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Merged
seanebum merged 37 commits into from
Feb 9, 2023
Merged

Release v1.2.0 #336

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81d50a0
Basic, untested commit of SConstruct files
jtcooper10 Nov 14, 2022
f6f2ab4
Changed all .c files to .cpp and .h files to .hpp
jtcooper10 Dec 18, 2022
3d0ce89
Update files to reference .cpp files, fix Makefile
jtcooper10 Dec 18, 2022
f8c12ec
Updated version to v1.1.3
BryanRumsey Jan 3, 2023
098e148
Fixed auto update docs github action.
BryanRumsey Jan 3, 2023
35b922a
Merge pull request #337 from StochSS/hotfix-auto-update-docs
briandrawert Jan 4, 2023
d726f35
Latest docs build.
github-actions[bot] Jan 4, 2023
f7b2435
Fixed issue with type_ids in XML mesh and mesh IO lattices.
BryanRumsey Jan 5, 2023
f59075f
Update SConscript and SConstruct files
jtcooper10 Jan 13, 2023
ae4107c
Configure SCons in solver object
jtcooper10 Jan 16, 2023
79503f0
Testing plotly fix
BryanRumsey Jan 16, 2023
ead8f55
Merge pull request #335 from StochSS/c-to-cpp-updates
briandrawert Jan 17, 2023
3f61120
Merge pull request #338 from StochSS/hotfix-file-lattice-type-ids
briandrawert Jan 17, 2023
9677869
Latest docs build.
github-actions[bot] Jan 17, 2023
f245738
Update __version__.py
BryanRumsey Jan 17, 2023
869fa75
Latest docs build.
github-actions[bot] Jan 17, 2023
bb0f309
Latest docs build.
github-actions[bot] Jan 17, 2023
6fd40fb
Fixed notebook plotting issues with plotly.
BryanRumsey Jan 18, 2023
b7875b3
fixed numerical error when decrementing radius.
BryanRumsey Jan 25, 2023
bbdc022
fixed numerical error when decrementing radius.
BryanRumsey Jan 25, 2023
f3af2a4
fixed numerical error when decrementing radius.
BryanRumsey Jan 25, 2023
60a87c8
Added warning for approx_rc == 0.
BryanRumsey Jan 25, 2023
1e78093
Changed the logger to a named logger.
BryanRumsey Jan 30, 2023
8dcd124
Fixed warning messages for approx_rc value of 0.
BryanRumsey Jan 30, 2023
c9673b4
Added flag to allow all types when executing compile prep.
BryanRumsey Jan 30, 2023
72ec726
Added handler for math errors for cartesian lattices.
BryanRumsey Jan 30, 2023
6351d0a
Merge pull request #342 from StochSS/hotfix-plotly-plotting
briandrawert Jan 31, 2023
7b56d1c
Latest docs build.
github-actions[bot] Jan 31, 2023
6d56050
Fixed issues with removing multiple particles from the domain.
BryanRumsey Jan 31, 2023
8ff2a26
Merge branch 'develop' of github.com:StochSS/SpatialPy into init-scons
jtcooper10 Feb 2, 2023
44f4df7
Update file extensions in SConscript files
jtcooper10 Feb 2, 2023
3c79cdf
Delete now-dead Makefiles
jtcooper10 Feb 2, 2023
2c40319
Fixed compile to work on Linux
briandrawert Feb 8, 2023
4fec4a2
Merge pull request #330 from StochSS/init-scons
BryanRumsey Feb 9, 2023
279f724
Latest docs build.
github-actions[bot] Feb 9, 2023
258242e
Merge pull request #344 from StochSS/hotfix-remove-action
briandrawert Feb 9, 2023
4da8f83
Latest docs build.
github-actions[bot] Feb 9, 2023
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13 changes: 9 additions & 4 deletions .github/workflows/update-docs.yml
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Expand Up @@ -2,7 +2,7 @@ name: Publish SpatialPy Docs

on:
push:
branches: [main]
branches: [develop]

jobs:
publish:
Expand All @@ -12,7 +12,7 @@ jobs:
- name: Initialize environment
uses: actions/checkout@v2
with:
ref: main
ref: develop
fetch-depth: 0

- name: Install Python
Expand All @@ -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
Expand All @@ -43,4 +48,4 @@ jobs:
uses: ad-m/github-push-action@master
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
branch: main
branch: develop
2 changes: 1 addition & 1 deletion docs/build/html/.buildinfo
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@@ -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
Binary file modified docs/build/html/.doctrees/classes/spatialpy.core.doctree
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4 changes: 2 additions & 2 deletions docs/build/html/_modules/index.html
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Expand Up @@ -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" />
Expand Down Expand Up @@ -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>

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48 changes: 25 additions & 23 deletions docs/build/html/_modules/spatialpy/core/boundarycondition.html
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24 changes: 13 additions & 11 deletions docs/build/html/_modules/spatialpy/core/cleanup.html
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Expand Up @@ -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" />

Expand Down Expand Up @@ -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>



Expand Down Expand Up @@ -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>
Expand All @@ -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>
Expand All @@ -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>
Expand All @@ -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>
Expand Down Expand Up @@ -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>

Expand Down
20 changes: 11 additions & 9 deletions docs/build/html/_modules/spatialpy/core/datafunction.html
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Expand Up @@ -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" />

Expand Down Expand Up @@ -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>



Expand Down Expand Up @@ -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>
Expand All @@ -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>
Expand All @@ -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>
Expand All @@ -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>

Expand Down
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