file, define the variables used in this code block in such a way that it avoids the DRY violation mentioned above.