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ForomePlatform · Jun 30, 2024 · 781fb38 · 781fb38
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diff --git a/doc/home.md b/doc/home.md
@@ -363,6 +363,17 @@ documentation for Dorieh platform
 Documentation utilities to simplify creation of consistent
 documentation for Dorieh platform 
 
+* [cwl2md](members/cwl2md) Generates [Markdown](https://www.markdownguide.org/basic-syntax/) 
+    documentation for a CWL tool or workflow
+* [collector](members/collector) Generates automatic 
+    [reStructuredText](https://docutils.sourceforge.io/rst.html) 
+    templates for all Python modules 
+* [copy_section](members/copy_section)  Copies a specified section from one markdown document
+    to another. This way we can collect summaries in one file<!-- end of section documentation utilities overview from dorieh.docutils -->
+
+Documentation utilities to simplify creation of consistent
+documentation for Dorieh platform 
+
 * [cwl2md](members/cwl2md) Generates [Markdown](https://www.markdownguide.org/basic-syntax/) 
     documentation for a CWL tool or workflow
 * [collector](members/collector) Generates automatic 

diff --git a/docs/.doctrees/TestingWorkflows.doctree b/docs/.doctrees/TestingWorkflows.doctree
diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/home.doctree b/docs/.doctrees/home.doctree
diff --git a/docs/TestingWorkflows.html b/docs/TestingWorkflows.html
@@ -59,11 +59,6 @@
 <li class="toctree-l2"><a class="reference internal" href="members/create_test.html">Utility to generate test queries</a></li>
 <li class="toctree-l2"><a class="reference internal" href="members/dbt_runner.html">Utility to generate test queries</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">Testing bundled workflows</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="pipelines.html">Data Processing Pipelines</a></li>
-<li class="toctree-l3"><a class="reference internal" href="pipeline/aqs.html">Full EPA AQS Processing Pipeline</a></li>
-<li class="toctree-l3"><a class="reference internal" href="pipeline/airnow.html">Full EPA AirNow Processing Pipeline (including downloading shapefiles)</a></li>
-<li class="toctree-l3"><a class="reference internal" href="pipeline/gridmet.html">Pipeline to aggregate data from Climatology Lab</a></li>
-<li class="toctree-l3"><a class="reference internal" href="pipeline/pm25_yearly_download.html">Pipeline to aggregate data in NetCDF format over given geographies</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#introduction-to-testing-and-prerequisites">Introduction to testing and prerequisites</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#before-running-any-test">Before running any test</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#testing-aqs-workflow">Testing AQS workflow</a><ul>
@@ -162,49 +157,8 @@ <h1>Testing bundled workflows<a class="headerlink" href="#testing-bundled-workfl
 </nav>
 <div class="admonition seealso">
 <p class="admonition-title">See also</p>
-<p><a class="reference internal" href="DBT.html"><span class="doc std std-doc">Database Testing Framework</span></a></p>
-</div>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="pipelines.html">Data Processing Pipelines</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="pipelines.html#introduction">Introduction</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipelines.html#running-workflows">Running Workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipelines.html#testing-workflows">Testing workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipelines.html#installing-python-dependencies">Installing Python dependencies</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipelines.html#published-and-tested-workflows">Published and tested workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipelines.html#developing-your-own-workflows">Developing your own workflows</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipelines.html#example-of-a-workflow">Example of a workflow</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="pipeline/aqs.html">Full EPA AQS Processing Pipeline</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/aqs.html#description">Description</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/aqs.html#inputs">Inputs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/aqs.html#outputs">Outputs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/aqs.html#steps">Steps</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="pipeline/airnow.html">Full EPA AirNow Processing Pipeline (including downloading shapefiles)</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/airnow.html#description">Description</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/airnow.html#inputs">Inputs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/airnow.html#outputs">Outputs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/airnow.html#steps">Steps</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="pipeline/gridmet.html">Pipeline to aggregate data from Climatology Lab</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/gridmet.html#description">Description</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/gridmet.html#inputs">Inputs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/gridmet.html#outputs">Outputs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/gridmet.html#steps">Steps</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="pipeline/pm25_yearly_download.html">Pipeline to aggregate data in NetCDF format over given geographies</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/pm25_yearly_download.html#description">Description</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/pm25_yearly_download.html#inputs">Inputs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/pm25_yearly_download.html#outputs">Outputs</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pipeline/pm25_yearly_download.html#steps">Steps</a></li>
-</ul>
-</li>
-</ul>
+<p><a class="reference internal" href="DBT.html"><span class="doc std std-doc">Database Testing Framework</span></a>
+<a class="reference internal" href="pipelines.html"><span class="doc std std-doc">Data Processing Pipelines</span></a></p>
 </div>
 <section id="introduction-to-testing-and-prerequisites">
 <h2><a class="toc-backref" href="#id7" role="doc-backlink">Introduction to testing and prerequisites</a><a class="headerlink" href="#introduction-to-testing-and-prerequisites" title="Permalink to this heading"></a></h2>
@@ -256,6 +210,10 @@ <h2><a class="toc-backref" href="#id8" role="doc-backlink">Before running any te
 </section>
 <section id="testing-aqs-workflow">
 <h2><a class="toc-backref" href="#id9" role="doc-backlink">Testing AQS workflow</a><a class="headerlink" href="#testing-aqs-workflow" title="Permalink to this heading"></a></h2>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="pipeline/aqs.html"><span class="doc std std-doc">Full EPA AQS Processing Pipeline</span></a></p>
+</div>
 <section id="before-running-the-test">
 <h3><a class="toc-backref" href="#id10" role="doc-backlink">Before running the test</a><a class="headerlink" href="#before-running-the-test" title="Permalink to this heading"></a></h3>
 <p>Create a scratch directory:</p>
@@ -299,6 +257,10 @@ <h3><a class="toc-backref" href="#id12" role="doc-backlink">Testing AQS workflow
 </section>
 <section id="testing-airnow-workflow">
 <h2><a class="toc-backref" href="#id13" role="doc-backlink">Testing Airnow workflow</a><a class="headerlink" href="#testing-airnow-workflow" title="Permalink to this heading"></a></h2>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="pipeline/airnow.html"><span class="doc std std-doc">Full EPA AirNow Processing Pipeline (including downloading shapefiles)</span></a></p>
+</div>
 <section id="id1">
 <h3><a class="toc-backref" href="#id14" role="doc-backlink">Before running the test</a><a class="headerlink" href="#id1" title="Permalink to this heading"></a></h3>
 <p>Create a scratch directory:</p>
@@ -344,7 +306,11 @@ <h3><a class="toc-backref" href="#id16" role="doc-backlink">Testing Airnow workf
 </section>
 <section id="testing-climate-workflow">
 <h2><a class="toc-backref" href="#id17" role="doc-backlink">Testing Climate workflow</a><a class="headerlink" href="#testing-climate-workflow" title="Permalink to this heading"></a></h2>
-<p>See also <a class="reference internal" href="Example-climate-workflow.html"><span class="doc std std-doc">Example of a workflow: aggregating a climate variable</span></a></p>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="Example-climate-workflow.html"><span class="doc std std-doc">Example of a workflow: aggregating a climate variable</span></a>
+<a class="reference internal" href="pipeline/gridmet.html"><span class="doc std std-doc">Pipeline to aggregate data from Climatology Lab</span></a></p>
+</div>
 <section id="id3">
 <h3><a class="toc-backref" href="#id18" role="doc-backlink">Before running the test</a><a class="headerlink" href="#id3" title="Permalink to this heading"></a></h3>
 <p>Create a scratch directory:</p>
@@ -386,7 +352,10 @@ <h3><a class="toc-backref" href="#id20" role="doc-backlink">Testing climate work
 </section>
 <section id="testing-exposure-workflow">
 <h2><a class="toc-backref" href="#id21" role="doc-backlink">Testing Exposure workflow</a><a class="headerlink" href="#testing-exposure-workflow" title="Permalink to this heading"></a></h2>
-<p>See also <a class="reference internal" href="Example-climate-workflow.html"><span class="doc std std-doc">Example of a workflow: aggregating a climate variable</span></a></p>
+<div class="admonition seealso">
+<p class="admonition-title">See also</p>
+<p><a class="reference internal" href="pipeline/pm25_yearly_download.html"><span class="doc std std-doc">Pipeline to aggregate data in NetCDF format over given geographies</span></a></p>
+</div>
 <section id="id5">
 <h3><a class="toc-backref" href="#id22" role="doc-backlink">Before running the test</a><a class="headerlink" href="#id5" title="Permalink to this heading"></a></h3>
 <p>Create a scratch directory:</p>

diff --git a/docs/_images/aggregate_one_file.png b/docs/_images/aggregate_one_file.png
diff --git a/docs/_images/airnow.png b/docs/_images/airnow.png
diff --git a/docs/_sources/TestingWorkflows.md.txt b/docs/_sources/TestingWorkflows.md.txt
@@ -8,18 +8,7 @@ local:
 
 ```{seealso}
 [Database Testing Framework](DBT)
-```
-
-```{toctree}
----
-maxdepth: 2
-
----
-pipelines
-pipeline/aqs
-pipeline/airnow
-pipeline/gridmet
-pipeline/pm25_yearly_download
+[](pipelines)
 ```
 
 ## Introduction to testing and prerequisites
@@ -78,6 +67,11 @@ you will need to replace `toil-cwl-runner` command with an appropriate alternati
 
 ## Testing AQS workflow
 
+```{seealso}
+[](pipeline/aqs)
+```
+
+
 ### Before running the test
 
 Create a scratch directory:
@@ -124,6 +118,11 @@ In the virtual environment that has Toil run the following command:
 
 ## Testing Airnow workflow
 
+```{seealso}
+[](pipeline/airnow)
+```
+
+
 ### Before running the test
 
 Create a scratch directory:
@@ -168,8 +167,11 @@ The command will be:
 
 
 ## Testing Climate workflow
-
-See also [](Example-climate-workflow)
+
+```{seealso}
+[](Example-climate-workflow)
+[](pipeline/gridmet)
+```
 
 ### Before running the test
 
@@ -212,7 +214,10 @@ If you have installed dorieh locally, run the following command
 
 ## Testing Exposure workflow
 
-See also [](Example-climate-workflow)
+```{seealso}
+[](pipeline/pm25_yearly_download)
+```
+
 
 ### Before running the test
 

diff --git a/docs/_sources/home.md.txt b/docs/_sources/home.md.txt
@@ -363,6 +363,17 @@ documentation for Dorieh platform
 Documentation utilities to simplify creation of consistent
 documentation for Dorieh platform 
 
+* [cwl2md](members/cwl2md) Generates [Markdown](https://www.markdownguide.org/basic-syntax/) 
+    documentation for a CWL tool or workflow
+* [collector](members/collector) Generates automatic 
+    [reStructuredText](https://docutils.sourceforge.io/rst.html) 
+    templates for all Python modules 
+* [copy_section](members/copy_section)  Copies a specified section from one markdown document
+    to another. This way we can collect summaries in one file<!-- end of section documentation utilities overview from dorieh.docutils -->
+
+Documentation utilities to simplify creation of consistent
+documentation for Dorieh platform 
+
 * [cwl2md](members/cwl2md) Generates [Markdown](https://www.markdownguide.org/basic-syntax/) 
     documentation for a CWL tool or workflow
 * [collector](members/collector) Generates automatic 

diff --git a/docs/home.html b/docs/home.html
@@ -464,6 +464,17 @@ <h3><a class="toc-backref" href="#id6" role="doc-backlink">Dorieh Documentation
 <li><p><a class="reference internal" href="members/copy_section.html"><span class="doc std std-doc">copy_section</span></a>  Copies a specified section from one markdown document
 to another. This way we can collect summaries in one file<!-- end of section documentation utilities overview from dorieh.docutils --></p></li>
 </ul>
+<p>Documentation utilities to simplify creation of consistent
+documentation for Dorieh platform</p>
+<ul class="simple">
+<li><p><a class="reference internal" href="members/cwl2md.html"><span class="doc std std-doc">cwl2md</span></a> Generates <a class="reference external" href="https://www.markdownguide.org/basic-syntax/">Markdown</a>
+documentation for a CWL tool or workflow</p></li>
+<li><p><a class="reference internal" href="members/collector.html"><span class="doc std std-doc">collector</span></a> Generates automatic
+<a class="reference external" href="https://docutils.sourceforge.io/rst.html">reStructuredText</a>
+templates for all Python modules</p></li>
+<li><p><a class="reference internal" href="members/copy_section.html"><span class="doc std std-doc">copy_section</span></a>  Copies a specified section from one markdown document
+to another. This way we can collect summaries in one file<!-- end of section documentation utilities overview from dorieh.docutils --></p></li>
+</ul>
 </section>
 <section id="data-processing-and-loading-pipelines">
 <h3><a class="toc-backref" href="#id7" role="doc-backlink">Data Processing and Loading Pipelines</a><a class="headerlink" href="#data-processing-and-loading-pipelines" title="Permalink to this heading"></a></h3>

diff --git a/docs/searchindex.js b/docs/searchindex.js