Update docs

cfr/reconjob.py

@@ -1018,11 +1018,11 @@ def run_graphem(self, save_recon=True, save_dirpath=None, save_filename=None,
                     load_precalc_solver=False, solver_save_path=None,
                     compress_params=None, verbose=False, output_indices=None,
                     **fit_kws):
-        ''' Run the GraphEM solver, essentially the :py:meth: `GraphEM.solver.GraphEM.fit` method
+        ''' Run the GraphEM solver, essentially the `GraphEM.solver.GraphEM.fit` method
 
-        Note that the arguments for :py:meth: `GraphEM.solver.GraphEM.fit` can be appended in the
+        Note that the arguments for `GraphEM.solver.GraphEM.fit` can be appended in the
         argument list of this function directly. For instance, to pass a pre-calculated graph, use
-        `estimate_graph=False` and `graph=g.adj`, where `g` is the :py:`Graph` object.
+        `estimate_graph=False` and `graph=g.adj`, where `g` is the `Graph` object.
 
         Args:
             save_dirpath (str): the path to save the related results

docs/_sources/cg-working-with-codebase.rst

@@ -21,6 +21,7 @@ You will need your own fork to work on the code.
 Go to the `cfr` repository and hit the Fork button.
 You will then want to clone your fork (i.e. download all the code to your local machine so you can edit it locally).
 At the command line, this would like something like::
+
     git clone https://github.com/your-user-name/cfr.git cfr-fork
     cd cfr-fork
     git remote add upstream https://github.com/fzhu2e/cfr.git
@@ -56,12 +57,12 @@ When you want to update the feature branch with changes in master after you crea
 
 Contributing new or updating existing functionalities
 """"""""""""""""""""""""""""""""""""""""""""""""""""""
-
-- Open an issue on GitHub (See above)
-- Integrate the new functionality or update the existing functionality. Make sure you:
-  - Re-use as many of `cfr`'s existing utilities as you can, introducing new package dependencies only as necessary.
-  - Create a docstring for your new function, describing arguments and returned variables, and showing an example of use. (Use an existing docstring for inspiration).
-- Test the functionality within a self-contained Jupyter notebook. If the functionality is related to the reconstruction method, **it is required to conduct a pseudoproxy experiment (PPE) using the `pseudoPAGES2k <https://fzhu2e.github.io/cfr/ug-pp2k.html>`_ dataset** so that the result is comparable to existing ones.
+.. note::
+    - Open an issue on GitHub (See above)
+    - Integrate the new functionality or update the existing functionality. Make sure you:
+    - Re-use as many of `cfr`'s existing utilities as you can, introducing new package dependencies only as necessary.
+    - Create a docstring for your new function, describing arguments and returned variables, and showing an example of use. (Use an existing docstring for inspiration).
+    - Test the functionality within a self-contained Jupyter notebook. If the functionality is related to the reconstruction method, **it is required to conduct a pseudoproxy experiment (PPE)** using the `pseudoPAGES2k dataset <https://www.nature.com/articles/s41597-023-02489-1>`_ so that the result is comparable to existing ones. For examples, please refer to `PPE: A PDA-based Reconstruction <https://fzhu2e.github.io/cfr/notebooks/pp2k-ppe-pda.html>`_ and `PPE: A GraphEM-based Reconstruction <https://fzhu2e.github.io/cfr/notebooks/pp2k-ppe-graphem.html>`_.
 
 
 Stylistic considerations

docs/_sources/index.rst

@@ -59,7 +59,7 @@ It provides a toolkit for
         :link: ug-psm
         :link-type: doc
 
-        Calibration and running of the Proxy System Models for multiple proxy types.
+        Proxy System Models for multiple proxy types.
 
     .. grid-item-card::  LMR
         :class-title: custom-title
@@ -68,7 +68,7 @@ It provides a toolkit for
         :link: ug-lmr
         :link-type: doc
 
-        Running the Last Millennium Reanalysis (LMR) workflow.
+        The Last Millennium Reanalysis (LMR) workflows.
 
     .. grid-item-card::  GraphEM
         :class-title: custom-title
@@ -77,7 +77,7 @@ It provides a toolkit for
         :link: ug-graphem
         :link-type: doc
 
-        Running the Graphical Expectation Maximization (GraphEM) workflow.
+        The Graphical Expectation Maximization (GraphEM) workflows.
 
     .. grid-item-card::  API
         :class-title: custom-title

docs/_sources/ug-lmr.rst

@@ -9,9 +9,4 @@ In this section, we will cover the below topics:
 
     notebooks/lmr-real-pages2k
     notebooks/lmr-assim-no-calib
-    notebooks/lmr-cli
-    .. notebooks/lmr-basics
-    .. notebooks/lmr-post
-    .. notebooks/lmr-cfg
-    .. notebooks/lmr-mc
-    .. notebooks/lmr-post
+    notebooks/lmr-cli

docs/_sources/ug-pp2k.rst

@@ -1,7 +1,7 @@
 
 pseudoPAGES2k
 ===================================
-This section shows the usage of the pseudoPAGES2k dataset with `cfr` as an example, including the below topics:
+This section shows the usage of the `pseudoPAGES2k dataset (Zhu et al., 2023) <https://www.nature.com/articles/s41597-023-02489-1>`_ with `cfr` as an example, including the below topics:
 
 .. toctree::
     :maxdepth: 1

docs/_sources/ug-psm.rst

@@ -10,6 +10,4 @@ PSM
     notebooks/psm-lake-VarveThickness
     notebooks/psm-coral-SrCa
     notebooks/psm-coral-d18O
-    notebooks/psm-tree-TRW
-    notebooks/psm-tree-seasonality
-    notebooks/psm-tree-memory
+    notebooks/psm-tree-TRW

docs/cg-working-with-codebase.html

@@ -465,13 +465,16 @@ <h2>Creating a branch<a class="headerlink" href="#creating-a-branch" title="Perm
 </section>
 <section id="contributing-new-or-updating-existing-functionalities">
 <h2>Contributing new or updating existing functionalities<a class="headerlink" href="#contributing-new-or-updating-existing-functionalities" title="Permalink to this heading">#</a></h2>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
 <ul class="simple">
 <li><p>Open an issue on GitHub (See above)</p></li>
-<li><p>Integrate the new functionality or update the existing functionality. Make sure you:
-- Re-use as many of <cite>cfr</cite>’s existing utilities as you can, introducing new package dependencies only as necessary.
-- Create a docstring for your new function, describing arguments and returned variables, and showing an example of use. (Use an existing docstring for inspiration).</p></li>
-<li><p>Test the functionality within a self-contained Jupyter notebook. If the functionality is related to the reconstruction method, <strong>it is required to conduct a pseudoproxy experiment (PPE) using the `pseudoPAGES2k &lt;https://fzhu2e.github.io/cfr/ug-pp2k.html&gt;`_ dataset</strong> so that the result is comparable to existing ones.</p></li>
+<li><p>Integrate the new functionality or update the existing functionality. Make sure you:</p></li>
+<li><p>Re-use as many of <cite>cfr</cite>’s existing utilities as you can, introducing new package dependencies only as necessary.</p></li>
+<li><p>Create a docstring for your new function, describing arguments and returned variables, and showing an example of use. (Use an existing docstring for inspiration).</p></li>
+<li><p>Test the functionality within a self-contained Jupyter notebook. If the functionality is related to the reconstruction method, <strong>it is required to conduct a pseudoproxy experiment (PPE)</strong> using the <a class="reference external" href="https://www.nature.com/articles/s41597-023-02489-1">pseudoPAGES2k dataset</a> so that the result is comparable to existing ones. For examples, please refer to <a class="reference external" href="https://fzhu2e.github.io/cfr/notebooks/pp2k-ppe-pda.html">PPE: A PDA-based Reconstruction</a> and <a class="reference external" href="https://fzhu2e.github.io/cfr/notebooks/pp2k-ppe-graphem.html">PPE: A GraphEM-based Reconstruction</a>.</p></li>
 </ul>
+</div>
 </section>
 <section id="stylistic-considerations">
 <h2>Stylistic considerations<a class="headerlink" href="#stylistic-considerations" title="Permalink to this heading">#</a></h2>

docs/index.html

@@ -445,7 +445,7 @@ <h1><cite>cfr</cite>: a Python package for Climate Field Reconstruction<a class=
 <div class="sd-card-body custom-body docutils">
 <div class="sd-card-title sd-font-weight-bold custom-title docutils">
 PSM</div>
-<p class="sd-card-text">Calibration and running of the Proxy System Models for multiple proxy types.</p>
+<p class="sd-card-text">Proxy System Models for multiple proxy types.</p>
 </div>
 <a class="sd-stretched-link reference internal" href="ug-psm.html"><span class="doc"></span></a></div>
 </div>
@@ -455,7 +455,7 @@ <h1><cite>cfr</cite>: a Python package for Climate Field Reconstruction<a class=
 <div class="sd-card-body custom-body docutils">
 <div class="sd-card-title sd-font-weight-bold custom-title docutils">
 LMR</div>
-<p class="sd-card-text">Running the Last Millennium Reanalysis (LMR) workflow.</p>
+<p class="sd-card-text">The Last Millennium Reanalysis (LMR) workflows.</p>
 </div>
 <a class="sd-stretched-link reference internal" href="ug-lmr.html"><span class="doc"></span></a></div>
 </div>
@@ -465,7 +465,7 @@ <h1><cite>cfr</cite>: a Python package for Climate Field Reconstruction<a class=
 <div class="sd-card-body custom-body docutils">
 <div class="sd-card-title sd-font-weight-bold custom-title docutils">
 GraphEM</div>
-<p class="sd-card-text">Running the Graphical Expectation Maximization (GraphEM) workflow.</p>
+<p class="sd-card-text">The Graphical Expectation Maximization (GraphEM) workflows.</p>
 </div>
 <a class="sd-stretched-link reference internal" href="ug-graphem.html"><span class="doc"></span></a></div>
 </div>

docs/ug-api.html

@@ -1905,10 +1905,10 @@ <h2>ReconJob<a class="headerlink" href="#reconjob" title="Permalink to this head
 <dl class="py method">
 <dt class="sig sig-object py" id="cfr.reconjob.ReconJob.run_graphem">
 <span class="sig-name descname"><span class="pre">run_graphem</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">save_recon</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_dirpath</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">load_precalc_solver</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">solver_save_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">compress_params</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_indices</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">fit_kws</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cfr.reconjob.ReconJob.run_graphem" title="Permalink to this definition">#</a></dt>
-<dd><p>Run the GraphEM solver, essentially the :py:meth: <cite>GraphEM.solver.GraphEM.fit</cite> method</p>
-<p>Note that the arguments for :py:meth: <cite>GraphEM.solver.GraphEM.fit</cite> can be appended in the
+<dd><p>Run the GraphEM solver, essentially the <cite>GraphEM.solver.GraphEM.fit</cite> method</p>
+<p>Note that the arguments for <cite>GraphEM.solver.GraphEM.fit</cite> can be appended in the
 argument list of this function directly. For instance, to pass a pre-calculated graph, use
-<cite>estimate_graph=False</cite> and <cite>graph=g.adj</cite>, where <cite>g</cite> is the <a href="#id1"><span class="problematic" id="id2">:py:`Graph`</span></a> object.</p>
+<cite>estimate_graph=False</cite> and <cite>graph=g.adj</cite>, where <cite>g</cite> is the <cite>Graph</cite> object.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">

docs/ug-pp2k.html

@@ -387,7 +387,7 @@ <h1>pseudoPAGES2k</h1>
 
   <section id="pseudopages2k">
 <h1>pseudoPAGES2k<a class="headerlink" href="#pseudopages2k" title="Permalink to this heading">#</a></h1>
-<p>This section shows the usage of the pseudoPAGES2k dataset with <cite>cfr</cite> as an example, including the below topics:</p>
+<p>This section shows the usage of the <a class="reference external" href="https://www.nature.com/articles/s41597-023-02489-1">pseudoPAGES2k dataset (Zhu et al., 2023)</a> with <cite>cfr</cite> as an example, including the below topics:</p>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/pp2k-pdb-load-viz.html">Loading and Visualization</a></li>

docsrc/cg-working-with-codebase.rst

@@ -21,6 +21,7 @@ You will need your own fork to work on the code.
 Go to the `cfr` repository and hit the Fork button.
 You will then want to clone your fork (i.e. download all the code to your local machine so you can edit it locally).
 At the command line, this would like something like::
+
     git clone https://github.com/your-user-name/cfr.git cfr-fork
     cd cfr-fork
     git remote add upstream https://github.com/fzhu2e/cfr.git
@@ -56,12 +57,12 @@ When you want to update the feature branch with changes in master after you crea
 
 Contributing new or updating existing functionalities
 """"""""""""""""""""""""""""""""""""""""""""""""""""""
-
-- Open an issue on GitHub (See above)
-- Integrate the new functionality or update the existing functionality. Make sure you:
-  - Re-use as many of `cfr`'s existing utilities as you can, introducing new package dependencies only as necessary.
-  - Create a docstring for your new function, describing arguments and returned variables, and showing an example of use. (Use an existing docstring for inspiration).
-- Test the functionality within a self-contained Jupyter notebook. If the functionality is related to the reconstruction method, **it is required to conduct a pseudoproxy experiment (PPE) using the `pseudoPAGES2k <https://fzhu2e.github.io/cfr/ug-pp2k.html>`_ dataset** so that the result is comparable to existing ones.
+.. note::
+    - Open an issue on GitHub (See above)
+    - Integrate the new functionality or update the existing functionality. Make sure you:
+    - Re-use as many of `cfr`'s existing utilities as you can, introducing new package dependencies only as necessary.
+    - Create a docstring for your new function, describing arguments and returned variables, and showing an example of use. (Use an existing docstring for inspiration).
+    - Test the functionality within a self-contained Jupyter notebook. If the functionality is related to the reconstruction method, **it is required to conduct a pseudoproxy experiment (PPE)** using the `pseudoPAGES2k dataset <https://www.nature.com/articles/s41597-023-02489-1>`_ so that the result is comparable to existing ones. For examples, please refer to `PPE: A PDA-based Reconstruction <https://fzhu2e.github.io/cfr/notebooks/pp2k-ppe-pda.html>`_ and `PPE: A GraphEM-based Reconstruction <https://fzhu2e.github.io/cfr/notebooks/pp2k-ppe-graphem.html>`_.
 
 
 Stylistic considerations

docsrc/index.rst

@@ -59,7 +59,7 @@ It provides a toolkit for
         :link: ug-psm
         :link-type: doc
 
-        Calibration and running of the Proxy System Models for multiple proxy types.
+        Proxy System Models for multiple proxy types.
 
     .. grid-item-card::  LMR
         :class-title: custom-title
@@ -68,7 +68,7 @@ It provides a toolkit for
         :link: ug-lmr
         :link-type: doc
 
-        Running the Last Millennium Reanalysis (LMR) workflow.
+        The Last Millennium Reanalysis (LMR) workflows.
 
     .. grid-item-card::  GraphEM
         :class-title: custom-title
@@ -77,7 +77,7 @@ It provides a toolkit for
         :link: ug-graphem
         :link-type: doc
 
-        Running the Graphical Expectation Maximization (GraphEM) workflow.
+        The Graphical Expectation Maximization (GraphEM) workflows.
 
     .. grid-item-card::  API
         :class-title: custom-title

docsrc/ug-lmr.rst

@@ -9,9 +9,4 @@ In this section, we will cover the below topics:
 
     notebooks/lmr-real-pages2k
     notebooks/lmr-assim-no-calib
-    notebooks/lmr-cli
-    .. notebooks/lmr-basics
-    .. notebooks/lmr-post
-    .. notebooks/lmr-cfg
-    .. notebooks/lmr-mc
-    .. notebooks/lmr-post
+    notebooks/lmr-cli

docsrc/ug-pp2k.rst

@@ -1,7 +1,7 @@
 
 pseudoPAGES2k
 ===================================
-This section shows the usage of the pseudoPAGES2k dataset with `cfr` as an example, including the below topics:
+This section shows the usage of the `pseudoPAGES2k dataset (Zhu et al., 2023) <https://www.nature.com/articles/s41597-023-02489-1>`_ with `cfr` as an example, including the below topics:
 
 .. toctree::
     :maxdepth: 1

docsrc/ug-psm.rst

@@ -10,6 +10,4 @@ PSM
     notebooks/psm-lake-VarveThickness
     notebooks/psm-coral-SrCa
     notebooks/psm-coral-d18O
-    notebooks/psm-tree-TRW
-    notebooks/psm-tree-seasonality
-    notebooks/psm-tree-memory
+    notebooks/psm-tree-TRW