update docs for v1.0.1

yumengch · Dec 10, 2024 · e47b4f8 · e47b4f8
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diff --git a/docs/API.html b/docs/API.html
@@ -7,16 +7,16 @@
 
     <title>API &#8212; pyPDAF  documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d1102ebc" />
-    <link rel="stylesheet" type="text/css" href="_static/basic.css?v=8e461078" />
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   <link rel="stylesheet" href="_static/custom.css" type="text/css" />
 
@@ -86,7 +86,7 @@ <h2><a class="toc-backref" href="#id10" role="doc-backlink">Initialisation and f
 <td><p>Allocating an array of <cite>obs_f</cite> derived types instances.</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.deallocate.html#pyPDAF.PDAF.deallocate" title="pyPDAF.PDAF.deallocate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.deallocate</span></code></a></p></td>
-<td><p>This function finalise the PDAF systems including freeing all memory used by PDAF.</p></td>
+<td><p>Finalise the PDAF systems including freeing some of the memory used by PDAF.</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.print_info.html#pyPDAF.PDAF.print_info" title="pyPDAF.PDAF.print_info"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.print_info</span></code></a></p></td>
 <td><p>Printing the wallclock time and memory measured by PDAF.</p></td>
@@ -299,13 +299,13 @@ <h3><a class="toc-backref" href="#id18" role="doc-backlink">obs_f setter functio
 <table class="autosummary longtable docutils align-default">
 <tbody>
 <tr class="row-odd"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.omi_set_doassim.html#pyPDAF.PDAF.omi_set_doassim" title="pyPDAF.PDAF.omi_set_doassim"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.omi_set_doassim</span></code></a></p></td>
-<td><p>This function sets the <cite>doassim</cite> attribute of <cite>obs_f</cite> typically used in user-supplied function <cite>py__init_dim_obs_pdaf</cite>.</p></td>
+<td><p>Setting the <cite>doassim</cite> attribute of <cite>obs_f</cite>.</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.omi_set_disttype.html#pyPDAF.PDAF.omi_set_disttype" title="pyPDAF.PDAF.omi_set_disttype"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.omi_set_disttype</span></code></a></p></td>
-<td><p>This function sets the <cite>disttype</cite> attribute of <cite>obs_f</cite> typically used in user-supplied function <cite>py__init_dim_obs_pdaf</cite>.</p></td>
+<td><p>Setting the <cite>disttype</cite> attribute of <cite>obs_f</cite>.</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.omi_set_ncoord.html#pyPDAF.PDAF.omi_set_ncoord" title="pyPDAF.PDAF.omi_set_ncoord"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.omi_set_ncoord</span></code></a></p></td>
-<td><p>This function sets the <cite>ncoord</cite> attribute of <cite>obs_f</cite> typically used in user-supplied function <cite>py__init_dim_obs_pdaf</cite>.</p></td>
+<td><p>Setting the <cite>ncoord</cite> attribute of <cite>obs_f</cite>.</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.omi_set_id_obs_p.html#pyPDAF.PDAF.omi_set_id_obs_p" title="pyPDAF.PDAF.omi_set_id_obs_p"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.omi_set_id_obs_p</span></code></a></p></td>
 <td><p>Setting the <cite>id_obs_p</cite> attribute of <cite>obs_f</cite>.</p></td>
@@ -417,7 +417,7 @@ <h3><a class="toc-backref" href="#id22" role="doc-backlink">Others</a><a class="
 <td><p>This sets the debug flag for OMI.</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.omi_gather_obs.html#pyPDAF.PDAF.omi_gather_obs" title="pyPDAF.PDAF.omi_gather_obs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.omi_gather_obs</span></code></a></p></td>
-<td><p>This function is typically called in the user-supplied function <cite>py__init_dim_obs_pdaf</cite>.</p></td>
+<td><p>Gather the dimension of a given type of observation across multiple local domains/filter processors.</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.omi_gather_obsstate.html#pyPDAF.PDAF.omi_gather_obsstate" title="pyPDAF.PDAF.omi_gather_obsstate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.omi_gather_obsstate</span></code></a></p></td>
 <td><p>This function is used to implement custom observation operators.</p></td>
@@ -432,7 +432,7 @@ <h3><a class="toc-backref" href="#id22" role="doc-backlink">Others</a><a class="
 <td><p>This function computes innovation and omit corresponding observations in assimilation if the innovation is too large.</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.omi_deallocate_obs.html#pyPDAF.PDAF.omi_deallocate_obs" title="pyPDAF.PDAF.omi_deallocate_obs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.omi_deallocate_obs</span></code></a></p></td>
-<td><p>It deallocates teh OMI-internal obsrevation arrays but this should not be called as it is called internally in PDAF.</p></td>
+<td><p>Deallocate OMI-internal obsrevation arrays</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.omi_check_error.html#pyPDAF.PDAF.omi_check_error" title="pyPDAF.PDAF.omi_check_error"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.omi_check_error</span></code></a></p></td>
 <td><p>This function returns the value of the PDAF-OMI internal error flag.</p></td>
@@ -473,7 +473,7 @@ <h3><a class="toc-backref" href="#id25" role="doc-backlink">Synthetic experiment
 <td><p>Generation of synthetic observations based on given error statistics and observation operator for diagonal observation error covariance matrix without post-processing, distributing analysis, and setting next observation step.</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.put_state_generate_obs.html#pyPDAF.PDAF.put_state_generate_obs" title="pyPDAF.PDAF.put_state_generate_obs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.put_state_generate_obs</span></code></a></p></td>
-<td><p>Generation of synthetic observations based on given error statistics and observation operator.</p></td>
+<td><p>Generation of synthetic observations based on given error statistics and observation operator without post-processing, distributing analysis, and setting next observation step.</p></td>
 </tr>
 </tbody>
 </table>
@@ -495,7 +495,7 @@ <h3><a class="toc-backref" href="#id26" role="doc-backlink">Statistical diagnost
 <td><p>Obtain a continuous rank probability score for an ensemble.</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.diag_CRPS_nompi.html#pyPDAF.PDAF.diag_CRPS_nompi" title="pyPDAF.PDAF.diag_CRPS_nompi"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.diag_CRPS_nompi</span></code></a></p></td>
-<td><p>Obtain a continuous rank probability score for an ensemble without using MPI parallelisation.</p></td>
+<td><p>A continuous rank probability score for an ensemble without using MPI parallelisation.</p></td>
 </tr>
 </tbody>
 </table>
@@ -561,7 +561,7 @@ <h3><a class="toc-backref" href="#id29" role="doc-backlink">Advanced manipulatio
 <td><p>This function sets the ensemble member index to given value.</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.set_comm_pdaf.html#pyPDAF.PDAF.set_comm_pdaf" title="pyPDAF.PDAF.set_comm_pdaf"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.set_comm_pdaf</span></code></a></p></td>
-<td><p>This function sets the MPI communicator of PDAF.</p></td>
+<td><p>Setting the MPI communicator used by PDAF.</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.set_offline_mode.html#pyPDAF.PDAF.set_offline_mode" title="pyPDAF.PDAF.set_offline_mode"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.set_offline_mode</span></code></a></p></td>
 <td><p>This function activates offline mode.</p></td>
@@ -586,7 +586,7 @@ <h3><a class="toc-backref" href="#id30" role="doc-backlink">Others</a><a class="
 <table class="autosummary longtable docutils align-default">
 <tbody>
 <tr class="row-odd"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.get_state.html#pyPDAF.PDAF.get_state" title="pyPDAF.PDAF.get_state"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.get_state</span></code></a></p></td>
-<td><p>Post-processing the analysis and distributing state vector back to the model.</p></td>
+<td><p>Distributing analysis state vector to an array.</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="_autosummary/pyPDAF.PDAF.assimilate_prepost.html#pyPDAF.PDAF.assimilate_prepost" title="pyPDAF.PDAF.assimilate_prepost"><code class="xref py py-obj docutils literal notranslate"><span class="pre">pyPDAF.PDAF.assimilate_prepost</span></code></a></p></td>
 <td><p>It is used to preprocess and postprocess of the ensemble.</p></td>
@@ -752,8 +752,7 @@ <h1 class="logo"><a href="index.html">pyPDAF</a></h1>
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="parallel.html">Parallelisation Strategy</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Manual.html">Userguide</a></li>
-<li class="toctree-l1"><a class="reference internal" href="implementation.html">Design Details</a></li>
+<li class="toctree-l1"><a class="reference internal" href="develop.html">Developer Guide</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">API</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#initialisation-and-finalisation">Initialisation and finalisation</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#fully-parallel-da-algorithms"><cite>Fully parallel</cite> DA algorithms</a></li>
@@ -772,7 +771,7 @@ <h1 class="logo"><a href="index.html">pyPDAF</a></h1>
 <h3>Related Topics</h3>
 <ul>
   <li><a href="index.html">Documentation overview</a><ul>
-      <li>Previous: <a href="implementation.html" title="previous chapter">Design Details</a></li>
+      <li>Previous: <a href="develop.html" title="previous chapter">Developer Guide</a></li>
       <li>Next: <a href="_autosummary/pyPDAF.PDAF.init.html" title="next chapter">pyPDAF.PDAF.init</a></li>
   </ul></li>
 </ul>
@@ -793,7 +792,7 @@ <h3>Related Topics</h3>
       &#169;2022 University of Reading and National Centre for Earth Observation.
 
       |
-      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.0.2</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.1.3</a>
       &amp; <a href="https://alabaster.readthedocs.io">Alabaster 1.0.0</a>
 
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diff --git a/docs/API_legacy.html b/docs/API_legacy.html
@@ -7,10 +7,10 @@
 
     <title>API (legacy) &#8212; pyPDAF  documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d1102ebc" />
-    <link rel="stylesheet" type="text/css" href="_static/basic.css?v=8e461078" />
+    <link rel="stylesheet" type="text/css" href="_static/basic.css?v=df3fedd5" />
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     <link rel="index" title="Index" href="genindex.html" />
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@@ -280,8 +280,7 @@ <h1 class="logo"><a href="index.html">pyPDAF</a></h1>
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="parallel.html">Parallelisation Strategy</a></li>
-<li class="toctree-l1"><a class="reference internal" href="Manual.html">Userguide</a></li>
-<li class="toctree-l1"><a class="reference internal" href="implementation.html">Design Details</a></li>
+<li class="toctree-l1"><a class="reference internal" href="develop.html">Developer Guide</a></li>
 <li class="toctree-l1"><a class="reference internal" href="API.html">API</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">API (legacy)</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#da-algorithms">DA algorithms</a></li>
@@ -314,7 +313,7 @@ <h3>Related Topics</h3>
       &#169;2022 University of Reading and National Centre for Earth Observation.
 
       |
-      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.0.2</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.1.3</a>
       &amp; <a href="https://alabaster.readthedocs.io">Alabaster 1.0.0</a>
 
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diff --git a/docs/Manual.html b/docs/Manual.html
@@ -5,17 +5,15 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Userguide &#8212; pyPDAF  documentation</title>
+    <title>&lt;no title&gt; &#8212; pyPDAF  documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d1102ebc" />
-    <link rel="stylesheet" type="text/css" href="_static/basic.css?v=8e461078" />
+    <link rel="stylesheet" type="text/css" href="_static/basic.css?v=df3fedd5" />
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-    <script src="_static/doctools.js?v=9a2dae69"></script>
+    <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="Design Details" href="implementation.html" />
-    <link rel="prev" title="Parallelisation Strategy" href="parallel.html" />
 
   <link rel="stylesheet" href="_static/custom.css" type="text/css" />
 
@@ -33,23 +31,7 @@
 
           <div class="body" role="main">
 
-  <section id="userguide">
-<h1>Userguide<a class="headerlink" href="#userguide" title="Link to this heading">¶</a></h1>
-<p>Here, only a few conventions and caveats are provided. For more detailed explanation and documentation of each routines, we recommend to <a class="reference external" href="http://pdaf.awi.de/trac/wiki">PDAF documentation</a>.</p>
-<section id="naming-conventions">
-<h2>Naming conventions<a class="headerlink" href="#naming-conventions" title="Link to this heading">¶</a></h2>
-<p>Since we expect Python users use:</p>
-<div class="highlight-Python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pyPDAF.PDAF</span> <span class="k">as</span> <span class="nn">PDAF</span>
-</pre></div>
-</div>
-<p>For all PDAF subroutines using name starting with <code class="docutils literal notranslate"><span class="pre">PDAF_</span></code> or <code class="docutils literal notranslate"><span class="pre">PDAFomi_</span></code>, the <code class="docutils literal notranslate"><span class="pre">PDAF</span></code> part is removed. For example, we expect <code class="docutils literal notranslate"><span class="pre">PDAF_get_state</span></code> is used as <code class="docutils literal notranslate"><span class="pre">PDAF.get_state</span></code> and <code class="docutils literal notranslate"><span class="pre">PDAFomi_gather_obs</span></code> is used as <code class="docutils literal notranslate"><span class="pre">PDAF.omi_gather_obs</span></code>. Hence, these prefixes in the subroutines are removed in <code class="docutils literal notranslate"><span class="pre">pyPDAF</span></code>.</p>
-</section>
-<section id="arguments-conventions">
-<h2>Arguments conventions<a class="headerlink" href="#arguments-conventions" title="Link to this heading">¶</a></h2>
-<p>The arguments may be slightly different between <code class="docutils literal notranslate"><span class="pre">PDAF</span></code> and <code class="docutils literal notranslate"><span class="pre">pyPDAF</span></code>. We recommend a check at the API reference for more details.</p>
-</section>
-</section>
-
+
 
           </div>
 
@@ -86,15 +68,10 @@ <h1 class="logo"><a href="index.html">pyPDAF</a></h1>
 </search>
 <script>document.getElementById('searchbox').style.display = "block"</script><h3>Navigation</h3>
 <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
-<ul class="current">
+<ul>
 <li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="parallel.html">Parallelisation Strategy</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">Userguide</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#naming-conventions">Naming conventions</a></li>
-<li class="toctree-l2"><a class="reference internal" href="#arguments-conventions">Arguments conventions</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="implementation.html">Design Details</a></li>
+<li class="toctree-l1"><a class="reference internal" href="develop.html">Developer Guide</a></li>
 <li class="toctree-l1"><a class="reference internal" href="API.html">API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="API_legacy.html">API (legacy)</a></li>
 </ul>
@@ -103,8 +80,6 @@ <h1 class="logo"><a href="index.html">pyPDAF</a></h1>
 <h3>Related Topics</h3>
 <ul>
   <li><a href="index.html">Documentation overview</a><ul>
-      <li>Previous: <a href="parallel.html" title="previous chapter">Parallelisation Strategy</a></li>
-      <li>Next: <a href="implementation.html" title="next chapter">Design Details</a></li>
   </ul></li>
 </ul>
 </div>
@@ -124,7 +99,7 @@ <h3>Related Topics</h3>
       &#169;2022 University of Reading and National Centre for Earth Observation.
 
       |
-      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.0.2</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.1.3</a>
       &amp; <a href="https://alabaster.readthedocs.io">Alabaster 1.0.0</a>
 
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