Merge pull request #336 from StochSS/develop

Release v1.2.0
StochSS · Feb 9, 2023 · 7b2dd09 · 7b2dd09
2 parents 4d7b5c4 + 4da8f83
commit 7b2dd09
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diff --git a/.github/workflows/update-docs.yml b/.github/workflows/update-docs.yml
@@ -2,7 +2,7 @@ name: Publish SpatialPy Docs
 
 on:
   push:
-    branches: [main]
+    branches: [develop]
 
 jobs:
   publish:
@@ -12,7 +12,7 @@ jobs:
     - name: Initialize environment
       uses: actions/checkout@v2
       with:
-        ref: main
+        ref: develop
         fetch-depth: 0
 
     - name: Install Python
@@ -27,10 +27,15 @@ jobs:
         python3 -m pip install numpy
         python3 -m pip install -r requirements.txt
 
+    - name: Refresh Repository
+      working-directory: .
+      run: |
+        git pull origin develop
+
     - name: Update the Docs
       working-directory: docs
       run: |
-        make build-docs
+        make html
 
     - name: Commit Changes
       working-directory: docs
@@ -43,4 +48,4 @@ jobs:
       uses: ad-m/github-push-action@master
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
-        branch: main
+        branch: develop
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: aa9a9a3c9380df45ffa4c7a40b7ba182
+config: e12fa66f30479b44f49efa882ed90e3f
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/.doctrees/classes/spatialpy.core.doctree b/docs/build/html/.doctrees/classes/spatialpy.core.doctree
diff --git a/docs/build/html/.doctrees/environment.pickle b/docs/build/html/.doctrees/environment.pickle
diff --git a/docs/build/html/.doctrees/index.doctree b/docs/build/html/.doctrees/index.doctree
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Overview: module code &#8212; SpatialPy 1.1.2 documentation</title>
+    <title>Overview: module code &#8212; SpatialPy 1.2.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../_static/alabaster.css" />
     <link rel="stylesheet" type="text/css" href="../_static/css/spatialpy_alabaster_customizations.css" />
@@ -131,7 +131,7 @@ <h1>All modules for which code is available</h1>
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
 
     </div>
 

diff --git a/docs/build/html/_modules/spatialpy/core/boundarycondition.html b/docs/build/html/_modules/spatialpy/core/boundarycondition.html
diff --git a/docs/build/html/_modules/spatialpy/core/cleanup.html b/docs/build/html/_modules/spatialpy/core/cleanup.html
@@ -5,14 +5,16 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>spatialpy.core.cleanup &#8212; SpatialPy 1.1.0 documentation</title>
+    <title>spatialpy.core.cleanup &#8212; SpatialPy 1.2.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/css/spatialpy_alabaster_customizations.css" />
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
     <script src="../../../_static/jquery.js"></script>
     <script src="../../../_static/underscore.js"></script>
+    <script src="../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
     <script src="../../../_static/doctools.js"></script>
+    <script src="../../../_static/sphinx_highlight.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" />
 
@@ -73,7 +75,7 @@ <h3 id="searchlabel">Quick search</h3>
     </form>
     </div>
 </div>
-<script>$('#searchbox').show(0);</script>
+<script>document.getElementById('searchbox').style.display = "block"</script>
 
 
 
@@ -112,7 +114,7 @@ <h1>Source code for spatialpy.core.cleanup</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">tempfile</span>
 
 <div class="viewcode-block" id="cleanup_tempfiles"><a class="viewcode-back" href="../../../classes/spatialpy.core.html#spatialpy.core.cleanup.cleanup_tempfiles">[docs]</a><span class="k">def</span> <span class="nf">cleanup_tempfiles</span><span class="p">():</span>
-    <span class="sd">&#39;&#39;&#39;</span>
+<span class="w">    </span><span class="sd">&#39;&#39;&#39;</span>
 <span class="sd">    Cleanup all tempfiles in spatialpy core, build, and results.</span>
 <span class="sd">    &#39;&#39;&#39;</span>
     <span class="n">cleanup_core_files</span><span class="p">()</span>
@@ -124,10 +126,10 @@ <h1>Source code for spatialpy.core.cleanup</h1><div class="highlight"><pre>
             <span class="n">cleanup_result_files</span><span class="p">(</span><span class="n">result_dir</span><span class="o">=</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">tempdir</span><span class="p">,</span> <span class="n">file_obj</span><span class="p">))</span></div>
 
 <div class="viewcode-block" id="cleanup_core_files"><a class="viewcode-back" href="../../../classes/spatialpy.core.html#spatialpy.core.cleanup.cleanup_core_files">[docs]</a><span class="k">def</span> <span class="nf">cleanup_core_files</span><span class="p">():</span>
-    <span class="sd">&#39;&#39;&#39;</span>
+<span class="w">    </span><span class="sd">&#39;&#39;&#39;</span>
 <span class="sd">    Cleanup all tempfiles in spatialpy core.</span>
 <span class="sd">    &#39;&#39;&#39;</span>
-    <span class="kn">from</span> <span class="nn">spatialpy.core</span> <span class="k">import</span> <span class="n">log</span> <span class="c1"># pylint: disable=import-outside-toplevel</span>
+    <span class="kn">from</span> <span class="nn">spatialpy.core</span> <span class="kn">import</span> <span class="n">log</span> <span class="c1"># pylint: disable=import-outside-toplevel</span>
 
     <span class="n">tempdir</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">gettempdir</span><span class="p">()</span>
     <span class="n">core_dir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">tempdir</span><span class="p">,</span> <span class="s2">&quot;spatialpy_core&quot;</span><span class="p">)</span>
@@ -136,13 +138,13 @@ <h1>Source code for spatialpy.core.cleanup</h1><div class="highlight"><pre>
     <span class="n">log</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;Spatialpy core directory was removed&quot;</span><span class="p">)</span></div>
 
 <div class="viewcode-block" id="cleanup_build_files"><a class="viewcode-back" href="../../../classes/spatialpy.core.html#spatialpy.core.cleanup.cleanup_build_files">[docs]</a><span class="k">def</span> <span class="nf">cleanup_build_files</span><span class="p">(</span><span class="n">build_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
-    <span class="sd">&#39;&#39;&#39;</span>
+<span class="w">    </span><span class="sd">&#39;&#39;&#39;</span>
 <span class="sd">    Cleanup all spatialpy_build directories.</span>
 
 <span class="sd">    :param build_dir: Path to the build directory to be removed. (optional)</span>
 <span class="sd">    :type build_dir: string</span>
 <span class="sd">    &#39;&#39;&#39;</span>
-    <span class="kn">from</span> <span class="nn">spatialpy.core</span> <span class="k">import</span> <span class="n">log</span> <span class="c1"># pylint: disable=import-outside-toplevel</span>
+    <span class="kn">from</span> <span class="nn">spatialpy.core</span> <span class="kn">import</span> <span class="n">log</span> <span class="c1"># pylint: disable=import-outside-toplevel</span>
 
     <span class="k">if</span> <span class="n">build_dir</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
         <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">build_dir</span><span class="p">)</span>
@@ -158,13 +160,13 @@ <h1>Source code for spatialpy.core.cleanup</h1><div class="highlight"><pre>
         <span class="n">log</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">{}</span><span class="s2"> build directories were removed&quot;</span><span class="p">,</span> <span class="n">count</span><span class="p">)</span></div>
 
 <div class="viewcode-block" id="cleanup_result_files"><a class="viewcode-back" href="../../../classes/spatialpy.core.html#spatialpy.core.cleanup.cleanup_result_files">[docs]</a><span class="k">def</span> <span class="nf">cleanup_result_files</span><span class="p">(</span><span class="n">result_dir</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
-    <span class="sd">&#39;&#39;&#39;</span>
+<span class="w">    </span><span class="sd">&#39;&#39;&#39;</span>
 <span class="sd">    Cleanup all spatialpy_result directories.</span>
 
 <span class="sd">    :param result_dir: Path to the result directory to be removed. (optional)</span>
 <span class="sd">    :type result_dir: string</span>
 <span class="sd">    &#39;&#39;&#39;</span>
-    <span class="kn">from</span> <span class="nn">spatialpy.core</span> <span class="k">import</span> <span class="n">log</span> <span class="c1"># pylint: disable=import-outside-toplevel</span>
+    <span class="kn">from</span> <span class="nn">spatialpy.core</span> <span class="kn">import</span> <span class="n">log</span> <span class="c1"># pylint: disable=import-outside-toplevel</span>
 
     <span class="k">if</span> <span class="n">result_dir</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
         <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">result_dir</span><span class="p">)</span>
@@ -197,8 +199,8 @@ <h1>Source code for spatialpy.core.cleanup</h1><div class="highlight"><pre>
       &copy;Copyright (C) 2019-2022.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 4.4.0</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
 
     </div>
 

diff --git a/docs/build/html/_modules/spatialpy/core/datafunction.html b/docs/build/html/_modules/spatialpy/core/datafunction.html
@@ -5,14 +5,16 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>spatialpy.core.datafunction &#8212; SpatialPy 1.1.0 documentation</title>
+    <title>spatialpy.core.datafunction &#8212; SpatialPy 1.2.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css" />
     <link rel="stylesheet" type="text/css" href="../../../_static/css/spatialpy_alabaster_customizations.css" />
     <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
     <script src="../../../_static/jquery.js"></script>
     <script src="../../../_static/underscore.js"></script>
+    <script src="../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
     <script src="../../../_static/doctools.js"></script>
+    <script src="../../../_static/sphinx_highlight.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" />
 
@@ -73,7 +75,7 @@ <h3 id="searchlabel">Quick search</h3>
     </form>
     </div>
 </div>
-<script>$('#searchbox').show(0);</script>
+<script>document.getElementById('searchbox').style.display = "block"</script>
 
 
 
@@ -106,10 +108,10 @@ <h1>Source code for spatialpy.core.datafunction</h1><div class="highlight"><pre>
 
 <span class="c1"># You should have received a copy of the GNU General Public License</span>
 <span class="c1"># along with this program.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</span>
-<span class="kn">from</span> <span class="nn">spatialpy.core.spatialpyerror</span> <span class="k">import</span> <span class="n">DataFunctionError</span>
+<span class="kn">from</span> <span class="nn">spatialpy.core.spatialpyerror</span> <span class="kn">import</span> <span class="n">DataFunctionError</span>
 
 <div class="viewcode-block" id="DataFunction"><a class="viewcode-back" href="../../../classes/spatialpy.core.html#spatialpy.core.datafunction.DataFunction">[docs]</a><span class="k">class</span> <span class="nc">DataFunction</span><span class="p">():</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Abstract class used to constuct the data function.</span>
 
 <span class="sd">    :param name: Name of the Data Function.</span>
@@ -118,14 +120,14 @@ <h1>Source code for spatialpy.core.datafunction</h1><div class="highlight"><pre>
 <span class="sd">    :raises DataFunctionError: If a name is not provided.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
-    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
         <span class="k">if</span> <span class="n">name</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="k">raise</span> <span class="n">DataFunctionError</span><span class="p">(</span><span class="s2">&quot;DataFunction must have a &#39;name&#39;&quot;</span><span class="p">)</span>
 
 <div class="viewcode-block" id="DataFunction.map"><a class="viewcode-back" href="../../../classes/spatialpy.core.html#spatialpy.core.datafunction.DataFunction.map">[docs]</a>    <span class="k">def</span> <span class="nf">map</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">point</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        This method must be overridden by the DataFunction subclass.</span>
 
 <span class="sd">        NOTE: The spatial location is evaulated at t=0 and is not \</span>
@@ -137,7 +139,7 @@ <h1>Source code for spatialpy.core.datafunction</h1><div class="highlight"><pre>
 <span class="sd">        :returns: Value of function at this spatial location.</span>
 <span class="sd">        :rtype: float</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">raise</span> <span class="n">DataFunctionError</span><span class="p">(</span><span class="n">f</span><span class="s2">&quot;</span><span class="si">{self.name}</span><span class="s2">: DataFunction.map() must be implemented.&quot;</span><span class="p">)</span></div></div>
+        <span class="k">raise</span> <span class="n">DataFunctionError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">: DataFunction.map() must be implemented.&quot;</span><span class="p">)</span></div></div>
 </pre></div>
 
           </div>
@@ -157,8 +159,8 @@ <h1>Source code for spatialpy.core.datafunction</h1><div class="highlight"><pre>
       &copy;Copyright (C) 2019-2022.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 4.4.0</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
 
     </div>